Thermodynamics Fundamentales Morales Rodriguez

THERMODYNAMICS
FUNDAMENTALS
AND
ITS APPLICATION
IN SCIENCE
Edited by
Ricardo Morales-Rodriguez
THERMODYNAMICS
FUNDAMENTALS AND ITS
APPLICATION IN SCIENCE
Edited by Ricardo Morales-Rodriguez
Thermodynamics Fundamentals and Its Application in Science
http://dx.doi.org/10.5772/2615
Contributors
Ahmet Grses, Mehtap Ejder-Korucu, Nikolai Bazhin, Yi Fang, Bohdan Hejna, A. Plastino,
Evaldo M. F. Curado, M. Casas, Zdeka Kolsk, Milan Zbransk, Alena Randov, Ronald J.
Bakker, Elisabeth Blanquet, Ioana Nuta, Lin Li, Rza Atav, L.E. Panin, Yu Liu, Kui Wang, Philippe
Vieillard, Nong-Moon Hwang, Jae-Soo Jung, Dong-Kwon Lee, Vasiliy Fefelov, Vitaly Gorbunov,
Alexander Myshlyavtsev, Marta Myshlyavtseva, Adela Ionescu, Paiguy Armand Ngouateu
Wouagfack, Rn Tchinda, Raul Mluan, Pedro Gmez Vilda, Xuejing Hou, Harvey J.M. Hou,
C.A.S. Silva, Hui-Zhen Fu, Yuh-Shan Ho
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Thermodynamics Fundamentals and Its Application in Science,

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Contents
Preface IX
Section 1 Classical Thermodynamics 1
Chapter 1 A View from the Conservation of

Energy to Chemical Thermodynamic 3
Ahmet Grses and Mehtap Ejder-Korucu
Chapter 2 Useful Work and Gibbs Energy 29

Nikolai Bazhin
Section 2 Statistical Thermodynamics 45
Chapter 3 Gibbs Free Energy Formula for Protein Folding 47

Yi Fang
Chapter 4 Information Capacity of Quantum Transfer

Channels and Thermodynamic Analogies 83
Bohdan Hejna
Chapter 5 Thermodynamics Microscopic Connotations 119

A. Plastino, Evaldo M. F. Curado and M. Casas
Section 3 Property Prediction and Thermodynamics 133
Chapter 6 Group Contribution Methods for Estimation of Selected

Physico-Chemical Properties of Organic Compounds 135
Zdeka Kolsk, Milan Zbransk and Alena Randov
Chapter 7 Thermodynamic Properties and Applications

of Modified van-der-Waals Equations of State 163
Ronald J. Bakker
Chapter 8 Thermodynamics Simulations Applied to

Gas-Solid Materials Fabrication Processes 191
Elisabeth Blanquet and Ioana Nuta
VI Contents
Section 4 Material and Products 215
Chapter 9 Application of Thermodynamics

and Kinetics in Materials Engineering 217
Lin Li
Chapter 10 Thermodynamics of Wool Dyeing 247

Rza Atav
Chapter 11 Mesomechanics and Thermodynamics of

Nanostructural Transitions in Biological Membranes
Under the Action of Steroid Hormones 263
L.E. Panin
Chapter 12 Thermodynamics of Resulting Complexes

Between Cyclodextrins and Bile Salts 305
Yu Liu and Kui Wang
Chapter 13 Thermodynamics of Hydration in Minerals:

How to Predict These Entities 339
Philippe Vieillard
Chapter 14 Thermodynamics and Kinetics in

the Synthesis of Monodisperse Nanoparticles 371
Nong-Moon Hwang, Jae-Soo Jung and Dong-Kwon Lee
Chapter 15 Statistical Thermodynamics of Lattice Gas

Models of Multisite Adsorption 389
Vasiliy Fefelov, Vitaly Gorbunov,
Alexander Myshlyavtsev and Marta Myshlyavtseva
Section 5 Non-Equilibrium Thermodynamics 417
Chapter 16 Influence of Simulation Parameters on the Excitable

Media Behaviour The Case of Turbulent Mixing 419
Adela Ionescu
Chapter 17 ECOP Criterion for Irreversible

Three-Heat-Source Absorption Refrigerators 445
Paiguy Armand Ngouateu Wouagfack and Rn Tchinda
Section 6 Thermodynamics in Diverse Areas 461
Chapter 18 Thermodynamics of Microarray Hybridization 463

Raul Mluan and Pedro Gmez Vilda
Chapter 19 Probing the Thermodynamics of Photosystem I by

Spectroscopic and Mutagenic Methods 483
Xuejing Hou and Harvey J.M. Hou
Contents VII
Chapter 20 Fuzzy Spheres Decays and Black Hole Thermodynamics 501

C.A.S. Silva
Chapter 21 Bibliometric Analysis of Thermodynamic Research:

A Science Citation Index Expanded-Based Analysis 519
Hui-Zhen Fu and Yuh-Shan Ho
Preface
This book is a result of a careful selection of scientific contributions involved in the

thermodynamic area and it is titled Thermodynamics - Fundamentals and Its
Application in Science. Thermodynamics is very important for the description of
phenomena in different fields on science. Therefore, this book contains chapters
describing the fundamentals and the diverse applications in different areas under
development, which allow the access of different kind of readers; for instance,
bachelor and postgraduate students, researchers, etc.
The book is divided in six sections and the classification was done according to the
purpose, relevance and approaches employed in the development of the contributions.
The first section describes the classical thermodynamics, where firstly an overview
about classical thermodynamics considering diverse fundamental concepts of the area
is described. This section also has a contribution presenting the mechanism of useful
work and heat production in reversible systems.
The second section includes some chapters based on statistical mechanics, for instance,
one of the chapters described the protein folding phenomena based on Gibbs free energy
through the use of quantum mechanics, topic of high importance currently. On the other
hand, another of the contributions in this section describes the information capacity of
quantum transfer channels and thermodynamics analogies. The last chapter of this
section introduces some axioms which allow one to derive the MaxEnt equations and
viceversa, giving an alternative foundation for equilibriums statistical mechanics.
The property prediction in thermodynamics is presented in the following section. A

chapter explaining the use and implementation of group contribution methods for
property prediction of organic compounds is firstly described. The description of pure
gases and multi/component fluid systems is presented in another chapter, which in
fact used a modified version of the Van der Waals equation. The last chapter is this
section illustrates the interest area of macroscopic modelling on the thermodynamics
simulation and gives some interesting examples in different domains in the material
and product design areas employing some predicted properties.
The fourth section contains the application of some thermodynamic insights in the
material and products area. One of the chapters introduces some computational
X Preface
results on the designing of advances material. A wool dyeing phenomenon described

by thermodynamics is presented in another contribution. On the other hand, some
authors talk about nanostructural transition in biological membranes under the action
of steroid hormones. In this section, a chapter highlighting the importance of
improving the understanding of molecular recognition mechanics in supramolecular
systems and the design and synthesis of new supramolecular systems based on
different kinds of cyclodextrins is also presented. The use of thermodynamics in the
mineral field is presented describing the hydration of minerals providing several
relationships illustrated by examples exhibiting great variability closely related to the
chemical and physical compound properties. The synthesis of monodisperse
nanoparticles is also described in one of the chapters of this section, relying on
thermodynamics and kinetic basis. The last chapter of the section talks about
thermodynamics of lattice gas models of multisite adsorption.
A section with chapters presenting non equilibrium approach is the fifth section of the
book. One of the chapters talks about the influence of certain parameters on excitable
media behaviour, specifically describing the turbulent mixing. Moreover, the other
chapter of this section presents an analytical method developed to achieve the
performance optimization of irreversible three-heat-sources absorption refrigeration
models having finite-rate of heat transfer, heat leakage and internal irreversibility
based on an objective function named ecological coefficient performance (ECOP).
The last section contains some chapters talking about diverse applications of
thermodynamics. For instance, one chapter discusses the importance of
thermodynamics in microarrays hybridization, due to thermodynamics factors affect
molecular interaction which in fact are not taken into account for the estimation of
genetic expression in current algorithms. Another chapter describes a case study
probing thermodynamics of electron transfer in photosystems using a combination of
molecular genetics and sophisticated biophysical techniques, in particular, pulsed
photoacoustic spectroscopy. The other chapter of this section address the black hole
thermodynamics in the context of topology change, as conceived for some classes of
quantum spaces called fuzzy spheres. The last chapter of the section and book shows a
bibliometric study about thermodynamic contributions giving a general picture about
the number of papers, institutions and countries working on certain thermodynamic
topics as well as the quality of the paper by their citations.
It is expected that the collections of these chapters contributes to the state of the art in
the thermodynamics area, which not only involve the fundamentals of
thermodynamics, but moreover, consider the wide applications of this area in several
fields.
Ricardo Morales-Rodriguez
Technical University of Denmark,
Denmark
Section 1
Classical Thermodynamics
Chapter 1
A View from the Conservation of

Energy to Chemical Thermodynamics
Ahmet Grses and Mehtap Ejder-Korucu
Additional information is available at the end of the chapter
1. Introduction
According to the conservation of energy law, energy, which is the capacity to do work or to
supply heat, can be neither created nor destroyed; it can only be converted from one form
into another. For example, the water in a reservoir of dam has potential energy because of its
height above the outlet stream but has no kinetic energy because it is not moving. As the
water starts to fall over the dam, its height and potential energy, (Ep) is energy due to
position or any other form of stored energy, decrease while its velocity and kinetic energy,
(EK) is the energy related to the motion of an object with mass m and velocity v, increase.
The total of potential energy plus kinetic energy always remains constant. When the water
reaches the bottom and dashes against the rocks or drives the turbine of a generator, its
kinetic energy is converted to other forms of energy-perhaps into heat that raises the
temperature of the water or into electrical energy [6]. If any fuel is burned in an open
medium, its energy is lost almost entirely as heat, whereas if it is burned in a car engine; a
portion of the energy is lost as work to move the car, and less is lost as heat. These are also
typical examples of the existence of the law.
Figure 1. Some examples showing the existence of the conservation of energy law
4 Thermodynamics Fundamentals and Its Application in Science
It is thought that the summation of the introduction as a detailed concept map related with
the conservation of energy would be better. This map in Fig.2 presents a concise view for
many concepts of thermodynamics and their relations.
Figure 2. A concept map for the conservation of energy law
The macroscopic part of universe under study in thermodynamics is called the system. The
parts of the universe that can interact with the system are called the surroundings [5]. In
order to describe the thermodynamic behavior of a physical system, the interaction between
the system and its surroundings must be understood. Thermodynamic systems are thus
classified into three main types according to the way they interact with the surroundings
(Fig.3); open system: matter and energy can be exchanged with the surroundings; closed
system: can exchange energy but not matter with the surroundings and isolated system:
cannot exchange matter or energy with the surroundings [4, 5]. Addition, a boundary that
does permit energy transfer as heat (such as steel and glass) is called diathermic and a
boundary that does not permit energy transfer as heat is called adiabatic [1;4].
The system may be homogeneous or heterogeneous. An exact definition is difficult, but it is
convenient to define a homogeneous system as one whose properties are the same in all
parts, or at least their spatial variation is continuous. A heterogeneous system consists of
A View from the Conservation of Energy to Chemical Thermodynamics 5
two or more distinct homogeneous regions or phases, which are separated from one another
by surfaces of discontinuity [4].
Figure 3. Systems and their surroundings; (a) open system (b) closed system and (c) isolated system.
Heating is a process in which the temperature of system, separated with diathermic border
from its surrounding, is increased. This process leads to passing system from a state of
lower energy to higher one. Heating process based on the energy difference between system
and its surrounding provides identify of an important property which indicates the flow
direction of energy. This property is called temperature. Temperature is a physical property
of matter that quantitatively expresses the common notions of hot and cold. Objects of low
temperature are cold, while various degrees of higher temperatures are referred to as warm
or hot. Heat spontaneously flows from bodies of a higher temperature to bodies of lower
temperature, at a rate that increases with the temperature difference and the thermal
conductivity. No heat will be exchanged between bodies at same temperature; such bodies
are said to be in "equilibrium. On the other hand, kinetic energy associated with the
random motion of particles is called thermal energy, and the thermal energy of a given
material is proportional to temperature. However, the magnitude of thermal energy in a
sample also depends on the number of particles in the sample and so it is an extensive
property. The water in a swimming pool and a cup of water taken from the pool has the
same temperature, so their particles have the same average kinetic energy. The water in the
pool has much more thermal energy than the water in the cup, simply because there are a
larger number of molecules in the pool. A large number of particles at a given temperature
have a higher total energy than a small number of particles at the same temperature [7].
Quantitatively, temperature which is an intensive property is measured with thermometers,
which may be calibrated to a variety of temperature scales [9].
If two thermodynamic systems, A and B, each of which is in thermal equilibrium

independently, are brought into thermal contact, one of two things will take place: either a
flow of heat from one system to the other or no thermodynamic process will result. In the
latter case the two systems are said to be in thermal equilibrium with respect to each other
[11]. When same treatment has been repeated other system, C, if there is thermal
equilibrium between B and C; the condition of thermodynamic equilibrium between them
may be symbolically represented as follows,
If A B and B C (1)
This observation has also been schematically shown in Fig.4
Figure 4. A schematic presentation of the zeroth law of thermodynamics.
Based on preceding observations, some of the physical properties of the system B

(Thermometer) can be used as a measure of the temperature, such as the volume of a fixed
amount of a liquid merqury or any alcohol under standard atmospheric pressure. The
zeroth law of thermodynamics is the assurance of the existence of a property called the
temperature [11].
The zeroth law allows us to assert the existence of temperature as a state function. Having
defined temperature, how do we measure it? Of course, you are familiar with the process of
putting a liquid-mercury thermometer in contact with a system, waiting until the volume
change of the mercury has ceased, indicating that thermal equilibrium between the
thermometer and the system has been reached [5].
It is necessary to know four common different temperature scales, namely Fahrenheit (0F),
Celsius (0C), Kelvin (K) and Rankine (0R). To convert these scales one another can be used
the following equations [9,10].
T / K / 0 C 273.15 (2)
oR oF 459.67 oF 1.8 oC 32 oR 1.8 K (3)
2. The first law of thermodynamic (the conservation of energy)

In thermodynamics, the total energy of a system is called its internal energy, U. The internal
energy is the total kinetic and potential energies of the particles in the system. It is denoted
by U the change in internal energy when a system changes from an initial state i with
internal energy Ui to a final state of internal energy Uf :
U U f Ui (4)
The internal energy is a state function in the sense that its value depends only on the current
state of the system and is independent of how that state has been prepared. In other words,
internal energy is a function of the properties as variables that determine the current state of
the system. Changing any one of the state variables, such as the pressure and temperature,
results in a change in internal energy. The internal energy is a state function that has
consequences of the greatest importance. The internal energy is an extensive property of a
system and is measured in joules (1 J = 1 kg m2 s2). The molar internal energy, Um, is the
internal energy divided by the amount of substance in a system, Um = U/n; it is an intensive
property and commonly reported in kilojoules per mole (kJ mol1) [12].
A particle has a certain number of motional degrees of freedom, such as the ability to
translate (the motion of its centre of mass through space), rotate around its centre of mass, or
vibrate (as its bond lengths and angles change, leaving its centre of mass unmoved). Many
physical and chemical properties depend on the energy associated with each of these modes
of motion. For example, a chemical bond might break if a lot of energy becomes
concentrated in it, for instance as vigorous vibration. According to it, the average energy of
each quadratic contribution to the energy is 1/2 kT. The mean energy of the atoms free to
move in three dimensions is kT and the total energy of a monatomic perfect gas is NkT, or
nRT (because N = nNA and R = NAk , NA: Avogadro's number and k: Boltzman's constant). I
t can therefore be written;
Um T Um 0 RT monatomic gas; translation only (5)
where Um(0) is the molar internal energy at T = 0, when all translational motions have ceased
and the sole contribution to the internal energy arises from the internal structure of the
atoms. This equation shows that the internal energy of a perfect gas increases linearly with
temperature. At 25C, 3/2 RT = 3.7 kJ mol1, so translational motion contributes about 4 kJ
mol1 to the molar internal energy of a gaseous sample of atoms or molecules.
When the gas consists of molecules, we need to take into account the effect of rotation and
vibration. A linear molecule, such as N2 and CO2, can rotate around two axes perpendicular
to the line of the atoms, so it has two rotational modes of motion, each contributing a term
1/2 kT to the internal energy. Therefore, the mean rotational energy is kT and the rotational
contribution to the molar internal energy is RT.
Um T Um 0 5 / 2 RT linear molecule ; translation and rotation only (6)
A nonlinear molecule, such as CH4 or H2O, can rotate around three axes and, again, each
mode of motion contributes a term 1/2 kT to the internal energy. Therefore, the mean
rotational energy is 3/2 kT and there is a rotational contribution of 3/2 RT to the molar
internal energy. That is,
Um T Um 0 3RT nonlinear molecule; translation and rotation only (7)
The internal energy now increases twice as rapidly with temperature compared with the
monatomic gas. Another way: for a gas consisting of 1 mol of nonlinear molecules to
undergo the same rise in temperature as 1 mol of monatomic gas, twice as more energy
must be supplied. Molecules do not vibrate significantly at room temperature and, as a first
approximation; the contribution of molecular vibrations to the internal energy is negligible

except for very large molecules such as polymers and biological macromolecules. None of
the expressions we have been derived depends on the volume occupied by the molecules:
there are no intermolecular interactions in a perfect gas, so the distance between the
molecules has no effect on the energy. That is, the internal energy of a perfect gas is
independent of the volume it occupies. The internal energy of interacting molecules in
condensed phases also has a contribution from the potential energy of their interaction.
However, no simple expressions can be written down in general. Nevertheless, the crucial
molecular point is that, as the temperature of a system is raised, the internal energy
increases as the various modes of motion become more highly excited [12].
By considering how the internal energy varies with temperature when the pressure of the
system is kept constant; many useful results and also some unfamiliar quantities can be
obtained. If it is divided both sides of eqn ((dU = (U/V)T dV + (U/T) v dT ) ((U/V)T = T
and T called as the internal pressure ; (U/T) v = Cv and it is called as heat capacity at
constant volume )) by dT and impose the condition of constant pressure on the resulting
differentials, so that dU/dT on the left becomes (U/T)p, So;
U / T p T V / T p Cv (8)
It is usually sensible in thermodynamics to inspect the output of a manipulation like this to

see if it contains any recognizable physical quantity. The differential coefficient on the right
in this expression is the slope of the plot of volume against temperature (at constant
pressure). This property is normally identified as thermal expansion coefficient, , of a
substance, which is defined as
1 / V V / T p (9)
When it is introduced the definition of into the equation for (U/T)p = T V + Cv ,this
equation is entirely general (provided the system is closed and its composition is constant).
It expresses the dependence of the internal energy on the temperature at constant pressure
in terms of Cv, which can be measured in one experiment, in terms of , which can be
measured in another, and in terms of the quantity T, for a perfect gas, T = 0, so
U / T p Cv (10)
That is, the constant-volume heat capacity of a perfect gas is equal to the slope of a plot of
internal energy against temperature at constant pressure as well as (by definition) to the
slope at constant volume. It can also be predicted that the change of internal energy with
temperature at constant pressure means a total energy change raised from increase in both
energy of kinetics and potential energy of particles in higher temperature. The translational
motion of particles against constant external pressure will lead to expansion, but thermal
expansion characteristics of substance control its magnitude. Thus, we can see that heating
in constant volume only changes internal energy as qv (U = qv), whereas its change in
constant pressure additionally includes changing of potential energy of particles due to

translation motion. That is, changes in constant pressure require a different definition of the
transferred energy [12].
3. From conservation of energy to heat and work

It has been found experimentally that the internal energy of a system may be changed either
by doing work on the system or by heating it. Whereas we may know how the energy
transfer has occurred (because we can see if a weight has been raised or lowered in the
surroundings, indicating transfer of energy by doing work, or if ice has melted in the
surroundings, indicating transfer of energy as heat), the system is blind to the mode
employed. Heat and work are equivalent ways of changing a systems internal energy. It is
also found experimentally that, if a system is isolated from its surroundings, then no change
in internal energy takes place. This summary of observations is now known as the First Law
of thermodynamics or the Conservation of Energy and is expressed as follows [1;12].
The internal energy of an isolated system is constant.
U 0 (11)
A system cannot be used to do work, leave it isolated, and then come back expecting to find
it restored to its original state with the same capacity for doing work. The experimental
evidence for this observation is that no perpetual motion machine, a machine that does
work without consuming fuel or using some other source of energy, has ever been built.
These remarks may be summarized as follows. If we write w for the work done on a system,
q for the energy transferred as heat to a system, and U for the resulting change in internal
energy, and then it follows that
U q w (12)
Equation summarizes the equivalence of heat and work and the fact that the internal energy is
constant in an isolated system (for which q = 0 and w = 0). The equation states that the change
in internal energy of a closed system is equal to the energy that passes through its boundary as
heat or work. It employs the acquisitive convention, in which w and q are positive if energy is
transferred to the system as work or heat and are negative if energy is lost from the system. In
other words, we view the flow of energy as work or heat from the systems perspective [1;12].
Heat (q)
Heat flows by virtue of a temperature difference. Heat will flow until temperature gradients
disappear [8]. When a heater is immersed in a beaker of water (the system), the capacity of the
system to do work increases because hot water can be used to do more work than cold water [1].
An exothermic process is a process that releases energy as heat. All combustion reactions
are exothermic. An endothermic process is a process that absorbs energy as heat. An
example of an endothermic process is the vaporization of water. An endothermic process in
a diathermic container results in energy flowing into the system as heat. An exothermic
process in a similar diathermic container results in a release of energy as heat into the
surroundings. If an endothermic process in nature was taken place by a system divided an
adiabatic boundary from its surroundings, a lowering of temperature of the system results;
conversely if the process is exothermic, temperature rises [1]. These are the expected results
of conversation of energy.
Work (w)
Energy is the essence of our existence as individuals and as a society. Just as energy is
important to our society on a macroscopic scale, it is critically important to each living
organism on a microscopic scale. The living cell is a miniature chemical factory powered by
energy from chemical reactions. The process of cellular respiration extracts the energy
stored in sugars and other nutrients to drive the various tasks of the cell. Although the
extraction process is more complex and more subtle, the energy obtained from fuel
molecules by the cell is the same as would be obtained from burning the fuel to power an
internal combustion engine [3].
The fundamental physical property in thermodynamics is work is done when an object is

moved against an opposing force. Doing work is equivalent into raising a weight
somewhere in the surrounding. An example of doing work is the expansion of a gas that
pushes out a piston and raises a weight. A chemical reaction that derives an electric current
through a resistance also does work, because the same current could be driven through a
motor and used to raise a weight [1].
Work is the transferred energy by virtue of a difference in mechanical properties from a

boundary between the system and the surroundings. There are many types of work; such as
mechanical work, electrical work, magnetic work, and surface tension [8].
The SI unit of both heat and work (kg m2/s2) is given the name joule (J), after the English
physicist James Prescott Joule (1818-1889) [6].
1 J = 1 kg m2/s2
In addition to the SI unit joule, some chemists still use the unit calorie (cal). Originally
defined as the amount of energy necessary to raise the temperature of 1 g of water by 1oC
(specially, from 14.5 oC to 15.5 oC), one calorie is now defined as exactly 4,184 J [6].
The workenergy theorem
In mechanics, the workenergy theorem demonstrates that the total work done on a system
is transformed into kinetic energy. This is represented in a very simple and meaningful
equation as follows:
Wtotal Ek (13)
in which, Wtotal is the total work done on the system, including the work carried out by all
the external forces (Wex), as well as the work developed by the internal forces within the
system (Win). Thus;
Wtotal Wex Win (14)
Now, if the external work is separated into two terms, namely the work done by the external
conservative forces (Wex,c), which are associated with an external potential energy (Ep,ex),
and the non-conservative external work (Wnon-ex), the whole external work can be written as:
Wex Wex,c Wnonex Ep,ex Wnonex (15)
Similarly, the work developed by the internal forces within the system can be also expressed
as the sum of a conservative work term plus the non-conservative internal work. Thus;
Win Win,c Wnonin Ep,in Wnonin (16)
Where, Ep,in is the internal potential energy of the system.
As for the kinetic energy of a system, mechanics shows that it can be considered as
consisting of two terms, as follows:
Ek 1 / 2 Mv 2CM Ek ,CM (17)
M being the total mass of the system,vCM the velocity of its center of mass, and Ek,CM the kinetic
energy of the system with respect to its center of mass. The first term on the right-hand side of
equation above represents the kinetic energy of the center of mass of the system, as if it had the
mass of the whole system. Thus, as the velocity vCM is taken with respect to an external
reference frame, this first term can be called the external kinetic energy of the system (Ek,ex),
whereas the second term would be its internal kinetic energy (Ek,in). Accordingly, the increase
of the kinetic energy of a system can be written in the following way:
Ek Ek,ex Ek,in (18)
Then, the substitution of equations 14, 15, 16 and 18 into equation 13 allows us to order
terms as follows:
Wex Ep ,ex Ek ,ex Ep ,in Ek ,in Win (19)
Equation 19 is a general developed expression of the workenergy theorem derived from

mechanics. It should be noticed that, though it does not describe the details of the energetic
terms, each of them is explicitly stated, which will be of great help both to define and to
understand the contribution of thermodynamics when establishing the first law [17].
Reversibility and Reversible changes
A reversible change in thermodynamics is a change that can be reversed by an infinitesimal

modification of a variable. One example of reversibility that we have encountered already is
the thermal equilibrium of two systems with the same temperature. The transfer of energy
as heat between the two is reversible because, if the temperature of either system is lowered
infinitesimally, then energy flows into the system with the lower temperature. If the
temperature of either system at thermal equilibrium is raised infinitesimally, then energy

flows out of the hotter system. There is obviously a very close relationship between
reversibility and equilibrium: systems at equilibrium are poised to undergo reversible
change. Suppose a gas is confined by a piston and that the external pressure, pex, is set equal
to the pressure, p, of the confined gas. Such a system is in mechanical equilibrium with its
surroundings because an infinitesimal change in the external pressure in either direction
causes changes in volume in opposite directions. If the external pressure is reduced
infinitesimally, the gas expands slightly. If the external pressure is increased infinitesimally,
the gas contracts slightly. In either case the change is reversible in the thermodynamic sense.
If, on the other hand, the external pressure differs measurably from the internal pressure,
then changing pex infinitesimally will not decrease it below the pressure of the gas, so will
not change the direction of the process. Such a system is not in mechanical equilibrium with
its surroundings and the expansion is thermodynamically irreversible [12].
To achieve reversible expansion we set pex equal to p at each stage of the expansion. In
practice, this equalization could be achieved by gradually removing weights from the piston
so that the downward force due to the weights always matches the changing upward force
due to the pressure of the gas. When we set pex = p, eqn (dw = pexdV) becomes
dw pexdV pdV reversible expansion work (20)
(Equations valid only for reversible processes are labeled with a subscript rev.) Although the
pressure inside the system appears in this expression for the work, it does so only because
pex has been set equal to p to ensure reversibility. The total work of reversible expansion
from an initial volume Vi to a final volume Vf is therefore
Vf
w pdV (21)
Vi
The integral can be evaluated once it is known how the pressure of the confined gas
depends on its volume [12].
At the isothermal, reversible expansion of a perfect gas, the work made by keeping the
system in thermal contact with its surroundings can be stated as follows;
Vf
w nRT dV / V nRTln V f / Vi (22)
Vi
When the final volume is greater than the initial volume, as in an expansion, the logarithm
in Eqn. 22 is positive and hence w < 0. In this case, the system has done work on the
surroundings and there is a corresponding reduction in its internal energy, but due to there
is a compensating influx of energy as heat, overall the internal energy is constant for the
isothermal expansion of a perfect gas, which clearly indicates the Conservation of Energy
Law. The equations also show that more work is done for a given change of volume when
the temperature is increased: at a higher temperature the greater pressure of the confined
gas needs a higher opposing pressure to ensure reversibility and the work done is
correspondingly greater (Fig. 5) [12].
Figure 5. The work done by a perfect gas when it expands reversibly and isothermally is equal to the
area under the isotherm p = nRT/V. The work done during the irreversible expansion against the same
final pressure is equal to the rectangular area shown slightly darker. It can be seen that the reversible
work is greater than the irreversible work [12].
Adiabatic changes
We are now equipped to deal with the changes that occur when a perfect gas expands
adiabatically. A decrease in temperature should be expected: because work is done but no
heat enters the system, the internal energy decrease, and therefore the temperature of the
working gas also decrease. In molecular terms, the kinetic energy of the particles decrease as
work is done, so their average speed decreases, and hence the temperature decrease. This
means that in the case of perfect gas, change in the distance between particles cannot be
responsible for the changing of internal energy but the Conservation of Energy Law
requires a measurable reduction in kinetic energy of particles, i.e. a reduction in their
velocities. The change in internal energy of a perfect gas when the temperature is changed
from Ti to T f and the volume is changed from Vi to Vf can be expressed as the sum of two
steps (Fig. 6).
In the first step, only the volume changes and the temperature is held constant at its initial
value. However, because the internal energy of a perfect gas is independent of the volume
the molecules occupy, the overall change in internal energy arises solely from the second
step, the change in temperature at constant volume. Provided the heat capacity is
independent of temperature, this change is

U CV T f Ti CV T (23)
Because the expansion is adiabatic, we know that q = 0; because U = q + w, it then follows

that U = ad. The subscript ad denotes an adiabatic process. Therefore, by equating the
two expressions we have obtained for U, we obtain
Wad CV T (24)
Figure 6. To achieve a change of state from one temperature and volume to another temperature and
volume, we may consider the overall change as composed of two steps. In the first step, the system
expands at constant temperature; there is no change in internal energy if the system consists of a perfect
gas. In the second step, the temperature of the system is reduced at constant volume. The overall change
in internal energy is the sum of the changes for the two steps [12].
That is, the work done during an adiabatic expansion of a perfect gas is proportional to the
temperature difference between the initial and final states. That is exactly what it can be
expected on molecular grounds and according to Conversation of Energy, because the
mean kinetic energy is proportional to T, so a change in internal energy arising from
temperature alone is also expected to be proportional to T [12].

1/ c
T f Ti Vi / V f (25)
where c = CV /R (CV :molar heat capacity in constant volume and R: universal gas constant). By
raising each side of this expression to the power c, an equivalent expression is
ViTi c V f T f c (26)
This result is often summarized in the form VTc = constant
4. From the conservation of energy to heat transfer, heat capacity and the
enthalpy
The process of heat moving from one object into another is called heat transfer. The
difference in temperature defines the direction in which the heat flows when two objects
come into contact; heat always flows from a hotter object at a higher temperature into a
colder object at a lower temperature. Heat transfer which can mainly occur in three ways,
namely conduction, convection and radiation changes the temperature of matter; it can also
cause changes in phase or state [7].
When energy is added to a substance and no work is done, the temperature of the substance
usually rises i.e. substance is heated; exception to the case in which a substance undergoes a
change of state-also called a phase transition, such as vaporization/condensation,
melting/freezing, and sublimation. The quantity of energy required to raise the temperature of
given mass of a substance by some amount varies from one substance to another. The amount
of increase also depends on the conditions in which heating takes place. Heat capacity (C) of a
substance is the quantity of energy required to raise its temperature by 1C or 1 K. The heat
capacity differs from substance to substance. In the case of a monatomic gas such as helium
under constant volume, if it is assumed that no electronic or nuclear quantum excitations
occur, each atom in the gas has only 3 degrees of freedom, all of a translational type. No
energy dependence is associated with the degrees of freedom which define the position of the
atoms. While, in fact, the degrees of freedom corresponding to the momenta of the atoms are
quadratic, and thus contribute to the heat capacity. In the somewhat more complex case of a
perfect gas of diatomic molecules, the presence of internal degrees of freedom is apparent.
Table1 shows C v values for some mono and diatomic gases at 1 atm and 25C.
Monoatomic Gases Cv (J/Kmol) Diatomic Gases Cv ( J/Kmol)

He 12.5 H2 20.18
Ne 12.5 CO 20.2
Ar 12.5 N2 19.9
Kr 12.5 Cl2 24.1
Xe 12.5 Br2 (vapor) 28.2
Table 1. C v values for some mono and diatomic gases at 1 atm and 25C.
From Table 1, it can be seen clearly that the heat capacities of all monoatomic gasses have
exactly same values, but they are lower than those of diatomic gasses which include the
contributions of translation vibration, and rotation.
The heat capacity is directly proportional to the amount of substance. Heat capacity is an
extensive property, meaning it is a physical property that scales with the size of a physical
system .That means by doubling the mass of substance, heat capacity can be doubled. The
heat required to increase the temperature from T1 to T2 of a substance can be calculated
using the following equation.
Q C x T (27)
The unit of heat capacity is JoC-1 or JK-1. For many experimental and theoretical purposes it is
more convenient to report heat capacity as an intensive property, as an intrinsically
characteristic property of a particular substance. This is most often accomplished by the
specification of the property per a unit of mass. In science and engineering, such properties
are often prefixed with the term specific. International standards now recommend that
specific heat capacity always refer to division by mass. The units for the specific heat
capacity are [C] = J/kg K in chemistry, the heat capacity is also often specified relative one
mole, the unit for amount of substance, and is called the molar heat capacity, having the
unit, J/mol K. For some considerations it is useful to specify the volume-specific heat
capacity, commonly called volumetric heat capacity, which is the heat capacity per unit
volume and has SI units [S] = J/m3 K. This is used almost exclusively for liquids and solids,
since for gasses it may be confused with specific heat capacity at constant volume.
In thermodynamics, two types of heat capacities are defined; Cp, the heat capacity at
constant pressure and C v, heat capacity at constant volume. The total energy of a system in
thermodynamics is called internal energy which specifies the total kinetic and potential
energy of particles in the system. Internal energy of a system can be changed either by doing
work on the system or heating it as a result of the conversation of energy law. The internal
energy of a substance increases when its temperature is increased. By considering the total
change in internal energy of a substance which is heated at constant pressure, the difference
between heat capacities at two different conditions can be meaningfully interpreted. Heat
capacity in terms of derivative at constant volume is expressed as follows:
Cv U / T v (28)
The first law of thermodynamics argues that the internal energy of a system which is heated
at constant-pressure differs from that at the constant-volume by the work needed to change
the volume of the system to maintain constant pressure. This work arises in two ways: One
is the work of driving back the atmosphere (external work); the other is the work of
stretching the bonds in the material, including any weak intermolecular interactions
(internal work). In the case of a perfect gas, the second makes no contribution.
In order to find out how the internal energy varies with temperature when the pressure
rather than the volume of the system is kept constant; it can be divided both sides of (dU =
(U/V)T dV + (U/T)v dT) by dT and thus;
U / T p U / V T V / T p U / T v (29)
It is usually sensible in thermodynamics to inspect the output of a manipulation like this to

see if it contains any recognizable physical quantity. The partial derivatives on the right in
this expression are the slope of the plot of volume against temperature at constant pressure,
the slope of the plot of internal energy against volume at constant temperature and the slope
of the plot of internal energy against temperature at constant volume, respectively. These
properties are normally tabulated as the expansion coefficient, , of a substance, which is
defined as =1/V (U/T) p, internal pressure, T, and constant volume heat capacity, C v,
respectively. Thus;
U / T p T V Cv (30)
Equation (30) is entirely general for a closed system, which may be in solid, liquid, or gas
states, with constant composition. It expresses the changing of internal energy with the
temperature at constant pressure depends on two terms on the right in this expression The
first term is related to the potential energy of particles and it comprises internal work made
against internal pressure due to thermal expansion which can be considered for all
substances in solid, liquid, or gas states, but weakness of inter-particles interactions in gas
state requires to take account of an additional contribution to identify the real change in
internal energy of any system in gas state heated at constant pressure. The fact that for a
perfect gas, T = 0 and so (U/T)p = Cv ,supports to this remark. The second term also is
interested in the kinetic energies of particles. That is, the energy at the constant-pressure of
any substance must defined by an another thermodynamic property or function and this
function must include external work made to external pressure due to volumetric expansion
of any system in gas state. This thermodynamic function which takes account of external
work is the enthalpy.
The enthalpy
The change in internal energy is not equal to the heat supplied when the system is free to
change its volume. Under these circumstances some of the energy supplied as heat to the
system is returned to the surroundings as expansion work, so U is less than q [1].
To determine E, it must be measured both heat and work which done by expanding of a
gas. It can be found the quantity of pV work done by multiplying the external pressure (P)
by the change in volume of the gas (V, or Vfinal - Vinitial). In an open flask (or a cylinder with
a weightless, frictionless piston), a gas does work by pushing back the atmosphere (Figure 7)
[18].
w pV (31)
Figure 7. Pressure-volume work. When the volume (V) of a system increases by an amount of V
against an external pressure (p), the system pushes back, and thus does pV work on the surroundings
(w = -p V) [18].
For changes at constant pressure, a thermodynamic variable called the enthalpy, H, is

mathematically defined as follows [1],
H U pV (32)
where U is the internal energy of the system, p is the pressure of the system, and V is the
volume of the system [3].
Since internal energy, pressure, and volume are all state functions, enthalpy is also a state
function. But what exactly is enthalpy? To help answer this question, consider a process
carried out at constant pressure and where the only work allowed is pressure-volume work
(w= - pV). Under this conditions, the expression
U qP w (33)
becomes
U qp pV (34)
or
qp U pV (35)
where qp, U and pV are the transferred energy as heat to the system heated at constant
pressure, change in internal energy and change in pV, respectively. Since p is constant; the
change in pV is due only to a change in volume. Thus
pV p V (36)
H qp (37)
Heat capacity in terms of derivative at constant pressure, i.e. changes in the energy of a
system heated at constant pressure is also expressed as follows:
C p H / T p (38)
The slope of a plot of internal energy against temperature at constant volume, for a perfect
gas CV is also the slope at constant pressure. In order to obtain an easy way to derive the
relation between Cp and CV for a perfect gas, both heat capacities can be used in terms of
derivatives at constant pressure:
Cp Cv H / T p U / T v H / T p U / T p (39)
Then, if (H = U + pV = U + nRT ) is introduced into the first term, which results in
Cp Cv U / T p nR U / T p
and C p Cv nR (40)
This means that in the case of a perfect gas, R, universal gas constant may be considered as
the work done to push back the atmosphere per unit increase in temperature. However, the
general relation between the two heat capacities for any pure substance is demonstrated as
follows;
C p Cv 2TV / T (41)
This formula is a thermodynamic expression, which means that it applies to any substance
(that is, it is universally true). It reduces to previous equation for a perfect gas when it was
set as = 1/T and T = 1/p
Because thermal expansion coefficients, , of liquids and solids are small, it is tempting to
deduce from last equation that for them CpCv. But this is not always so, because the
compressibility T might also be small, so 2/T might be large. That is, although only a little
work need be done to push back the atmosphere, a great deal of work may have to be done
to pull atoms apart from one another as the solid expands. As an illustration, for water at 25
0C, Eqn (41) gives Cp = 75.3 J/Kmol compared with Cv = 74.8 J/Kmol. In some cases, the two
heat capacities differ by as much as 30 per cent [21]. The constant-pressure heat capacity Cp
differs from the constant-volume heat capacity Cv by the work needed to change the volume
of the system to maintain constant pressure. This work arises in two ways. One is the work
of driving back the atmosphere (external work); the other is the work of stretching the bonds
in the material, including any weak intermolecular interactions (internal work). In the case
of a perfect gas, the second makes no contribution. This suggests that the difference between
two heat capacities is related to both internal work and external work done by the particles
of a substance as an expended result of the conservation of energy.
By considering the variation of H with temperature at constant volume, the validity of the
enthalpy function can be differently verified. Firstly; for a closed system of constant
composition, H is expressed in the total differential of T and p;
dH ( H / p T dp H / T p dT (42)
and then, divided this equation though by dT;
H / T v H / p T p / T v Cp (43)
The manipulation of this expression provides more involved equation which can be applied
to any substance. Because all the quantities that appear in it can be measured in suitable
experiments.
H / T v (1 / T ) C p (44)
where the isothermal compressibility, , is defined as
T 1 / V V / p T (45)
and the Joule Thomson coefficient, , is defined as
(T / p)H (46)
This expression derived for the changing of the enthalpy with temperature at constant
volume suggests that change in H with increased temperature at constant V is lower than
that at constant p and the difference between them depend on some characteristic
properties of particles, such as , and ,, indicating its relation with the absence of
external work.
The measurement of an enthalpy change
An enthalpy change can be measured calorimetrically by monitoring the temperature

change that accompanies a physical or chemical change occurring at constant pressure. A
calorimeter for studying processes at constant pressure is called an isobaric calorimeter. A
simple example is a thermally insulated vessel open to the atmosphere: the heat released in
the reaction is monitored by measuring the change in temperature of the contents. For a
combustion reaction an adiabatic flame calorimeter may be used to measure T when a
given amount of substance burns in a supply of oxygen. Another route to H is to measure
the internal energy change using a bomb calorimeter, and then to convert U to H.
Because solids and liquids have small molar volumes, for them both pVm , external work
and internal work is so small that the molar enthalpy and molar internal energy are almost
identical (Hm = Um + pVm Um). Consequently, if a process involves only solids or liquids, the
values of H and U are almost identical. Physically, such processes are accompanied by a
very small change in volume; the system does negligible work on the surroundings when
the process occurs, so the energy supplied as heat stays entirely within the system, as a
expended result of the conversation of energy.
Calorimeters
The heat that is given out or taken in, when a chemical reaction occurs can be measured
using a calorimeter. A simple, constant-pressure calorimeter (Coffee-cup calorimeter) for
measuring heat for reactions in solution is shown in Fig. 8. This figure also shows a bomb
calorimeter. The container is an expanded polystyrene cup with a lid. This material provides
insulation which ensures that heat loss to, or gains from the surroundings is minimized; the
outer cup in Fig. 8 provides additional insulation. As the reaction takes place, the
thermometer records any change in temperature.
(a) (b)
Figure 8. Calorimeter types; (a) Coffee-cup calorimeter [18] and (b) Bomb calorimeter [22].
The relationship between the temperature change and the energy is given as follows;
Energy change in J m g .C J / gK . T K (47)
where C is the specific heat capacity of the solution. Since the reaction is carried out at
constant pressure, the energy is equal to the enthalpy change. For dilute aqueous solutions,
it is usually sufficient to assume that the specific heat capacity of the solution is the same as
for water: Cwater 4.18 J/gK. It is assumed that no heat is used to change the temperature of the
calorimeter itself. Where a calorimeter is made from expanded polystyrene cups, this is a
reasonable assumption because the specific heat capacity of the calorimeter material is so
small. However, the approximation is not valid for many types of calorimeter and such
pieces of apparatus must be calibrated before use. Measurements made in the crude
apparatus shown together with in Figure 8 are not accurate, and more specialized
calorimeters, such as bomb calorimeter must be used if accurate results are required [18;19].
A bomb calorimeter is ideally suited for measuring the heat evolved in a combustion
reaction. The system is everything within the double-walled outer jacket of the calorimeter.
This includes the bomb and its contents, the water in which the bomb is immersed, the
thermometer, the stirrer, and so on. Before using above equation, it must be emphasized
that a rise in temperature of a system insulated with its surrounding does not occur by any
heat transferred from the surroundings to the system because of the temperature difference
between them. The difference in temperature observed during the measuring may be arisen
from the change in the composition of system and considered as if the involved reaction
occurs as exothermic or endothermic in diathermic condition. At constant pressure (where
only pV work is allowed), the change in enthalpy H of the system is equal to the energy
flow as heat. This means that for a reaction studied at constant pressure, the flow of heat is a
measure of the change in enthalpy for the system. For this reason, the terms heat of reaction
and change in enthalpy are used interchangeably for reactions studied at constant pressure.
For a chemical reaction, the enthalpy change is given by the equation
H H products Hreactants (48)
In a case in which the products of a reaction have a greater enthalpy than the reactants, H
will be positive. Thus heat will be absorbed by the system, and the reaction is endothermic.
On the other hand, if the enthalpy of the products is less than that of the reactants, H will
be negative. In this case the overall decrease in enthalpy is achieved by the generation of
heat, and the reaction is exothermic [3]. Energy diagrams for exothermic and endothermic
reactions are shown in Figure 9.
Standard enthalpy change
The standard enthalpy change of a reaction refers to the enthalpy change when all the
reactants and products are in their standard states. The notation for this thermochemical
quantity is rH0 (T) where the subscript r stands for reaction, the superscript o means
standard state conditions, and (T) means at temperature T. This type of notation is found
for other thermodynamic functions that we meet later on.
(a) (b)
Figure 9. Energy diagrams for exothermic (a) and endothermic reactions (b) [20].
The standard state of a substance is its most thermodynamically stable state under a
pressure of 1 bar (1.00 x 105 Pa) and at a specified temperature, T. Most commonly, T =
298.15 K, and the notation for the standard enthalpy change of a reaction at 298.15K is then
rH0 (298.15 K). It is usually sufficient to write rH0 (298 K) [19].
Standard enthalpies of formation

The standard enthalpy of formation (Hf0) of a compound is defined as the change in
enthalpy that accompanies the formation of one mole of a compound from its elements with
all substances in their reference states. The reference state of a element is its most
thermodynamically stable state under a pressure of 1 bar (1.00 x 105 Pa) and at a specified
temperature, T.
A degree symbol on a thermodynamic function, for example, H, indicates that the
corresponding process has been carried out under standard conditions. The standard state
for a substance is a precisely defined reference state. Because thermodynamic functions
often depend on the concentrations (or pressures) of the substances involved, it must be
used a common reference state to properly compare the thermodynamic properties of two
substances. This is especially important because, for most thermodynamic properties, it can
be measured only changes in the property
Enthalpy is a state function, so it can be chosen any convenient pathway from reactants to
products and then sums the enthalpy changes along the chosen pathway. A convenient
pathway, shown in Fig. 10, involves taking the reactants apart to the respective elements in
their reference states in reactions (a) and (b) and then forming the products from these
elements in reactions (c) and (d). This general pathway will work for any reaction, since
atoms are conserved in a chemical reaction [3].
From Fig. 10, it can be seen that reaction (a), where methane is taken apart into its elements,
CH4 g C s 2 H 2 g (49)
is just the reverse of the formation reaction for methane:
C s 2 H 2 g CH 4 g H 0 f 75 kJ / mol (50)
Since reversing a reaction means changing the sign of H, but keeping the magnitude the
same, H for reaction (a) is H0f, or 75 kJ. Thus H0 (a) = 75 kJ.
It can be secondarily considered reaction (b). Here oxygen is already an element in its
reference state, so no change is needed. Thus H0 (b) = 0.
Figure 10. In this pathway for the combustion of methane, the reactants are first taken apart in
reactions (a) and (b) to form the constituent elements in their reference states, which are then used to
assemble the products in reactions (c) and (d) [3].
The next steps, reactions (c) and (d), use the elements formed in reactions (a) and (b) to form
the products. That is, reaction (c) is simply the formation reaction for carbon dioxide:
C s O2 g CO2 g H 0 f 394 kJ / mol (51)
and
H 0( c ) H 0 f for CO2 g 394 kJ / mol (52)
Reaction (d) is the formation reaction for water:
H 2 g 1 / 2O2 g H 2O l H 0 f 286 kJ / mol (53)
However, since 2 moles of water are required in the balanced equation, it must be formed 2
moles of water from the elements:
2 H2 g O2 g 2 H2O (54)
Thus
H 0( d ) 2 x H 0 f for H 2O l 2 286 kJ / 572 kJ / mol (55)
It has now been completed the pathway from the reactants to the products. The change in
enthalpy for the reaction is the sum of the H values (including their signs) for the steps:
H 0 reaction H 0( a) H 0 b H 0( c ) H 0( d ) (56)
H 0 f for CH 4 g 0 H 0 f for CO2 g 2 x H 0 f for H 2O l ]

(57)
75 kJ 0 394 kJ 572 kJ 891 kJ
This process is diagramed in Fig. 11. It can be seen that the reactants are taken apart and
converted to elements [not necessary for O2 (g)] that are then used to form products. It can be
seen that this is a very exothermic reaction because very little energy is required to convert the
reactants to the respective elements but a great deal of energy is released when these elements
form the products. This is why this reaction is so useful for producing heat to warm homes
and offices. If it is examined carefully the pathway used in this example, it can be understood
that first, the reactants were broken down into the elements in their reference states and then
the products were then constructed from these elements. This involved formation reactions
and thus enthalpies of formation. The entire process can be summarized as follows:
H 0 reaction p H 0 f products p H 0 f ( reactants ) (58)
where, is stoichiometric coefficients for both reactants and products. The enthalpy change
for a given reaction can be calculated by subtracting the enthalpies of formation of the
reactants from the enthalpies of formation of the products.
Figure 11. A schematic diagram of the energy changes for the reaction CH4 (g) + 2O2 (g) CO2 (g) +
2H2O (l) [3].
Hesss law
Another way to calculate values of H for reactions involves manipulating equations for
other reactions with known H values. When chemical equations are added to yield a
different chemical equation, the corresponding H values are added to get the H for the
desired equation. This principle is called Hesss law and it is an application of the first law
of thermodynamic or the conservation of energy. For example, it can be calculated the H
for the reaction of carbon with oxygen gas to yield carbon dioxide from the values for the
reaction of carbon with oxygen to yield carbon monoxide and that of carbon monoxide plus
oxygen to yield carbon dioxide [9].
Desired
C s O2 g CO2 g (59)
Given
C s 1 / 2 O2 g CO g H 110 kJ (60)
CO g 1 / 2 O2 g CO2 g H 283 kJ (61)
Adding the two chemical equations given:
C( s) CO( g ) O2( g ) CO2( g ) CO( g ) (62)
Eliminating CO from both sides results in the desired equation:
C s O2 g CO2 g (63)
Therefore, adding these two H values will give the H desired:
H 110 kJ 283 kJ 393 kJ (64)
It must be noticed that enthalpies of formation have not been used explicitly in this process [9].
The Hesss law is shown schematically in Fig 12 [3].
Figure 12. A schematic diagram of Hesss law. The same change in enthalpy occurs when nitrogen and
oxygen react to form nitrogen dioxide, regardless of whether the reaction occurs in one (red) or two
(blue) steps [3].
The overall reaction can be written in one step, where the enthalpy change is represented by
H1 [3].
N2 g 2O2 g 2 NO2 g H1 68 kJ (65)

This reaction also can be carried out in two distinct steps, with enthalpy changes designated
by H2 and H3:
N2 g O2 g 2 NO g H2 180 kJ (66)
2 NO g O2 g 2 NO2 g H3 112 kJ (67)
Net reaction:
N2 g 2O2 g 2 NO2 g H2 H3 68 kJ (68)
The sum of the two steps gives the net, or overall, reaction and that
H1 H 2 H 3 68 kJ (69)
The temperature dependence of reaction enthalpies

The standard enthalpies of many important reactions have been measured at different
temperatures. However, in the absence of this information, standard reaction enthalpies at
different temperatures may be calculated from heat capacities and the reaction enthalpy at
some other temperature (Fig. 13). In many cases heat capacity data are more accurate than
reaction enthalpies. It follows from eqn (dH = CpdT at constant pressure) that, when a
substance is heated from T1 to T2, its enthalpy changes from
H (T1) to
T2
H T2 H T1 CpdT (70)
T1
(It has been assumed that no phase transition takes place in the temperature range of
interest.) Because this equation applies to each substance in the reaction, the Standard
reaction enthalpy changes from H0r (T1) to
T2
Hr 0 T2 Hr 0 T1 CpdT (71)
T1
where Cp is the difference of the molar heat capacities of products and reactants under
standard conditions weighted by the stoichiometric coefficients that appear in the chemical
equation [12];
C p C p( Products ) C p Reactants (72)
Equation 71 is known as Kirchhoffs law. It is normally a good approximation to assume

that Cpr is independent of the temperature, at least over reasonably limited ranges.
Although the individual heat capacities may vary, their difference varies less significantly.
In some cases the temperature dependence of heat capacities is taken into account by using
equation below.
C p a bT c / T 2 (73)
Figure 13. An illustration of the content of Kirchhoffs law. When the temperature is increased, the
enthalpy of both the products and the reactants increases. In each case, the change in enthalpy depends
on the heat capacities of the substances. The change in reaction enthalpy reflects the difference in the
changes of the enthalpies [12].
Author details
Ahmet Grses
Ataturk University, K.K. Education Faculty, Department of Chemistry, Erzurum, Turkey
Mehtap Ejder-Korucu
Kafkas University, Faculty of Science and Literature, Department of Chemistry, Kars, Turkey
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[8] Lee. H-G., Chemical Thermodynamics for Metals and Materials. Imperial College Press.
1999.
[9] Goldberg. D. E., Fundamentals of Chemistry. Fifth edition. The McGraw-Hill. 2007
[10] Powers. J. M., Lecture Notes on Thermodynamics. Notre Dame, Indiana; USA. 2012
[11] Tanaka. T., The Laws of Thermodynamics. Cambridge Universty Press.
[12] Atkins. P., and de Paula. J., Atkns Physical Chemistry. Oxford Universty Press 2009.
[13] Laider, Keith, J. (1993). The World of Physical Chemistry (http:/ / books. google. com)
Oxford University Press. ISBN 0-19-855919-4.
[14] International Union of Pure and Applied Chemistry, Physical Chemistry Division.
"Quantities, Units and Symbols in Physical Chemistry" (http:/ / old. iupac. org/
publications/ books/ gbook/ gren book). Blackwell Sciences. p. 7. "The adjective specific
before the name of an extensive quantity is often used to mean divided by mass."
[15] International Bureau of Weights and Measures (2006), The International System of Units
(SI) (http:/ / www. bipm. org) (8th ed.), ISBN 92-822-2213-6,
[16] Gilbert. T. R., 7.chemistry-the science in context-second edition. 2008.
[17] Minguez. J. M., The work-energy theorem and the first law of thermodynamics.
International Journal of Mechanical engineering Education 33/1.
[18] Silberg. M. S., Principles of General Chemistry. McGraw-Hill Higher Education. 2007.
[19] Housecroft. C. E and Constable. E. C., Chemistry: An Introduction to Organic, Inorganic
and Physical Chemistry. 3rd Edition. Pearson Prentice Hall. 2006.
[20] Jones. A., Clement. M., Higton. A., and Golding. E., Access to Chemistry. Royal Society
of Chemistry. 1999.
[21] Atkins. P. W., Physical Chemistry. Oxford University Press. Sixth Edition. 1998.
[22] Mortimer. R. G., Physical Chemistry. Third edition. Academic Press in an imprint of
Elsevier.2008.
Chapter 2
Useful Work and Gibbs Energy
Nikolai Bazhin
1. Introduction
Devices for performing chemical reactions are widely used to produce heat and work. Heat,
in turn, produces work, e.g., in the form of electric energy in the so-called heat engines. It is
the well-known fact that the efficiency of heat engines is restricted by Carnot principle.
Therefore, it is generally recognized that heat cannot be fully converted to work. The
efficiency of electric energy production due to the burning of fossil fuel of various kinds
varies from 30 to 50 %.
On the other hand, there are galvanic and fuel cells whose efficiency can reach theoretically
unity if it implies the ratio between the electric energy produced and the value of a change
in Gibbs energy during chemical reactions occurring in a cell. These devices operate at
constant temperature and pressure. It is concluded then that the devices, similar to a
galvanic cell, cannot work at constant and uniform temperature according to the principle of
heat engine. These devices assumed to operate only due to the direct transformation of
chemical reaction energy, described by a change in the Gibbs energy, into work [1]. This
viewpoint causes, however, numerous contradictions. The goal of this work is to analyze in
detail the mechanism of useful work and heat production in chemical systems functioning at
constant temperature and pressure.
2. Fundamental functions
In this Section, the fundamental functions of thermodynamics will be characterized, as the
fundamental functions play the important role in the description of the process of the
energy transformation. This notion includes four functions, i.e., internal energy, enthalpy,
Helmholtz energy, and Gibbs energy. All of them are the state functions of energy
dimension. It is generally believed that the value with energy dimension describes energy
but this is by no means always the case. Below, the fundamental functions will elucidate
whether these are energy values or not.
2.1. Internal energy

According to IUPAC [2], "internal energy U is the quantity the change in which is equal to
the sum of heat, q, brought to the system and work, w, performed on it,
U q w ". Because of various transformations, the internal energy can be converted to
other kinds of energy. However, the initial quantity of internal energy should be conserved
due to the law of energy conservation. Conservation is the most important characteristic of
energy. Hence U is energy.
2.2. Enthalpy
According to IUPAC, "enthalpy, H =U + pV is the internal energy of a system plus the product
of pressure and volume. Its change in a system is equal to the heat, brought to the system at
constant pressure [2]. It is worth noting that the change in the value describing energy
always corresponds to the change in energy and not only in some special cases. Generally, a
change in enthalpy may be inconsistent with the change in real physical values. Let us
consider, e.g., the process of ideal gas heating at constant volume. The quantity of heat,
taken in by ideal gas from the heat bath, q , equivalently changes only the internal gas
energy, U q , and simultaneously causes changes in gas enthalpy, H U pV q .
However, this change fails to reflect the changes in any physically significant values. Thus,
the enthalpy is not energy but a function of state having the dimension of energy. It is easier
and more correct to assume that the enthalpy is the part of a calculating means used to
describe thermodynamic processes.
2.3. Helmholtz energy

According to IUPAC, "Helmholtz energy (function), A, is the internal energy minus the
product of thermodynamic temperature and entropy: A = U - TS. It was formerly called
free energy" [2]. Let us see why this quantity was called free energy. According to the first
law [3]
U q w , (1)
where q is the heat, entering the system, and w is the total work performed on the system by
the surroundings. Usually, the total work is given as the sum of two terms: expansion work
( pV ) and so-called useful work ( wuseful )
w pV wuseful . (2)
If the process occurs at constant volume, the expansion work is absent and w describes the
useful work. In the case of reversible process [3]
q T S. (3)
Thus, eq. (1) is of the form in the case of reversible process

Useful Work and Gibbs Energy 31
wuseful U T S (U TS) A , (4)
where A is the change in Helmholtz energy at constant temperature and volume. Since
the term "energy" means the capacity of the system to perform work, from eq. (4) it is
formally concluded that A is the energy (but in this case eq. (4) can have the second
explanation A is the numerical characteristic of work and not the work itself). Further,
from eq. (4) it was concluded that only the part of internal energy U minus TS can be used to
produce work. Therefore, the TS quantity was called "bound energy" and (U - TS) "free
energy". The meaning of these notions will be considered in more detail using the Gibbs
energy as an example because it is more often used in chemical applications.
2.4. Gibbs energy

According to IUPAC [2], "Gibbs energy (function), G ( H TS) , is the enthalpy minus the
product of thermodynamic temperature and entropy. It was formerly called free energy or
free enthalpy". The reasons for the appearance of the term "Gibbs energy" are similar to
those discussed when considering the Helmholtz energy except for the fact that the Gibbs
energy describes the reversible useful work performed at constant temperature and
pressure. This is readily observed by substituting eq. (3) and eq. (2) into eq. (1) with regard
to V p 0
wuseful H T S ( H TS) G , (5)
where G is the change in Gibbs energy at constant temperature and pressure in the
reversible process.
Unfortunately, the word "energy" as defined by IUPAC for a Gibbs energy (and also for a
Helmholtz energy), causes great confusion. The Gibbs energy G = H TS consists of two
terms, the enthalpy and the entropy one. The origin of both of the terms is quite different
despite the same dimension. The enthalpy, considered above, is not energy.
Consider now the problem of TS nature. In the case of the reversible process T S q , but in
the case of the irreversible process T S q and additional contributions to T S can arise
without change in energy. For example, it is well known the increase of the entropy in the
process of ideal gas expansion in vacuum without heat consumption (q = 0).
Let us consider another example. Let the ideal gas-phase system involves a spontaneous
process of the monomolecular transformation of substance A into B. As suggested a change in
enthalpy tends to zero in this reaction. Thus, the internal energy, temperature, pressure, and
volume will not undergo changes in this process. However, the entropy will increase due to
the entropy of the mixing, because the entropy is a function of state. The value of the TS
product will increase accordingly. However, the energy and even the bound energy cannot
arise from nothing, whereas the entropy, being a function of state, can increase thus reflecting
a change in system state without any changes in the internal system energy. Therefore, the TS
term is not the energy, which also implies the absence of the term "bound" energy.
Since neither enthalpy nor TS are the energy quantities, the difference between them cannot
represent energy. Thus, G cannot represent energy precisely in terms of this notion. Note that
in the irreversible process, occurring at constant temperature and pressure, the Gibbs energy
decreases and thus, is not conserved. This is readily demonstrated by e.g., the aforementioned
example of a monomolecular transformation of substance A into B. Thus, conservation, as the
most important criterion for energy quantity, fails for the Gibbs energy. It is concluded then
that the Gibbs energy is not energy [4] but a function of state. In this regard, the Gibbs energy
does not differ from heat capacity. The notions of the non-existing in reality quantities of free
energy" and "bound energy" cause only confusion and are, at present, obsolete [5].
Nevertheless, the notions that the Gibbs energy is the energy and thus, obeys conservation
laws, prove to be long-lived, which causes erroneous interpretation of a number of
processes some of which are of paramount importance.
Let us consider now the reaction of adenosine triphosphate (ATP) hydrolysis in water
solution which is of great concern in biochemistry
ATP + H2O = ADP + Pi.
Under the standard conditions [6] rG o 7, r H o 4 kcalmol-1. According to D. Haynie

[6, p. 143], "measurement of the enthalpy change of ATP hydrolysis shows that H o 4
kcalmol-1. That is, the hydrolysis of one mole of ATP at 25 results in about 4 kcalmol-1
being transferred to a solution in the form of heat and about 3 kcalmol-1 remaining with
ATP and Pi in the form of increased random motion."
The heat of 4 kcalmol-1 is actually released into solution due to hydrolysis. Unfortunately, it is
then assumed that the Gibbs energy is conserved which makes his difference in r H o and
rG o of 3 calmol-1 be located on the degrees of freedom of product molecules. However, in
this connection, the product molecules could appear in the non-equilibrium excited states and
transfer this energy to solvent molecules which would result in the emission of 7 kcalmol-1
rather than 4 kcalmol-1 which contradicts the experiment. There are no additional 3 calmol-1
on the degrees of freedom of A and Pi because the Gibbs energy is not conserved.
2.5. Conclusions
Thus, among the four quantities, that claims to be called energy quantity, only the internal
energy deserves this name. The other functions, i.e., enthalpy , Helmholtz energy A, and
Gibbs energy G are the parts of a mathematical apparatus for calculating various quantities,
such as useful work, equilibrium constants, etc. This also means that the useful work is only
calculated by using functions A and G, but cannot arise from the change in either the
Helmholtz or the Gibbs energy. The physical nature of the work performed should be
considered separately. Since the Helmholtz energy and the Gibbs energy are not energies,
then, to avoid misunderstanding, it is better to exclude the word energy from the name of
corresponding functions and to use the second variant of the name of these functions
according to IUPAC: a Helmholtz function and a Gibbs function [7].
3. Direct conversion of chemical reaction energy to useful work

This Section is devoted to the discussion of the generally accepted theory of the direct
conversion of energy [1, 8] produced by chemical reaction to useful work. For simplicity,
hereafter exergonic ( rG 0) and exothermic ( r H 0) reactions will be considered.
The useful work of the chemical reaction occurring at constant temperature and pressure in
the reversible conditions can be calculated through the change in the Gibbs function (5). When
the interest is the useful work performed by the system in the environment ( wuseful ) , then
wuseful r H T rS rG. (6)
From eq. (6) it follows formally that the useful work of the reversible system in the
environment is the sum of the enthalpy member ( r H ) and the entropy member T rS . In
this connection it is interesting to discuss the various situations which arise in dependence
on the relation between ( r H ) and T rS .
From eq. (6) it follows, that for rS 0 the useful work in the environment exceeds ( r H ) :
wuseful r H . Therefore, the system must drag the thermal energy from the environment
in the volume T rS to perform useful work. What is the physical reason for thermal energy
consumption? Why does the system consume thermal energy of volume T rS neither more
or less? How can two different contributions produce the same useful work?
The second case of rS 0 is also of interest. In this case wuseful r H and the system
must evolve the part of reaction heat to the environment. Why cannot the system use the
total reaction heat for useful work production if this energy is at its disposal? Why can the
system transfer energy of volume T rS and neither more or less to the environment?
The third case is r H 0 . Here the system can use only the thermal energy of the
environment to produce useful work.
In the fourth case rS 0 and the system performs work formally due to the reaction heat
( r H ) without exchanging thermal energy with the environment. But it is not the case.
As mentioned in the Introduction, at present, it is generally accepted that the high efficiency
of reversible devices is inconsistent with the notions that heat can be used to produce work
and that such devices realize the direct conversion of chemical system energy into work. But
below it will be shown that in all the cases, the useful work results from the heat of volume
rG dragged from the environment.
4. A mechanism of useful work production - A Vant Hoff Equilibrium

Box
In this Section, it will demonstrate the mechanism of producing useful reversible work
which involves no notions of the direct conversion of reaction energy into useful work. To
this end, let us consider a Vant Hoff equilibrium box (VHEB) [9 11]. A thermodynamic
system must provide realization of the reversible process. This means that all changes in the
system are infinitely slow at infinitely minor deviation from equilibrium.
It is assumed that in the system the following reaction occurs
i Ai j Bj , (7)
i j
where A i are the reagents and B j are the products. The reaction takes place in the reactor
(Fig. 1) where the reagents and products are in equilibrium. The chemical process is
afforded by reservoirs with reagents and products contained in the system. For simplicity,
the reagents and products are assumed to be in standard states. The system should have
instruments to transport both the reagents from standard vessels to reactor and the products
from reactor to standard vessels. In addition, the system should have tools to perform work,
because the reversible process must be followed by reversible work production. The
instruments and tools for performing work can be used together. The reactor, transporting
instruments, and tools for performing work can be placed either separately or together. To
provide constant and uniform temperature, it is necessary to locate the system, including
reactor, standard vessels, transporting instruments, and tools in a thermostat, which can
also imply the environment of constant temperature.
Figure 1. Production of useful work and heat in a closed reversible system. Ast (Bst) indicate the
reagents Ai (products Bj) in the standard states; Aeq (Beq) indicate the reagents Ai (products Bj) in the
equilibrium states, which correspond to the equilibrium at the reactor; the green figures in circles
indicate the step numbers (see text)
Let us consider reversible chemical process in a closed system (Fig. 1). The realization of the
reversible chemical process consists in reversible transformation of the reagents to products
via chemical reaction. Let us consider the closed system.
4.1. Closed system

The process of reversible work production includes six stages.
Step 1. A small amount of substance Ai is removed from the vessel with reagent Ai in the
standard state upon reversible process. Gaseous substances can be removed from a
standard vessel and put into a portable cylinder with pistons [11]; solid or liquid
substances are placed in lock chambers.
Then, the change in the Gibbs function and the work are zero ( G1i 0, w1i 0) because a
minor portion of substance Ai is in the same standard state as the residual reagent.
Step 2. Reagent Ai is transformed reversibly from the standard into the equilibrium state in
the reactor. For example, for ideal gas, the gas pressure will vary from a standard value
to the equilibrium partial value in the reactor. In this stage, the reversible work w2 i is
produced and G2 i 0 . The work w2 i can be done only due to thermostat heat
because there are no other energy sources in the system (reaction is in the equilibrium).
This work depends on the difference in the physical states of reagent Ai in the initial
and equilibrium states. All reagents Ai participate in all stages in quantities
proportional to i . For ideal gas, the useful work is
w2 i i RT ln( pi ,eq / pi ,st ), (8)
where pi ,eq is the equilibrium pressure of i-th gas in the reactor, and pi ,st is the pressure of
i-th gas in a standard vessel. For gaseous components, e.g., the process of reversible gas
expansion (compression) in a portable cylinder for producing the maximum useful work,
must proceed to the value pi ,eq . If expansion (compression) stops at pi pi ,eq , then the inlet
of gas into the reactor causes irreversible gas expansion and thus, the useful work will be
less than the maximum one. When due to expansion (compression) the final pressure is less
than pi ,eq , then the inlet of gas into the reactor causes the irreversible inlet of the i-th gas
from an equilibrium mixture in the reactor to the portable cylinder, which also leads to a
decrease in useful work. The solid and liquid substances can be transported by lock
chambers. The pressure above either solid or liquid substances is varied from 1 bar to the
value of the total equilibrium pressure in the reactor. The pressure is created using a minor
portion of equilibrium reaction mixture.
The thermostat enthalpy varies as follows: H 2 i ,thermostat w2 i .
Step 3. Reagent Ai is reversibly introduced into the reactor. Gaseous components are
introduced into the reactor through semipermeable membranes using portable cylinders
[11]; the solid or liquid ones by means of lock chambers. Hence, G3 i 0, w3i 0 .
The useful work production and the change in thermostat enthalpy ( H 2,thermostat ) take
place only at step 2:
w2 H 2,thermostat , (9)
where w2 w2i and H 2,thermostat H 2i ,thermostat .

i i
The same procedure is used to bring products from the standard vessels to reactor.
Step 4. An equivalent amount of product BJ is reversibly removed from the reactor. After
this step is G4 j 0, w4 j 0 .
Step 5. Product BJ, removed from the reactor, is reversibly transformed from the
equilibrium state into the standard one to perform work w5 j . The change in the Gibbs
function is not zero, G5 j 0 . The change in the thermostat enthalpy is
H 5 j ,thermostat w5 j .
Step 6. Product BJ, removed from the reactor, is reversibly introduced into the standard
vessel. In this case is G6 j 0 and w6 j 0 .
The change in the thermostat enthalpy upon thermal energy conversion into useful work at
step 5 is
w5 H 5,thermostat , (10)
where and w5 w5 j , H 5,thermostat H 5 j ,thermostat

j j
The change in the thermostat enthalpy at the second and fifth steps obeys the equation
H 2,thermostat H 5,thermostat Qdragged , (11)
where Qdragged is the heat dragged by tools.
For the reversible process, the maximal useful work is numerically equal to rG , eq. (5)
and, hence, the heat dragged by tools from thermostat in the volume
wuseful w2 w5 rG r H T rS Qdragged . (12)
The process has resulted in the useful work of the reaction, rG , but the reaction did not
occur yet. To put it otherwise, reaction work was performed without reaction. Only the
thermal energy of the thermostat (environment) may be the source of work. This means that
the process of useful work production and the reaction itself may be temporally and
spatially separated. Thus, eq. (6) numerically connects reaction parameters and the
magnitude of the work. However, no reaction energy is needed to produce the work. There
is no need to subdivide energy sources into reaction source ( r H ) and thermal T rS ,
because there is only one energy source: the thermal energy of thermostat (environment).
For ( rS 0) , the thermal energy dragged by the tools exceeds r H , (Qdragged r H ) ; in

the case of ( rS 0) , the dragged thermal energy is less than r H (Qdragged r H ) ; in
the case of ( rS 0) the energy extracted is equal to r H (Qdragged r H ) and for
( r H 0) the dragged thermal energy is of volume T rS (Qdragged T rS) . The volume of
extracted thermal energy is controlled by chemical equilibrium via rG .
Thus, the mixture in the reactor is moved off balance to be restored later. As a result, the
reaction heat is emitted into the thermostat. Indeed, because of the elementary chemical act
in the reactor, the energy released concentrates at the degrees of freedom of the product
molecules. As the reactor temperature is constant, this energy is dissipated in the reactor
and transferred to the thermostat which causes a r H change in thermostat enthalpy. The
total change in thermostat enthalpy is
H thermostat w2 w5 r H . (13)
The cycle is over. Equations (12, 13) can be used to calculate the total change in thermostat
enthalpy
H thermostat rG r H T rS. (14)
The change in thermostat enthalpy is controlled only by reaction entropy [11].
4.2. The main principles of reversible device functioning in useful work

production
This consideration demonstrates the main characteristics of the reversible process of useful
work production at constant temperature and pressure in closed systems:
1. The useful work arises from the stage of the reversible transport of reagents from reservoir
to reactor and from the stage of the reversible transport of products from the reactor.
2. The only energy source of useful work is the thermal energy of thermostat (or
environment).
3. The heat released by chemical reactions is dissipated to the thermostat; the reaction heat
is infinitely small in comparison with the volume of the thermostat thermal energy;
therefore no reaction heat is really needed to produce work.
4. Although the useful work is produced by the cooling of one body (thermostat), the
second law of thermodynamics is not violated, because the process is followed by a
change in the amount of reagents and products.
5. The useful work is produced by heat exchange with thermostat (environment)
according to the scheme
reaction heat thermal thermostat energy useful work (scheme I)
6. The maximal useful work is equal the heat dragged by tools from thermostat.
7. Useful work depends on the difference in the concentrations of standard and
equilibrium states of reagents and products. Therefore, the amount of extracted energy
can be calculated via the change in the Gibbs function.
8. There is no direct conversion of the Gibbs energy into useful work. Gibbs energy is
equal numerically the thermal energy dragged by systems from the environment for
doing work.
4.3. The energy limit of chemical reactions - Open systems

Usually, the total energy which can be produced by chemical system, is r H . However,
this holds for closed systems only. For open systems, the case is quite different [11].
The open system is depicted in Fig. 2. As compared with the closed one (Fig. 1), the open
system consists of two thermostats: the first one contains a reactor and the second one
contains standard vessels with substances A and B and tools. The second thermostat can be
replaced by the environment. In the process, steps 1, 2, 5, and 6 occur in the second
thermostat (environment); steps 3 and 4 take place in the first one. Thus, the heat is released
in the first thermostat only and the work is performed by thermal energy of the second
thermostat (environment). The processes of heat and work production are spatially
separated! The energy potential of the open system obeys the equation
q wuseful r H rG (15)
Figure 2. Production of useful work and heat in the open reversible system. The designations see in the
subscription to Fig. 1
In the case of coal burning, it is possible to obtain the double total energy [11]. Thus,
understanding the mechanism of useful work production in the reversible process allows us
to predict an increase in the energy potential of chemical reactions in the open system.
It is worth noting that the open system under study is not a heat pump. The heat pump
consumes energy to transfer heat from a cold body to the warm one. The open system
studied does not consume external energy and produces heat due to chemical reactions in
one thermostat and performs work by extraction of thermal energy from the second one.
4.4. Conclusions
The chemical reaction heat is always released in the reversible chemical processes and
passes to the environment independent of the fact whether the system produces work or
not, whether it is closed or open. The discussed mechanism of useful work production in the
reversible systems did not use such notions as "free energy", "bound energy", "direct Gibbs
energy conversion". The useful work arises only due to the heat exchange with a thermal
basin in the process, described by the scheme I. The total energy of chemical system can be
high and equal to r H rG .
5. The mechanism of electric work production in a galvanic cell

The current theory of galvanic cells [1, 3, 8] is based on a direct transformation of the energy
( rG ) of oxidation-reduction reactions into electric work. However, using VHEB as an
example, It is clear that the energy of chemical reactions is first converted into the thermal
energy of thermostat (environment) and then the thermal energy is extracted from the
thermostat and transformed into work by means of special devices. It is assumed then that in
galvanic cells, useful work is produced via the mechanism similar to the VHEB one [12, 13].
The rG value is used to calculate electric work which does not, however, mean that the
electric work is performed at the expense of the Gibbs energy, all the more it was shown that
the Gibbs energy is not energy. The electric work of a galvanic cell results from the electrodes
discharged. Electric charging of electrodes is caused by chemical reactions in electrodes.
The mechanism of electric energy production in galvanic cells will be solved by analyzing the
behavior of one ion. But it does not denote that thermodynamics will be applied to a real single
ion: thermodynamic parameters of one ion imply the averaged parameters of many ions.
5.1. A galvanic cell

For simplicity a Daniell cell will be considered, consisting of zinc (1) and copper (2)
electrodes (Fig. 3). The activity of salts in solutions is denoted by 1 and 2 , respectively. Let
the cell with an open, external circuit be in equilibrium. Close now the external circuit for
the moment and two electrons will transfer from the zinc to the copper electrode. The
balance of the cell is distorted. Consider now the establishment of equilibrium on the zinc
electrode (Fig 3). To this end, the zinc ion must leave a metallic plate and escape into the
bulk. The dissolving of zinc ions is described by the change in a Gibbs function
rG1 rG1o RT ln a1 , (16)

where rG1o is a standard change in the Gibbs function upon dissolving. The ion penetrates
further into solution with execution of the work ( w1g ) in the electric field
Met11 ,
w1g nF sol (17)
where n is the number of electrons, participating in the reactions, F is the Faraday constant,
Met11 is the difference in potentials of solution and metal. The work described in
and sol
equation (17), is the electric work spent to charge an electrode. It is performed at the
extraction of the thermal energy of solution due to the absence of other energy sources in the
system. Since in equilibrium, the chemical potential of ions in solution equals the chemical
potential of metal, it is possible to derive the equation for electrochemical equilibrium
rG1o RT ln a1 nF Met1
sol
1 0, (18)
which readily gives the expression for both the work performed on the first electrode and its
galvanic potential [3]
Met11 rG1 RT ln a1 ,
w1g nF sol o
(19)
rG1o RT ln a1
Met11
sol . (20)
nF nF
The latter is the potential for a half-cell. Thus, the approach, based on the consideration of
the behavior of one ion, provides a common expression for electrode potential.
Figure 3. Establishment of equilibrium on the electrodes

The change in electrode enthalpy involves dissolution enthalpy and thermal energy
consumption upon ion transport into solution. The equation for dissolution enthalpy is
readily obtained from eq. (16)
ln a1
r H1 r H1o RT 2 , (21)
T
where r H1o is a standard change in enthalpy during ion dissolving. The total change in the
enthalpy of the first electrode ( H1,thermostat ) is the sum of the expressions r H1 and wg1
ln a1
H1,thermostat r H1 wg1 T rS1o RT ln a1 RT 2 T rS1 , (22)
T
where rS1o is a standard change in entropy upon ion dissolving and rS1 is the change in
entropy upon ion dissolving on the first electrode which amounts to
ln a1
rS1 rS1o R ln a1 RT . (23)
T
As follows from eq. (22), the change in enthalpy, related to the first electrode, is independent
of the processes, occurring on the second one. Therefore, studying either release or
absorption of heat on a separate electrode, one may calculate the change in entropy due to
the escape of the ions of the same type into the bulk.
A corresponding expression for the second electrode is of the same form but index "1"
should be substituted by index "2":
rG2 rG2o RT ln a2 , (24)
w2 g nF Met2
sol
2 rG2o RT ln a2 (25)
rG2o RT ln a2
Met2 2
sol . (26)
nF nF
ln a2
r H 2 r H 2o RT 2 , (27)
T
ln a2
rS2 rS2o R ln a2 RT , (28)
T
ln a2
H 2,thermostat r H 2 w2 g T rS2o RT ln a2 RT 2 T rS2 . (29)
T
In the operation of the galvanic cell, the processes on the second electrode are oppositely
directed which should be taken into account in consideration of the thermodynamic cell
parameters.
Equations (20) and (26) allow to get the Nernst equation for the potential of the cell [3]
rG o RT a1
Met2 2 Met11
E sol
sol
ln , (30)
nF nF a2
where E the cell potential, rG o rG1o rG2o .
The electric work of the galvanic cell ( wel ) results from the transformation of the potential
energy of the charged electrodes into electric energy. The potential energy arises from the
thermal energy of both of the electrodes upon ions transport into solution and equals
a1
wel w1g w2 g rG o RT ln wuseful . (31)
a2
The change in thermostat enthalpy is of the form
H thermostat H1,thermostat H 2,thermostat T rS , (32)
which is in fair agreement with similar expression, described by eq. (14), for the VHEB. The
detailed equation for H thermostat can be get after substitution corresponding expressions
(22) and (29) into (32)
ln a2 ln a1
H thermostat T ( rS1o rS2o ) RT ln( a2 / a1 ) RT 2 ( ). (33)
T T
The sum of eqs. (31) and (33) gives the total energy (electric work + heat), produced by the
galvanic cell
ln a2 ln a1
wel Hthermostat r H o RT 2 ( ). (34)
T T
From eq.(34) it follows that the total energy produced by the galvanic cell is equal to the heat
emitted by oxidation-reduction reaction.
Thus, the approach, based on the analysis of the behavior of one ion gives the same results
as the present-day theory. However, it uses not a mysterious, direct transformation of the
chemical energy ( rG ) into electric work, but the concept of chemical energy conversion
into the thermal one, and then, the thermal energy of thermostat (environment) is converted
into the potential energy of charged electrodes [12, 13]. The electric energy of the galvanic
cell arises according to the scheme:
reaction heat thermal thermostat energy potential energy of charged electrodes
electric energy.
Thus, in various systems with uniform temperature, useful work is produced by the same
mechanism through the exchange of thermal energy with thermostat (environment). No
direct conversion of chemical energy into useful work is observed. Unfortunately, in the
galvanic cell, the processes of heat release and useful work production cannot be spatially
separated, because both of them occur in a double layer. Therefore, galvanic cells are
unpromising in production of a double amount of energy.
5.2. A concentration cell

Consider now a concentration cell, consisting of two electrodes, e.g., the zinc ones of
different solution activity. Standard changes in the Gibbs function, enthalpy, and entropy
for the concentration cell tend to zero due to the same chemical nature of both of the
electrodes. By definition, it has been considered that a2 a1 . From eq. (31) it follows
wel RT ln( a2 / a1 ) wuseful , (35)
which is a usual expression for the electric energy of the concentration cell. From eq. (34) it
follows
ln a2 ln a1
wel Hthermostat RT 2 ( ). (36)
T T
For the system in which the activities are temperature-independent, the electric energy
arises from the thermal thermostat energy (environment)
wel H thermostat wuseful , (37)
which is in fair agreement with conventional concepts.
6. Useful work of the systems with concentration gradient

An ideal system with concentration gradient has no potential energy because the mixing
does not result in heat release and H 0 . Nevertheless, the system with concentration
gradient can be used, as any non-equilibrium system, to produce useful work if this system
is supplied with special tools for extracting heat from the environment with a simultaneous
transformation of the extracted thermal energy into work upon the system approaches to the
equilibrium. The volume of useful work is equal to the volume of the heat extracted from
the environment
wuseful H thermostat (38)
The useful work of the system with a concentration gradient wuseful obeys expressions (35)
and (38). The concentration cell is a good example of such a system.
7. General conclusions
Any non-equilibrium state can serve as an energy source. The thermostat (environment) is
an active participant of the process of reversible useful work production in devices
operating at constant temperature. The heat released by chemical reactions, always
dissipates in the thermostat (environment). The useful work is produced by special tools
that provide the extraction of the thermal energy of the thermostat (environment) and the
transformation of thermal energy into work at the process of the restoration of the chemical
equilibrium. The volume of the useful work is equal, in reversible conditions, to the change
in Gibbs function. A spatial separation of reactor and tools can lead to a substantial increase
in the energy produced. The direct conversion of the Gibbs energy into useful work does not
exist. The concepts of free and bound energy become unnecessary.
Author details
Nikolai Bazhin
Institute of Chemical Kinetics and Combustion, Novosibirsk State University, Institutskaya 3,
Novosibirsk, Russia
8. References
[1] Denbigh K (1971) The Principles of Chemical Equilibrium, 3rd ed., The University
Press: Cambridge, 494 p.
[2] IUPAC Green Book (1996) Quantities, Units and Symbols in Physical Chemistry 48 p.
[3] Atkins P (2001) The Elements of Physical Chemistry, 3rd ed., Oxford University Press,
Oxford,.549 p.
[4] Lower S. (2010) Chemistry. Available http://www.chem1.com/acad/webtext/
virtualtextbook.html
[5] Gokcen NA, Reddy RG (1996) Thermodynamics, Second edition, Springer, 416 p.
[6] Haynie DN (2008), Biological Thermodynamics, 2nd ed., Cambridge University Press,
422 p.
[7] Haywood RW (1980) Equilibrium Thermodynamics for Engineers and Scientists, J.
Wiley, N.Y., 456 p.
[8] Adam NK (1956) Physical Chemistry, Oxford, Clarendon Press, 658 p.
[9] Physical Chemistry (1980) Gerasimov YaI, Ed., Chimiya, oscow (in Russian), 1279 p.
[10] Steiner LE (1948) Introduction to Chemical Thermodynamic, 2nd ed.; McGraw-Hill
Book Company, New York, 516 p.
[11] Bazhin NM, Parmon VN (2007) Conversion of the Chemical Reaction Energy into
Useful Work in the Vant Hoff Equilibrium Box. J. Chem. Ed. 84: 1053 1055
[12] Bazhin NM, Parmon VN (2007) Ways of Energy Conversion in Electrochemical Cells.
Doklady Physical Chemistry 417: 335-336
[13] Bazhin NM (2011) Mechanism of electric energy production in galvanic and
concentration cells. J. Eng. Thermophysics 20: 302-307
Section 2
Statistical Thermodynamics
Chapter
Chapter 3
0
Gibbs Free Energy Formula

for Protein Folding
Yi Fang
1. Introduction
Proteins are lifes working horses and natures robots. They participate in every life process.
They form supporting structures of cell, bre, tissue, and organs; they are catalysts, speed up
various life critical chemical reactions; they transfer signals so that we can see, hear, and smell;
they protect us against intruders such as bacteria and virus; they regulate life cycles to keep
that everything is in order; etc., just mention only a few of their functions.
The rst thing drawing our attention of proteins are their size. Proteins are macromolecules,
that is, large molecules. Non-organic molecules usually are small, consisting of from a couple
of atoms to a couple of dozen atoms. A small protein will have thousands of atoms, large ones
have over ten thousand atoms. With their huge number of atoms, one can imaging that how
complicated should be of a protein molecule. Fortunately, there are some regularities in these
huge molecules, i.e., proteins are polymers building up by monomers or smaller building
blocks. The monomers of proteins are amino acids, life employs 20 different amino acids to
form proteins. In cell, a series of amino acids joined one by one into amino acids sequences.
The order and length of this amino acid sequence is translated from DNA sequences by the
universal genetic code. The bond joining one amino acid to the next one in sequence is peptide
bond (a covalent bond) with quite regular specic geometric pattern. Thus amino acids
sequences are also called peptide chains. But the easy translation and geometric regularities
stop here. The peptide chain has everything required to a molecule, all covalent bonds are
correctly formed. But to perform a proteins biological function, the peptide chain has to form
a specic shape, called the proteins native structure. Only in this native structure a protein
performs its biological function. Proteins fall to wrong shapes not only will not perform its
function, but also will cause disasters. Many disease are known to be caused by some proteins
taking wrong structure.
How the peptide chain take its native structure? Is there another genetic code to guide the
process of taking to the native structure? In fact, at this stage, lifes most remarkable drama
48 2Thermodynamics Fundamentals and Its Application in Science Will-be-set-by-IN-TECH
takes stage. Once synthesized, the peptide chain of a protein spontaneously (some need the
help of other proteins and molecules) fold to its native structure. This process is called protein
folding. At this stage, everything is governed by simple but fundamental physical laws.
The protein folding problem then can be roughly divided into three aspects: 1. folding
process: such that how fast a peptide chain folds, what are the intermediate structures
between the initial shape and the native structure. 2. the mechanics of the folding, such as
what is the deriving force. 3. the most direct application to biological study is the prediction
of the native structure of a protein from its peptide chain. All three parts of the protein folding
problem can have a unied treatment: writing down the Gibbs free energy formula G (X) for
any conformation X = (x1 , , xi , , x M ) R3M of protein, where xi R3 is the atom ai s
atomic center.
The fundamental law for protein folding is the Thermodynamic Principle: the amino acid
sequence of a protein determines its native structure and the native structure of the protein
has the minimum Gibbs free energy among all possible conformations as stated in Annsen
(1973). Let X be a conformation of a protein, is there a natural Gibbs free energy function
G (X)? The answer must be positive, as G. N. Lewis said in 1933: There can be no doubt
but that in quantum mechanics one has the complete solution to the problems of chemistry."
(quoted from Bader (1990), page 130.) Protein folding is a problem in biochemistry, why such
a formula G (X) has not been found and what is the formula? This chapter is trying to give the
answers.
First, the Gibbs free energy formula is given, it has two versions, the chemical balance version
(1) and the geometric version (2).
1.1. The formula

Atoms in a protein are classied into classes Hi , 1 i H, according to their levels of
hydrophobicity. The formula has two versions, the chemical balance version is:
H
G (X) = e Ne (X) + i Ni (X), (1)
i =1
where Ne (X) is the mean number of electrons in the space included by the rst hydration
shell of X, e is its chemical potential. Ni (X) is the mean number of water molecules in the
rst hydration layer that directly contact to the atoms in Hi , i is the chemical potential.
Let MX (see F IGURE 3) be the molecular surface for the conformation X, dening MX i MX
as the set of points in MX that are closer to atoms in Hi than to any atoms in Hj , j = i. Then
the geometric version of G (X) is:
H
G (X) = e e V (X ) + dw e e A( MX ) + i i A( MX ),
i
e , i > 0, (2)
i =1
where V (X ) is the volume of the domain X enclosed by MX , dw the diameter of a water

molecule, and A( MX ) and A( MXi ) the areas of MX and MXi , e [V (X ) + dw A( MX )] = Ne ,
i A( MXi ) = Ni (X), 1 i H. The e and i are independent of X, they are the average
numbers of particles per unit volume and area.
for Protein Folding Gibbs Free Energy Formula for Protein Folding3 49
Before the actual derivation is given, some basic facts should be stated, such as
hydrophobicity, protein structures, and the environment in which the protein folds. Brief
description of the methods in the experimental measurements and theoretical derivation of
the Gibbs free energy of the protein folding is introduced to give the motivation and idea
of the derivation. By making critics on the previous derivation, the necessary concepts
would be claried, what are important in the derivation would be identied, and would
set the thermodynamic system that most t the reality currently known about the protein
folding process. Then both classical and quantum statistical derivations were given, the only
difference is that in the classical statistically derived formula, the volume and the whole
surface area terms in formula (2) are missing. Thus it is that only quantum statistical method
gives us the volume and whole surface terms in formula (2). After the derivations, some
remarks are made. A direct application of the Gibbs free energy formula (2) is the ab initio
prediction of proteins natives structures. Gradient formulas of G (X) are given to be able
to apply the Newtons fastest descending method. Finally, it should be emphasized that the
gradient G (X) not only can be used to predict the native structure, it is actually the force
that forces the proteins to fold as stated in Ben-Naim (2012). In Appendix, integrated gradient
formulas of G (X) on the molecular surface are given.
2. Proteins
2.1. Amino acids
There are 20 different amino acids that appear in natural proteins. All amino acids have a
common part, or the back bone consisting of 9 atoms in F IGURE 1 (except the R).
NH2 is the amino group and COOH is the carboxyl group of the back bone. Single amino
acid is in polar state, so the amino group gains one more hydrogen from the carboxyl group,
or perhaps the amino group losses one electron to the carboxyl group. Geometrically it is
irrelevant since after forming peptide bonds the amino group will loss one H to become NH
and the carboxyl group will loss one OH to become CO. Thus an amino acid in the sequence
is also called a residue.
H H O
\ | ||
N C C
/ | |
H R O H
Figure 1. An generic amino acid.
The group R in F IGURE 1 is called side chain, it distinguishes the 20 different amino acids. A
side chain can be as small as a single hydrogen atom as in Glycine, or as large as consisting of
18 atoms including two rings as in Tryptophan. 15 amino acids have side chains that contain
more than 7 atoms, i.e., more atoms than that of the back bone in an amino acid sequence.
Except Glycine, a C carbon in a side chain forms a covalent bond with the central carbon C
of the back bone.
2.2. Hydrogen bonds

A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative
atom (the accepter), like nitrogen, oxygen or uorine (thus the name hydrogen bond", which
must not be confused with a covalent bond to hydrogen). The hydrogen must be covalently
bonded to another electronegative atom (forming a donor group) to create the hydrogen
bond. These bonds can occur between molecules (intermolecular), or within different parts
of a single molecule (intramolecular). The hydrogen bond is stronger than the van der Waals
interaction, but weaker than covalent or ionic bond. Hydrogen bond occurs in both inorganic
molecules such as water and organic molecules such as DNA, RNA, and proteins.
Some amino acids side chains contain hydrogen bond donors or acceptors that can form
hydrogen bond with either other side chains in the same protein (intramolecular hydrogen
bond) or with surrounding water molecules (inter-molecular hydrogen bond). Those amino
acids whose side chains do not contain either donors or acceptors of hydrogen bond are
classied as hydrophobic.
2.3. Hydrophobicity levels

Every atom in a protein belongs to a moiety or atom group, according to the moietys level
of ability to form hydrogen bond, the atom is assigned a hydrophobicity level. All the
hydrophobicity scales are tested or theorized in some aspects of individual amino acid, either
as a independent molecule or as a residue in a protein, in various environments such as
solvent, PH value, temperature, pressure, etc. That is just like taking a snap shot of an
object with complicated shape. All snap shots are different if taking from different angles
of view. Therefore, there are many different classications of hydrophobicity, for example, in
Eisenberg and McLachlan (1986) there are ve classes, C, O/N, O , N+ , S. Let a protein have
M atoms {a1 , , ai , , a M }. One can assume that there are H hydrophobic classes, such
that {a1 , , ai , , a M } = iH=1 Hi .
2.4. Protein structures

Let a molecule have M atoms, listed as (a1 , , ai , , a M ). A presentation of a structure X of
this molecule is a series atomic centers (nuclear centers) of the atoms ai , xi R3 . Hence it can
be written as a point in R3M , X = (x1 , , xi , , x M ). The space R3M then is called the control
space. The real shape of the structure X is realized in R3 , called the behavior space as dened in
Bader (1990), it is a bunch of overlapping balls (spheres), PX = iM =1 B ( xi , ri ), where ri is the
van der Waals radius of the atom ai and B(x, r ) is the closed ball {y : |y x| r } R3 , of
center x and radius r.
Protein native structures are complicated. Unlike the famous double-helix structure of DNA
structure, the only general pattern for protein structure is no pattern at all. To study the
native structures of proteins people divide the structures in different levels and make structure
classications.
The amino acid sequence of a protein is called its primary structure. Regular patterns of
local (along the sequences) structures such as helix, strand, and turn are called the secondary
structure which contain many intramolecular hydrogen bonds in regular patterns. The global
assembly of these secondary structures, connected by turns and irregular loops, is called
the tertiary structure. For proteins having multiple amino acid sequences or structurally
associated with other molecules there are also quaternary structures, see Branden and Tooze
(1999) and Finkelstein and Ptitsyn (2002).
The secondary structures are local structures, they are usually in helix, strand, and turn. A
common feature of them is that they have regular geometric arrangement of their main chain
atoms, such that there are good opportunities to form hydrogen bonds between different
residues. Several strands may form sheet, stabilized by regular pattern of hydrogen bonds.
Turns and loops are necessary for the extended long chain to transfer to a sphere like shape.
Turns are short, 3 or 4 residues long. Loops involves many residues, but without any regular
pattern of hydrogen bonds. Loops often form the working place of the protein, therefore
appear on the out surface of the native structure.
Figure 2. PX is a bunch of overlapping balls, called the space-lling model, or CPK model.
3. Some functions in thermodynamics

A thermodynamic system consists of particles in a region R3 and a bath or environment
surrounding it. A wall, usually the boundary separating the system with its surrounding.
If no energy and matter can be exchanged through the wall, the system is an isolated system.
If only energy can be exchanged, the system is a closed system. If both energy and matter can
be exchanged with the surrounding, the system is an open system.
For an open system of variable particles contacting with surrounding thermal and particle
bath, let U, T, S, P, V, and N be the inner energy, temperature, entropy, pressure, volume,
chemical potential, and the number of particles of the system respectively, then
dU = TdS PdV + dN, (3)
By Legendre transformations various extensive quantities can be derived,
F = U TS, G = U TS + PV, = F N = U TS N (4)
where F, G, and are Helmholtz, Gibbs free energies, and thermodynamic potential
respectively. Then
dF = SdT PdV + dN, dG = SdT + VdP + dN, d = SdT PdV Nd. (5)
Which shows that U = U (S, V, N ), F = F ( T, V, N ), G = G ( T, P, N ), = ( T, V, ).

All extensive quantities satisfy a linear homogeneous relation, i.e., consider a scaling
transformation which enlarges the actual amount of matter by a factor , then all extensive
quantities are multiplied by a factor . U, S, V, N, F, G, are extensive, while T, P, are
intensive. Thus
U = U (S, V, N ), F = F ( T, V, N ), G = G ( T, P, N ), ( T, V, ) = ( T, V, ).
(6)

From equations in (5) ( V ) T, = P. By equations in (6)

d()
= =V = PV (7)
d V T,
and
( T, V, ) = PV. (8)
Equation (8) is true for any open thermodynamics system.
4. Statistical mechanics
Thermodynamics is a phenomenological theory of macroscopic phenomena that neglects the
individual properties of particles in a system. Statistical mechanics is the bridge between
the macroscopic and microscopic behavior. In statistical mechanics, the particles in a system
obey either classical or quantum dynamic laws, and the macroscopic quantities are statistical
averages of the corresponding microscopic quantities. If the particles obey classical dynamical
law, it is the classical statistical mechanics. If the particles obey quantum dynamical law, it
is the quantum statistical mechanics. But the averaging to get macroscopic quantities from
microscopic ones are in the same principle and formality.
Protein folding studies the structure of the protein molecule, what is the native structure and
why and how the protein folds to it. All these aspects are specic properties of a particle,
the protein molecule. To get the Gibbs free energy formula G (X) for each conformation X,
statistical mechanics is needed with careful specication of the thermodynamic system.
4.1. The canonic ensemble

Statistical mechanics uses ensembles of all microscopic states under the same macroscopic
character, for example, all microscopic states corresponding to the same energy E. The
probability of this ensemble then is proportional to
p E exp( E), (9)
where = 1/kT, k the Boltzmann constant and T the temperature. If there are only a series
energy levels E1 , E2 , , then the probability distribution for canonic ensemble is
exp( Ei )
pi = . (10)

n=1 exp( En )
Various of thermodynamic quantities, such as the inner energy of the system, can be put as
the means:
1 Ei exp( Ei )
U = Ei = i= . (11)
n=1 exp( En )
If only the Halminltonian H (q, p) is known, where q = (q1 , , qi , , q N ) N is
the position of the N particles in the thermodynamic system R3 under study, and
p = (p1 , , pi , , p N ) momentums of these particles, the canonical phase-space density of
the system then is
exp[ H (q, p)] exp[ H (q, p)]

pc (q, p) = = . (12)
1
N dq N R3N exp [ H ( q, p )] dp N Z ( T, V, N )
N!h3N
where N! is the Gibbs corrector because that the particles in the system is indistinguishable.
Z ( T, V, N ) is called the canonic partition function, it depends on the systems temperature T,
volume V, and particle number N. Note that under the assumption of the canonic ensemble,
they are all xed for the xed thermodynamical system . Especially, V = V () = dq
implicitly set that R3 has a volume.
Then the entropy S is

k
S = S() = k ln pc = dq N [ H (q, p) + ln Z ( T, V, N )] pc (q, p)dp N
N!h3N N R3N
1
= [ H + kT ln Z ( T, V, N )] . (13)
T
From which the Helmholtz free energy F = F () and the Gibbs free energy G = G () are
obtained,
F = U TS = kT ln Z ( T, V, N ), G = PV + F = PV kT ln Z ( T, V, N ). (14)
Therefore, to obtain the Gibbs free energy one has to really calculate ln Z ( T, V, N ), a task that
often cannot be done.
4.2. The grand canonic ensemble

The grand canonic ensemble or macroscopic ensemble deals with an open thermodynamic
system , i.e., not only energy can be exchanged, matter particles can also be exchanged
between and environment. Therefore, the particle number N in is variable.
In classical mechanics, suppose that the phase space is (q, p) N R3N . Let H be the
Hamiltonian, the grand canonic phase-space density is
exp[ ( H N )] exp[ ( H N )]
p gc (q, p, N ) = = ,
1
N dq
N =0 N!h3N
N
R3N exp[ ( H ( q, p ) N ]dp
N Z ( T, V, )
(15)
where V = V () is the volume of the system. By denition the entropy is

S() = k ln p gc = k dq N { [ H (q, p) N ] + ln Z } p gc (q, p)dp N
N =0 R3N
N
1
= [ H N + kT ln Z ] . (16)
T
Here H = U is the inner energy of the system , N = N () is the mean number of
particles in . More importantly, the function kT ln Z ( T, V, ) is nothing but the grand
canonic potential , from equation (8) it is just PV. Thus
G = U + PV TS = N . (17)
5. Experimental measuring and theoretical derivation of the Gibbs free

energy of protein folding
The newly synthesized peptide chain of a protein automatically folds to its native structure in
the physiological environment. Change of environment will make a protein denatured, i.e.,
the protein no longer performs its biological function. The facts that denaturation does not
change the protein molecule, that the only thing changed is its structure, was rst theorized by
Hisen Wu based on his own extensive experiments, Hisen Wu (1931). It was found that after
removing the agents that caused the change of environment, some protein can automatically
retake its native structure, this is called renaturation or refolding. After many experiments
in denaturation and renaturation, Annsen summarized the Thermodynamic Principle as
the fundamental law of the protein folding, Annsen (1973). Annsens work actually
show that protein refolds spontaneously after removing denaturation agents. Therefore, in
the physiological or similar environment, the native structure has the minimum Gibbs free
energy; and in a changed environment, the denatured structure(s) will have the smaller
Gibbs free energy. The Thermodynamic Principle of protein folding then is the general
thermodynamics law, if a change happens spontaneously, then the end state will have smaller
Gibbs free energy than the initial state.
To apply the Thermodynamic Principle in the research of protein folding, it is necessary to

know the Gibbs free energy formula G (X) for each conformation X. Until now, theoretical
derivation of G (X) is unsuccessful and rarely being tried. Most knowledge of the Gibbs free
energy of protein folding comes from experiment observations.
5.1. Experimental measuring of

G
The basic principle of experimentally measuring
G, the difference in Gibbs free energy
between the native and the denatured structures of a protein is as follows. For protein
molecules in a solution, the criterion of the protein is in the native structure is that it performes
its biological function, otherwise the protein is denatured or not in the native structure. The
level of biological function indicates the degree of the denaturation. Let B be the native
structure, denote its molar concentration as [ B]. Denote A as an non-native structure of the
same protein in the solution and [ A] its molar concentration.
Three things to be borne in mind: 1. the environment is the physiological environment or
similar one such that the protein can spontaneously fold; 2: individual molecule cannot be
directly measured, so the measuring is in per mole term, R = NA k instead of k should be used,
where NA is the Avogadros number; 3: the environment in reality has constant pressure P,
hence the enthalpy H = U + PV can replace the inner energy U, where V is the volume of the
system (it is a subset of the whole R3 ).
As expressed in (9), the probabilities of the protein takes the conformations A and B are

H H
p A WA exp A , PB WB exp B , (18)
RT RT
where H A = U A + PV and HB = UB + PV are the enthalpy per mole for A and B, WA (WB )
is the number of ways of the enthalpy H A (HB ) can be achieved by microscopic states. The
quantities [ A] and [ B] are assumed to be measurable in experiment. Therefore their ration
K = [ A]/[ B] is also measurable. Then

G o = RT ln K. (19)
To see that equation (19) is true, note that the ratio K is equal to the ratio p A /p B and the
entropies per mole are S A = R ln WA , SB = R ln WB , therefore

p HB H
RT ln K = RT ln A = RT A RT (ln WA ln WB )
pB RT RT
= H A HB T ( R ln WA R ln WB ) = H A HB T (S A SB )
= H A TS A ( HB TSB ) = G A GB =
G o . (20)
But in reality, the ratio K is measurable in experiment is only theoretical, since in physiological
environment K = 0, i.e., almost all protein molecules take the native structure B.
There is no way to change the native structure B to A while keeping the environment
unchanged. In experiments, one has to change the environment to get the protein denatured,
56 10
Thermodynamics Fundamentals and Its Application in Science Will-be-set-by-IN-TECH
that is, to change its shape from the native structure B to another conformation A. Heating the
solution is a simple way to change the environment, during the heating, the system absorb an
amount of heat H, the systems temperature increased from T0 to T1 . Then
G ( A, T1 ) G ( B, T0 ) = f ( H ), (21)
where f ( H ) is a function depending on H and its value is obtained from experiment. What
really needed is

G = G ( A, T0 ) G ( B, T0 ). (22)
To get
G, interpolation to equation (21) is used to estimate the value in T0 . Other methods
of changing environment face the same problem, i.e., interpolation has neither theoretical nor
observation basis.
Equation (19) may give the reason why
G is used whenever referring the Gibbs free energy.
For experiment, only
G can be got. In theoretical derivation, this rule no longer to be
followed and moreover, without a base structure to compare to, the notation
G will look
strange.
More importantly, it should be emphasized again, that the Thermodynamic Principle really
says that in the physiological environment the native structure has the minimum Gibbs free
energy; and in other environment, the native structure no longer has the minimum Gibbs free
energy. Summarizing, it is
G ( B, T0 ) < G ( A, T0 ), G ( A, T1 ) < G ( B, T1 ). (23)
It should always keep in mind that before comparison, rst clarify the environment.
When deriving the Gibbs free energy formula, the rst thing is also to make clear what is the
environment. Another reality that should be borne in mind is that during the protein folding
process, the environment does not change.
Remember that after removing the denaturation agent some proteins will spontaneously
refold to their native structure, this is called the refolding or renaturation. Distinguish the
original protein folding problem and protein refolding problem is another important issue.
Only in the refolding case, a theoretical derivation can make the environment change, for
example, lower the temperature to the room temperature (around 300K). Some discussions
on protein folding are really talking about refolding, because they start from changing the
environment from nonphysological to physiological.
While experiment has no way to change the native structure without disturbing the
environment, theory can play a role instead. Formulas (1) and (2) give us the chance to
compare
G, as long as the accurate chemical potentials values are known.
5.2. Theoretical consideration of the protein folding problem

Protein folding is a highly practical eld. Very few attention was paid to its theoretical part.
For example, almost nobody has seriously considered the Gibbs free energy formula. Instead,
all kinds of empirical models are tried in computer simulation, without any justication in
fundamental principle.
for Protein Folding 11 57
Gibbs Free Energy Formula for Protein Folding
One attempt to theoretically get the Gibbs free energy formula from canonic ensemble is
summarized by Lazaridis and Karplus (2003), the theoretical part of it is reported below
and why it is not successful will be briey pointed out. Their notations such as R = X as
conformation, A = F as the Helmholtz free energy, Q = Z as the partition function, = h,
etc., will be kept in this section.
Treating the protein folding system as the set of all conformations plus surrounding water
molecules with a phase point (R, r), where r are coordinates of N water molecules plus their
orientations. The Hamiltonian H can be decomposed as
H = Hmm + Hmw + Hww , (24)
where mm means interactions inside the protein, mw between protein and water molecules,
and ww water to water, all in the atomic level. Triplet interactions mmm, mmw, etc., can also
be considered, but for simplicity only take the pairwise atomic interactions.
Applying the canonic ensemble, the canonic partition function is

exp( H )dr N dR M Z
Q= = ,
N!
3M 3N N! 3N
3M
and the Helmholtz free energy is given by

A = kT ln Q = kT ln exp( H )dr N dR M + kT ln( N!3M 3N ). (25)
To separate the contributions made by water molecules and the conformations, the effective
energy W is dened,

exp( Hmw Hww )dr N
exp( W ) = exp( Hmm ) = exp( Hmm ) exp( X ), (26)
exp( Hww )dr N
Dene
exp( Hmw ) exp( Hww )dr N
exp( Hmw ) o = . (27)
exp( Hww )dr N
The effective energy W (R) is:
W (R) = Hmm (R) + X (R) = Hmm (R) kT lnexp( Hmw ) o Hmm (R) +
Gslv (R). (28)
The term
Gslv (R) is called the solvation free energy while Hmm is the intra-macromolecular
energy.
After changing R to interior coordinates q, it is stated that

Z = V8 2 exp( Hww )dr N exp( W )dq, (29)
because the interior coordinates has only 3M 6 dimension, the integration of the remaining
6 dimension over the system getting the value V8 2 , implying that each xi in R can be any
point in the system that has volume V. As usual, the probability of nding the system at the
58 12
conguration (q) is:

exp[ W (q)]
p(q) = . (30)
exp[ W (q)]dq
Consequently,

p(q) ln p(q)dq = ln Z + ln exp( Hww )dr N + ln(V8 2 ) p(q)W (q)dq, (31)
From equation (25),

3M
A = kT exp( Hww )dr N + kT ln + p(q)W (q)dq + kT p(q) ln p(q)dq
V8 2

3M
= Ao + kT ln + W TSconf , (32)
V8 2

where Ao = kT exp( Hww )dr N is the pure Helmholtz free energy of pure solvent; the
term TSconf = kT p(q) ln p(q)dq is the contribution of the congurational entropy of the
macromolecule to the free energy.
The Gibbs free energy is G = A + PV. Since the volume is thought negligible under ambient
conditions so Gibbs and Helmholtz free energies are considered identical.
Now for any subset of A , integrals restricted on A gives the Helmholtz energy A A , i.e.,

3M
A A = Ao + kT ln + W A TSconf
A . (33)
V8 2
Thus for two different subsets A and B, the difference in the Helmholtz free energy is

A = A B A A = W B W A T (Sconf
B Sconf
A )
=
Hmm +

Gslv T
Sconf . (34)
Especially, If A is the denatured state and B the native state, both of which have to be dened
in some way and both of which include many congurations, Eq. (34) gives the free energy of
folding."
5.3. Critics of the derivation in Lazaridis and Karplus (2003)

Protein folding is considered a very practical research eld, dominating activities are
computer simulations with empirical models. There are very few theoretical discussions about
protein folding. This derivation in Lazaridis and Karplus (2003) is a rare example deserving
an analysis to see why for decades there has been no theoretic progress in this eld. Many
lessons can be learned from this example.
One important lesson from the derivation Lazaridis and Karplus (2003) is that when dealing
with thermodynamics and statistical mechanics, the thermodynamic system must be clearly
dened. The system will occupy a space in R3 , what is it? How to delimit it?
More importantly, it is not just one conformation R, but all conformations of a single protein
are considered in the derivation. As a single point R R3M , no structural features of the
conformation R are considered, i.e., this particle is structureless. Remember that the research
object is the conformation of the protein, we cannot treat them as structureless particles. Yes,
classical derivations such as the ideal gas system are dened this way, that is because that
the interest is not in the individual particles structure but the macroscopic properties of
the idea gas. The lesson then is that instead of considering all conformations together in a
system, specic thermodynamic system has to be tailored for each individual conformation
R. And such a system contains only one conformation R, with its structure geometry, and
other particles such as water molecules, thus the Gibbs free energy of such a system will be
indexed by R, G = G (R).
Perhaps the biggest lesson to be learned is that when solving a problem, one should
concentrate on the specic features of the problem to design the ways to attack it, not just
imitate successful classical examples.
The derivation of Lazaridis and Karplus (2003) gives the effective energy W (R) as
some substitute of the Gibbs free energy without theoretic basis for its relation to the
Thermodynamic Principle. Moreover, the formula W (R) tells us nothing of how to calculate
it, all are buried in multiple-integrations without clear delimitation. Being the only function
for individual conformation R, it was pointed out in Lazaridis and Karplus (2003) that
The function W denes a hyper-surface in the conformation space of the macromolecule
in the presence of equilibrated solvent and, therefore, includes the solvation entropy. This
hyper-surface is now often called an energy landscape. It determines the thermodynamics
and kinetics of macromolecular conformational transitions." From this comment it can be
seen that the authors are not against individual quantities such as W (R) and think they are
important to the study of protein folding. Changing the effective energy" W (R) to the Gibbs
free energy G (R), the comment really makes sense. The lesson should be learned is that never
invent theoretical concepts without rm theoretical basis. Another one is that always keep in
mind that useful Gibbs free energy formula should be calculable.
From now on, the notation X = R will be used to represent a conformation. To put the
Thermodynamic Principle in practice, not merely as a talking show, what really needed is
G (X), the Gibbs free energy of each individual conformation X, not the effective energy W (R).
One hopes that the formula G (X) should be calculable, not buried in multiple integrations. To
get such a formula, the grand canonic ensemble and eventually the quantum statistics have to
be applied.
6. Necessary preparations for the derivation of the Gibbs free energy

formula
Summarizing what have learned from the critics of the derivation in Lazaridis and Karplus
(2003), in any attempt of derivation of the Gibbs free energy formula one has to: 1. clearly state
all assumptions used in the derivation; and 2. for each conformation X, set a thermodynamic
system TX associated with X; 3. use the grand canonic ensemble.
60 14
6.1. The assumptions

All assumptions here are based on well-known facts of consensus among protein folding
students. Let U be a protein with M atoms (a1 , , ai , , a M ). A structure (conformation) of
U is a point X = (x1 , , xi , , x M ) R3M , xi R3 is the atomic center (nuclear) position of
ai . Alternatively, the conformation X corresponds to a subset in R3 , PX = iM =1 B ( x i , r i ) R
3
where ri s are van der Waals radii.
1. The proteins discussed here are monomeric, single domain, self folding globular proteins.
2. Therefore, in the case of our selected proteins, the environment of the protein folding, the
physiological environment, is pure water, there are no other elements in the environment,
no chaperonins, no co-factors, etc. This is a rational simplication, at least when one
considers the environment as only the rst hydration shell of a conformation, as in our
derivation of the G (X).
3. During the folding, the environment does not change.
4. Annsen (1973) showed that before folding, the polypeptide chain already has its main
chains and each residues covalent bonds correctly formed. Hence, our conformations
should satisfy the following steric conditions set in Fang (2005) and Fang and Jing (2010):
there are ij > 0, 1 i < j M such that for any two atoms ai and a j in PX =
kM=1 B(xk , rk ),
ij |xi x j |, no covalent bond between ai and a j ;

(35)
dij ij |xi x j | dij + ij , dij is the standard bond length between ai and a j .
All conformations satisfying the steric conditions (35) will be denoted as X and in this
chapter only X X will be considered.
5. A water molecule is treated as a single particle centered at the oxygen nuclear position
w R3 , and the covalent bonds in it are xed. In the Born-Oppenheimer approximation,
only the conformation X is xed, all particles, water molecules or electrons in the rst
hydration shell of PX , are moving.
6. As in section 2.3, there are H hydrophobic levels Hi , i = 1, , H, such that iH=1 Hi =
( a1 , , a i , , a M ).
6.2. The thermodynamic system TX

Let dw be the diameter of a water molecule and MX be the molecular surface of PX as dened
in Richards (1977) with the probe radius dw /2, see F IGURE 3. Dene
RX = {x R3 : dist(x, MX ) dw } \ PX (36)
as the rst hydration shell surrounding PX , where dist(x, S) = infyS |x y|. Then TX =
PX RX will be our thermodynamic system of protein folding at the conformation X.
Figure 3. Two dimensional presenting of molecular surface Richards (1977) and solvent accessible
surface Lee and Richards (1971). This gure was originally in Fang and Jing (2010).
Let Ii {1, 2, , M } be the subset such that a j Hi if and only if j Ii . Dene PX i =

j Ii B(x j , r j ) PX and as shown in F IGURE 4,
RX i = {x RX : dist(x, PXi ) dist(x, PX \ PX i )}, 1 i H. (37)
Let V () be the volume of R3 , then
H
RX = iH=1 RX i , V (RX ) = V (RX i ), and for i = j, V (RX i RX j ) = 0. (38)
i =1
Since MX is a closed surface, it divides R3 into two regions X and X such that X =
X = MX and R3 = X MX X . Note that PX X and all nuclear centers of atoms in
the water molecules in RX are contained in X . Moreover, X is bounded, therefore, has
a volume V (X ). For S R3 , denote S as the closure of S. Dene the hydrophobicity
subsurface MX i , 1 i H, as
MX i = MX R X i . (39)
Let A(S) be the area of a surface S R3 , then
H
MX = iH=1 MX i , A ( MX ) = A( MX i ), and if i = j, then A( MX i MX j ) = 0. (40)
i =1
Although the shape of each atom in a molecule is well dened by the theory of atoms in
molecules as in Bader (1990) and Popelier (2000), what concerning us here is the overall
62 16
RX i PX
MX
RX m
RX i
Water
Figure 4. Note that RXi generally are not connected, i.e., having more than one block.
shape of the structure PX . The cutoff of electron density 0.001au in Bader (1990) and
Popelier (2000) gives the overall shape of a molecular structure that is just like PX , a bunch
of overlapping balls. Moreover, the boundary of the 0.001au cutoff is very similar to
the molecular surface MX which was dened by Richards (1977) and was shown has more
physical meaning as the boundary surface of the conformation PX in Tun et. al. (1992) and
Jackson and Sternberg (1993).
7. Gibbs free energy formula: Classical statistical mechanics derivation

The grand canonic ensemble or macroscopic ensemble will be applied to derive the desired
Gibbs free energy formula G (X). In addition to let the number of water molecules vary, the
assumptions is that the chemical potential will be different for water molecules contacting
to different hydrophobicity levels Hi (or falling in RX i ). Counting the numbers Ni of water
molecules that contact to atoms in Hi , the N and in equation (15) should be modied
to N = ( N1 , , Ni , , NH ), = (1 , , i , , H ). Let (q, p) RXM R3M be the
water molecules phase space for a xed N, where M = iH=1 Ni . Let HX = HX (q, p) be the
Hamiltonian. The grand canonic phase density function will be
exp{ [ HX (q, p) iH=1 i Ni ]}

pX (q, p, N ) =

M =0
1
M!h3M Ni = M iH=1 Ni dq Ni R3M exp{ [ HX iH=1 i Ni ]}dp3M
RX i
exp{ [ HX (q, p) iH=1 i Ni ]}

= . (41)
Z ( T, V, )
The entropy S(X) = S(TX ) is
H
S = k ln pX = k N
dq Ni ln pX pX dp M
M=0 N1 ++ NH = M i =1 RX i R3M
i

H H
= k N
dq Ni
i Ni HX (q, p) ln Z pX dp M (42)
M =0 N1 ++ NH = M i =1 RX i
i
i =1

H
1
= H i Ni + kT ln Z ( T, V, ) (43)
T i =1

H
1
= U (TX ) i Ni (TX ) + kT ln Z ( T, V, )
T i =1
where U (X) = U (TX ) = H is the inner energy, Ni (X) = Ni the mean number of water
molecules in RX i . By equation (8), kT ln Z ( T, V, ) = ( T, V, ) = PV (TX ). Therefore, from
G = U + PV TS,
H
G (X) = G (TX ) = U (X) + PV (TX ) TS(TX ) = Ni (X). (44)
i =1
The Gibbs free energy given in formula (44) does not involve any integration at all, just
counting the number of water molecules contacting atoms in Hi . Furthermore, against the
effective energy, potential function Hmm plays no role at all, a surprise indeed. But formula
(44) also is not easy to calculate, counting the number of water molecules actually need more
knowledge of the conformations boundary, the molecular surface MX . Formula (44) can be
directly transfered into a geometric version.
7.1. Converting formula (44) to a geometric version

Since every water molecule in RX i has contact with the surface MX i , Ni (X) is proportional to
the area A( MX i ). Therefore, there are i > 0, such that
i A( MX i ) = Ni (X), 1 i H. (45)
Substitute in (44),
H
G (X) = G (TX ) = i i A( MX i ). (46)
i =1
64 18
For each conformation X, the molecular surface MX is calculable, see Connolly (1983). The
areas A( MX ) and A( MX i ) are also calculable. Therefore, unlike the formula given in (34), this
formula is calculable. Moreover, our derivation theoretically justied the surface area models
that will be discussed later, only difference is that the molecular surface area is used here
instead of the solvent accessible surface area.
But still something is missing. That is, the volume V (TX ), an important thermodynamic
quantity, does not show here at all. It seems that no way to put the V (TX ) here in the classical
statistical mechanics. To resolve this, the quantum statistical mechanics is necessary.
8. A quantum statistical theory of protein folding

In 1929 Dirac wrote: The underlying physical laws necessary for the mathematical theory of
... the whole of chemistry are thus completely known, and the difculty is only that the exact
application of these laws leads to equations much too complicated to be soluble." (quoted from
Bader (1990), page 132). Yes, the multidimensional Shrdinger equation for protein folding
is beyond our ability to solve, no matter how fast and how powerful our computers are. But
mathematical theory guarantees that there is a complete set of eigenvalues (energy levels) and
eigenfunctions to the Shrdinger equation in the Born-Oppenheimer approximation. Then
consider that in the statistical mechanics, ensembles collect all (energy) states of the same
system. Although one cannot have exact solutions to the Shrdinger equation, the eigenvalues
of it are theoretically known. Thus one can apply the grand canonical ensemble to obtain the
desired Gibbs free energy formula G (X). This is the main idea of the derivation.
8.1. The Shrdinger equation

For any conformation X X, let W = (w1 , , wi , , w N ) R3N be the nuclear centers
of water molecules in RX and E = (e1 , , ei , , e L ) R3L be electronic positions of all
electrons in TX . Then the Hamiltonian for the system TX is
M
h2 h2 N 2 h2 L
H = T + V = 2me i
2i i 2i + V (X, W, E), (47)
i =1
2mi 2mw i=1 =1
where mi is the nuclear mass of atom ai , mw and me are the masses of water molecule and
electron; 2i is Laplacian in corresponding R3 ; and V the potential.
8.2. The rst step of the Born-Oppenheimer approximation

Depending on the shape of PX , for each i, 1 i H, the maximum numbers NX i of
water molecules contained in RX i vary. Theoretically all cases are considered, i.e., there are
0 Ni NX i water molecules in RX i , 1 i H. Let M0 = 0 and Mi = ji Nj and
Wi = (w Mi1 +1 , , w Mi1 + j , , w Mi ) RXNii , 1 i H, and W = (W1 , W2 , , W MH )
N
iH=1 RX ii denote the nuclear positions of water molecules in RX . As well, there will be all
possible numbers 0 Ne < of electrons in TX . Let E = (e1 , e2 , , e Ne ) R3Ne denote their
nuclear positions. For each xed X X and N = ( N1 , , NH , Ne ), the Born-Oppenheimer
approximation has the Hamiltonian

h2 1 MH 2 1 Ne 2
2 mw j me
HX = j + + V (X, W, E). (48)
=1 =1

The eigenfunctions iX,N (W, E) L20 (iH=1 RXNii TXNe ) = HX,N , 1 i < , comprise an
orthonormal basis of HX,N . Denote their eigenvalues (energy levels) as EX,N
i , then HX iX,N =
i
EX,N iX,N .
8.3. Grand partition function and grand canonic density operator

Since the numbers Ni and Ne vary, the grand canonic ensemble should be adopted. Let i be
the chemical potentials, that is, the Gibbs free energy per water molecule in RX i . Let e be
electron chemical potential. The grand canonic density operator is like in equation (15), or see
Greiner et. al. (1994) and Dai (2007)

H
X = exp HX i Ni e Ne (X) . (49)
i =1
where (X) is the grand canonic potential in equation (8) with the index X and the grand
partition function is

H
exp[ (X)] = Trace exp HX i Ni e Ne
i =1

H
= exp i
EX,N i Ni e Ne . (50)
i,N i =1
8.4. The Gibbs free energy G (X)

As in equation (16), under the grand canonic ensemble the entropy S(X) = S(TX ) of the
system TX is

H
S(X) = kTrace(X ln X ) = k ln X = k HX (X) i Ni e Ne
i =1

H
1
= HX (X) i Ni e Ne
T i =1

H
1
= U (X) (X) i Ni (X) e Ne (X) . (51)
T i =1
66 20
Denote Ni = Ni (X) as the mean number of water molecules in RX i , 1 i H, and Ne =

Ne (X) the mean number of electrons in TX . The inner energy HX of the system TX is denoted
as U (X) = U (TX ). By equation (8) and the remark after it (X)( T, V, 1 , , H , e ) =
PV (X), where V (X) = V (TX ) is the volume of the thermodynamic system TX . Thus by
equation (51) the Gibbs free energy G (X) = G (TX ) in formula (1) is obtained:
H
G (X) = G (TX ) = PV (X) + U (X) TS(X) = i Ni (X) + e Ne (X). (52)
i =1
8.5. Converting formula (1) to geometric form (2)

As in the classical statistical mechanics case,
i A( MX i ) = Ni (X), 1 i H. (53)
Similarly, there will be a e > 0 such that e V (TX ) = Ne (X). By the denition of TX and X , it
is roughly V (TX \ X ) = dw A( MX ). Thus
Ne (X) = e V (TX ) = e [V (X ) + V (TX \ X )] = e V (X ) + dw e A( MX ). (54)
Substitute equations (45) and (54) into formula (1), formula (2) is obtained.
9. Some remarks
The question to applying fundamental physical laws directly to the protein folding problem
is, can it be done? It should be checked that how rigorous is the derivation and be asked that
are there any fundamental errors? Possible ways to modify the formula or the derivation will
also be discussed.
By applying quantum statistics the protein folding problem is theoretically treated. A theory is
useful only if it can make explanations to the observed facts and if it can simplify and improve
research methods as well as clarify concepts. It will be shown that G (X) can do exactly these.
If the same theoretical result can be derived from two different disciplines, it is often not just
by chance. An early phenomenological mathematical model Fang (2005), starting from purely
geometric reasoning, has achieved formula (2), with just two hydrophobic levels, hydrophobic
and hydrophilic.
A theory also has to be falsiable, that is making a prediction to be checked. The fundamental
prediction is that minimizing formula (1) or (2) the native structures will be obtained for the
amino acid sequences of proteins considered in the assumptions of the formulas. That can
only be done after the actual values of the chemical potentials appear in the formulas, for the
physiological environment, are determined.
9.1. How rigorous is the derivation?

Two common tools in physics, the rst step of the Born-Oppenheimer approximation in
quantum mechanics and the grand canonic ensemble in statistical physics, are applied to
obtain formula (1).
9.1.1. The Born-Oppenheimer approximation

The Born-Oppenheimer approximation treats the electrons as if they are moving in the eld
of xed nuclei. This is a good approximation because, loosely speaking, electrons move much
faster than nuclei and will almost instantly adjust themselves to a change in nuclear position."
Popelier (2000). Since the mass of a water molecule is much less than the mass of a protein, this
approximation can be extended to the case of when X changes the other particles, electrons
and water molecules, will quickly adjust themselves to the change as well.
9.1.2. The statistical physics in general and the grand canonic ensemble in particular
Up to now there is no evidence to show that statistical physics itself is responsible for any
mistakes," the Preface of Dai (2007). Via the ensemble theory of statistical mechanics only
one protein molecule and particles in its immediate environment are considered, it is justied
since as pointed out in Dai (2007) page 10, When the duration of measurement is short, or
the number of particles is not large enough, the concept of ensemble theory is still valid." And
among different ensembles, Generally speaking, the grand canonic ensemble, with the least
restrictions, is the most convenient in the mathematical treatment." Dai (2007) page 16. In
fact, the canonic ensemble has been tried and ended with a result that the eigenvalues of the
quantum mechanics system have to be really calculated, to do it accurately is impossible.
The derivations in this chapter only puts together the two very common and sound practices:
the Born-Oppenheimer approximation (only the rst step) and the grand canonic ensemble,
and apply them to the protein folding problem. As long as protein folding obeys the
fundamental physical laws, there should not be any serious error with the derivation.
9.2. Equilibrium and quasi-equilibrium

A proteins structure will never be in equilibrium, in fact, even the native structure is only a
snapshot of the constant vibration state of the structure. The best description of conformation
X is given in Chapter 3 of Bader (1990). Simply speaking, a conformation X actually is any
point Y such that all yi are contained in a union of tiny balls centered at xi , i = 1, , M.
In this sense, it can only be anticipated that a quasi-equilibrium description (such as the
heat engine, Bailyn (1994) page 94) of the thermodynamic states of the protein folding. This
has been built-in in the Thermodynamical Principle of Protein Folding. So the quantities
such as S(X), (X), and G (X) can only be understood in this sense. That is, observing
a concrete folding process one will see a series of conformations Xi , i = 1, 2, 3, . The
Thermodynamic Principle then says that measuring the Gibbs free energy G (Xi ) one will
observe that eventually G (Xi ) will converge to a minimum value and the Xi will eventually
approach to the native structure. While all the time, no conformation Xi and thermodynamic
system TXi are really in equilibrium state.
9.3. Potential energy plays no role in protein folding

Formulas (1) and (2) theoretically show that hydrophobic effect is the driving force of
protein folding, it is not just solvent free energy besides the pairwise interactions such as
the Coulombs, etc., as all force elds assumed. Only in the physiological environment the
68 22
hydrophobic effect works towards to native structure, otherwise it will push denaturation as
discussed in explanation of folding and unfolding. Formulas (1) and (2) show that the Gibbs
free energy is actually independent of the potential energy, against ones intuition and a bit of
surprising. The explanation is that during the folding process, all covalent bonds in the main
chain and each side chain are kept invariant, the potential energy has already played its role
in the synthesis process of forming the peptide chain, which of course can also be described
by quantum mechanics. According to Annsen (1973), protein folding is after the synthesis of
the whole peptide chain, so the synthesis process can be skipped and the concentration can be
focused on the folding process.
The steric conditions (35) will just keep this early synthesis result, not any X =
(x1 , , xi , , x M ) is eligible to be a conformation, it has to satisfy the steric conditions
(35). The steric conditions not only pay respect to the bond length, it also reect a lot of
physic-chemical properties of a conformation: They are dened via the allowed minimal
atomic distances, such that for non-bonding atoms, the allowed minimal distances are: shorter
between differently charged or polarized atoms; a little longer between non-polar ones; and
much longer (generally greater than the sum of their radii) between the same charged ones,
etc. For example, minimal distance between sulfur atoms in Cysteine residues to form
disulde bonds is allowed. And for any newly found intramolecular covalent bond between
side chains, such as the isopeptide bonds in Kang and Baker (2011), the steric conditions can
be easily modied to allow the newly found phenomenon.
The drawback of the steric conditions is that the minimization in equation (57) becomes a
constrained minimization.
9.4. Unied explanation of folding and denaturation

Protein denaturation is easy to happen, even if the environment is slightly changed, as
described by Hsien Wu (1931). (Hsien Wu (1931) is the 13th article that theorizes the results
of a series experiments, and a preliminary report was read before the Xlllth International
Congress of Physiology at Boston, August 19-24, 1929, and published in the Am. J. Physiol. for
October 1929. In which Hsien Wu rst suggested that the denatured protein is still the same
molecule, only structure has been changed.) Annsen in various experiments showed that
after denaturation by changed environment, if removing the denature agent, certain globular
proteins can spontaneously refold to its native structure, Annsen (1973). The spontaneous
renaturation suggests that protein folding does not need outside help, at least to the class of
proteins in this chapter. Therefore, the fundamental law of thermodynamics asserts that in the
environments in which a protein can fold, the native structure must have the minimum Gibbs
free energy. The same is true for denaturation, under the denatured environment, the native
structure no longer has the minimum Gibbs free energy, some other structure(s), will have
the minimum Gibbs free energy. Thus let En present environment, any formula of Gibbs free
energy should be stated as G (X, En) instead of just G (X), unless the environment is specied
like in this chapter. Let En N be the physiological environment and EnU be some denatured
environment, X N be the native structure and XU be one of the denatured stable structure in
EnU , then the thermodynamic principle for both of protein folding and unfolding should be
that
G (X N , En N ) < G (XU , En N ), G (X N , EnU ) > G (XU , EnU ). (55)
To check this, an experiment should be designed that can suddenly put proteins in a different
environment. Formulas (1) and (2) should be written as G (X, En N ). Indeed, the chemical
potentials e and i s are Gibbs free energies per corresponding particles, = u + Pv Ts.
Two environment parameters, temperature T and pressure P, explicitly appear in , the
inner energy u and entropy s may also implicitly depend on the environment. According
to formulas (1) and (2), if i < 0, then make more Hi atoms to expose to water (make larger
A( MX i )) will reduce the Gibbs free energy. If i > 0, then the reverse will happen. Increase
or reduce the Hi atoms exposure to water (A( MX i )), the conformation has to change. The
conformation changes to adjust until a conformation X N is obtained, such that the net effect of
any change of the conformation will either increase some Hi atoms exposure to water while
i > 0 or reduce Hi atoms exposure to water while i < 0. In other words, the G (X, En N )
achieves its minimum at G (X N , En N ). Protein folding, at least for the proteins considered in
the assumptions, is explained very well by formulas (1) and (2).
In changed environment, the chemical potentials e and i s in formulas (1) and (2) changed
their values. With the changed chemical potentials, G (X, EnU ) has the same form as
G (X, En N ) but different chemical potentials. Therefore, the structure XU will be stable,
according to the second inequality in (55), the process is exactly the same as described for
the protein folding if the changing environment method does not include introducing new
kinds (non-water) of particles, for example, if only temperature or pressure is changed.
Even in the new environment including new kinds of particles, formulas (1) and (2) can still
partially explain the denaturation, only that more obstructs prevent the protein to denature
to XU , but any way it will end in some structure other than the X N , the protein is denatured.
Actually, this is a hint of how to modify the current formulas to extend to general proteins.
9.5. Explain hydrophobic effect and the role played by hydrogen bonding
In 1959, by reviewing the literature Kauzmann concluded that the hydrophobic effect
is the main driving force in protein folding, Kauzmann (1959). Empirical correlation
between hydrophobic free energy and aqueous cavity surface area was noted as early as by
Reynolds et.al. (1974), giving justication of the hydrophobic effect. Various justications
of hydrophobic effect were published, based on empirical models of protein folding, for
example, Dill (1990). But the debate continues to present, some still insist that it is the
hydrogen bond instead of hydrophobic effect plays the main role of driving force in protein
folding, for example, Rose et. al (2006). The theoretically derived formulas (1) and (2) can
explain why the hydrophobic effect is indeed the driving force. A simulation of reducing
hydrophobic area alone by Fang and Jing (2010) shows that the result is the appearance of
regularly patterned intramolecular hydrogen bonds associated to the secondary structures.
In fact, according to formulas (1) and (2), if i < 0, then make more Hi atoms to appear in
the boundary of PX will reduce the Gibbs free energy. If i > 0, then the reverse will happen,
reducing the exposure of Hi atoms to water will reduce the Gibbs free energy. This gives a
theoretical explanation of the hydrophobic effect. The kinetic formulas Fi = xi G (X) (will
be discussed later) is the force that push the conformation to change to the native structure.
The mechanics stated above works through the chemical potentials i for various levels of
hydrophobicity. In physiological environment, all hydrophobic Hi s will have positive i , all
70 24
hydrophilic Hi s will have negative i . Thus changing conformation PX such that the most
hydrophilic Hi (i = min(1 , , H )) gets the rst priority to appear on the boundary,
and the most hydrophobic Hi (i = max(1 , , H )) gets the rst priority to hide in the
hydrophobic core to avoid contacting with water molecules, etc. One should keep in mind
that all the time, the steric conditions (35) have to be obeyed.
But the hydrophobic effect is actually partially working through hydrogen bond formation.
This is well presented in the chemical potentials in formulas (1) and (2). In fact, the values of
the chemical potentials reect the ability of the atoms or atom groups to form hydrogen bond,
either with another atom group in the protein or with water molecules. This gives a way
to theoretically or experimentally determine the values of hydrophilic chemical potentials:
checking the actual energy value of the hydrogen bond.
According to Fikelstein and Ptitsyn (2002), energies of hydrogen bonds appearing in protein
(intermolecular or intramolecular) are (the positive sign means that to break it energy is
needed) and their energies are:
OH : : : O (21 kJ mol1 or 5.0 kcal mol1 ); OH : : : N (29 kJ mol1 or 6.9 kcal mol1 );
NH : : : N (13 kJ mol1 or 3.1 kcal mol1 ); NH : : : O (8 kJ mol1 or 1.9 kcal mol1 ).
For hydrophobic ones, it will be more complicated, common sense is that it reduces the
entropy that certainly comes from the inability of forming hydrogen bonds with water
molecules. Hence although hydrophobic effect is the driving force of protein folding, it works
through the atoms ability or inability to form hydrogen bonds with water molecules.
How to explain the intramolecular hydrogen bonds? It seems that formulas (1) and (2) do not
address this issue. The possible theory is that the amino acid sequence of a protein is highly
selectable in evolution, in fact only a tiny number of amino acid sequences can really become
a protein.
Indeed, suppose in average each species (or kind" of prokaryote) has 105 proteins (Homo
sapiens has around 3 105 ), and assume that per protein has 100 variants (versions with
tiny difference in the peptide sequence of the protein), then there are at most 1047 peptide
sequences that can really produce a natural protein. Now further suppose that only one in
1013 theoretically protein producing peptide sequences on the earth get a chance to be realized,
then there will be at most 1060 possible protein producing peptide sequence. A huge number!
The number of peptide sequences of length less than or equal to n is
n
20n+1 20 20
N (n) = 20i = = = 20n+0.0171
(20n 1) = 101.301(n+0.0171) . (56)
i =1
19 19
The longest amino acid sequence in the record of ExPASy Proteomics Server has 35,213
residues. Then N (35, 213) > 101.335,213 > 1045060 and the ratio of the number of potentially
protein producing peptide sequences to the number of all possible sequence of length up to
35,213 is less than 1060 /1045060 = 1045000 , so tiny a number that it is undistinguishable from
zero. Even assuming that the longest peptide sequence is only 400, the ratio is still less than
10460 . How small a chance that a random peptide sequence happens to be a proteins peptide
sequence!
With these highly specially selected peptide sequences, one can assume that while shrinking
the various hydrophobic surfaces to form a hydrophobic core, residues are put in positions
to form secondary structures and their associated hydrogen bonds. This sounds a little bit
too arbitrary. But the huge number of candidate peptide sequences makes the evolutional
selection not only possible but also probable. Moreover, a simulation of shrinking
hydrophobic surface area alone indeed produced secondary structures and hydrogen bonds.
The simulation was reported by Fang and Jing (2010). Without calculating any dihedral
angles or electronic charges, without any arbitrary parameter, paying no attention to any
particular atoms position, by just reducing hydrophobic surface area (there it was assumed
that there are only two kinds of atoms, hydrophobic and hydrophilic), secondary structures
and hydrogen bonds duly appeared. The proteins used in the simulation are 2i9c, 2hng, and
2ib0, with 123, 127, and 162 residues. No simulation of any kind of empirical or theoretical
models had achieved such a success. More than anything, this simulation should prove that
hydrophobic effect alone will give more chance of forming intramolecular hydrogen bonds.
Indeed, pushing hydrophilic atoms to make hydrogen bonds with water molecules will give
other non-boundary hydrophilic groups more chance to form intramolecular hydrogen bonds.
Again formula (2) can partly explain the success of this simulation, when there are only two
hydrophobic classes in formula (2), the hydrophobic area presents the main positive part of
the Gibbs free energy, reducing it is reducing the Gibbs free energy, no matter what is the
chemical potentials real value.
9.6. Explanation of the successes of surface area models

In 1995, Wang et al (1995) compared 8 empirical energy models by testing their ability to
distinguish native structures and their close neighboring compact non-native structures. Their
models WZS are accessible surface area models with 14 hydrophobicity classes of atoms,
14i =1 i Ai . Each two combination of three targeting proteins were used to train WZS to get
i , hence there are three models WZS1, WZS2, and WZS3. Among the 8 models, all WZSs
performed the best, distinguishing all 6 targeting proteins. The worst performer is the force
eld AMBER 4.0, it failed in distinguishing any of the 6 targets.
These testing and the successes of various surface area models such as Eisenberg and
MacLachlan (1986), showed that instead of watching numerous pairwise atomic interactions,
the surface area models, though looking too simple, have surprising powers. Now the formula
(2) gives them a theoretic justication. On the other hand, the successes of these models also
reenforce the theoretical results.
There is a gap between the accessible surface area model in Eisenberg and Maclanchlan (1986)
and the experiment results (surface tension), as pointed out in Tun et. al. (1992). The gap
disappeared when one uses the molecular surface area to replace the accessible surface area,
in Tun et. al. (1992) it was shown that molecular surface area assigned of 72-73 cal/mol/2
perfectly ts with the macroscopic experiment data. Later it was asserted that the molecular
surface is the real boundary of protein in its native structure by Jackson and Sternberg (1993).
By the denition of X , as shown in F IGURE 3 and F IGURE 4, water molecules contact to
PX must be outside the molecular surface MX . Since the assessable surface is in the middle
of the rst hydration shell, it is better to use the molecular surface MX as the boundary of
72 26
the conformation PX . Moreover, the conversion of the mean numbers Ni (X) to surface area,
Ni (X) = i A( MX .i ), only works for the molecular surface, not for the accessible surface. This
can explain the conclusions that molecular surface is a much better boundary than accessible
surface as stated in Tun et. al. (1992) and Jackson and Sternberg (1993).
In fact, the advantage of the solvent accessible surface is that by denition of it one knows
exactly each atom occupies which part of the surface, therefore, one can calculate its share in
surface area. This fact may partly account why there are so many models based on the solvent
accessible surface, even people knew the afore mentioned gap. For other surfaces, one has to
dene the part of surface that belongs to a specic hydrophobicity class. This was resolved in
Fang (2005) via the distance function denition as is used here.
All surface area models neglected one element, the volume of the structure. As early as
in the 1970s, Richards and his colleagues already pointed out that the native structure of
globular proteins is very dense, or compact, (density = 0.75, Richards (1977)). To make
a conformation denser, obviously we should shrink the volume V (X ). The model in
Fang (2005) introduced volume term but kept the oversimplication of all atoms are either
hydrophobic or hydrophilic. The derivation of formulas (1) and (2) shows that volume term
should be counted, but it may be that e e is very small, in that case, volume maybe really is
irrelevant.
9.7. Coincidence with phenomenological mathematical model

If a theoretical result can be derived from two different disciplines, its possibility of
correctness will be dramatically increased. Indeed, from a pure geometric consideration, a
phenomenological mathematical model, G (X) = aV (X ) + bA( MX ) + cA( MX 1 ), a, b, c > 0 (it
was assumed that there are only two hydrophobicity levels, hydrophobic and hydrophilic, the
hydrophilic surface area A( MX 2 ) is absorbed in A( MX ) by A( MX 2 ) = A( MX ) A( MX 1 )),
was created in Fang (2005). It was based on the well-known global geometric characteristics
of the native structure of globular proteins: 1. high density; 2. smaller surface area; 3.
hydrophobic core, as demonstrated and summarized in Richards (1977) and Novotny et.al
(1984). So that to obtain the native structure, one should shrink the volume (increasing
the density) and surface area, and form better hydrophobic core (reducing the hydrophobic
surface area A( MX 1 )) simultaneously and cohesively.
The coincidence of formula (2) and the phenomenological mathematical model of Fang (2005)
cannot be just a coincidence. Most likely, it is the same natural law reected in different
disciplines. The advantage of formula (2) is that everything there has its physical meaning.
10. Applications
After the derivation it is suitable to point out some immediate applications of the formula
G ( X ).
10.1. Energy surface or landscape

An obvious application is the construction of Gibbs free energy surface or landscape.
Empirical estimate is no longer needed, the Gibbs free energy formula G : X R gives
a graph (X, G (X)) over the space X (all eligible conformations for a given protein), and
this is nothing but the Gibbs free energy surface. Mathematically it is a 3M dimensional
hyper-surface. Its characteristics concerned by students of energy surface theory, such as how
rugged it is? how many local minimums are there? is there a funnel? etc., can be answered by
simple calculations of the formula.
Since the function G is actually dened on the whole R3M (on an domain of R3M containing all
X is enough), mathematical tools can be explored to study its graph, and compare the results
with the restricted conformations. One important question is: Does the absolute minimum
structure belongs to X?
10.2. Structure prediction

Prediction of protein structures is the most important method to reveal proteins functions
and working mechanics, it becomes a bottle neck in the rapidly developing life science. With
more and more powerful computers, this problem is attacked in full front. Various models,
homologous or ab initio, full atom model or coarse grained, with numerous parameters of
which many are quite arbitrary, are used to achieve the goal. Although our computer power
growths exponentially, prediction power does not follow that way. At this moment, one
should take a deep breath and remind what the great physicist Fermi said: There are two
ways of doing calculations in theoretical physics. One way, and this is the way I prefer, is to
have a clear physical picture of the process that you are calculating. The other way is to have a
precise and self consistent mathematical formalism." And I remember my friend Johnny von
Neumann used to say, with four parameters I can t an elephant, and with ve I can make
him wiggle his trunk." Quoted from Dyson (2004).
These remarks should also apply to any scientic calculation, not just theoretical physics.
Look at the current situation, all ab initio prediction models are actually just empirical with
many parameters to ensure some success. Fermis comments remind us that a theory should
be based on fundamental physical laws, and contain no arbitrary parameters. Look at
formulas (1) and (2), one sees immediately that they are neat, precise and self consistent
mathematical formulas. Furthermore, they including no arbitrary parameter, all terms in them
have clear physical meanings. Chemical potentials e and i s, geometric constants e and i s,
can be evalued by theory or experiments, they are not arbitrary at all.
But a theory has to be developed, tested, until justied or falsied. For interested researchers,
the tasks are to determine the correct values of the chemical potentials in formula (1) and
the geometric ratios e and i in formula (2). There are many estimates to them, but they
are either for the solvent accessible surface area such as in Eisenberg and MaLachlan (1986)
hence not suit to the experiment data as pointed out in Tun et. al., or do not distinguish
different hydrophobicity levels as in Tun et. al. (1992). To get the correct values of the
chemical potentials and geometric constants, commonly used method of training with data
can be employed, in which one can also test the formulas ability of discriminating native and
nearby compact non-native structures. After that, a direct test is to predict the native structure
from the amino acid sequence of a protein by minimizing the following:
G (X N ) = inf G (X). (57)

X X
74 28
This is the rst time that a theoretically derived formula of the Gibbs free energy is available.
Before this, all ab intitio predictions are not really ab initio. A combined (theoretical and
experimental) search for the values of chemical potentials will be the key for the success of
the ab initio prediction of protein structure.
10.3. Gradient
With formula (2) as the Gibbs free energy, the minimization in equation (57) can be pursued
by Newtons fastest descending method. To state the result, some denitions are necessary.
10.3.1. Molecular graphs

Given a molecule U, let V be the set of atoms in U and N = |V | be the number of atoms and
label the atoms as a1 , a2 , , a N . For 1 i, j N, dene Bij = n if atoms i and j are connected
by a bond with valency n (one can imagine that n is not necessarily a whole number), if i and
j do not form a bond, then Bij = 0. The molecule formula of U in chemistry can be seen as a
graph G (U ) = (V, E), where V acts as the vertex set of G (U ) and E is the edge set of G (U ).
An edge in E is denoted by {i, j}, If two atoms ai and a j are connected by a covalent bond,
i.e., Bij = n 1, then {i, j} E is an edge. Call G (U ) the molecular graph of U. F IGURE 1 is
a molecular graph if the side chain R consisting of only one atom, such as in the amino acid
Glycine.
A graph G is connected if from any vertex v one can follow the edges in the graph to arrive
any other vertex. If a graph is not connected, then it has several connected components, each
is itself a connected graph. All molecular graphs are connected.
10.3.2. Rotatable bonds

Let b = a a be a covalent bond in the molecule U connecting two atoms a and a . The bond
b is rotatable if and only if: 1. the valency of b is not greater than 1; 2. in the molecular graph
G (U ), if one deletes {, }, the remaining graph G (U )\{, } = (V, E\{, }) has exactly two
connected components and neither component has rotational symmetry around the bond b.
10.3.3. Derivatives of G (X)

Let xi = ( xi , yi , zi ), write F = xi G (X) = ( Gxi , Gyi , Gzi )(X). The calculation of Gxi (X),
for example, is via Lie vector eld induced by moving the atomic position xi . In fact, any
innitesimal change of structure X will induce a Lie vector eld L : X R3 . For example,
moving xi from xi to xi + (xi , 0, 0) while keep other nuclear center xed, will induce L xi :
X R3 , such that L xi (xi ) = (1, 0, 0) and L xi (x j ) = (0, 0, 0) for j = i. Similarly Lyi and Lzi can
be described as well. Then write Gxi = GL , etc. and
xi
xi G (X) = ( GLx , GLy , GLz )(X), (58)

i i i
Rotating around a covalent bond bij also induce a Lie vector eld Lbij : X R3 . In fact if ai a j
form the covalent bond bij , then the bond axis is
x j xi
bij = . (59)
| x j xi |
If bij is rotatable, denoting all nuclear centers in one component by Rbij and others in Fbij . One
can rotate all centers in Rbij around bij for certain angle while keep all centers in Fbij xed. The
induced Lie vector eld Lb will be ij
Lb (xk ) = (xk xi ) bij , if xk Rb ; (60)

ij ij
Lb (xk ) = 0, if xk Fb . (61)

ij ij
Any such a Lie vector eld L will generate a family of conformations Xt =

(x1 t , , xi t , , x M t ), where xk t = xk + tL(xk ), k = 1, , M. Moreover, the Lie vector
eld L can be generated to the molecular surface MX , as shown in Appendix A.
The derivative GL (X) is given by
H
GL (X) = e e VL (X ) + dw e e AL ( MX ) + i i AL ( MX i ), (62)
i =1
with
VL (X ) = L Nd
H2 , AL ( MX ) = 2 H (L N
)dH 2 , (63)
MX MX
is the outer unit normal of MX , H the mean curvature of MX , and H2 the Hausdorff
where N
measure. Dene f t,i : R3 R as f t i (x) = dist(x, MXt i ) dist(x, MXt \ MXt i ), and dene on
MX
f t i d f 0,i

MX f 0,i = f 0,i ( f 0,i N ) N, f 0,i = , = L f 0,i + f 0,i

, (64)
t t=0 dt
then let be the unit outward conormal vector of MX i (normal to MX i but tangent to MX ),

d f 0,i

AL ( MX i ) = 2 H (L N
)dH +
2 L dt
dH 1 . (65)
MX i MX i | MX f 0,i |
The Xt is all the information needed in calculating the molecular surface MXt , see Connolly
(1983). To calculate, the above formulas have to be translated into formulas on the molecular
surface MX . These translations are given in Appendix A, they are calculable (all integrals are
integrable, i.e., can be expressed by analytic formulas with variables X) and were calculated
piecewise on MX .
10.3.4. The gradient

Let a protein U have L rotatable bonds (b1 , , bi , , b L ). Let i denote the dihedral angle
around the rotatable bond bi . A conformation X of U can be expressed in terms of these
rotatable dihedral angles = (1 , , i , , L ), then
G ( X ) = G ( ), (66)
76 30
and the gradient of G can be written as

G G G
G () = , , , , () = ( GL , , GL , , GL )(X). (67)
1 i L b1 bi bL
If the rotation around bi with rotating angle sGL (X) on Rbi and x atoms in Fbi be denoted
bi
as Mi , new conformation Ys = M L M L1 . . . M1 will be obtained, where s > 0 is a suitable
step length. That is to say, the dihedral angles of Ys are
[1 sGL (X), , i sGL (X), , L sGL (X)].

b1 bi bL
The order of rotations in fact is irrelevant, i.e., by any order, the same conformation Ys will
always be obtained, as proved in Fang and Jing (2008) and Appendix A. This way one can fast
change the structure by simultaneous rotate around all rotatable bonds.
This actually is the Newtons fastest descending method, it reduces the Gibbs free energy
G (X) most efciently. Afore mentioned simulations of Fang and Jing (2010) used this method.
10.4. Kinetics
There are evidence that some proteins native structure is not the global minimum of the Gibbs
free energy, but only a local minimum. If the native structure of a protein achieves the global
minimal value of the Gibbs free energy, the folding process is thermodynamic; if it is only a
local minimum, the folding process is kinetic, Lazaridis and Karplus (2003).
With the formula (2) and the gradient just obtained, one actually has the kinetic in hand.
In fact, for any atomic position xi , the kinetic force is Fi (X) = xi G (X), Dai (2007).
With formula (2) these quantities are readily calculable as mentioned above. The resulting
Newtons fastest descending method will help us nd the native structure, either in the
thermodynamic case or in the kinetic case, here the thermodynamic and kinetic cases are
combined by the Gibbs free energy formula (2) and its derivatives.
The moving along G method was used in the simulation in Fang and Jing (2010).
11. Conclusion
A quantum statistical theory of protein folding for monomeric, single domain, self folding
globular proteins is suggested. The assumptions of the theory t all observed realities of
protein folding. The resulting formulas (1) and (2) do not have any arbitrary parameters
and all terms in them have clear physical meaning. Potential energies involving pairwise
interactions between atoms do not appear in them.
Formulas (1) and (2) have explanation powers. They give unied explanation to folding and
denaturation, to the hydrophobic effect in protein folding and its relation with the hydrogen
bonding. The formulas also explain the relative successes of surface area protein folding
models. Relation between kinetic and thermodynamic of protein folding is discussed, driving
force formula comes from the Gibbs free energy formula (2) are also given. Energy surface
theory will be much easier to handle. The concept of
G is claried.
Appendix
A. Calculations on the molecular surface
A.1. Rotation order
Let PX = iN=1 B(xi , ri ) and x0 and x1 be bonded by b , the rotation line of b is x0 +
x0
t |xx1 = x0 + tb . Each b divides {x1 , , x M } into two groups F and R , balls in
1 x0 |
R will be rotated while balls in F will be xed. Note that these partitions are independent
of PX , they only depend on the molecular graph of the protein molecule. Let M be this
rotation-xation, it will be shown that
M M (X) = M M (X), X (x1 , x2 , , x M ), 1 , L. (1)
The formula of rotating a point X around a line L : y = x + tb (|b| = 1) by an angle is

R( X ) = x + A( )( X x). Let I be the identity matrix, B = bb T and Zb the matrix such that
the outer product b X = Zb X, then the orthonormal matrix A( ) = (1 cos ) B + cos I +
sin Zb .
The topology of a protein molecule guarantees that if two bonds b and b such that R R ,
then {x0 , x1 } R . Let b1 and b2 be two bonds and L1 : x = x1 + tb1 and L2 : x = x2 + tb2
be the two rotating lines and X (x1 , x2 , , x N ). To prove equation (1), there are only two
cases to consider: R1 R2 and R1 R2 = . In any case, if X F1 F2 , then M1 M2 ( X ) =
M2 M1 ( X ) = X. If X R1 R2 , then
M2 M1 ( X ) = x2 + A2 (2 )(x1 x2 )+ A2 (2 )A1 (1 )( X x1 ). (2)
On the other hand b1 and hence L1 itself will be rotated by M2 , L3 = M2 ( L1 ) = x3 + tb3 ,

where x3 = x2 + A2 (2 )(x1 x2 ), b3 = A2 (2 )b1 . Since X R1 R2 and M2 ( X ) R1 (in
the new conformation M2 ( P) where rotation around b1 is rotation around L3 ), M1 M2 ( X )
will be the rotation R3 around L3 of M2 ( X ) by angle 1 , thus
M1 M2 ( X ) = x2 + A2 (2 )(x1 x2 ) + A3 (1 )A2 (2 )( X x1 ). (3)
Let v R3 be an arbitrary vector, writing A1 (1 ) = A1 , A2 (2 ) = A2 , and A3 (1 ) = A3 ,

then
A2 A1v=(1 cos 1 )(b1 v)A2 b1 + cos 1 A2 v + sin 1 A2 (b1 v). (4)
For any orthonormal matrix O, (Ob1 )(Ov) = b1 v, O(b1 v) = (Ob1 )(Ov). Then by
b 3 = A 2 ( 2 ) b 1 ,
A3 A2 v = (1 cos 1 )[b3 (A2 v)]b3 + cos 1 (A2 v) + sin 1 b3 (A2 v)

= (1 cos 1 )(b1 v)A2 b1 + cos 1 A2 v + sin 1 A2 (b1 v). (5)
Since v was arbitrary, equations (2) to (5) show equation (1) is true.
If R1 R2 = and X R2 , then X and M2 ( X ) F1 hence M1 M2 ( X ) = M2 ( X ) =
M2 M1 ( X ).
78 32
The molecular surface is consisted of faces. Thus all integrals can be integrated piecewise
on faces. There are three kinds of faces, convex, concave, and saddle, Connolly (1983).
The formulas on each kind of face are given below. The notation x means L(x) with L the
corresponding Lie vector eld. All van der Waals radii ri , as well as the probe radius r p , are
constants.
A.2. Convex face

A convex face is a piece of spherical surface lying on some Si = B(xi , ri ) and bounded by
circular arcs , = 1, , n F , let v0 and v1 be s vertices and c and r the center and radius
of s circle, r the arc length of , e3 = (z1 , z2 , z3 ) be the unit vector in the direction
v0 c
of (v0 c )(v1 c ), d = e3 (c xi ), e1 = r ij = ( x1 , x2 , x3 ), e2 = e3 e1 =
(y1 , y2 , y3 ), 1 n F . A point x on F has the form x = xi ri N and X (x) = x ri N,
by N N 0 and the general divergence formula on sphere,

1 M
ri ( X N ) H dH 2 = X N dH 2 = xi ( X , Y , Z ), (6)
F F ri =1
where
r2
X = { z1 + sin [cos ( x2 y3 + x3 y2 ) + sin (y2 y3 x2 x3 )}
2
+r d z2 [y3 sin x3 (1 cos )] , (7)
r2
Y = { z2 + sin [cos ( x3 y1 + x1 y3 ) + sin (y1 y3 x1 x3 )]}
2
+r d z3 [y1 sin x1 (1 cos )] , (8)
r2
Z = { z3 + sin [cos ( x1 y2 + x2 y1 ) + sin (y1 y2 x1 x2 )]}
2
+r d z1 [y2 sin x2 (1 cos )] . (9)
A.3. Concave face

A concave face F is a spherical polygon on the probe sphere S when S is simultaneously
tangent to 3 balls B(xi , ri ), 1 i 3. F is expressed by parameters ti 0, i = 1, 2, 3,
t1 x1 + t2 x2 + t3 x3 p
x = p + rN = p + r , t1 + t2 + t3 = 1. (10)
| t1 x1 + t2 x2 + t3 x3 p |
t1 x1 ( t ) + t2 x2 ( t ) + t3 x3 ( t ) p ( t )
t (x) = p(t) + rN (t) = p(t) + r , (11)
|t1 x1 (t) + t2 x2 (t) + t3 x3 (t) p(t)|

dt (x)
X (x) = dt = p + r N. Using |p(t) xi (t)| = ri + r = constant, let bi = (xi p) xi ,
t =0
x1 p
b = (b1 , b2 , b3 ) T , A = x2 p , then det A = 0, p = A1 b. By X N = p N,
x3 p
3
1
r ( X N ) H dH 2 = X N dH2 = p ( Xi , Yi , Zi ). (12)
F F r i =1
Here the Xi , Yi , and Zi are the same as in equations (7) to (9).

Assume that x1 has different water association with x2 and x3 , let Ri = ri + r, dij = |xi x j |,
yij = ( R2i R2j )/2dij . Then f P (x) = (x p) nk , where nk = (xk x1 )/d1k is the directed
unit normal of the dividing plane Pk (passing through p and t1k = 12 (x1 + xk ) + y1k nk and
perpendicular to it), k = 2, 3. The projection of W F on the x1 x2 x3 plane is in the form of
one or two curves k , ({ j, k } = {2, 3})
d1j cos d1k + 2y1k

tk = Ak t j + Bk , 0 t j z j , Ak = , Bk = , (13)
d1k 2d1k
(x2 x1 )(x3 x1 )
where cos = . F W is a spherical polygon with arcs , 1 n, including
d13
d12
some k as above, so W F ( X N ) HdH2 has the similar form as that in equation (12).
Let Ak = x j x1 + Ak (xk x1 ), Bk = Bk (xk x1 ) + (x1 p), Ck = Bk Ak . Treating Ak and
Bk as constants and setting Hk = p Ck , Jk = Ak Ck , and Kk = Bk Ck . Let ak t2j + bk t j + ck =
|Ak t j + Bk |2 > 0, then k = 4ak ck bk2 > 0. By = Ntj N/| Ntj | and dH1 = r | Ntj |dt j ,

2rH 2ak z j + bk b
X dH1= k arctan arctan k
(W F )k k k k

2r2 Jk bk z j + 2ck
+ 2 ck (14)
k a z2 + b z + c
k j k j k

2r2 Kk 2ak z j + bk bk
+ .
k ak z2j + bk z j + ck ck
Let Uk = (Ak nk ), Vk = (Bk nk ), Wk = |Ck nk | > 0, then

d fP
(2a z + bk )Vk
2r 2
k j b V
dt
dH 1 = k k
k | M P f P | Wk a k z j + bk z j + c k
2 ck

(bk z j + 2ck )Uk
+ 2 ck Uk , (15)
ak z2j + bk z j + ck
where the sign is determined by orientation.

80 34
A.4. Saddle face

A saddle face F is generated when the probe S simultaneously tangents to two balls B(x1 , r1 )
and B(x2 , r2 ), and rolls around the axis e2 = x2d12x1 . The starting and stopping positions of
the probe center is p and q. Let y = [(r1 + r )2 (r2 + r )2 ]/2d12 and t = 12 (x1 + x2 ) + ye2 ,
R = |p t|, e1 = (p t)/R, e3 = e1 e2 , then F is parametrized by 0 s , 1 2 ,
x(, ) = t + ( R r cos )(cos e1 + sin e3 ) + r sin e2 , (16)
where let s = arccos[(p t) (q t)/R2 ], then s = s or 2 s . 1 =

arctan[(d12 + 2y)/2R], 2 = arctan[(d12 2y)/2R]. These data are uniquely determined
by the conformation P, see Connolly (1983). Let k (t) and s (t) be similarly dened for
(t) (t)( )+2 (t)( 2 )
the conformation Pt , one can dene t () = s , t ( ) =
s 1 2
2 1 , and
U () = cos e1 + sin e3 , then for the same 0 s and 1 2 ,
t (x) = t(t) + [ R r cos t ( )]U (t ()) + r sin t ( )e2 (t). (17)
Let U = cos e1 + sin e3 , U = sin e1 + cos e3 , then
X (x) = t + ( R + r sin )U + ( R r cos )(U + U )

+r cos e2 + r sin e2 . (18)
On F, N = cos U () + sin e2 , dH2 = r ( R r cos )dd, 2H = rR 2r cos . Let J =

( Rr cos )
s
J (s ) = 0 U ()d, then

4 X NdH2 = 4rR(s t e2 RJ e2 )(cos 1 cos 2 )
F
+ 4rR(s R + t J )(sin 1 sin 2 ) (19)
2
r (s t e2 RJ e2 )(cos 21 cos 22 )
+ r2 (s R + t J )[2(1 2 ) + sin 21 sin 22 ],

2 ( X N ) HdH2 = 2R(s t e2 R e2 )(cos 1 cos 2 )
F
+ 2R(s R + t J )(sin 1 sin 2 ) (20)
r (s t e2 RJ e2 )(cos 21 cos 22 )
+ r (s R + t J )[2(1 2 ) + sin 21 sin 22 ].
Assume that x1 is hydrophobic and x2 is not, then the dividing plane P passing through p and
t and is perpendicular to e2 . The curve W F is given by x() = t + ( R r )U (), 0 s ,
on which dH1 = ( R r )d. The hydrophobic surface integral on F then is the same as in
d (t) 1 2 2 1
equation (20), except 1 = 0. Since on W F, = N N = e2 , dt |t=0 = 0 = 2 1 , by
equation (18),

X dH1 = ( R r )s (r 0 + t e2 ) ( R r )2 e2 J, (21)
W F
d f Pt (t ( X ))
Let n j = e2 , then f Pt (t (x)) = [t (x) t(t)] n j (t), | MP f P | = n j = 1, and dt | t =0 =
[t ( X ) t(t)] e2 + [( R r )U ] e2 = r 0 .
d fP
dt
dH1 = ( R r )s r 0 . (22)
WP F | MP f P |
Author details
Yi Fang
Department of Mathematics, Nanchang University, 999 Xuefu Road, Honggutan New District,
Nanchang, 330031, China
12. References
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Protein Chem. 14, 1-63 (1959).
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protein models. Implications for structure predictions. J. Mol. Biol. 177, 787-818.
[22] Popelier, P. (2000) Atoms in Molecules: An Introduction. (Prentice Hall).
[23] Reynolds, J. A., Gilbert, D. B., and Tanford, C. (1974) Empirical correlation between
hydrophobic free energy and aqueous cavity surface area. Proc. Natl. Acad. Sci. USA
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[24] Richards, F. M. (1977) Areas, volumes, packing, and protein structure. Ann. Rev. Biophys.
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Chapter
Chapter 4
0
Information Capacity of Quantum Transfer

Channels and Thermodynamic Analogies
Bohdan Hejna
1. Introduction
We will begin with a simple type of stationary stochastic1 systems of quantum physics using
them within a frame of the Shannon Information Theory and Thermodynamics but starting
with their algebraic representation. Based on this algebraic description a model of information
transmission in those systems by dening the Shannon information will be stated in terms
of variable about the system state. Measuring on these system is then dened as a spectral
decomposition of measured quantities - operators. The information capacity formulas, now
of the narrow-band nature, are derived consequently, for the simple system governed by
the BoseEinstein (BE) Law [bosonic (photonic) channel] and that one governed by the
Fermi-Dirac (FD) Law [fermionic (electron) channel]. The not-zero value for the average input
energy needed for information transmission existence in FD systems is stated [11, 12].
Further the wideband information capacity formulas for BE and FD case are stated.
Also the original thermodynamic capacity derivation for the wideband photonic channel
as it was stated by LebedevLevitin in 1966 is revised. This revision is motivated by
apparent relationship between the BE (photonic) wideband information capacity and the
heat efciency for a certain heat cycle, being further considered as the demonstrating model
for processes of information transfer in the original wideband photonic channel. The
information characteristics of a model reverse heat cycle and, by this model are analyzed, the
information arrangement of which is set up to be most analogous to the structure of the
photonic channel considered, we see the necessity of returning the transfer medium (the
channel itself) to its initial state as a condition for a sustain, repeatable transfer. It is not
regarded in [12, 30] where a single information transfer act only is considered. Or the return is
1
We deal with such a system which is taking on at time t = 0, 1, . . . states t from a state space . If for any t0 the
t0 + T
1
relative frequencies IB of events B is valid that
T IB (t ) tends for T to probabilities pt0 ( B) we speak
t = t 0 +1
about a stochastic system. If these probabilities do not depend on the beginning t0 , a stationary stochastic system is
spoken about.
regarded, but by opening the whole transfer chain for covering these return energy needs from
its environment not counting them in - not within the transfer chain only as we do now. The result
is the corrected capacity formula for wideband photonic (BE) channels being used for an information
transfer organized cyclicaly.
2. Information transfer channel

An information, transfer channel K is dened as an arranged tripartite structure [5]
Def Def Def

K = [ X, , Y ] where X = [ A, p X ()] , Y = [ B, pY ()] and (1)

- X is an input stochastic quantity, a source of input messages a A+ = X , a transceiver,

- Y is an output stochastic quantity, a source of output messages b B+ = Y , a receiver,
- output messages b Y are stochastic dependent on input messages a X and they are
received by the receiver of messages, Y,
- is the maximal probability of an error in the transfer of any symbol x A in an input
message a X
[the maximal probability of erroneously receiving y B (inappropriate for x) in an output
message b Y ],
- A denotes a nite alphabet of elements x of the source of input messages,
- B denotes a nite alphabet of elements y of the source of output messages,
- p X () is the probability distribution of evidence of any symbol x A in an input message,
- pY () is the probability distribution of evidence of any symbol y B in an output message.
The structure ( X, K, Y ) or (X , K, Y ) is termed a transfer (Shannon) chain. The symbols H ( X )
and H (Y ) respectively denote the input information (Shannon) entropy and the output information
(Shannon) entropy of channel K, discrete for this while,
Def Def
H (X) = p X ( x ) ln p X ( x ), H (Y ) = pY (y) ln pY (y) (2)
x A y B
The symbol H ( X |Y ) denotes the loss entropy and the symbol H (Y | X ) denotes the noise entropy
of channel K. These entropies are dened as follows,
Def Def
H ( X |Y ) = p X,Y ( x, y) ln p X |Y ( x |y), H (Y | X ) = p X,Y ( x, y) ln pY | X (y| x ) (3)
A B A B
where the symbol p| (|) denotes the condition and the symbol p, (, ) denotes the
simultaneous probabilities. For mutual (transferred) usable information, transinformation T ( X; Y )
or T (Y; X ) is valid that
T ( X; Y ) = H ( X ) H ( X |Y ) and T (Y; X ) = H (Y ) H (Y | X ) (4)
From (2) and (3), together with the denitions of p| (|) and p, (, ), is provable prove
that the transinformation is symmetric. Then the equation of entropy (information) conservation
is valid
H ( X ) H ( X |Y ) = H (Y ) H (Y | X ) (5)
Information Capacity of Quantum Transfer Information Capacity
Channels and Thermodynamic of Quantum
Analogies Transfer Channels and Thermodynamic Analogies3 85
The information capacity of the channel K (both discrete an continuous) is dened by the
equation
Def
C = sup I ( X; Y ) (6)
over all possible probability distributions q(), p().It is the maximum (supremum) of the
medium value of the usable amount of information about the input message x within the
output message y.
Remark: For continuous distributions (densities) p[] (), p[|] (|) on intervals X , Y R,
x X , y Y is

H (X) = p X ( x ) ln p X dx, (7)
X
H (Y ) = pY (y) ln pY (y) dy (8)
Y

H ( X |Y ) = p X,Y ( x, y) ln p X |Y ( x |y) dxdy,
X Y

H (Y | X ) = p X,Y ( x, y) ln p(y| x ) dxdy
X Y
Equations (4), (5 are valid for both the quantities H () and H (|), as well as for their respective
changes H ()[= H ()] and H (|)[= H (|)].
3. Representation of physical transfer channels

The most simple way of description of stationary physical systems is an eucleidian space of
their states expressed as linear operators.2 This way enables the mathematical formulation of the
term (physical) state and, generally, the term (physical) quantity.
Physical quantities , associated with a physical system represented by the Eucleidian space
are expressed by symmetric operators from the linear space L() of operators on , A
L() [7]. The supposition is that any physical quantity can achieve only those real values
which are the eigenvalues of the associated symmetric operator (symmetric matrix [i,j ]n,n , n =
dim ). They are elements of the spectrum S() of the operator . The eigenvalues S()
R of the quantity being measured on the system = depend on the (inner) states of
this system .
The pure states of the system = are represented by eigenvectors . It is valid that
the scalar project (, ) = 1; in quantum physics they are called normalized wave functions.
The mixed states are nonnegative quantities A; their trace [of an square matrix (operator)
] is dened
n
Def
Tr() = i,i and, for is valid that Tr() = 1. (9)
i =1
The symmetric projector {} = [({})] (orthogonal) on the onedimensional subspace
({}) of the space is nonnegative quantity for which Tr( {}) = 1 is valid. The projector
{} represents [on the set of quantities A L()] the pure state of the system . Thus, an
arbitrary state of the system can be dened as a nonnegative quantity A for which
Tr() = 1 is valid. For the pure state is then valid that 2 = and the state space of the
system is dened as the set of all states of the system .
2
The motivation is the axiomatic theory of algebraic representation of physical systems [7].
3.1. Probabilities and information on physical systems

3.1.0.1. Theorem:
For any state the pure states i = {i } and numbers q(i |) 0 exists, that
n n
q(i |) 0, = q(i|) i where q(i|) = 1 (10)
i =1 i =1
3.1.0.2. Proof:
Let D () = { D : S()} is a disjoint decomposition of the set {1, 2, ..., n} of indexes of
the base {1 , 2 , ..., n } of . The set {i : i D } is an orthogonal basis of the eigenspace
( |) of the operator [for its eigenvalue S()]. Then
card D = dim ( |) 1 and [( |)] = {i }, S() (11)

i D
Let q(i |) = is taken for all i D , S(). By the spectral decomposition theorem [9],
n
= = [( |)] = {i } = q(i|) {i } (12)
S() S() S() i D i =1
n n
Tr() = q(i|) Tr( {i }) = q(i|) = 1
i =1 i =1
The symbol q(|) denotes the probability distribution into pure, canonic components i of is
called:
canonic distribution (q-distribution) of the state .3
Further the two distribution dened on spectras of A and A will be dealt:
dimensional distribution (d-distribution) of the state 4
Def dim ( |) dim ( |)

d( |) = = , S() (13)
dim n
distribution of measuring (p-distribution) of the quantity A in the state ,
Def
p(||) = Tr( ), S() (14)
where { : S()} is the spectral decomposition of the unit operator 1. Due the nonnegativity
of is p(||) = Tr( ) 0. By spectral decomposition of 1 and by denition of the
trace Tr() is
p(||) = Tr = Tr(1) = 1 (15)

S() S()
Thus the relation (14) denes the probability distribution on the spectrum of the operator
S ( ).
3
Or, the system spectral distribution SSD [11].
4
Or, the system distribution of the system spectral dimension SDSD [11].
The special case of the p-distribution is that for measuring values of , ,

p( ||) = Tr( ) = dim ( |), S() (16)
It is the case of measuring the itself. Thus, by the equation (14), the term measuring means
just the spectral decomposition of the unit operator 1 within the spectral relation with
[4, 20]. The act of measuring of the quantity A in (the system) state gives the value
from the spectrum S() with the probability p(||) = Tr( ) given by the p-distribution,
p(||) = Tr( ) = 1 (17)

S() S()
The measured quantity in the state is a stochastic quantity with its values [occuring with
probabilities p(||)] from its spectrum S(). For its mathematical expectation, medium value
is valid
E() = Tr( ) = Tr = Tr() = (, ) (18)

S() S()
Nevertheless, in the pure state = {} the values i = S() are measured, Tr(i ) =
(i , i ) = ii .
Let is an arbitrary stationary physical system and A is its arbitrary state. The
physical entropy H() of the system in the state is dened by the equality
Def
H() = Tr( ln ) (19)
When { : S()} is the decomposition of 1 spectral equivalent with , then it is valid
that
ln = ln and H() = ln dim ( |) (20)
S() S()
3.1.0.3. Theorem:
For a physical system in any state is valid that
n
p( ||)
H() = q(i |) ln q(i |) = H [q(|)] = ln n p( ||) ln
i =1 S()
d( |)
= ln n I [ p(||)
d(|)] (21)
where H () is the Shannon entropy, I (
) is the information divergence, p(||) is the
p-distribution for the state , q(|) is the q-distribution for the state and d(|) is the
d-distribution for the state , n = dim .
3.1.0.4. Proof:
The relations in (21) follows from (20) and from denition (10) of the distribution q(|). From
denitions (13) and (16) of the other two distributions follows that [12, 38]
n dim ( |)
I [ p(||)
d(|)] = dim ( |) ln
dim ( |)
S()
= dim ( |) ln n H() = ln n H() (22)

S()
Due to the quantities X, Y, X |Y, Y | X describing the information transfer are in our algebraic

description denoted as follows, X = , Y = or Y = (
), ( X |Y ) = (|), (Y | X ) = (|).
The laws of information transfer are writable in this way too:
C = sup I (; ), I (||) T (; ) (23)

,
I (; ) = I (; ) = H() H (|) = H (
) H (|) = H() + H (
) H (, )
H (, ) = H (, ) = H() + H (|) = H (
) + H (|) (24)
4. Narrow-band quantum transfer channels

Let the symmetric operator of energy of quantum particle is considered, the spectrum of
which eigenvalues i is S(). Now the equidistant energy levels are supposed. In a pure state
i of the measured (observed) system the eigenvalue i = i , > 0. Further, the output
quantity of the observed system is supposed (the system is cell of the phase space BE or
FD) with the spectrum of eigenvalues S() = {0 , 1 , ..., } being measured with probability
distribution Pr() = { p(0), p(1), p(2), ...}

p(k i ) pro k i
p(k ||i ) = (25)
0 k<i
Such a situation arises when a particle with energy i is excited by an impact from the output
environment. The jump of energy level of the impacted particle is from i up to i+ j , i + j = k.
The output i+ j for the excited particle is measured (it is the value on the output of the channel
K= . This transition j occurs with the probability distribution
Pr( j), j {0, 1, 2, ...} (26)
Let be considered the narrowband systems (with one constant level of a particle energy) of
BE or FD type [27] (denoted further by BE, , FD, ).
In the BE system, bosonic, e.g. the photonic gas the BE distribution is valid

Pr( j) = (1 p) p j , j {0, 1, ...}, p (0, 1), p k (27)
In the FD system, fermionic, e.g. electron gas the FD distribution is valid
pj
Pr( j) = , j {0, 1}, p (0, 1), p k (28)
1+ p
where parameter p is variable with absolute temperature > 0; k is the Boltzman constant.
Also a collision with a bundle of j particles with constant energies of each and absorbing
the energy j of the bundle is considerable. E.g., by (e.g. BE, is the photonic gas)
the monochromatic impulses with amplitudes i S are transferred, nevertheless generated
from the environment of the same type but at the temperature TW , TW > T0 where T0 is the
temperature of the transfer system = K (the noise temperature).
It is supposed that both pure states i in the place where the input message is being coded
- on the input of the channel
= K and, also, the measurable values of the quantity being
observed on the place where the output message is decoded - on the output of the channel =K
are arrangable in such a way that in a given i-th pure state i of the system = K only
the values k S(), k = i + j are measurable and, that the probability of measuring the k-th
value is Pr( j) = Pr (k i ). This probability distribution describes the additive noise in the given
channel = K. Just it is this noise which creates observed values from the output spectrum
S() = {i , i+1 , ...} being the selecting space of the stochastic quantity .
The pure states with energy level i = i are achievable by sending i particles with energy
of each. When the environment, through which these particles are going, generates a bundle
of j particles with probability Pr( j) then, with the same probability the energy i+ j = k is
decoded on the output.
It is supposed, also, the innite number of states i , innite spectrum S() of the measured

quantity , then S() = {0, 1, 2, ...}, S() = D (); [S() = S, k = ].
The narrowband, memory-less (quantum) channel, additive (with additive noise) operating
on the energy level S() is dened by the tripartite structure (1),
K = {[S , q(i |)], p(||i ), [S , p(||)]}. (29)
4.1. Capacity of BoseEinstein narrowband channel

Let now i i, i = 0, 1, ... are pure states of a system BE,
= K and let is output quantity
taking on in the state i values S with probabilities
p(||i ) = (1 p) pi (30)
Thus the distribution p(||i ) is determined by the forced (innerinput) state i = {i }

representing the coded input energy at the value i = i S(), = const. For the medium
value W of the input i is valid

W= i q(i|) = E(), W = W (31)
i =0
The quantity W is the medium value of the energy coding the input signal i.
For the medium value of the number of particles j = i 0 with BE statistics is valid

d 1 p
j (1 p) p j = (1 p) p j p j1 = (1 p) p dp 1 p = 1 p
j =0 j =0
The quantity E() is the medium value of the output quantity and
E() = p(||) (32)

S()
where p(||) is the probability of measuring the eigenvalue = k of the output variable .
n
K
This probability is dened by the state = q(i |) i of the system BE, =
i =0
n n
p(||) = q(i|) p(||i ) = (1 p) q(i|) pi [= Tr( )] (33)
i =0 i =0
From the differential equation with the condition for = 0
p(||) = p( 1||) p + (1 p) q(|), 1; p(0||) = (1 p) q(0|) (34)
follows, for the medium value E() of the output stochastic variable , that
E() = p( 1||) p + (1 p) q(|) (35)

1 1
= p( 1||) p + W (1 p) = p E() + p p( 1||) + W (1 p)
1 1
p
E() (1 p) = p + W (1 p) E() = + W, W = E() > 0, 0 (36)
1+ p
The quantity H (
i ) is the p-entropy of measuring for the input i S being represented
by the pure state i of the system BE,
H (
i ) = (1 p) p j ln[(1 p) p j ] (37)
jS
= (1 p) ln(1 p) p j (1 p) p ln p j p j1
j j

d 1 h( p)
= ln(1 p) (1 p) p ln p = , i S
dp 1 p 1 p

where h( p) = (1 p) ln(1 p) p ln p is the Shannon entropy of Bernoulli distribution
{ p, 1 p}.
The quantity H (|) is the conditional Shannon entropy of the stochastic quantity in the
state of the system BE, , not depending on the (the noise entropy)
n n
h( p) h( p)
H (|) = q(i|) H (
i ) = q(i|) 1 p =
1 p
(38)
i =0 i =0
For capacity CBE of the channel K

= BE is, following the capacity denition, valid
h( p)
CBE = sup H (
) H (|) = sup H (
) (39)
0 0
1 p
where the set 0 = { , E() = W 0} represents the coding procedure of the input
i S. The quantity H (
) = H ( p(||)) is the p-entropy of the output quantity . Its
supremum is determined by the Lagrange multipliers method:

H (
) = p(||) ln p(||) = p ln p , p = p(||) (40)
S() S()
The conditions for determinating of the bound extreme are
p = 1, p = E() = const. (41)

S() S()
The Lagrange function
L = p ln p 1 p + 1 2 p + 2 E() (42)

L
which gives the condition for the extreme, = ln p 1 1 2 = 0, yielding in
p
e 1 1 e 1 1
p = e11 e2 = p(||) and further, in p = = =1 (43)
e 2 1 e 2
Then for the medium value E() the following result is obtained

E() = p = e 1 1
e 2 = e 1 1
2 e
2
(44)

1 e 1 1 e 2
= e 1 1 = e 2
=
2 1 e 2 (1 e 2 )2 1 e 2

By (35), (36) and for the parametr p=e k = const. ( = const. = const.) E() is a function

of W only. For 2 = is e2 = p(W ) and E() is the medium value for with the
kTW
geometric probability distribution
p() = p(||) = [1 p(W )] p(W ) , S() (45)

depending only on or, on the absolute temperature TW respectively. Thus for E() is
kTW
valid that
p(W )
E() = , p(W ) = e kTW (46)
1 p(W )
From (35) and (46) is visible that p(W ) or TW respectively is the only one root of the equation

p(W ) p e kTW e kT0
= + W , resp. =
+W (47)
1 p(W ) 1 p
1 e kTW 1 e kT0
From (34) and (45) follows that for state 0 or, for the q-distribution q(|) respectively, in
which the value H (
) is maximal [that state in which achieves the distribution q(|) =
p()], is valid that
1 p(W ) 1 p(W )
q(|) = , = 0 and q(|) = [ p(W ) p] p(W )1 , > 0 (48)
1 p 1 p
For the effective temperatutre TW of coding input messages the distribution (45) supremizes
(maximizes) the p-entropy H (
) of and, by using (37) with p(W ), is gained that
h[ p(W )]
sup H (
) = (49)
0
1 p(W )
From (39) and (49) follows [12, 37] the capacity CBE, of the narrowband channel K
= BE
h[ p(W )] h( p)
CBE, = (50)
1 p(W ) 1 p
92 10
By (35), (36) and (46) the medium value W of the input message i S is derived,
p(W ) p
W= (51)
1 p(W ) 1 p
By (31) the condition for the minimal average energy WKrit needed for coding the input
message is
W 0 resp. W = W 0, S() (52)

W WKrit , WKrit = 0 (53)
The relations (35), (36), (46) and (52), (53) yield in
p(W ) p
E() = and, then p(W ) p, 1 p(W ) 1 p (54)
1 p(W ) 1 p
From (47) and (54) follows that for the dened direction of the signal (messaage) transmission
at the temperature TW of its sending and decoding is valid that
p(W ) p
> , p(W ) > p, W > 0 (55)
1 p(W ) 1 p
kT kT
p(W ) = e W e 0 = p and thus TW T0 (56)
4.2. Capacity of FermiDirac narrowband channel

Let is now considered, in the same way as it was in the BE system, the pure states i i
of the system which are coding the input messages i = 0, 1, ... and the output stochastic
quantity having its selecting space S. On the spectrum S probabilities of realizations S
are dened,
p i
p(||i ) = , p (0, 1), i = 0, 1, ... (57)
1+ p
expressing the additive stochastic transformation of an input i into the output for wich is
valid = i or = i + 1.5 The uniform energy level = const. of particles is considered.
The quantity W is the mathematical expectation of the energy coding the input signal
W = W, W = i q(i|) = E() (58)

iS
The medium value of a stochastic quantity with the FD statistic is given by
pj p
j
1+ p
=
1+ p
(59)
j{0,1}
The quantity E() is the medium value of the output quantity ,
E() = p(||) (60)

S()
5
In accordance with Pauli excluding principle (valid for fermions) and a given energetic level S().
Analogies 11 93
Transfer Channels and Thermodynamic Analogies
where p(||) is probability of realization of S in the state of the system

FD,
=K,
n n
1
= q(i|) i , p(||) = q(i|) p(||i ) = q(i |) pi (61)
iS i =0
1 + p i =0
From the differential equation
q( 1|) p + q(|)
p(||) = , 1 (62)
1+ p
with the condition for

1
= 0, p(0||) = q(0|)
1+ p
follows that for the medium value E() of the output stochastic variable is valid that
p 1
1 + p p
E() = q( 1|) + q(|) (63)
1 1 + 1
p p 1
1 + p
= ( 1) q( 1|) + q( 1|) + W
1 1 + p 1
1 + p
p p 1 p
= W + + W E() = + W , W = E(), 0
1+ p 1+ p 1+ p 1+ p
The quantity H (
i ) is the p-entropy of measuring for the input i S being represented
by the pure state i of the system FD,
1
pj pj 1 1 p p
H (
i ) = ln = ln ln (64)
j =0
1 + p 1 + p 1 + p 1 + p 1 + p 1 + p

p p p p p
= 1 ln 1 ln =h , i S
1+ p 1+ p 1+ p 1+ p 1+ p
The quantity H (|) is the conditional (the noise) Shannon entropy of the stochastic quantity
in the system state , but, independent on this ,
n

p p
H (|) = q(i |) H (
i ) = q(i |) h =h (65)
i =0 i
1+ p 1+ p
For capacity CFD, of the channel K

=FD, is, by the capacity denition in (23)-(24), valid
that

p
CFD = sup H (
) H (|) = sup H (
) h (66)

1+ p
0 0
where the set 0 = { : E() = W > 0} represents the coding procedure.

The quantity H (
) = H ( p(||)) is the p-entropy of the stochastic quantity in the state
of the system FD, . Its supremum is determined by the Lagrange multipliers method in
the same way as in BE case and with the same results for the probility distribution p(||)
(geometric) and the medium value E()
94 12
p() = p(||) = [1 p(W )] p(W ) , S() (67)

p(W )
E() = , p(W ) = e kTW
1 p(W )

Again , the value E() depends on , or on absolute temperature TW respectively, only. By
kTW
using E() in (63) it is seen that p(W ) or TW respectively is the only one root of the equation
[12, 30]

p(W ) p e kTW e kT0
= + W , resp. =
+W (68)
1 p(W ) 1+ p
1 e kTW 1 + e kT0
For the q-distribution q(|) = p() of states 0 , for which the relation (62) and (67) is
gained, follows that
q( 1|) p + q(|)
= [1 p(W )] p(W ) , S with conditions (69)
1+ p
q(0|) = (1 + p) [1 p(W )] and q(1|) = (1 + p) [1 p(W )] [ p(W ) p];

1
q(|) = (1 + p) [1 p(W )] (1)i p(W )i pi + (1) p , > 1
i =0
For the effective temperatutre TW of coding the input messages the distribution (67) supremises
(maximizes) the p-entropy H (
) of is valid, in the same way as in (49), that
h[ p(W )]
sup H (
) = (70)
0
1 p(W )
By using (70) in (66) the formula for the CFD, capacity [12, 37] is gained

h[ p(W )] p
CFD, = h (71)
1 p(W ) 1+ p
The medium value W of the input i = 0, 1, 2, ... is limited by a minimal not-zero and
positive bottom value WKrit . From (58), (63) and (68) follows
p(W ) p
E() = , p(W ) = e kTW e kT0 = p and thus TW T0 (72)
1 p(W ) 1 p

2
p(W ) p 2p2 2e kT0
W= 0, W = WKrit , resp. W = W 2
(73)
1 p(W ) 1 + p 1 p 2
1 e kT0
For the average coding energy W, when the channel CFD, acts on a uniform energetic level
, is
2p2
W WKrit = (74)
1 p2
For the FD channel is then possible speak about the effect of the not-zero capacity when the
difference between the coding temperatures TW and the noise temperature T0 is zero.6 This
phennomenon is, by necessity, given by properties of cells of the FD phase space.
6
Not not-zero capacity for zero input power as was stated in [37]. The (74) also repares small missprint in [11].
Analogies 13 95
5. Wideband quantum transfer channels

Till now the narrowband variant of an information transfer channel K ,
S(), card S() = 1 has been dealt. Let is now considered the symmetric operator of energy
of a particle, having the spectrum of eigenavalues

h 2h nh rh
S() = 0, , , ..., , ... = , card S() = n + 1 (75)
r=0, 1, ..., n
where > 0 denotes the time length of the input signal and h denotes Planck constant. The
multiband physical transfer channel K, memory-less, with additive noise is defend by the
(arranged) set of narrowband, independent components K , S(),

K= K =
S() S()
i , p( | |,i ), = i, p(||i ), (76)
i=
S()
i = [S, q (i | )],
S()
i S = {0, 1, 2, ...}
=
S() =
S()
[S, p( | | )], S = {0, 1 , 2, ...}
Due the independency of narrowband components K the vector quantities i , , , j are

independent stochastic quantities too.
The simultaneous q-distribution of the input vector of i and the simultaneous p-distribution
of measuring the output vector of values (of the individual narrowband components K )
are
q (i | ) = q(i |), =
S()
, i S (i ) (77)
S()
p( | | ) = p(||), =
S()
, S() (78)
S()
The system of quantities (the set of states of the narrowband components K ) is the state
of the multiband channel K in which the (canonic) q-distribution of the system K is dened.
Values i , j ,
= j + i ; = , j = j , i = i ; j = i 0, S(), cardS > 1

S() S() S()
(79)
are the numbers of the input, output and additive (noise) particles of the multiband channel
K. In this channel the stochastic transformation of the input i into the output is performed,
being determined by additive stochastic transformations of the input i into the output in
individual narrowband components K .
Realizations of the stochastic systems i, , , j are the vectors (sequences) i, , , j
i = (i )S() , = ( )S() , = ( )S() , j = ( j )S() ; i, , j

S()
S, (80)
i , , j S, S( ), = ,i , S()
i S
96 14
For the probability of the additive stochastic transformation (77), (78) of input i into the output
is valid
p( | |,i ) = p(||i ), = j + i, i S(i ), j S( j), S() (81)

S()
The symbol ,i denotes the pure state coding the input i S of a narrowband component
K and the state i = S() ,i codes the input i for which
q(i |) = q = q ( ) (82)
S()
For the multiband channel K the following quantities are dened:7

the p-entropy of the output
H (
) = H (
) = p( | | ) ln p( | | ) (83)
S() S() S
sup H (
)
S()
for which, following the output narrowband BE and FD components K K, is valid that
h[ p (W )]
sup H (
) = sup H (
) = sup H (
) = (84)
S()
1 p (W )
0 0 S() S()
the conditional noise entropy (entropy of the multiband BE | FD noise)

h( p ) p
H (|) = H ( | ) = q(i |,i ) H (
,i ) = h (85)
1 p 1 + p
S() S() iS S()
kT kT
where p (W ) = e 0W , p = e 0 , TW T0 > 0 and h( p) = p ln p (1 p) ln(1
p ).
the transinformation T (; ) and the information capacity C (K),
C (K ) = sup T (; ) = sup H (
) H (|) (86)
0 0

h[ p (W )] h( p ) p
= h
S()
1 p (W ) S() 1 p 1 + p
The set 0 = { ; E( ) = W 0} represents a coding procedure of the input i

S()
of the K into i , [by transforming each input i into pure state ,i , S()].
7
Using the chain rule for simultaneous probabilities it is found that for information entropy of an independent stochastic

system X = ( X1 , X2 , ..., Xn ) is valid that H ( X ) = H ( Xi | X1 , ...Xi1 ) = H ( Xi ). Thus the physical entropy H()
i i
of independent stochastic system, = { } , is the sum of H [q(| )] over S too.
Analogies 15 97
5.1. Transfer channels with continuous energy spectrum

Let a spectrum of energy with the nite cardinality n + 1 and a nite time interval > 0 are
considered

rh h rh
S() = { r }r=0, 1, ..., n = , = , r = = r , (87)
r=0, 1, ..., n
n h h
card S() = = n + 1, n = n = n , = = const.
n n
For a transfer channel with the continuous spectrum of energies of particles and with the
n
bandwidth equal to card S() = , is valid that
h
rh 1 d
lim r = lim = lim r = r d resp. lim = , S() = 0, n ) (88)
h
But the innite wideband and innite number of particles ( , n ) will be dealt
with. Then

rh rh
S() = { r }r=0, 1, ... = = lim r = lim = lim r = r d (89)
r=0, 1, ... 0
and thus the wideband spectrum S() of energies is
1 d
lim = , S() = 0, ) (90)
h

With the denotation = , i = i , j = j , i , j S, S, S() For the p-entropy of
the output of the wideband transfer channel KBE|FD is valid that
1 1
p( | | ) ln p( | | )(91)
H (
) = lim H (
) = lim

S() S() S

1
=
h 0
p(| | ) ln p(| | ) d
S

1 1 h[ p (W )]

sup H (
) = lim sup H (
) = d

S()
h 0 1 p (W )
For conditional entropy of the wideband transfer channel KBE|FD [entropy of the
wideband noise independent on the system (KBE|FD ) state ] and for its information
capacity is valid, by (85) and (86)
1 1
q(i|,i ) H (
,i )
H (|) = lim H ( | ) = lim (92)

S() S() iS

1 1 h( p ) p
= H ( | ) d = h d
h 0 h 0 1 p 1 + p

1 h[ p (W )] 1 h( p ) p
C ( KBE|FD ) = = d h d (93)
h 0 1 p (W ) h 0 1 p 1 + p
98 16
By (52) and (74) the average number of particles on the input of a narrowband component
K is

2p2
W = i q(i | ) 0 (94)
iS 1 p2
and then for the whole average number of input particles W of the wideband transfer
channel K is obtained
1 1
W = W d, W = W d (95)
h 0 h 0
where W is whole input energy and TW is the effective coding temperature being supposingly at
the value TW , TW = TW , S().
5.2. BoseEinstein wideband channel capacity

By derivations (86) and (92), (93) is valid that [12]

1 h[ p (W )] 1 h( p )
C ( KBE ) = d d (96)
h 0 1 p (W ) h 0 1 p
For the rst or, for the second integral respectively, obviously is valid

1 h[ p (W )] 2 kTW 1 h( p ) 2 kT0
d = resp. d = (97)
h 0 1 p (W ) 3h h 0 1 p 3h
Then, for the capacity of the wideband BE transfer channel KBE is valid
2 k 2 kTW TW T0 2 kTW
C ( KBE ) = ( TW T0 ) = = max , TW T0 (98)
3h 3h TW 3h
and for the whole average output energy is valid
1
1 p (W ) 1 p (W ) k2 TW
2
ln(1 t) 2 k2 TW
2

lim = d = dt =

S()
1 p (W ) h 0 1 p (W ) h 0 t 6h
(99)
For the whole average energy of the BE noise must be valid

1 p 1 p 2 k2 T0 2

lim = d = (100)

S()
1 p h 0 1 p 6h
From the relations (79) among the energies of the output , of the noise j and the input i ,
2 k2 TW
2
2 k2 T0 2
= +W (101)
6h 6h

6hW
the effective coding temperature TW is derivable, TW = T0 1+ . Using it in (98)
2 k2 T0 2
gives

2 kT0 6hW
C ( KBE ) = 1+ 1 (102)
3h 2 k2 T0 2
Analogies 17 99
For T0 0 the quantum aproximation of C (KBE ), independent on the heat noise energy
(deminishes whith tempertures aiming to absolute 0 K)

4 k2 T 2 2W 2 kT 2W
lim C (KBE ) = lim 0
+ 2 0
= (103)
T0 0 T0 0 9h2 3h 3h 3h
The classical approximation of C (KBE ) is gaind for temperatures T0 0 (T0

respectively). It is near to value W , the Shannon capacity of the wideband Gaussian
kT0
channel with the whole noise energy kT0 and with the whole average input energy W. For T0
from (101), great enough, is gained that8

. 2 kT0 3hW W
C ( KBE ) = = (104)
3h 2 k2 T0 2 kT0
5.3. FermiDirac wideband channel capacity

By derivations (86) and (92), (93) is valid that [12]

1 h[ p (W )] 1 p 2 kTW 1 p
C ( KFD ) = d h d = h d
h 0 1 p (W ) h 0 1 + p 3h h 0 1 + p
(105)
For the second integral obviously is valid

1 p 2 kT0
h d = (106)
h 0 1 + p 6h
By guring (105) the capacity of the wideband FD channel KFD is gained,

2 k T0
C ( KFD ) = TW (107)
3h 2
and for TW > T0 is writable
2TW T0
C (KFD ) = C (KBE ) (108)
2TW 2T0
For the whole average output energy is valid the same as for the BE case,

1 p (W ) 2 k2 TW
2
d = (109)
h 0 1 p (W ) 6h
For the whole average FD wideband noise energy is being derived
kT
1 p 1 e 0 k2 T0 2 e x
lim

1 + p = h kT
d =
h
x
1 + e x
dx (110)
S() 0 1+e 0 0
1
k2 T0 2 ln t 2 k2 T0 2
= dt =
h 0 t+1 12h
. 6hW
8
For | x | < 1, 1 + x = 1 + 12 x 18 x2 + . . . = 1 + 12 x where x = < 1.
2 k2 T0 2
100 Thermodynamics
18 Fundamentals and Its Application in Science Will-be-set-by-IN-TECH
From the relation (79) among the whole output, input, and noise energy,
2 k2 TW2
2 k2 T0 2
= +W (111)
6h 12h

1 6hW
follows the effective coding temperature TW = T0 + . Using it in (107) the
2 k2 T0 2
2
result is [24]
2 kT0 1 6hW 1
C ( KFD ) = + (112)
3h 2 2 k2 T0 2 2
For T0 0 the quantum approximation capacity C (KFD ), independent on heat noise energy
kT0 is gaind (the same as in the BE case (103),

4 k2 T 2 1 2W 2 kT 1 2W
lim C (KFD ) = lim 0
+ 2 0
= (113)
T0 0 T0 0 9h 2 2 3h 3h 2 3h
The classical approximation of the capacity C (KFD ) is gained for T0 09

2 kT0 1 12hW 1 . 2 kT0 1 6hW 1
C ( KFD ) = 1+ = 1 + (114)
3h 2 2 k2 T0 2 2 3h 2 2 k2 T0 2 2

2 kT0 W 2 kT0
= 21 + 2 2 1 , W = const. Wcrit
6h kT0 T0 6h
By (74) the condition for the medium value of the input particles of a narrowband component
2p2
K , S(), of the channel KFD is valid, W , from which the condition for
1 p2
the whole input energy of the wideband channel KFD follows. By (95) it is gaind, for
TW T0 > 0, that10
2 kT
1 1 2p2 . 2 e 0 2 k2 T0 2
W lim
S ( )
W lim

= 2 kT
d= = Wcrit>0 (115)
S() 1 p
2 h 12h
0 1 e 0
6. Physical information transfer and thermodynamics

Whether the considered information transfers are narrowband or wideband, their
algebraic-information description remains the same. So let be considered an arbitrary
stationary physical system of these two bandtypes as usable for information transfer.
n
Let a system state = q(i| ) {i } of the system is the successor (follower,
i =1
n
equivocant) of the system state = q(i|) {i } , is written. The
i =1
.
9
For 1 + x = 1 + 12 x when | x | < 1; x = 12hW .
2 k2 T0 2
10
If, in the special case of FD channel, it is considered that the value W given by the number of electrons as the average
energy of the modulating current entering into a wire, over a time unit, then it is the average power on the electric
resistor R = 1 too.
Analogies 19 101
n
distribution q(i | ) = p(i| j) q( j|), p(i | j) = (i , j )2 = u2ji and , ensures existence
j =1
of the transformation matrix [ui,j ] of a base of the space = {}in=1 into the base { }in=1 .11
From the relation also is visible that it is reexive and transitive relation between states
and, thus, it denes (a partial) arrangment on the set space . The terminal, maximal state for
this arrangement is the equilibrial state + of the system : it is the successor of an arbitrary
system state, including itself.
The statistic, Shannon, information) entropy H () is a generalization of the physical
entropyH(). The quantity I-divergence I (
) is, by (21), a generalization of the physical
quantity I ( p
d) = H(+ ) H() where the state
1 n
+ =
n i
i for i = {i }, i = 1, 2, ..., n (116)
=1
is the equlibrial state of the system . The probability distribution into the canonic components
i of + is uniform and thus
H(+ ) = ln n = ln dim () (117)
Information divergence I ( p
d) 0 expresses the distance of the two probability distributions
q(|) and q(|+ ) of states (stochastic quantities)
= [S, q(|)] and + = [S, q(|+ )] (118)
In the physical sense the divergence I ( p

d) is a measure of a not-equilibriality of the state
of the physical (let say a thermodynamic) system . Is maximized in the initial (starting),
not-equilibrium state of the (time) evolution of the . It is clear that I ( p
d) T (; )
6.0.0.5. H-Theorem, I I. Second Principle of Thermodynamics:
Let for states , of the system is valid that . Then
H( ) H() (119)
and the equality arises for = only [12, 38].

6.0.0.6. Proof:
(a) For a strictly convex function f (u) = u ln u the Jensen inequality is valid [23]

n n
f p(i | j) q( j|) p(i| j) f [q( j|)], i = 1, 2 , ..., n (120)
j =1 j =1

n n n n
f p(i| j) q( j|) p(i| j) f [q( j|)]
i =1 j =1 i =1 j =1
n n n
= f [q( j|)] = q( j|) ln q( j|) = H [q(|)] = H() due to p (i | j ) = 1
j =1 j =1 i =1
11
It is the matrix of the unitary operator u(t) expressing the time evolution of the system .
102 Thermodynamics
and for distributions q(i | ) is valid H( ) H():

n n n
f p(i| j) q( j|) = q(i| ) ln q(i| ) = H( ) [ H()]
i =1 j =1 i =1
(b) The equality in (119) arises if and only if the index permutation [i (1), i (2), ..., i (n)] exists
that p(i | j) = [i |i ( j)], j = 1, 2, ..., n; then q[i ( j)| ] = q( j|), j = 1, 2, ....
Let a xed j is given. Then, when 0 = p(i | j) = (i , j )2 , i = i ( j), the orthogonality is valid

(j | j ) (i |i ) , j = { j } = j , i = {i } = i (121)
i =i ( j )
and, consequently, j [i( j) |i( j) ], p[i ( j)| j] = (i( j) , j )2 = 1. It results in j = i( j) . This

prooves that the equality H( ) = H() implies the equality q( j|) {j } = q[i ( j)|] {i( j) }
and = .
H-theorem says, that a reversible transition is not possible between any two different states
= . From the inequality (119) also follows that any state of the system is the
successor of itself, and, that any reversibility of the relation (the transition
) is not possible within the system only, it is not possible without openning this
system . The difference

H(+ ) H() = max H( ) H() = H q(|+ ) H [q(|)] (122)

reppresents the information-theoretical expressing of the Brillouin (maximal) entropy

defect H (the Brillouin negentropic information principle [2, 30]). For the state + is valid
that + , . It is also called the terminal state or the (atractor of the time evolution)
of the system .12
6.0.0.7. Gibbs Theorem:
For all , of the system is valid
H() Tr( ln ) (123)
and the equality arises only for = [38].

6.0.0.8. Proof:
n n
Let for , is valid that = q(i |) {i }, = q(i |) {i } and let the operators
i =1 i =1
, are commuting = , D () = { D : S()}, D () = { D : S()}, are
their spectral decompositions. Let be the state the successor of , and relations
p(||) = q(i | ) = p(|| ) and H( ) H() are valid. For the matrix (ij ) of the
i D
12
In this sense, the physical entropy H() (19), (21) determines the direction of the thermodynamic time arrow [2],
H( ) H() H
= 0, t = t t > 0. The equality occurs in the equlibrial (stationary) state + of the system
t t
and its environment.
Analogies 21 103
n
operator in the base {1 , 2 , ..., n } is obtained that ij = uki ukj q(k|) and thus for
k =1
operators ln and Tr( ln ) is valid that

n n n
ln = ln q(i |) {i } and Tr( ln ) = u2ki q(k|) ln q(i |) (124)
i =1 i =1 k =1
n
= q(i | ) ln q(i |)
i =1
For the information divergence of the distributions q(| ), q(|) and the entropy H( ) is
valid that
n
q(i | ) n
I [q(| )
q(|)] = q(i| ) ln 0, H( ) q(i | ) ln q(i |). (125)
i =1 q(i |) i =1
By (119) for is writable that H() H( ) Tr( ln ). By (123) Tr( ln )

H( ) H() are valid; the rst equality is for
I [q(| )
q(|)] = 0, H( ) = H(), q(i | ) = q(i |), i = 1, 2, ..., n, = (126)
the second equality is for = . The Gibbs theorem expresses, in the deductive
(matematical-logical) way, the phenomenon of Gibbs paradox.13
From formulas (47), (55), (56) and (68), (72), (73) for the narrow-band BE and FD capacities
follows that

kT TW T0
TW T0
e W e kT0
1, e kT0 TW
e0 ; > 0, T0 > 0 TW T0
= max 0
TW
(127)
and it is seen that the quantity temperature is decisive for studied information transfers. The
last relation envokes, inevitably, such an opinion, that these transfers are able be modeled by
a direct reversible Carnot cycle with efciency max (0, 1). Conditions leading to C[|] < 0
mean, in such a direct thermodynamic model, that its efciency should be max < 0. This is
the contradiction with the Equivalence Principle of Thermodynamics [19]; expresses only that the
transfer is running in the opposite direction (as for temperatures).
As for BE channel; for the supposition W < 0 the inequalities TW < T0 and p(W ) < p
would be gained which is the contradiction with (35), (36) and (47). It would be such a situation
with the information is transferred in a different direction and under a different operation mode. Our
sustaining on the meaning about the original organization of the transfer, for TW > T0 , then
leads to the contradiction mentioned above saying only that we are convinced mistakenly
about the actual direction of the information transfer. In the case TW = T0 for the capacity
CBE from (50) is valid that CBE = 0. Then W = WKrit [= 0] for p(W ) = p.
2p2
As for FD channel; for the supposition W < TW < T0 and p(W ) < p is
1 p2
gained which is the contradiction with (68). For TW = T0 is for CFD from (71) valid
13
Derived by the information-thermodynamic way together with the I. and I I. Thermodynamic Principle and with the
Equivalence Principle of Thermodynamics in [16, 17, 19].
104 Thermodynamics
h( p) p
CFD = + ln p ln(1 + p).14
1 p 1+ p
Let be noticed yet the relations between the wideband BE and FD capacities and the model
heat efciency max . For the BE capacity (98) is gained that

2 kTW TW T0 2 kTW 2 kTW
C ( KBE ) = = max = Cmax (KBE ) (128)
3h TW 3h max 1 3h
Cmax (KBE ) = sup H (
) = H (i ) = H()

C (KBE ) > 0, TW > T0 , C ( KBE ) 0, TW T0

TW T0
(max 0)
2 kTW
It is the information capacity for such a direct Carnot cycle where H ( X ) = =
3h
Cmax (KBE ).
For the wide-band FD capacity from (105) is valid
2 kTW 2 kT0
C ( KFD ) = , TW T0 and for TW > T0 , (129)
3h 6h
2 kTW 2TW T0 2 kTW 2TW T0
C ( KFD ) = = max
3h 2TW 3h 2( TW T0 )
2TW T0
= C ( KBE )
2( TW T0 )
T0 2 kTW
Due to 1 max = is valid T0 = TW (1 max ) and also C (KFD ) = (1 + max ).
TW 6h
Then,
2 kTW
C (KFD ) = , (130)
max 1 3h
1 1 2 kTW
C ( KFD ) H (i ) = H() =
TW T0
2 2 6h
(max 0)
2
kTW 2 kTW 1
C ( KFD ) , = H(), H()
6h 3h 2
Again the phenomenon of the not-zero capacity is seen here when the difference between
the coding temperature TW and the noise temperature T0 is zero. Capacities C (KFD ) 0
T
are, surely, considerable for TW 0 , T0 and being given by the property of the FD phase
2
space cells. Capacities C (KBE ) < 0 and C (KFD ) < 0 are without sense for the given
direction of information transfer.
14
Nevertheless the capacity CFD for this case W < WKrit is set in [12, 13]. Similar results as this one and (74) are gained
for the MaxwellBoltzman (MB) system in [13].
Analogies 23 105
Nevertheless, it will be shown that all these processes themselves are not organized cyclically by
themselves.
Further the relation between the information transfer in a wideband BE (photonic) channel
organized in a cyclical way and a relevant (reverse) heat cycle will be dealt with. But, rstly, the
way in which the capacity formula for an information transfer system of photons was derived
in [30] will be reviewed.
6.1. Thermodynamic derivation of wideband photonic capacity

A transfer channel is now created by the electromagnetic radiation of a system L = KLL of
photons being emitted from an absolute black body at temperature T0 and within a frequency
bandwidth of = R+ , where is the frequency. Then the energy of such radiation is the
energy of noise. A source of input messages, signals transmits monochromatic electromagnetic
impulses (numbers ai of photons) into this environment with an average input energy W.
This source is dened by an alphabet of input messages, signals { ai }in=1 , with a probability
distribution pi = p( ai ), i = 1, 2, ... , n.15 The output (whole, received) signal is created by additive
superposition of the input signal and the noise signal. The input signal ai , within a frequency
, is represented by the occupation number m = m(), which equates to the number of photons
of an input eld with an energy level () = h. The output signal is represented by the
occupation number l = l (). The noise signal, created by the number of photons emitted by
absolute black body radiation at temperature T0 , is represented by the occupation number
n = n(). The medium values of these quantities (spectral densities of the input, noise and
output photonic stream) are denoted as m, n and l. In accordance with the Planck radiation
law, the spectral density r of a photonic stream of absolute black body radiation at temperature
and within frequency , is given by the Planck distribution,
h
p(, ) p(, T0 ) p(, TW )
r () = , n() = , l () = , p(, ) = e k (131)
1 p(, ) 1 p(, T0 ) 1 p(, TW )
Thus, for the average energy P of radiation at temperature within the bandwidth = R+
is gained that

2 k2 2 dP() 2 k2
P() = (, )d = where (, ) = r ()h and = . (132)
0 6h d 3h
Then, for the average noise energy P1 at temperature T0 , and for the average output energy P2
at temperature TW , both of which occur within the bandwidth = R+ is valid that
2 k2 T0 2 2 k2 TW 2
P1 ( T0 ) = , P2 ( TW ) = . (133)
6h 6h
The entropy H of radiation at temperature is derived from Clausius denition of heat entropy
and thus
1 dP() 2 k 2P( )
H= d = = (134)
0 k d 3h k
15
To distinguish between two frequencies mutually deferring at an innitesimally small d is needed, in accordance
with Heisenberg uncertainty principle, a time interval spanning the innite length of time, t ; analog of the
thermodynamic stationarity.
106 Thermodynamics
Thus, for the entropy H1 of the noise signal and for the entropy H2 of the ouptut signal on the
channel L is
2 kT0 2P 2 kTW 2P2
H1 = = 1 , H2 = = (135)
3h kT0 3h kTW
The information capacity CTW ,T0 of the wide-band photonic transfer channel L is given by the
maximal entropy defect [2, 30]) by
TW TW
1 dP() 2 k 2 k
CT0 ,TW = H2 H1 = d = d = ( TW T0 ) . (136)
T0 k d 3h T0 3h
For P2 = P1 + W, where W is the average energy of the input signal is then valid that

2 k2 TW 2 2 k2 T0 2 6h W
= + W TW = T0 1 + (137)
6h 6h 2 k2 T0 2
Then, in accordance with (102), (103), (104) [30]

2 kT0 6h W
CT0 ,W (KLL ) = 1+ 1 (138)
3h 2 k2 T0 2
7. Reverse heat cycle and transfer channel

A reverse and reversible Carnot cycle Orrev starts with the isothermal expansion at temperature
T0 (the diathermic contact [31] is made between the system L and the cooler B ) when L is
receiving the pumped out, transferred heat Q0 from the B . During the isothermal compression,
when the temperature of both the system L and the heater A is at the same value TW , TW >
T0 > 0, the output heat QW is being delivered to the A
QW = Q0 + A (139)
where A is the input mechanical energy (work) delivered into L during this isothermal
compression. It follows from [2, 8, 28] that when an average amount of information I is
being recorded, transmitted, computed, etc. at temperature , there is a need for the average

energy W k I; at this case W = A. Thus Orrev is considerable as a thermodynamic
model of information transfer process in the channel K
= L [14]. The following values are
changes of the information entropies dened on K16 :
QW A Q0
H (Y ) = output (= I ), H ( X ) = input, H (Y | X ) = noise (140)
kTW kTW kTW
where k is Boltzman constant. The information transfer in K = L is without losses caused by
the friction, noise heat (Q0x = 0) and thus H ( X |Y ) = 0.
By assuming that for the changes (140) and H ( X |Y ) = 0 the channel equation (4), (5) and (23)
is valid The result is
A QW
T ( X; Y ) = 0 = max = H ( X ) (141)
kTW kTW
Q0 + A Q0 A
T (Y; X ) = = = H ( X ).
kTW kTW kTW
16
In information units Hartley, nat, bit; H () = H (), H (|) = H (|).
Analogies 25 107
But the other information arrangement, description of a revese Carnot cycle will be used further,
given by
Q0 H ( X ), QW H (Y ) and A H (Y | X ), H ( X |Y ) = 0 (142)
In a general (reversible) discrete heat cycle O (with temperatures of its heat reservoires
changing in a discrete way) considered as a model of the information transfer process in an
transfer channel K = L [17, 19] is, for the elementary changes H (k ) [maxk ] of information
entropies of L, valid that17
Q(k )
H (k ) [maxk ] = [maxk ] , k = 1, 2, ..., n (143)
kk
where n 2 is the maximal number of its elementary Carnot cycles Ok .18 The change of heat
of the system L at temperatures k is Q(k ).
In a general (reversible) continuous cycle O [with temperatures changing continuously, n
in the previous discrete system, at will be Q( )] considered as an information transfer
process in a transfer channel K = L is valid that
Q()
d
=
Q() Q( )
dH () = andH ()= d( ); Q()= Q( )d (144)
k k 0 k 0
For the whole cycle Orrev , TW > T0 > 0, let be H ( X |Y ) = 0 and then

S( TW ) S( T0 ) A( ) TW 2QW
H (X) = = = dH () = ( TW T0 ) (145)
k k Orrev k T0 kTW 2
TW TW
S( TW ) QW (W ) 2QW
H (Y ) = = = dH () = [ H ( X ) = H (Y ) max ]
k 0 kW 0 kTW
TW TW T0
H (Y | X ) = H (Y ) H ( X ) = dH () dH () = dH ()
0 T0 0
T0
QW ( ) S( T0 ) 2QW 2QW T0
= = = T0 = = H (X)
0 k k kTW 2 kTW TW
TW T0 TW
T (Y; X ) = H (Y ) H (Y | X ) = dH () dH () = dH ()
0 0 T0
A( ) 2QW
= = max = H (Y ) max = H ( X ) = I
Orrev k kTW
Obviously, T ( X; Y ) = H ( X ) H ( X |Y ) = T (Y | X ). Further it is obvious that T ( X; Y ) is the

capacity CTW ,T0 of the channel K = L too,
TW
A( ) QW ( )
CTW ,T0 = T ( X; Y ) = H ( X ) = = (146)
Orrev k T0 k
2QW
= ( TW T0 ), CTmax
W ,T0
= H (Y )
kTW 2
h
17
In reality for the least elementary heat change Q = h is right where h = and h is Planck constant.
2
18
It is provable that the Carnot cycle itself is elenentary, not dividible [18].
108 Thermodynamics
7.1. Triangular heat cycle

Elementary change d of temperature of the environment of the general continuous cycle O
and thus of its working medium L (both are in the diathermic contact at ) causes the elementary
reversible change of the heat Q() delivered, (radiated) into L, just about the value Q( ),
W
Q() Q( )
Q( ) = d, Q(W ) = d (147)
0
The heat Q(W ) is the whole heat delivered (reversibly) into L (at the end temperature
W ). For the innitezimal heat Q( ) delivered (reversibly) into L at temperature and in
accordance with the Clausius denition of heat entropy SL [22] is valid that
Q()
Q( ) = dSL ( ), dSL () = (148)

For the whole change of entropy SL (W ), or for the entropy SL (W ) respectively,
delivered into the medium L by its heating within the temperature interval (0, W , is valid
that
W W W Q( ) d
Q()
SL (W ) = dSL () = = = SL (W ) (149)
0 0 0
Def
when SL (0) = 0 is set down. By (148) for the whole heat Q(W ) deliverd into L within
the temperature interval (0, W also is valid that
W
Q(W ) = dSL ( ) (150)
0
0 + W
Then, by medium value theorem19 is valid that (0,
W)
= = W and
2 2
S L ( W )
Q(W ) = dSL ( ) = [SL (W ) SL (0)] (0, (151)
S L (0) W)
For the extremal values T0 a TW of the cooler temperature of O and by (151)

T0 TW

Q0 = Q( T0 ) = QW ( ) and QW = Q( TW ) = QW ( ) (152)
0 0
SL ( T0 )
T0
Q 0 = dSL ( ) = [SL ( T0 ) SL (0)] (0,T ) , (0,T ) =
S L (0) 0 0 2
SL ( TW )
TW
Q W = dSL ( ) = [SL ( TW ) SL (0)] (0,T ) , (0,T =
S L (0) W W) 2
With SL (0) = 0 for the (end) temperatures , T0 , TW of L and the relevant heats and their
entropies is valid
2Q( )
Q( ) = SL ( ) and then SL ( ) = (153)
2
TW 2QW
QW = SL ( TW ) and then SL ( TW ) =
2 TW
T0 2Q0
Q0 = SL ( T0 ) and then SL ( T0 ) =
2 T0
19
Of Integral Calculus.
Analogies 27 109
For the change SL of the thermodynamic entropy SL of the system L, at the

tememperature running through the interval T0 , TW , by gaining heat from its environment
(the environment of the cycle O ), is valid

T
Q W Q 0 W Q ( )
SL = SL ( TW ) SL ( T0 ) = 2 = (154)
TW T0 T0
By (149) for the entropy SL (W ) of L at variable temperature 0, W , W TW , is

gained that
W

SL () d 1 W
S L ( W ) = = 2 dS L () (155)
0 2 2 0
W W
1 1 d
= S L ()d + SL ()
2 0 2 0
and then
W W
d 2Q(W )
S L ( W ) = SL ( ) = dSL ( ) =
0 0 W
d
and thus SL ( ) = dSL ( ) (156)

By the result of derivation (155)-(156) for an arbitrary temperature of medium L is valid
that20
2Q( ) l
SL ( ) = l , l = 2
Q( ) = 2 , = (157)
2
Obviously, from (154) for T0 , TW is derivable that
T0
SL = l ( TW T0 ) = l TW (1 ), = (158)
TW
Let such a reverse cycle is given that the medium L of which takes, through the elementary
isothermal expansions at temperatures T0 , TW , the whole heat Q0
TW TW
l 2
Q0 = Q() = ld = TW T02 = QW Q(159)
0
T0 T0 2
or, with medium values
TW SL ( TW )
Q0 = Q() = dSL ()
T0 SL ( T0 )

TW + T0 Q W Q 0
= W(T ,T [SL ( TW ) SL ( T0 )] = 2
0 W) 2 TW T0
and thus equivalently
T0
Q0 = ( TW + T0 ) [ TW T0 ] = TW 2 (1 2 ), =
TW
For a reverse reversible Carnot cycle O rrev , equivalent with the just considered general
continuous heat cycle O , drawing up the same heat Q0 , consumpting the same mechanical

f (x) d f (x) dx
20
If dx = d f ( x ), or = , then ln | f ( x )| = ln | x | + ln L, L > 0, ln | f ( x )| = ln( L | x |), f (x) =
x f (x) x
l x, l R.
110 Thermodynamics
work A and giving, at its higher temperature tW (the average temperature of the heater of
T0 + TW
our general cycle), the same heat QW , is valid that Q0 = QW where = 2
is
tW
the transform ratio.
Then
2tW l 2tW
QW = Q0 = TW 2 T0 2 = l tW ( TW T0 ) (160)
T0 + TW 2 T0 + TW

T + TW
A = QW (1 ) = l tW ( TW T0 ) 1 0 (161)
2tW
l
= ( TW T0 ) (2tW T0 TW )
2
For the elementary work A(, ) corresponding with the heat Q() pumped out (reversibly)
from L at the (end, output) temperature of L and for the entropy SL () of the whole
environment of O (including L with O ) is valid
d Q() d
A(, d)
SL () = = = dSL () = l d (162)

A(, d) = SL ()d = l d and A(d, d) = l dd = dSL ()d() = A

ld d = l ( T0 )d = A(, d; T0 ) (163)
T0
For the whole work A(W ; T0 ) consumpted by the general reverse cycle O between
temperatures T0 and W , being coverd by elementary cycles (162), is valid that
W W W
A(W ; T0 ) = dSL ( ) d = ld d = l ( T0 )d(164)
T0 T0 T0 T0 T0
l l l 2l
= (W 2 T0 2 ) l T0 (W T0 ) = W 2 + T0 2 T0 W = (W T0 )2
2 2 2 2
T
= A = TW (1 ) , when it is valid that W = TW , = 0
2 2
O(W ,T0 ) TW
But, then for the results for A in (160), (161) and (164) follows that
TW + W
tW = = TW and then tW = TW = const. (165)
2

Thus our general cycle O is of a triangle shape, O = Orrev with the apexes
[lT0 , T0 ], [lTW , TW ], [lT0 , TW ] (166)
1 1
and its efciency is 1 = = max . Thus, the return to the initial (starting) state of
2 2
the medium L is possible by using the oriented abscissas (in the S T diagram)

[lTW , TW ], [lT0 , TW ] and [lT0 , TW ], [lT0 , T0 ] (167)
Analogies 29 111
For works A(, d; T0 ) of elementary Carnot cycles covering cycle Orrev (166), the range
of their working temperatures is d and, for the given heater temperature T0 , W is,
by (162)-(163) valid that
d d
A(, d; T0 ) = QW () = l ( T0 ) = l ( T0 )d (168)

= [SL ( ) SL ( T0 )] d
QW () = l ( T0 ) and for used in (160) is gained that
+ T0
Q0 () = QW () () = l ( T0 ) = 2 T0 2
2
For the whole heats Q0 a QW being changed mutually between the working medium L
of the whole triangular cycle Orrev and its environment (166), and for the work A, in its
T + TW
equivalent Carnot cycle O rrev with working temperatures 0 and TW , will be valid
2
that21
TW
l 2 2 l 2
Q0 = ld d= TW (1 ) = W = l ( TW T0 ) T0 + ( TW T0 ) (169)
T0 0 2 2
TW TW
QW = ld d = l ( TW T0 ) TW = l TW 2 (1 )
T0 0
T
1 TW W
A = ld d = lTW 2 (1 ) l TW 2 (1 ) (170)
2 T0 T0
l l
= l TW 2 (1 ) [1 (1 + )] = TW 2 (1 )2 = A
2 2 Orrev
7.2. Capacity corections for wideband photonic transfer channel

The average output energy P2 (W ) of the message being received within interval (0, TW of
the temperature of the medium L = KLL from [30], when 0 < 0 W and 0 T0
and W TW are valid, is given by the sum of the input average energy W (W , 0 ) and the
average energy P1 (0 ) of the additive noise
P2 (W ) = P1 (0 ) + W (W , 0 ) (171)
The output message bears the whole average output information H2 (W ). By the medium
value theorem is possible, for a certain maximal temperature W TW of the temperature
(0, W , consider that the receiving of the output message is performed at the average
W
(constant) temperature W = . Then for the whole change of the output information
2

entropy H2 = H2 (W ) [the thermodynamic entropy SL (W ) in information units] is valid
P2 (W ) P ( ) + W ( W , 0 )
H2 (W ) = = 1 0 = H1 (W , 0 ) + H [W (W , 0 )] (172)
kW kW
2 k2 2 k2
21
Further it willbe layed down = , l= = 2 .
6h 3h
112 Thermodynamics
By (153) is valid that Q( ) = 2 and Q( ) = ld. Thus for (0, T0 a

(0, TW is valid
Q(W ) l 2ld
dHW (Y ) = = dW , dHW (Y | X ) = (173)
kW k kW
TW
With W = TW and 0 = T0 and with the reducing temperature is possible to write
2

P2 = W + P1 = QW = TW 2 = Y (174)
TW
l l P 2(W + P1 ) 2TW lT 2
H2 = H (Y ) = dW = T = T2 = = = W
0 k k W k 2W kTW kTW k

P1 = Q0 = T0 2 = Y | X
T0
2ld l P 2T0 2 lT 2
H1 = H (Y | X ) = = T0 2 = T1 = = 0
0 kTW kTW k 2W kTW kTW

W = Q W Q 0 = X
W 2
H [W ( TW , T0 )] = H ( X ) = T = ( TW 2 T0 2 ) (175)
k 2
W kTW
By the channel equation (4), (5) and by equations (23)-(24) and also by denitions (174)-(175)
and with the loss entropy H ( X |Y ) = 0 it must be valid for the transinformation T (; ) that
l
T (Y; X ) = H (Y ) H (Y | X ) = ( TW T0 ) (1 + ) = H ( X ) (176)
k
2 k2 T
T ( X; Y ) = H ( X ) H ( X |Y ) = H ( X ) = T ( X, Y ) and by using l = , = 0,
3h TW
2 k 2 k
T (Y; X ) = T (1 2 ) = T (1 ) (1 + ) = CT0 ,W (KLL ) (1 + )
3h W 3h W
For the given extremal temperatures T0 , TW the value T ( X; Y ) stated this way is the only
one, and thus also, it is the information capacity C T0 ,TW (W ) of the channel KLL (the rst
correction)

2 kT0 6h W
C T0 ,TW = (W ) = T ( X; Y ) = 1+ 1 (1 + ) (177)
3h 2 k2 T0 2
The information capacity correction (177) of the wideband photonic channel KLL [30],
stated this way, is (1 + )-times higher than the formulas (102) and (138) say. The reason is

in using two different information descriptions of the oriented abscissa [l0, 0], [lTW , TW ] in

derivation (138) and (177) which abscissa [l0, 0], [lTW , TW ] is on one line in S T diagram and
is composed from two oriented abscissas,

[l0, 0],[lT0 , T0 ] and [lT0 , T0 ], [lTW , TW ] (178)
The rst abscissa represents the phase of noise generation and the second one the phase of input
signal generation. The whole composed abscissa represents the phase of whole output signal
generation.
Analogies 31 113
For the sustaining, in the sense repeatable, cyclical information transfer, the renewal of the
initial or starting state of the transfer channel KLL = L, after any individual information
transfer act - the sending input and receiving output message has been accomplished, is
needed.
Nevertheless, in derivations of the formulas (102), (177) and (138) this return of the physical
medium L, after accomplishing any individual information transfer act, into the starting state
is either not considered, or, on the contrary, is considered, but by that the whole transfer
chain is opened to cover the energetic needs for this return transition from another, outer
resources than from those ones within the transfer chain itself. In both these two cases
the channel equation is fullled. This enables any individual act of information transfer be
realized by external and forced out, repeated starting of each this individual transfer act.22 23
If for the creation of a cycle the resources of the transfer chain are used only, the need
for another correction, this time in (177) arises. To express it it will be used the full cyclical
thermodynamic analogy K of KLL used cyclically, K LL . The information transfer will be
modeled by the cyclical thermodynamic process Orrev of reversible changes in the channel
K = K LL
= L and without opening the transfer chain. (Also K = K BE ).
7.2.1. Return of transfer medium into initial state, second correction

Now the further correction for capacity formulas (102), (138) and (177) will be dealt with for
that case that the return of the medium L into its initial, starting state is performed within the
transfer chain only. It will be envisiged by a triangular reverse heat cycle Orrev created by the
oriented abscissas within the apexes in the S T diagram (166), [lT0 , T0 ], [lTW , TW ], [lT0 , TW ].
The abstract experiment from [30] will be now, formally and as an analogy, realized by this
reverse and reversible heat cycle Orrev O rrev , described informationaly, and thought as
modeling information transfer process in a channel K = K LL|BE
= L. Thus the denotation
K K is usable. By (153)-(157) it will be
2 k2 2 l l l
Q( ) = = 2 , QW = TW 2 , Q0 = T0 2 (179)
6h 2 2 2
The working temperature 0 of cooling and W of heating are changing by (157),
1
0 = SL (0 ) T0 , TW and W = TW = const. (180)
l
and the heat entropy SL () of the medium L is changing by (155)-(156),
Q( ) 1 2Q( )
dSL = d and then SL ( ) = l = (181)

Using integral (149) it is possible to write that

Q( )
Q() = Q( ) = d = ld (182)
0 0 0
22
For these both cases is not possible to construct a construction-relevant heat cycles described in a proper information way.
23
But the modeling by the direct cycle such as in (128) is possible for the I I. Principle of Thermodynamics is valid in any
case and giving the possibility of the cycle description.
114 Thermodynamics
For the whole heats Q0 and QW being changed mutually between L with the cycle Orrev
and its environment and, for the whole work A for the equivalent Carnot cycle O rrev with
T + TW
working temperatures 0 and TW is valid, by (169)-(170), that
2
l
W = Q0 = T 2 (1 2 ) = X, QW = l TW 2 (1 ) = Y (183)
2 W
l
QW Q0 = A = T 2 (1 )2 = Y | X
2 W
For the whole work A delivered into the cycle Orrev , at the temperature TW , and the
entropy SL of its working medium L is valid

A A TW d
= = l ( T0 ) (184)
TW Orrev TW T0 TW
TW TW TW
A 1 d d
= dSL ( ) = [SL ( TW ) SL ( T0 )]
Orrev TW 2 T0 T0 TW T0 2TW
l l A
= ( TW T0 )2 = TW (1 )2 =
2TW 2 TW
Following (4), (5) and (23) and the triangular shape of the cycle Orrev , the changes of
information entropies by expressions (142), (169)-(170) are dened, valid for the equivalent
O rrev 24 , see (142),
TW TW
Def Q0 Q( ) d 1
H (X) = = = ld` d (185)
kTW T0 0 kTW T0 0 kTW
TW TW TW TW
Def QW Q( ) d 1
H (Y ) = = = ld` d
kTW T0 0 kTW T0 0 kTW
TW TW
Def A 1 TW Q( ) d 1 TW 1
H (Y | X ) = = = ld d
kTW 2 T0 T0 kTW 2 T0 T0 kTW
TW TW TW
l
T (Y; X ) = H (Y ) H (Y | X ) = 2 d d d
2kTW T0 0 T0
2 k
and by gguring these formulas with l = is gained that
3h
l 2 kTW
H (X) = TW (1 2 ) = (1 2 )
2k 6h
l 2 kTW
H (Y ) = TW (1 ) = (1 )
k 3h
l kTW
2 A
H (Y | X ) = T (1 )2 = (1 )2 =
2k W 6h Orrev kTW
l l 2 l
T (Y; X ) = T (1 ) T (1 ) = T (1 ) (2 1 + )
k W 2k W 2k W
l 2 kTW
= TW (1 2 ) = (1 2 ) = H ( X ) = T ( X; Y )
2k 6h
H ( X |Y ) = 0
24
In accordance with the input energy delivered and the extremal temperatures used in [30].
Analogies 33 115
It is visible that the quantity H (Y ) [= H ( X ) + H (Y | X )] is introduced correctly, for by (185) is

valid that
l l l
H (Y ) = T (1 )2 + T (1 2 ) = T (1 ) (1 + 1 + )(186)
2k W 2k W 2k W
l
= TW (1 )
k
For the transinformation and the information capacity of the transfer organized this way is
valid (177),
1
T ( X; Y ) = C T0 ,TW (W ) (187)
2
With the extremal temperatures T0 and TW the information capacity C T0 ,TW (W ) is given by
T ( X; Y ) = C T0 ,TW (W ) and then Cmax = lim C T0 ,TW (W ) = H (Y ) (188)

T0 TW

From the difference Q0 = W = Q0 QW (in L) follows that the temperature
6h W
TW = T0 1 + .
2 k2 T0 2
Then, for the transinformation, in the same way as in (187), is now valid

2 k 2
2 k 1+ 2 kT0 6h W 1+
T ( X; Y ) = 1 = ( TW T0 ) = 1+ 1
6h 3h 2 3h 2 k2 T0 2 2
(189)
The transiformation T ( X; Y ) is the capacity C (K ) and it is possible to write

2 kT0 6h W
T ( X; Y ) = C (K ) = C T0 ,TW (W ) = 1+ 1 ( T0 + TW ) (190)
6hTW 2 k2 T0 2
W W
= C TW (W ) = = C T0 (W ) = = C ( K LL|BE )
kTW 6h W
kT0 1+
2 k2 T0 2
2
which value is 2 less than (177) and less than (138).
1+
For T0 0 the quantum approximation C (W ) of the capacity C T0 ,TW (W ) is obtained,
independent on the noise energy (the noise power deminishes near the abslute 0 K)

4 k2 T 2 W 2 kT
C (W ) = lim 0
+ 2 0 (1 + ) = W (191)
T0 0 62 h2 6h 6h 6h
The classical aproximation CT0 (W ) of C T0 ,TW (W ) is gained for T0 0. This value is near
Shannon capacity of the wideband Gaussian channel with noise energy kT0 and with the
whole average input energy (energy) W; in the same way as in (104) is now gained

. 2 kT0 3h W W W
CT0 (W ) = (1 + ) = (1 + ) (192)
6h 2 k2 T0 2 2kT0 kT0
116 Thermodynamics
The mutual difference of results (189) and and (102), (138) [12, 30] is given by the necessity of
the returning the transfer medium, the channel K = K LL| B E
= L into its initial state
after each individual information transfer act has been accomplished and, by the relevant
temperatutre reducing of the heat Q0 [by TW in (183)-(189)]. Thus, our thermodynamic
cyclical model K = Orrev for the repeatible information transfer through the channel
K LL|BE is of the information capacity (189), while in [12, 30] the information capacity of
the one-act information transfer is stated.25 By (189) the whole energy costs for the cyclical
information transfer considered is countable.26
8. Conclusion
After each completed transmission of an input message and receipt of an output message
(one-act transfer) the transferring system must be reverted to its starting state, otherwise the
constant (in the sense repeatable) ow of information could not exist. The author believes
that either the opening of the chain was presupposed in the original derivation in [30], or
that the return of transferring system to its starting state was not considered at all, it was not
counted-in. In our derivations this needed state transition is considered be powered within
the transfer chain itself, without its openning. Although our derivation of the information
capacity for a cyclical case (using the cyclic thermodynamic model) results in a lower value
than the original one it seems to be more exact and its result as more precise from the theoretic
point of view, extending and not ceasing the previous, original result [12, 30] which remains of
its technology-drawing value. Also it forces us in being aware and respecting of the global costs
for (any) communication and its evaluation and, as such, it is of a gnoseologic character.
Author details
Bohdan Hejna
Institute of Chemical Technology Prague, Department of Mathematics, Studentsk 6, 166 28 Prague 6,
Czech Republic
9. References
[1] Bell, D. A. Teorie informace; SNTL: Praha, 1961.
[2] Brillouin, L. Science and Information Theory; Academia Press: New York, 1963.
[3] Cholevo, A. S. On the Capacity of Quantum Communication Channel. Problems of
Information Transmission 1979, 15 (4), 311.
[4] Cholevo, A. S. Verojatnostnyje i statisticeskije aspekty kvantovoj teorii; Nauka: Moskva, 1980.
[5] Cover, T. M.; Thomas, J. B. Elements of Information Theory; Wiley: New York, 1991.
[6] Davydov, A. S. Kvantov mechanika; SPN: Praha, 1978.
[7] Emch, G. G. Algebraiceskije metody v statisticeskoj mechanike i kvantovoj teorii polja; Mir:
Moskva, 1976.
25
For one-act information transfer the choose between two information descriptions is possible which result in capacity
(138) or (177).
2
26
For the energy T ( X; Y ) TW on the output the energy TW greater is needed on the input of the transfer channel
1+
2
which is in accordance with the I I. Principle of thermodynamics for > 1 is valid.
1+
Analogies 35 117
[8] Gershenfeld, N. Signal entropy and the thermodynamics of computation. IBM Systems
Journal 1996, 35 (3/4), 577586. DOI 10.1147/sj.353.0577.
[9] Halmos, P. R. Konecnomernyje vektornyje prostranstva; Nauka: Moskva, 1963.
[10] Haek, O.; Noicka, J. Technick mechanika pro elektrotechnick obory II.; SNTL: Praha, 1968.
[11] Hejna, B.; Vajda, I. Information transmission in stationary stochastic systems. AIP Conf.
Proc. 1999, 465 (1), 405418. DOI: 10.1063/1.58272.
[12] Hejna, B. Informacn kapacita stacionrnch fyziklnch systmu. Ph.D. Dissertation,
TIA AV CR, Praha, FJFI CVUT, Praha, 2000.
[13] Hejna, B. Generalized Formula of Physical Channel Capacities. International Journal of
Control, Automation, and Systems 2003, 15.
[14] Hejna, B. Thermodynamic Model of Noise Information Transfer. In AIP Conference
Proceedings, Computing Anticipatory Systems: CASYS07 Eighth International
Conference; Dubois, D., Ed.; American Institute of Physics: Melville, New York, 2008;
pp 6775. ISBN 978-0-7354-0579-0. ISSN 0094-243X.
[15] Hejna, B. Proposed Correction to Capacity Formula for a Wide-Band Photonic Transfer
Channel. In Proceedings of International Conference Automatics and Informatics08; Atanasoff,
J., Ed.; Society of Automatics and Informatics: Soa, Bulgaria, 2008; pp VII-1VIII-4.
[16] Hejna, B. Gibbs Paradox as Property of Observation, Proof of II. Principle of
Thermodynamics. In AIP Conf. Proc., Computing Anticipatory Systems: CASYS09:
Ninth International Conference on Computing, Anticipatory Systems, 38 August 2009;
Dubois, D., Ed.; American Institute of Physics: Melville, New York, 2010; pp 131140.
ISBN 978-0-7354-0858-6. ISSN 0094-243X.
[17] Hejna, B. Informacn termodynamika I.: Rovnovn termodynamika prenosu informace;
VCHT Praha: Praha, 2010. ISBN 978-80-7080-747-7.
[18] Hejna, B. Informacn termodynamika II.: Fyzikln systmy prenosu informace; VCHT Praha:
Praha, 2011. ISBN 978-80-7080-774-3.
[19] Hejna, B. Information Thermodynamics, Thermodynamics - Physical Chemistry of Aqueous
Systems, Juan Carlos Moreno-Pirajan (Ed.), ISBN: 978-953-307-979-0, InTech, 2011
Available from:
http://www.intechopen.com/articles/show/title/information-thermodynamics
[20] Helstroem, C. W. Quantum Detection and Estimation Theory; Pergamon Press: London,
1976.
[21] Hork, Z.; Krupka, F. Technick fyzika; SNTL/ALFA: Praha, 1976.
[22] Hork, Z.; Krupka, F. Technick fysika; SNTL: Praha, 1961.
[23] Jaglom, A. M.; Jaglom, I. M. Pravdepodobnost a teorie informace; Academia: Praha, 1964.
[24] Chodasevic, M. A.; Sinitsin, G. V.; Jasjukevic, A. S. Ideal fermionic communication channel in
the number-state model;Division for Optical Problems in Information technologies, Belarus
Academy of Sciences, 2000.
[25] Kalck, J.; Skora, K. Technick termomechanika; Academia: Praha, 1973.
[26] Karpuko, F. V.; Chodasevic, M. A. Sravnitelnoje issledovanije skorostnych charakteristik
bozonnych i fermionnych kommunikacionnych kanalov; Vesc NAN B, The National Academy
of Sciences of Belarus, 1998.
[27] Landau, L. D.; Lifschitz, E. M. Statistical Physics, 2nd ed.; Pergamon Press: Oxford, 1969.
[28] Landauer, M. Irreversibility and Heat Generation in the Computing Process. IBM J. Res.
Dev. 2000, 44 (1/2), 261.
[29] Lavenda, B. H. Statistical Physics; Wiley: New York, 1991.
118 Thermodynamics
[30] Lebedev, D.; Levitin, L. B. Information Transmission by Electromagnetic Field.

Information and Control 1966, 9, 122.
[31] Mark, Z. Termodynamika a statistick fyzika; CVUT: Praha, 1995.
[32] Marx, G. vod do kvantov mechaniky; SNTL: Praha, 1965.
[33] Moore, W. J. Fyzikln chemie; SNTL: Praha, 1981.
[34] Prchal, J. Signly a soustavy; SNTL/ALFA: Praha, 1987.
[35] Shannon, C. E. A Mathematical Theory of Communication. The Bell Systems Technical
Journal 1948, 27, 379423, 623656.
[36] Sinitsin, G. V.; Chodasevic, M. A.; Jasjukevic, A. S. Elektronnyj kommunikacionnyj kanal v
modeli svobodnogo vyrodennogo fermi-gaza; Belarus Academy of Sciences, 1999.
[37] Vajda, I. Teria informcie a tatistickho rozhodovania; Alfa: Bratislava, 1982.
[38] Watanabe, S. Knowing and Guessing; Wiley: New York, 1969.
Chapter
Chapter 5
0
Thermodynamics Microscopic Connotations
A. Plastino, Evaldo M. F. Curado and M. Casas
1. Introduction
Thermodynamics is the science of energy conversion. It involves heat and other forms of
energy, mechanical one being the foremost one. Potential energy is the capacity of doing
work because of the position of something. Kinetic energy is due to movement, depending
upon mass and speed. Since all objects have structure, they possess some internal energy
that holds such structure together, a kind of strain energy. As for work, there are to kinds
of it: internal and external. The later is work done on something". The former is work
effected within something, being a capacity. Heat is another king of energy, the leit-motif of
thermodynamics. Thermodynamics studies and interrelates the macroscopic variables, such
as temperature, volume, and pressure that are employed to describe thermal systems and
concerns itself with phenomena that can be experimentally reproducible.
In thermodynamics one is usually interested in special systems states called equilibrium ones.
Such states are steady ones reached after a system has stabilized itself to such an extent that
it no longer keeps changing with the passage of time, as far as its macroscopic variables
are concerned. From a thermodynamics point of view a system is dened by its being
prepared in a certain, specic way. The system will always reach, eventually, a unique state
of thermodynamic equilibrium, univocally determined by the preparation-manner. Empiric
reproducibility is a fundamental requirement for physics in general an thermodynamics in
particular. The main source of the strength, or robustness, of thermodynamics, lies on the fact
does it deals only with phenomena that are experimentally reproducible.
Historically, thermodynamics developed out the need for increasing the efciency of early
steam engines, particularly through the work of the French physicist Nicolas Sadi-Carnot
(1824) who believed that a heat engines efciency was to play an important role in helping
France win the Napoleonic Wars. Scottish physicist Lord Kelvin was the rst to formulate a
succint denition of thermodynamics in 1854: Thermodynamics is the subject of the relation
of heat to forces acting between contiguous parts of bodies, and the relation of heat to electrical
agency". Chemical thermodynamics studies the role of entropy in the process of chemical
reactions and provides the main body of knowledge of the eld. Since Boltzmann in the 1870s,
120 Thermodynamics
statistical thermodynamics, or statistical mechanics, that are microscopic theories, began to

explain macroscopic thermodynamics via statistical predictions on the collective motion of
atoms.
1.1. Thermodynamics laws

The laws of physics are established scientic regularities regarded as universal and invariable
facts of the universe. A law" differs from hypotheses, theories, postulates, principles,
etc., in that it constitutes an analytic statement. A theory starts from a set of axioms from
which all laws and phenomena should arise via adequate mathematical treatment. The
principles of thermodynamics, often called its laws", count themselves amongst the most
fundamental regularities of Nature [1]. These laws dene fundamental physical quantities,
such as temperature, energy, and entropy, to describe thermodynamic systems and they
account for the transfer of energy as heat and work in thermodynamic processes. An
empirically reproducible distinction between heat and work constitutes the hard-core" of
thermodynamics. For processes in which this distinction cannot be made, thermodynamics
remains silent. One speaks of four thermodynamics laws:
The zeroth law of thermodynamics allows for the assignment of a unique temperature to
systems that are in thermal equilibrium with each other.
The rst law postulates the existence of a quantity called the internal energy of a system
and shows how it is related to the distinction between energy transfer as work and energy
transfer as heat. The internal energy is conserved but work and heat are not dened as
separately conserved quantities. Alternatively, one can reformulate the rst law as stating
that perpetual motion machines of the rst kind can not exist.
The second law of thermodynamics expresses the existence of a quantity called the entropy
S and states that for an isolated macroscopic system S never decreases, or, alternatively,
that perpetual motion machines of the second kind are impossible.
The third law of thermodynamics refers to the entropy of a system at absolute zero
temperature (T = 0) and states that it is impossible to lower T in such a manner that
reaches the limit T = 0.
Classical thermodynamics accounts for the exchange of work and heat between systems with
emphasis in states of thermodynamic equilibrium. Thermal equilibrium is a condition sine
qua non for macroscopically specied systems only. It shoul be noted that, at the microscopic
(atomic) level all physical systems undergo random uctuations. Every nite system will
exhibit statistical uctuations in its thermodynamic variables of state (entropy, temperature,
pressure, etc.), but these are negligible for macroscopically specied systems. Fluctuations
become important for microscopically specied systems. Exceptionally, for macroscopically
specied systems found at critical states, uctuations are of the essence.
1.2. The Legendre transform

The Legendre transform is an operation that transforms one real-valued function of f a real
variable x into another f T , of a different variable y, maintaining constant its information
Thermodynamics Microscopic Connotations Thermodynamics Microscopic Connotations3 121
content. The derivative of the function f becomes the argument to the function f T .
f T (y) = xy f ( x ); y = f ( x ) reciprocity. (1)
The Legendre transform its own inverse. It is used to get from Lagrangians the Hamiltonian
formulation of classical mechanics.
Legendre reciprocity relations constitute thermodynamics essential formal ingredient [2]. In
general, for two functions I and one has
M
I ( A1 , . . . , A M ) = + k Ak , (2)
k =1
with the Ai extensive variables and the i intensive ones. Obviously, the Legendre transform
main goal is that of changing the identity of our relevant independent variables. For we
have
M
( 1 , . . . , M ) = I k Ak . (3)
k =1
The three operative reciprocity relations become [2]
I I M
Ak
k
= Ak ;
Ak
= k ;
i
= k i
, (4)
k
the last one being the so-called Euler theorem.
1.3. The axioms of thermodynamics

Thermodynamics can be regarded as a formal logical structure whose axioms are empirical
facts [2], which gives it a unique status among the scientic disciplines [1]. The four
axioms given below are equivalent to the celebrated laws of thermodynamics of the prevous
Subsection [2].
For every system there exists a quantity E, the internal energy, such that a unique Es value
is associated to each and every state s. The difference Es1 Es2 for two different states
s1 and s2 in a closed system is equal to the work required to bring the system, while
adiabatically enclosed, from one state to the other.
There exist particular states of a system, the equilibrium ones, that are uniquely
determined by E and by a set of extensive macroscopic parameters A , = 1, . . . , M.
The number and characteristics of the A depends on the nature of the system.
For every system there exists a state function S( E, A ) that (i) always grows if internal
constraints are removed and (ii) is a monotonously (growing) function of E. S remains
constant in quasi-static adiabatic changes.
122 Thermodynamics
S and the temperature T = [ E S ] A1 ,...,A M vanish for the state of minimum energy and are
non-negative for all other states.
From the second and 3rd. Postulates one extracts the following two essential assertions
1. Statement 3a) for every system there exists a state function S, a function of E and the A
S = S( E, A1 , . . . , A M ). (5)
2. Statement 3b) S is a monotonous (growing) function of E, so that one can interchange the
roles of E and S in (5) and write
E = E(S, A1 , . . . , A M ), (6)
Eq. (6) clearly indicates that
E E
dE = dS + dA dE = TdS + P dA , (7)
S
A
with P generalized pressures and the temperature T dened as [2]

E
T= . (8)
S [ A ]
Eq. (7) will play a key-role in our future considerations. If we know S( E, A1 , . . . , An ) or,
equivalently because of monotonicity, E(S, A1 , . . . , An )) we have a complete thermodynamic
description of a system [2]. For experimentalists, it is often more convenient to work with
intensive variables dened as follows [2].
Let S A0 . The intensive variable associated to the extensive Ai , to be called Pi are the
derivatives
E
P0 T = [ ] , 1/T = . (9)
S A1 ,...,An
E
Pj j /T = [ ] . (10)
A j S,A1 ,...,A j1 ,A j+1 ,...,An
Any one of the Legendre transforms that replaces any s extensive variables by their associated
intensive ones (, s will be Lagrange multipliers in SM)
Lr1 ,...,rs = E Pj A j , ( j = r1 , . . . , rs )
j
contains the same information as either S or E. The transform Lr1 ,...,rs is a function of
n s extensive and s intensive variables. This is called the Legendre invariant structure of
thermodynamics. As we saw above, this implies certain relationships amongst the relevant
systems variables, called the reciprocity relations (RR), that are crucial for the microscopic
discussion of Thermodynamics.
2. Classical statistical mechanics

In 1903 Gibbs formulated the rst axiomatic theory for statistical mechanics [1, 3], revolving
around the concept of phase space. The phase space (PS) precise location is given by
generalized coordinates and momenta. Gibbs postulates properties of an imaginary (Platonic)
ad-hoc notion: the ensemble" (a mental picture). The ensemble consists of extremely many
(N) independent systems, all identical in nature with the one of actual physical interest,
but differing in PS-location. That is, the original system is to be mentally repeated many
times, each with a different arrangement of generalized coordinates and momenta. Here
Liouvilles theorem of volume conservation in phase space for Hamiltonian motion plays a
crucial role. The ensemble amounts to a distribution of N PS-points, representative of the
actual system. N is large enough that one can properly speak of a density D at any PS-point
= q1 , . . . , q N ; p1 , . . . , p N , with D = D (q1 , . . . , q N ; p1 , . . . , p N , t) D (), with t the time, and,
if we call d the volume element,

N= d D; t. (11)
Randomly extracting a system from the ensemble, the probability of selecting it being located
in a neighborhood of would yield
P() = D ()/N. (12)
Consequently,
P d = 1. (13)
Liouvilles theorem follows from the fact that, since phase-space points can not be
destroyed", if
2
N12 = D d, (14)
1
then
dN12
= 0. (15)
dt
An appropriate analytical manipulation involving Hamiltons canonical equations of motion
then yields the theorem in the form [1]
N N
D D
D + pi + q = 0, (16)
i
pi i
qi i
entailing the PS-conservation of density.

Equilibrium means simply D = 0, i. e.,
N N
D D
pi
pi + q = 0.
qi i
(17)
i i
124 Thermodynamics
2.1. The classical axioms

Gibbs refers to PS-location as the phase" of the system [1, 3]. The following
statements completely explain in microscopic fashion the corpus of classical equilibrium
thermodynamics [1].
The probability that at time t the system will be found in the dynamical state characterized
by equals the probability P() that a system randomly selected from the ensemble shall
possess the phase will be given by Eq. (12) above.
All phase-space neighborhoods (cells) have the same a priori probability.
D depends only upon the systems Hamiltonian.
The time-average of a dynamical quantity F equals its average over the ensemble,
evaluated using D.
3. Information
Information theory (IT) treats information as data communication, with the primary goal
of concocting efcient manners of encoding and transferring data. IT is a branch of
applied mathematics and electrical engineering, involving the quantication of information,
developed by Claude E. Shannon [4] in order to i) nd fundamental limits on signal
processing operations such as compressing data and ii) nding ways of reliably storing
and communicating data. Since its 1948-inception it has considerably enlarged its scope
and found applications in many areas that include statistical inference, natural language
processing, cryptography, and networks other than communication networks. A key
information-measure (IM) was originally called (by Shannon) entropy, in principle unrelated
to thermodynamic entropy. It is usually expressed by the average number of bits needed
to store or communicate one symbol in a message and quanties the uncertainty involved
in predicting the value of a random variable.Thus, a degree of knowledge (or ignorance)
is associated to any normalized probability distribution p(i ), (i = 1, . . . , N ), determined
by a functional I [{ pi }] of the { pi } [47] which is precisely Shannons entropy. IT was la
axiomatized in 1950 by Kinchin [8], on the basis of four axioms, namely,
I is a function ONLY of the p(i ),

I is an absolute maximum for the uniform probability distribution,
I is not modied if an N + 1 event of probability zero is added,
Composition law.
As for the last axiom, consider two sub-systems [1 , { p1 (i )}] and [2 , { p2 ( j)}] of a composite
system [, { p(i, j)}] with p(i, j) = p1 (i ) p2 ( j). Assume further that the conditional
probability distribution (PD) Q( j|i ) of realizing the event j in system 2 for a xed i event
in system 1. To this PD one associates the information measure I [ Q]. Clearly,
p(i, j) = p1 (i ) Q( j|i ). (18)

Then Kinchins fourth axiom states that

I ( p ) = I ( p1 ) + p1 ( i ) I Q ( j | i ) . (19)
i
An important consequence is that, out of the four Kinchin axioms one nds that Shannonss
measure
N
S = p(i ) ln [ p(i )], (20)
i =1
gives us the only way of complying with Kinchins axioms.
4. Statistical mechanics and information theory

It has been argued [9] that the statistical mechanics (SM) of Gibbs is a juxtaposition of
subjective, probabilistic ideas on the one hand and objective, mechanical ideas on the other.
From the mechanical viewpoint, the vocables statistical mechanics" suggest that for solving
physical problems we ought to acknowledge a degree of uncertainty as to the experimental
conditions. Turning this problem around, it also appears that the purely statistical arguments
are incapable of yielding any physical insight unless some mechanical information is a priori
assumed [9]. This is the conceptual origin of the link SM-IT pioneered by Jaynes in 1957 via
his Maximum Entropy Principle (MaxEnt) [5, 6, 10] which allowed for reformulating SM in
information terms. Since ITs central concept is that of information measure (IM)
Descartes scientic methodology considers that truth is established via the agreement
between two independent instances that can neither suborn nor bribe each other: analysis
(purely mental) and experiment [11]. The analytic part invokes mathematical tools and
concepts: Mathematics world Laboratory. The mathematical realm is called Platos
Topos Uranus (TP). Science in general, and physics in particular, may thus be seen as a
[TP Experiment"] two-way bridge. TP concepts are related to each other in the form of
laws" that adequately describe the relationships obtaining among suitable chosen variables
that describe the phenomenon at hand. In many cases these laws are integrated into a
comprehensive theory (e.g., classical electromagnetism, based upon Maxwells equations)
[1, 1215].
Jaynes MaxEnt ideas describe thermodynamics via the link [IT as a part of TP] [Thermal
experiment], or in a more general scenario: [IT] [Phenomenon at hand]. It is clear that the
relation between an information measure and entropy is [IM] [Entropy S]. One can then
assert that an IM is not necessarily an entropy, since the rst belongs to the Topos Uranus and
the later to the laboratory. Of course, in some special cases an association I M entropy S
can be established. Such association is both useful and proper in very many situations [5].
If, in a given scenario, N distinct outcomes (i = 1, . . . , N) are possible, three alternatives are to
be considered [6]:
1. Zero ignorance: predict with certainty the actual outcome.

2. Maximum ignorance: Nothing can be said in advance. The N outcomes are equally likely.
126 Thermodynamics
3. Partial ignorance: we are given the probability distribution { Pi }; i = 1, . . . , N.
If our state of knowledge is appropriately represented by a set of, say, M expectation values,
then the best", least unbiased probability distribution is the one that [6]
reects just what we know, without inventing" unavailable pieces of knowledge [5, 6]
and, additionally,
maximizes ignorance: the truth, all the truth, nothing but the truth [6].
Such is the MaxEnt rationale. In using MaxEnt, one is not maximizing a physical entropy, but
only maximizing ignorance in order to obtain the least biased distribution compatible with
the a priori knowledge.
Statistical mechanics and thereby thermodynamics can be formulated on an information
theory basis if the density operator is obtained by appealing to Jaynes maximum entropy
principle (MaxEnt), that can be stated as follows:
Assume that your prior knowledge about the system is given by the values of M expectation
values < A1 >, . . . , < A M >. In such circumstances is uniquely determined by extremizing
I () subject to M constraints given, namely, the M conditions < A j >= Tr [ A j ], a procedure
that entails introducing M Lagrange multipliers i . Additionally, since normalization of
is necessary, a normalization Lagrange multiplier should be invoked. The procedure
immediately leads one [6] to realizing that I S, the equilibrium Boltzmanns entropy, if
the a priori knowledge < A1 >, . . . , < A M > refers only to extensive quantities. Of course, I,
once determined, affords for complete thermodynamical information for the system of interest [6].
5. A new micro-macroscopic way of accounting for thermodynamics

Gibbs and MaxEnt approaches satisfactorily describe equilibrium thermodynamics. We will
here search for a new, different alternative able to account for thermodynamics from rst
principles. Our idea is to give axiom-status to Eq. (7), which is an empirical statement. Why?
Because neither in Gibbs nor in MaxEnts axioms we encounter a direct connection with
actual thermal data. By appealing to Eq. (7) we would instead be actually employing
empirical information. This is our rationale.
Consequently, we will concoct a new SM-axiomatics by giving postulate status to the
following macroscopic statement:
Axiom (1)
dE = TdS + P dA . (21)

This is a macroscopic postulate to be inserted into a microscopic axiomatics corpus.
We still need some amount of microscopic information, since we are building up a microscopic
theory. We wish to add as little as possible, of course (Ockhams razor). At this point it is useful
to remind the reader of Kinchins postulates, recounted above. We will content ourselves with
borrowing for our theoretical concerns just his his rst axiom. Thus, we conjecture at this
point, and will prove below, that the following assertion sufces for our theoretical purposes:
Axiom (2) If there are W microscopic accessible states labelled by i, whose microscopic
probability we call pi , then
S = S ( p 1 , p 2 , . . . , pW ) . (22)
Thus, we are actually taking as a postulate something that is actually known from both
quantum and classical mechanics.
Axiom (3) The internal energy E and the external parameters A are to be considered as
the expectation values of suitable operators, that is, the hamiltonian H and the hermitian
operators R (i.e., A < R >). Thus, the A (and also E) will depend on the eigenvalues
of these operators and on the probability set. (Note that energy eigenvalues depend of course
upon the R .
The reader will immediately realize that Axiom (2) is just a way of re-expressing Boltzmanns
atomic" conjecture. Thus, macroscopic quantities become statistical averages evaluated using
a microscopic probability distribution [16]. Our present three new axioms are statements of
fact. What do we mean? That they are borrowed from either experiment or pre-existent
theories. Somewhat surprisingly, our three axioms do not actually incorporate any knew
knowledge at all. The merely re-express known previous notions. Ockhams razor at its best!
Our theory could no be more economical.
We need now to prove that the above three postulates allow one to reconstruct the imposing
edice of statistical mechanics. We will tackle this issue by showing below that they our
axioms are equivalent to those of Jaynes [17]. At this point we need to recall the main goal
of statistical mechanics, namely, nding the probability distribution (or the density operator)
that best describes our physical system. In order to do so Jaynes appealed to his MaxEnt
postulate, that we restate below for the sake of xing notation.
MaxEnt axiom: assume your prior knowledge about the system is given by the values of M
expectation values
A1 < R1 >, . . . , A R < R M > . (23)
Then, is uniquely xed by extremizing the information measure I () subject to
normalization plus the constraints given by the M conditions constituting our assumed
foreknowledge
A =< R >= Tr [ R ]. (24)
This leads, after a Lagrange-constrained extremizing process, to the introduction of M
Lagrange multipliers , that one assimilates to the generalized pressures P . The truth, the
whole truth, nothing but the truth [6]. Jaynes rationale asserts that if the entropic measure
that reects our ignorance were not of maximal character, we would actually be inventing
information not at hand.
While working through his variational process, Jaynes discovers that, after multiplying by
Boltzmanns constant k B the right-hand-side of his expression for the information measure, it
converts itself into an entropy, I S, the equilibrium thermodynamic one, with the caveat
that A1 =< R1 >, . . . , A M =< R M > refer to extensive quantities. Having , his universal
form I () yields complete microscopic information with respect to the system of interest. To achieve
our ends one needs now just to prove that the new axiomatics, with (21) and (22), is equivalent
to MaxEnt.
128 Thermodynamics
6. New connection between macroscopic and microscopic approaches

In establishing our new connections between the micro- and macro-scenarios we shall work
with the classical instance only, since the corresponding quantum treatment constitute in this
sense just a straightforward extension.
Our main idea is to pay attention to the generic change pi pi + dpi as constrained by Eq. (
21). In other word, we insist on studying the change dpi that takes place in such a manner that
(21) holds. Our main macroscopic quantities S, A j , and E will vary with dpi . These changes
are not arbitrary but are constrained by (21). Note here an important advantage to be of our
approach. We need not specify beforehand the information measure employed.
Since several possibilities exist (see for instance Gell-Mann and Tsallis [18]), this entails that
the choice of information nature is not predetermined by macroscopic thermodynamics. For
a detailed discussion of this issue see Ferri, Martinez, and Plastino [19].
The pertinent ingredients at hand are
an arbitrary, smooth function f ( p) permitting one expressing the information measure via
I S({ pi }) = p i f ( p i ), (25)
i
such that S({ pi }) is a concave function,
M quantities A representing values of extensive quantities R , that adopt, for a
micro-state i, the value ai with probability pi ,
still another arbitrary smooth, monotonic function g( pi ) (g(0) = 0; g(1) = 1). With
the express purpose of employing generalized, non-Shannonian entropies, we slightly
generalize here the expectation-value denitions by recourse to g via (26):
W
A R = ai g( pi ); = 2, . . . , M, (26)
i
W
E=
i g ( p i ) , (27)
i
where
i is the energy associated to the microstate i.
We take A1 E and pass to a consideration of the probability variations dpi that should
generate accompanying changes dS, dA , and dE in, respectively, S, the A , and E.
The essential issue at hand is that of enforcing compliance with
W
dE TdS + dA = 0, (28)
=1
with T the temperature and generalized pressures. By recourse to (25), (26), and (27) we i)
recast now (28) for
Thermodynamics Microscopic Connotations 11 129
pi pi + dpi , (29)
and ii) expand the resulting equation up to rst order in the dpi .
Remembering that the Lagrange multipliers are identical to the generalized pressures P
of Eq. (7), one thus encounter, after a little algebra [2026],
(1)
Ci = [M=1 ai +
i ]
(2) S
Ci = T p i
(1) (2)
i [Ci + Ci ]dpi i Ki dpi = 0, (30)
so that, appropriately rearranging things

(1)
Ti = f ( pi ) + pi f ( pi )
(2)
Ti = [(M=1 ai +
i ) g ( pi ) K ],
( 1/kT ), (31)
and we are in a position to recast (30) in the fashion

(1) (2)
Ti + Ti = 0; ( f or any i ), (32)
an expression whose importance will become manifest later on.

Eqs. (30) or (32) yield one and just one pi expression, as demonstrated in Refs. [2026].
However, it will be realized below that, at this stage, an explicit expression for this probability
distribution is not required.
We pass now to traversing the opposite road that leads from Jaynes MaxEnt procedure and
ends up with our present equations. This entails extremization of S subject to constraints in E,
A , and normalization. For details see [2026].
Setting 1 = 1/T one has
M
pi [ S H R pi ] = 0, (33)
=2 i
(normalization Lagrange multiplier ) is easily seen in the above cited references to yield as a
solution the very set of Eqs. (30). The detailed proof is given in the forthcoming Section. Eqs.
(30) arise then from two different approaches:
our methodology, based on Eqs. (21) and (22), and

following the well known MaxEnt route.
Accordingly, we see that both MaxEnt and our axiomatics co-imply one another. They are
indeed equivalent ways of constructing equilibrium statistical mechanics. As a really relevant
fact
130 Thermodynamics
One does not need to know the analytic form of S[ pi ] neither in Eqs. (30) nor in (33).
7. Proof
Here we prove that Eqs. (30) can be derived from the MaxEnt approach (33). One wishes to
extremize S subject to the constraints of xed valued for i) U, ii) the M values A (entailing
Lagrange multipliers (1) and (2) M ), and iii) normalization (Lagrange multiplier ). One
has also
A = R = pi ai , (34)
i
with ai = i |R |i the matrix elements in the basis i of R . The ensuing variational problem
one faces, with U = i pi
i , is

M
{ pi } S U A pi = 0, (35)
=1 i
that immediately leads, for = , to

M
pm pi f ( pi ) [ pi ( ai +
i ) + p i ] = 0, (36)
i =1
so that the the following two quantities vanish
f ( pi ) + pi f ( pi ) [ (M=1 ai +
i ) + ]
if K,
f ( pi ) + pi f ( pi ) (M=1 ai +
i ) + K ]
(1) (2)
0 = Ti + Ti . (37)
We realize now that (32) and the last equality of (37) are one and the same equation. MaxEnt
does lead to (32).
8. Conclusions
We have formally proved above that our axiomatics allows one to derive MaxEnt equations
and viceversa. Thus, our treatment provides an alternative foundation for equilibrium
statistical mechanics. We emphasized that, opposite to what happens with both Gibbs and
Jaynes axioms, our postulates have zero new informational content. Why? Because they are
borrowed either from experiment or from pre-existing theories, namely, information theory
and quantum mechanics.
The rst and second laws of thermodynamics are two of physics most important empirical
facts, constituting pillars to our present view of Nature. Statistical mechanics (SM) adds an
underlying microscopic substratum able to explain not only these two laws but the whole
of thermodynamics itself [2, 6, 2730]. Basic SM-ingredient is a microscopic probability
Thermodynamics Microscopic Connotations 13 131
distribution (PD) that controls microstates-population [27]. Our present ideas yield a detailed
picture, from a new perspective [2026], of how changes in the independent external
thermodynamic parameters affect the micro-state population and, consequently, the entropy
and the internal energy.
Acknowledgement
This work was partially supported by the MEC Grant FIS2005-02796 (Spain).
Author details
A. Plastino
Universidad Nacional de La Plata, Instituto de Fsica (IFLP-CCT-CONICET), C.C. 727, 1900 La Plata,
Argentina
Physics Departament and IFISC-CSIC, University of Balearic Islands, 07122 Palma de Mallorca, Spain
Evaldo M. F. Curado
Centro Brasileiro de Pesquisas Fisicas, Rio de Janeiro, Brazil
M. Casas
Physics Departament and IFISC-CSIC, University of Balearic Islands, 07122 Palma de Mallorca, Spain
9. References
[1] R. B. Lindsay and H. Margenau, Foundations of physics, NY, Dover, 1957.
[2] E. A. Desloge, Thermal physics NY, Holt, Rhinehart and Winston, 1968.
[3] J. Willard Gibbs, Elementary Principles in Statistical Mechanics, New Haven, Yale
University Press, 1902.
[4] C. E. Shannon, Bell System Technol. J. 27 (1948) 379-390.
[5] E. T. Jaynes Papers on probability, statistics and statistical physics, edited by R. D.
Rosenkrantz, Dordrecht, Reidel, 1987.
[6] A. Katz, Principles of Statistical Mechanics, The information Theory Approach, San Francisco,
Freeman and Co., 1967.
[7] T. M. Cover and J. A. Thomas, Elements of information theory, NY, J. Wiley, 1991.
[8] A. Plastino and A. R. Plastino in Condensed Matter Theories, Volume 11, E. Ludea (Ed.),
Nova Science Publishers, p. 341 (1996).
[9] D. M. Rogers, T. L. Beck, S. B. Rempe, Information Theory and Statistical Mechanics Revisited,
ArXiv 1105.5662v1.
[10] D. J. Scalapino in Physics and probability. Essays in honor of Edwin T. Jaynes edited by W.
T. Grandy, Jr. and P. W. Milonni (Cambridge University Press, NY, 1993), and references
therein.
[11] B. Russell, A history of western philosophy (Simon & Schuster, NY, 1945).
[12] P. W. Bridgman The nature of physical theory (Dover, NY, 1936).
[13] P. Duhem The aim and structure of physical theory (Princeton University Press, Princeton,
New Jersey, 1954).
[14] R. B. Lindsay Concepts and methods of theoretical physics (Van Nostrand, NY, 1951).
132 Thermodynamics
[15] H. Weyl Philosophy of mathematics and natural science (Princeton University Press,
Princeton, New Jersey, 1949).
[16] D. Lindley, Boltzmanns atom, NY, The free press, 2001.
[17] W.T. Grandy Jr. and P. W. Milonni (Editors), Physics and Probability. Essays in Honor of
Edwin T. Jaynes, NY, Cambridge University Press, 1993.
[18] M. Gell-Mann and C. Tsallis, Eds. Nonextensive Entropy: Interdisciplinary applications,
Oxford, Oxford University Press, 2004.
[19] G. L. Ferri, S. Martinez, A. Plastino, Journal of Statistical Mechanics, P04009 (2005).
[20] E. Curado, A. Plastino, Phys. Rev. E 72 (2005) 047103.
[21] A. Plastino, E. Curado, Physica A 365 (2006) 24
[22] A. Plastino, E. Curado, International Journal of Modern Physics B 21 (2007) 2557
[23] A. Plastino, E. Curado, Physica A 386 (2007) 155
[24] A. Plastino, E. Curado, M. Casas, Entropy A 10 (2008) 124
[25] International Journal of Modern Physics B 22, (2008) 4589
[26] E. Curado, F. Nobre, A. Plastino, Physica A 389 (2010) 970.
[27] R.K. Pathria, Statistical Mechanics (Pergamon Press, Exeter, 1993).
[28] F. Reif, Statistical and thermal physics (McGraw-Hill, NY, 1965).
[29] J. J.Sakurai, Modern quantum mechanics (Benjamin, Menlo Park, Ca., 1985).
[30] B. H. Lavenda, Statistical Physics (J. Wiley, New York, 1991); B. H. Lavenda,
Thermodynamics of Extremes (Albion, West Sussex, 1995).
Section 3
Property Prediction and Thermodynamics

Chapter 6
Group Contribution Methods for Estimation

of Selected Physico-Chemical Properties
of Organic Compounds
Zdeka Kolsk, Milan Zbransk and Alena Randov
1. Introduction
Thermodynamic data play an important role in the understanding and design of chemical
processes. To determine values of physico-chemical properties of compounds we can apply
experimental or non-experimental techniques. Experimental techniques belong to the most
correct, accurate and reliable. All experimental methods require relevant technical
equipment, time necessary for experiment, sufficient amount of measured compounds of
satisfactory purity. Compound must not affect technical apparatus and should not be
decomposed during experiment. Other aspect is a valid legislation, which limits a usage of
dangerous compounds by any users.
If due to any of these conditions mentioned above causes the experiment cannot be realized,
some non-experimental approaches can be applied.
2. Non-experimental approaches to determine physico-chemical

properties of compounds
If due to any of conditions results in that experimental determination cannot be realized and
data on physico-chemical property are necessary, we have to employ some non-
experimental approaches, either calculation methods or estimation ones. Due to the lack of
experimental data for several industrially important compounds, different estimation
methods have been developed to provide missing data. Estimation methods include those
based on theory (e.g. statistical thermodynamics or quantum mechanics), various empirical
relationships (correlations of required property with variable, experimentally determined
compound characteristics, e.g. number of carbon atoms in their molecule, molecular weight,
normal boiling temperature, etc.), and several classes of additivity-principle methods
(Baum, 1989; Pauling et al., 2001). Estimation methods can be divided into several groups
from many aspects, e.g. into methods based on theoretical, semi-theoretical relations and the
empirical ones. Books and papers of last decades divide estimation methods depending on
the required input data into QPPR or QSPR approaches (Baum, 1989). QPPR methods
(Quantity-Property-Property-Relationship) are input data-intensive. They require for
calculation of searched value property knowledge of other experimental data. We can use
them successfully only when we have input data. On the other hand QSPR (Baum, 1989)
methods (Quantity-Structure-Property-Relationship) need only knowledge of the chemical
structure of a compound to predict the estimated property. QSPR methods use some
structural characteristics, such as number of fragments (atoms, bonds or group of atoms in a
molecule), topological indices or other structural information, molecular descriptors, to
express the relation between the property and molecular structure of compound (Baum,
1989; Pauling et al., 2001; Gonzles et al., 2007a). Empirical and group contribution methods
seem to be the most suitable (Pauling et al., 2001; Majer et al., 1989) due to their simplicity,
universality and fast usage.
2.1. Group contribution methods

Group contribution methods are presented as empirical QSPR approaches. The easiest
models were based on study of property on number of carbon atoms nC or methylen groups
nCH2 in molecules of homological series. In Fig. 1 is presented dependence of normal boiling
temperature Tb on number of carbon atoms nC (bottom axis) or methylen groups nCH2 (top
axis) in molecules of homological series n-alkanols C1-C12 (Majer & Svoboda, 1985; NIST
database). As we can see, this dependence is clearly linear in some range of nC=C2-C10. But
increasing discrepancy is evident either for low number of carbon atoms C1 or for higher
one nC>C10. Due to these departures from linear behaviour some parameters covering
structural effects on property were inclusive to these easy models (e.g. Chickos et al., 1996).
From these approaches structural fragments and subsequently group contribution methods
have been established.
Group contribution methods are based on the so called additive principle. That means
any compound can be divided into fragments, usually atoms, bonds or group of atoms, etc.
All fragments have a partial value called a contribution. These contributions are calculated
from known experimental data. Property of a compound is obtained by a summing up the
values of all contributions presented in the molecule. Example of division of molecule of
ethanol into atomic, bond and group fragments is presented in Fig. 2. When we divide this
molecule into atomic fragments, the total value of property X of ethanol is given by
summing up the values for two carbon atom contributions X(C), six hydrogen atom
contributions X(H) and one oxygen atom contribution X(O). The second way is the division of
ethanol molecules into the following bond fragments with their contribution: X(C-C), X(C-O),
X(C-H) and X(O-H). Due to increasing quality and possibility of computer technique a
fragmentation into more complex group structural fragments is applied in present papers
(Baum, 1989; Pauling et al., 2001). Some of ways to divide the molecule ethanol into group
structural fragments are presented in Fig. 2. Ethanol molecule can be divided either into: (i)
Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds 137
CH3-, -CH2- and -OH, or: (ii) CH3- and CH2OH. More complex compounds are described
by more complex structural fragments.
Figure 1. Dependence of normal boiling temperature of n-alkanols in homological series C1-C12
Figure 2. Example of division of ethanol molecule into atomic, bond and group structural fragments
Group contribution methods are essentially empirical estimation methods. A large variety
of these models have been designed during last centuries, differing in a field of their
applicability and in the set of experimental data. They were developed to estimate, e.g.
critical properties (Lydersen, 1955; Ambrose, 1978; Ambrose, 1979; Joback & Reid, 1987;
Gani & Constantinou, 1996; Poling et al., 2001; Marrero & Gani, 2001; Brown et al., 2010;
Monago & Otobrise, 2010; Sales-Cruz et al., 2010; Manohar & Udaya Sankar, 2011; Garcia
et al., 2012), parameters of state equations (Pereda et al., 2010; Schmid & Gmehling, 2012),
acentric factor (Constantinou & Gani, 1994; Brown et al., 2010; Monago & Otobrise, 2010),
activity coefficients (Tochigi et al., 2005; Tochigi & Gmehling, 2011), vapour pressure
(Poling et al., 2001; Miller, 1964), liquid viscosity (Joback & Reid, 1987; Conte et al., 2008;
Sales-Cruz et al., 2010), gas viscosity (Reichenberg, 1975), heat capacity (Joback & Reid,
1987; Ruzicka & Domalski, 1993a; Ruzicka & Domalski, 1993b; Kolsk et al., 2008),
enthalpy of vaporization (e.g. Chickos et al., 1995; Chickos & Wilson, 1997; Marrero &
Gani, 2001; Kolsk et al. 2005, etc.), entropy of vaporization (Chiskos et al., 1998; Kolsk et
al. 2005), normal boiling temperature (Joback & Reid, 1987; Gani & Constantinou, 1996;
Marrero & Gani, 2001), liquid thermal conductivity (Nagvekar & Daubert, 1987), gas
thermal conductivity (Chung et al., 1984), gas permeability and diffusion coefficients
(Yampolskii et al., 1998), liquid density (Campbell & Thodos, 1985; Sales-Cruz et al., 2010;
Shahbaz et al., 2012), surface tension (Brock, 1955; Conte et al., 2008; Awasthi et al., 2010),
solubility parameters of fatty acid methyl esters (Lu et al., 2011), flash temperatures (Liaw
& Chiu, 2006; Liaw et al., 2011). Large surveys of group contribution methods for
enthalpy of vaporization and liquid heat capacity have been presented in references
(Zbransk et al., 2003; Kolsk, 2004; Kolsk et al., 2005; Kolsk et. al, 2008; Zbransk et
al, 2010a). Group-contribution-based property estimation methods ca be also used to
predict the missing UNIFAC group-interaction parameters for the calculation of vapor-
liquid equilibrium (Gonzles at al., 2007b).
Group contribution methods can be used for pure compounds, even inorganic compounds
(e.g. Williams, 1997; Briard et al., 2003), organometallic compounds (e.g. Nikitin et al., 2010)
and also for mixtures (e.g. Awasthi et al., 2010; Papaioannou et al., 2010; Teixeira et al., 2011;
Garcia et al., 2012). Also e.g. estimation of thermodynamic properties of polysacharides was
presented (Lobanova et al., 2011). Discussion about determination of properties of polymers
has been also published (Satyanarayana et al., 2007; Bogdanic, 2009; Oh & Bae, 2009).
Property models based on the group contribution approach for lipid technology have been
also presented (Daz-Tovar et al., 2007).
During last years also models for ionic liquids and their variable properties were developed,
e.g. for density, thermal expansion and viscosity of cholinium-derived ionic liquids (Costa et
al., 2011; Costa et al., 2012), viscosity (Adamov et al., 2011), the glass-transition temperature
and fragility (Gacino et al., 2011), experimental data of mixture with ionic liquid were
compared with group contribution methods (Cehreli & Gmehling, 2010) or thermophysical
properties were studied (Gardas et al., 2010).
Some of these group contribution methods were developed for only limited number of
compounds, for some family of compounds, e.g. for fluorinated olefins (Brown et al., 2010),
hydrocarbons (Chickos et al., 1995), fatty acid methyl esters (Lu et al., 2011), etc., most of
approaches were established for a wide range of organic compounds.
2.1.1. Group contribution methods by Marrero-Gani

In this chapter for most of estimations the modified group contribution method by Marrero
and Gani (Marrero & Gani, 2001; Kolsk et al., 2005; Kolsk et. al. 2008) was applied, which
has been originally developed for estimation of different thermodynamic properties at one
temperature only (Constantinou & Gani, 1996; Marrero & Gani, 2001). Determination of
group contribution parameters is performed in three levels, primary, secondary and third.
At first, all compounds are divided into the primary (first) order group contributions. This
primary level uses contributions from simple groups that allow description of a wide
variety of organic compounds. Criteria for their creation and calculation have been
described (Marrero & Gani, 2001; Kolsk et al., 2005; Kolsk et al., 2008). The primary level
groups, however, are insufficient to capture a proximity effect (they do not implicate an
influence of their surroundings) and differences between isomers. Using primary level
groups enables to estimate correctly properties of only simple and monofunctional
compounds, but the estimation errors for more complex substances are higher. The primary
level contributions provide an initial approximation that is improved at the second level and
further refined at the third level, if that is possible and necessary. The higher levels (second
and third) involve polyfunctional and structural groups that provide more information
about a molecular structure of more complex compounds. These higher levels are able to
describe more correctly polyfunctional compounds with at least one ring in a molecule, or
non-ring chains including more than four carbon atoms in a molecule, and multi-ring
compounds with a fused or non-fused aromatic or non-aromatic rings. The differences
between some isomers are also able to distinguish by these higher levels. Complex
polycyclic compounds or systems of fused aromatic or nonaromatic rings are described by
the third order contributions. They are still bigger and more complex than the first, even the
second order ones. The multilevel scheme enhances the accuracy, reliability and the range of
application of group contribution method for an almost all classes of organic compounds.
After these all three levels the total value of predicted property X is obtained by the
summing up of all group contributions, which occur in the molecule. First order groups,
second and third order ones, if they are in.
n m o
X x N C M D z O E (1)
0 i xi j xj k xk
i 1 j 1 k 1
where X stands the estimated property, x0 is an adjustable parameter for the relevant
property, Cxi is the first-order group contribution of type i, Dxj is the second-order group
contribution of type j, Exk is the third-order group contributions of the type k and Ni, Mj, Ok
denote the number of occurrences of individual group contributions. The more detail
description of parameters calculation is mentioned in original papers (Marrero & Gani, 2001;
Kolsk et al., 2005; Kolsk et al., 2008)
To develop reliable and accurate group contribution model three important steps should be
realized: (i) to collect input database, rather of critically assessed experimental data, from
which parameters, group contributions, would be calculated; (ii) to design structural
fragments for description of all chemical structures for compounds of input database; (iii) to
divide all chemical structures into defined structural fragments correctly. It can be realized
either manually, when databases of chemical structures and structural fragments inclusive
several members only, either via computer program, when databases contain hundreds of
compounds and structural fragments are more complex. To calculate group contribution
parameters for thermophysical properties the ProPred program has been used (Marrero,
2002). Description and division chemical structures for other estimations have been made
handy. Molecular structures for electronical splitting of all compounds from the basic data
set were input in the Simplified Molecular Input Line Entry Specification, so-called the
SMILES format (Weininger et al., 1986; Weininger, 1988; Weininger et al., 1989; Weininger,
1990).
For more universal usage of computer fragmentation a suitable computer program has been
developed (Kolsk & Petrus, 2010). The main goal of the newly developed program is to
provide a powerful tool for authors using group contribution methods for automatic
fragmentation of chemical structures.
2.2. Estimation of selected physico-chemical properties of compounds

The models for estimation of several physical or physico-chemical properties of pure
organic compounds, such as enthalpy of vaporization, entropy of vaporization (Kolsk et al.,
2005), liquid heat capacity (Kolsk et al., 2008) and a Nafion swelling (Randov et al, 2009) is
presented below. Most of them are developed to estimate property at constant temperature
298.15 K and at normal boiling temperature (Kolsk et al., 2005; Kolsk et al., 2008; Randov
et al., 2009), liquid heat capacity as a temperature dependent (Kolsk et al., 2008). Hitherto
unpublished results for estimation of a flash temperature or organic compounds and for
determination of reactivation abbility of reactivators of acetylcholinesterase inhibited by
inhibitor are presented in this chapter.
2.2.1. Enthalpy of vaporization and entropy of vaporization

Enthalpy of vaporization, HV, entropy of vaporization, SV are important thermodynamic
quantities of a pure compound, necessary for chemical engineers for modelling of many
technological processes with evaporation, for extrapolation and prediction of vapour
pressure data, or for estimation of the other thermodynamic properties, e.g. solubility
parameters. It can be also used for extrapolation and prediction of vapour pressure data.
There are several methods to determine these properties, experiment-based and model-
based. Experiment-based methods, such as calorimetry or gas chromatography, provide
generally reliable data of good accuracy. In the case of model-based methods, we can
distinguish several groups of methods on the basis of the input information they require.
Methods based on the Clausius-Clapeyron equation and vapour pressure data, variable
empirical correlations, methods based on the tools of statistical thermodynamics or
quantum mechanics. During last decades the group contribution methods are widely used
for their universality and simplicity. More rich survey of estimation methods for enthalpy of
vaporization is presented in papers (Kolsk, 2004; Kolsk et al., 2005).
Large databases of critically assessed data have been used for group contribution
calculations: data for 831 compounds have been used for estimations at 298.15 K, and data
for 589 compounds have been used for estimations at the normal boiling temperature.
Organic compounds were divided into several classes (aliphatic and acyclic saturated and
unsaturated hydrocarbons, aromatic hydrocarbons, halogenated hydrocarbons, compounds
containing oxygen, nitrogen or sulphur atoms and miscellaneous compounds). Especially
calorimetrically measured experimental data from the compilation (Majer & Svoboda, 1985)
and data from some other sources mentioned in original paper (Kolsk et al., 2005) were
employed.
Results for estimations of these three properties are presented in the following Tables, Table
1 for enthalpy of vaporization at 298.15 K, Table 2 for enthalpy of vaporization at normal
boiling temperature and Table 3 for entropy of vaporization at normal boiling temperature,
NC means a number of compounds used for development of model and contributions
calculation, NG is number of applied structural fragments (groups), AAE is absolute average
error and ARE is average relative error (Kolsk et al., 2005).
Table 1 shows that values for 831 compounds were used for estimation of enthalpy of
vaporization at 298.15 K. When only first level groups were used, the prediction was
performed with the AAE and the ARE of 1.3 kJ/mol and 2.8%, resp. Values of 116 group
contributions were calculated at this step. Then, 486 compounds were described by the
second order groups. Prediction of these compounds improved after the use of these
contributions from the value of 1.3 kJ/mol to 0.8 kJ/mol (from 2.8% to 1.8%) in comparison
when using only the first level groups. At the end only 55 compounds were suitable for
refining by the third order groups. The results were refined from the values of 1.4 kJ/mol to
1.1 kJ/mol (from 2.5% to 2.1%). The total prediction error was cut down from the value of 1.3
kJ/mol to 1.0 kJ/mol for AAE and from 2.8% to 2.2 % for ARE after usage of all three-level
groups, as it is obvious from this table. A similar pattern of results for other predicted
properties are presented in Tables 2 and 3.
Estimation level NC NG AAE / kJ/mol ARE / %

FIRST 831 116 1.3 2.8
SECOND 486 91 0.8 1.8
486 compounds after only the FIRST (1.3) (2.8)
THIRD 55 15 1.1 2.1
55 compounds After FIRST + SECOND (1.4) (2.5)
ALL LEVELS 831 222 1.0 2.2
Table 1. Results for estimation of enthalpy of vaporization at 298.15 K (Kolsk et al., 2005)
Estimation level NC NG AAE / kJ/mol ARE / %

FIRST 589 111 1.2 3.2
SECOND 377 100 0.9 2.5
THIRD 23 14 1.1 2.1
ALL LEVELS 589 225 0.9 2.6
Table 2. Results for estimation of enthalpy of vaporization at normal boiling temperature (Kolsk et al.,
2005)
Estimation level NC NG AAE / J/(Kmol) ARE / %

FIRST 589 111 2.1 2.2
SECOND 377 100 1.8 1.9
THIRD 23 14 1.9 1.9
ALL LEVELS 589 225 1.7 1.8
Table 3. Results for estimation of entropy of vaporization at normal boiling temperature (Kolsk et al.,
2005)
As an example of the use of all three levels we have chosen the molecule of 1,1,4,7-
tetramethylindane. Its chemical structure is shown in Fig. 3 and its division into individual
first, second and third order groups with the result for vaporization enthalpy at 298.15 K is
presented in Table 4. When we sum up all group contribution of the first level, we have got
value of 64.48 kJ/mol. The first level provides an initial approximation with the relative error
of estimated value exceeding 5 % in comparison with experimental value 61.37 kJ/mol.
Estimated value of vaporization enthalpy at 298.15 K is then improved at the second level
and further refined at the third level, after those the relative error reduced to 1.2 %.
Figure 3. Chemical structure of 1,1,4,7-tetramethylindane

Estimation Group Its Group contribution value for

Group fragment definition
level fragment no. frequency HV at 298.15 K / kJ/mol
FIRST x0 Adjustable parameter 1 9.672
1 CH3 2 2.266
13 aCH 2 4.297
aC fused with nonaromatic
15 2 6.190
subring
18 aC-CH3 2 8.121
107 CH2 (cyclic) 2 4.013
109 C (cyclic) 1 3.667
Estimated
64.48
value
SECOND 55 Ccyc-CH3 2 -1.355
Estimated
63.59
value
aC-CHncyc (fused rings) (n
THIRD 6 2 0.279
in 0..1)
19 AROM.FUSED[2]s1s4 1 -0.615
Estimated
62.13
value
Table 4. Results for estimation of enthalpy of vaporization at 298.15 K for 1,1,4,7-tetramethylindane, aC
means carbon atom in aromatic ring, abbreviation cyc is used for cycle (Kolsk et al., 2005)
Group contribution methods by Ducros (Ducros et al., 1980; Ducros et al., 1981; Ducros &
Sannier, 1982; Ducros & Sannier, 1984), by Chickos (Chickos et al., 1996), the empirical
method, equations nos. 6 and 7 by Vetere (Vetere, 1995) and method by Ma and Zhao (Ma &
Zhao, 1993) were used for comparison of results obtained in this work for estimation at
298.15 K and at normal boiling temperature, resp. While the new approach (Kolsk et al.,
2005) was applied for enthalpy of vaporization at 298.15 K for 831 organic compounds with
the ARE of 2.2 %, the Ducross method could be applied to only 526 substances with the
ARE of 3.1 % and the Chickoss one for 800 compounds with the ARE of 4.7 %. For
comparison of the results of estimation at the normal boiling temperature the new model
provided for 589 compounds, the ARE was 2.6 % for enthalpy of vaporization and 1.8 % for
entropy of vaporization (Kolsk et al., 2005), the Veteres method was capable of estimating
the values of for the same number of compounds with the following results: 4.6 % (Eq. 6,
Vetere, 1995) and 3.4 % (Eq. 7, Vetere, 1995), model by Ma and Zhao (Ma & Zhao, 1993) for
549 compounds with the ARE of 2.5 %. The error for the enthalpy of vaporization, based on
an independent set of various 74 compounds not used for correlation, has been determined
to be 2.5%. Group contribution description and values for next usage of readers are
presented in original paper (Kolsk et al., 2005).
2.2.2. Liquid heat capacity

Isobaric heat capacity of liquid Clp is an important thermodynamic quantity of a pure
compound. Its value must be known for the calculation of an enthalpy difference required
for the evaluation of heating and cooling duties. Liquid heat capacity also serves as an input
parameter for example in the calculation of temperature dependence of enthalpy of
vaporization, for extrapolation of vapour pressure and the related thermal data by their
simultaneous correlation, etc.
In work (Kolsk et al., 2008) the three-level group contribution method by Marrero and Gani
(Marrero & Gani, 2001) mentioned above, which is able to calculate liquid heat capacity at
only one temperature 298.15 K, was applied, and this approach has been extended to
estimate heat capacity of liquids as a function of temperature. Authors have employed the
combination of equation for the temperature dependence of heat capacity and the model by
Marrero and Gani to develop new model (Kolsk et al., 2008).
For parameter calculation 549 organic compounds of variable families of compounds were
taken. In Table 5 are presented results of this estimation. NG means number of applied
structural groups and ARE is the average relative error. More detailed results are presented
in original paper (Kolsk et al., 2008).
Estimation level NG ARE / %

First 111 1.9
Second 88 1.6
Third 25 1.5
Table 5. Results for estimation of liquid heat capacity in temperature range of pure organic compounds
(Kolsk et al., 2008)
Also these estimated values were compared with results obtained by other estimation
methods (Zbransk & Rika, 2004; Chickos et al., 1993) for the basic dataset (compounds
applied for parameter calculation) and also for 149 additional compounds not used in the
parameter calculation (independent set). The first method (Zbransk & Rika, 2004) was
applied for all temperature range, the method proposed by Chickos (Chickos et al., 1993)
was only used for temperature 298.15 K with the following results: new model was applied
for 404 compounds with ARE of 1.5 %, the older method by Zbransk (Zbransk &
Rika, 2004) for the same number of compounds with the ARE of 1.8 % and the Chickoss
one for 399 compounds with the ARE of 3.9 %.
For the heat capacity of liquids authors used recommended data from the compilations by
(Zbransk et al., 1996; Zbransk et al., 2001). Because the experimental data are presented
permanently, it is necessary to update database of critically assessed and recommended
data. Therefore authorss work has been also aimed at updating and extending two
publications prepared earlier within the framework of the IUPAC projects (Zbransk et al.,
1996; Zbransk et al., 2001). These publications contain recommended data on liquid heat
capacities for almost 2000 mostly organic compounds expressed in terms of parameters of
correlating equations for temperature dependence of heat capacity. In new work (Zbransk
et al., 2010b) authors collected experimental data on heat capacities of pure liquid organic
and inorganic compounds that have melting temperature below 573 K published in the
primary literature between 1999 and 2006. Data from more than 200 articles are included
into the database. Compounds were divided into several families, such as hydrocarbons
(saturated, cyclic, unsaturated, aromatic), halogenated hydrocarbons containing atoms of
fluorine, chlorine, iodine, bromine, compounds containing oxygen (alcohols, phenols,
ethers, ketones, aldehydes, acids, esters, heterocycles, other miscellaneous compounds),
compounds containing nitrogen (amines, nitriles, heterocycles, other miscellaneous
compounds), compounds containing sulphur (thioles, sulphides, heterocycles) and
compounds containing silicon. Also data of organometallic compounds, compounds
containing atoms of phosphorus and boron as well as some inorganic compounds were
included. Also the list of families of compounds has been extended by a new group denoted
as ionic liquids due to an increased interest in physical-chemical properties of these
compounds in recent years. Data for approximately 40 ionic liquids were included.
Altogether new data for almost 500 compounds, out of them about 250 compounds were not
covered the in previous works (Zbransk et al., 1996; Zbransk et al., 2001), were
compiled and critically evaluated.
2.2.3. Nafion swelling

Prediction of the physical and chemical properties of pure substances and mixtures is a
serious problem in the chemical process industries. One of the possibilities for prediction of
the properties is the group contribution method. The anisotropic swelling of Nafion 112
membrane in pure organic liquids (solvents) was monitored by an optical method. Nafion is
a poly(tetrafluoroethylene) (PTFE) polymer with perfluorovinyl pendant side chains ended
by sulfonic acid groups. The PTFE backbone guarantees a great chemical stability in both
reducing and oxidizing environments. Nafion membrane is important in chemical industry.
It is used in fuel cells, membrane reactors, gas dryers, production of NaOH, etc. (Randov et
al., 2009). In many applications Nafion is immersed in liquid, which significantly affects the
membrane properties, namely swelling and transport properties of permeates (Randov et
al., 2009). The change in the size of the membrane sample is taken as a measure of swelling.
All experimental data were presented (Randov et al., 2009) and these results were used as a
basis for application of the group contribution method to the relative expansion in
equilibrium. From a total of 38 organic liquids under study, 26 were selected as an
evaluational set from which the group and structural group contributions were assigned.
The remaining 12 compounds were used as the testing set.
Due to limited number of compounds the more complex and known group contribution
methods could not been taken. Authors have to develop new group structural fragments.
The proposed method utilizes the four kinds of the structural units: constants, C-backbone,
functional groups, and molecular geometry (Randov et al., 2009). Constants were presented
as alcohols, ketones, ethers, esters, carboxylic acids. As C-backbone were taken groups CH3,
-CH2- and >CH-. Functional groups as hydroxyl OH-, carbonyl -C=O and ether O- and
fragments for molecular geometry for cycles and branched chains were taken. The relative
expansions Aexp (for the drawing direction) and/or Bexp (for the perpendicular direction)
were calculated from the side lengths of the dry membrane sample (a10, a20, b10, b20) and the
side lengths of the swelled membrane sample in equilibrium (a1, a2, b1, b2) according to the
eq. (3). Description of mentioned sizes is presented in Fig. 4.
Figure 4. Description of membrane dimensions a10, a20, b10, b20 side lengths of the dry membrane and a1,
a2, b1, b2 side lengths of the swelled membrane in equilibrium (Randov et al., 2009)
a1 a10 a2 a20 b1 b10 b2 b20

ua1 , ua 2 , ub1 , ub 2 (3)
a10 a20 b10 b20
Calculation approach is presented in original paper (Randov et al., 2009). Value of 1.5% in
relative expansions was determined to be the experimental error. Maximum differences
between the experimental and calculated relative expansions in both sets did not exceed the
value of 3% (Randov et al., 2009).
The values of 13 contributions for individual membrane relative expansions were

determined on the basis of experimental data on relative expansion of Nafion membrane.
Obtained results are in good agreement with experimental data. Maximum differences
between experimental and calculated values are nearly the same, only twice greater than the
experimental error.
2.2.4. Flash temperature of organic compounds

The flash temperature Tf and lower flammability limit (LFL) are one of the most important
variables to consider when designing chemical processes involving flammable substances.
These characteristics are not fundamental physical points. Flash temperature is one of the
most important variables used to characterize fire and explosion hazard of liquids. The flash
temperature is defined as the lowest temperature at which vapour above liquid forms
flammable mixture with air at a pressure 101 325 Pa. Usual approach for flash temperature
estimation is linear relationship between flash temperature Tf and normal boiling
temperature Tb (Dvok, 1993). Some models for flash temperature were presented earlier
(Liaw & Chiu, 2006; Liaw et al., 2011).
In this work to estimate flash temperature of organic compound authors applied the
modified group contribution method (Kolsk et al., 2005) and calculate group contribution
values data for 186 compounds (Steinleitner, 1980) were used. The database for calculation
of parameters contains data for aliphatic and acyclic saturated and unsaturated
hydrocarbons, aromatic hydrocarbons, alcohols, halogenated hydrocarbons, compounds

containing oxygen, nitrogen or sulphur atoms and miscellaneous compounds. To collect
more data for development of reliable method was not able due to that all databases collect
some values obtained via closed cup type measuring method and others measured by open
cup one and data both of methods vary.
Flash temperature was calculated by relationship (4) similar to eq. (1):
n m o
Tf Tf NiCi M j D j z Ok Ek (4)
i 1 j 1 k 1
where Tf is an adjustable parameter, Ci is the first-order group contribution of type i, Dj is

the second-order group contribution of type j, Ek is the third-order group contribution of the
type k and Ni, Mj, Ok denote the number of occurrences of individual group contributions.
Determination of contributions and of adjustable parameters was performed by a three-step
regression procedure (Marrero & Gani, 2001). To evaluate the method error the following
statistical quantities for each compound, absolute error AE (eq. 5) and relative error ARE (eq.
6) were used:
AE Tf Tf exp Tf est (5)
T
f exp Tf est
RE Tf 100 (6)
Tf exp

where subscripts exp and est mean experimental and estimated value of the flash
temperature. 186 compounds from the basic data set were described by the first level group
contributions (Kolsk et al., 2005). From this large database only 114 compounds could be
selected to be described by the original second level groups as defined earlier (Kolsk et al.,
2005). The total absolute and the relative average errors for all 186 compounds were equal to
6.3 K and 2.0 %. Results for individual estimation levels are presented in Table 6.
Estimation level NC AAE / K ARE / %

FIRST 186 7.9 2.4
SECOND 105 5.7 1.8
THIRD 11 2.9 0.8
ALL LEVELS 186 6.5 2.0
Table 6. Results for Estimation of flash temperature, NC is number of compounds
Individual calculated structural fragments of the first, second and third estimation levels are
presented in Tables 7-9, resp.
Structural Contribution Structural Contribution Structural Contribution

fragment /K fragment /K fragment /K
Tf 194.35 aCH 12.39 aC-OH 85.26
CH3 5.38 aC 21.15 CH2Cl 45.56
CH2 13.28 aC 26.84 CHCl 42.83
CH 15.77 aC 31.53 CCl 37.51
C 13.59 aN 25.51 CHCl2 67.42
CH2=CH 11.51 aC-CH3 28.32 CCl3 100.38
CH=CH 34.57 aC-CH2 37.11 aC-Cl 50.70
CH2=C 19.63 aC-CH 37.38 aC-F 53.47
CH=C 27.52 aC-C 19.88 aC-Br 64.97
C=C 29.27 aC-CH=CH2 50.66 -I 78.85
CH#C 14.94 OH 64.22 -Br 59.25
C#C 15.04 -SH 55.62 CH=CH 18.21
-F 2.99 CH2 10.89 CH=C 37.59
-Cl 29.32 CH 22.89 N 52.99
CH2SH 56.33 C -9.50 O -3.39
Table 7. Group contribution of the first level for estimation of flash temperature
Structural fragment Contribution Structural Contribution Structural fragment Contribution

/K fragment /K /K
CHm=CHn-Cl
(CH3)2CH -1.45 (m,n in 0..2) -0.50 CHcyc-OH -1.31
aC-CHn-X (n in
(CH3)3C -3.98 1..2) X: Halogen 1.04 Ccyc-CH3 -0.23
aC-CHn-OH (n
CH(CH3)CH(CH3) 7.68 in 1..2) 5.51 >Ncyc-CH3 -1.11E-17
CH(CH3)C(CH3)2 22.69 aC-CH(CH3)2 1.80 AROMRINGs1s2 -2.24
CHn=CHm-CHp=CHk
(k,m,n,p in 0..2) 0.53 aC-CF3 0.13 AROMRINGs1s3 1.72
CH3-CHm=CHn (m,n in (CHn=C)cyc-
0..2) -2.01 CH3 (n in 0..2) 0.46 AROMRINGs1s4 -0.84
CH2-CHm=CHn (m,n in
0..2) 2.23 CHcyc-CH3 -5.70 AROMRINGs1s2s4 -2.84
CHp-CHm=CHn (m,n in
0..2; p in 0..1) 3.78 CHcyc-CH2 17.80 AROMRINGs1s2s4s5 6.22
CHcyc-CH=CHn 8.52
CHOH -3.92 (n in 1..2) PYRIDINEs3s5 9.98E-18
CHcyc-C=CHn
COH -4.98 (n in 1..2) -1.20 (CH=CHOCH=CH)cyc -4.24
CHm(OH)CHn(OH)
(m,n in 0..2) 13.41 CHcyc-Cl 1.59 (3 F) -0.13
(perFlouro) 2.66E-17
Table 8. Group contribution of the second level for estimation of flash temperature
Structural Contribution Contribution Structural Contribution

Structural fragment
fragment /K /K fragment /K
OH-(CHn)m-OH CHcyc-CHcyc
-33.36 -1.87 AROM.FUSED[2] 8.69
(m>2, n in 0..2) (different rings)
aC-aC (different
-6.04 CH multiring 0.98 AROM.FUSED[4a] -26.07
rings)
aC-CHm-aC
aC-CHncyc (fused
-4.34 (different rings) (m 12.92
rings) (n in 0..1)
in 0..2)
Table 9. Group contribution of the third level for estimation of flash temperature
2.2.5. Reactivation ability of some reactivators of acetylcholinesterase

In the last years regarding to valid legislation on dangerous compounds it is necessary to
know many of important characteristics of chemical compounds. Due to this new models for
their estimation were developed. New models for estimation of reactivation ability of
reactivators for acetylcholinesterase inhibited by (i) chloropyrifos (O,O-diethyl O-3,5,6-
trichloropyridin-2-yl phosphorothioate) as a representative of organophosphate insecticide
and by (ii) sarin ((RS)-propan-2-yl methylphosphonofluoridate) as a representative of nerve
agent is now presented. Both of these family compounds, organophosphate pesticide and
nerve agent, are highly toxic and have the same effect to living organisms, which is based on
an inhibition of acetylcholinesterase (AChE). New compounds able to reactivate the
inhibited AChE, so-called reactivators of AChE, are synthesized. Reactivation ability of
these reactivators is studied using standard reactivation in vitro test (Kua & Kassa, 2003).
Reactivation ability of reactivators means the percentage of original activity of AChE (Kua
& Patoka, 2004). New models for determination values of reactivation ability of reactivators
AChE inhibited by (i) chloropyrifos and (ii) sarin have been developed. Concentration of
reactivators was c=110-3 moldm-3. In comparison with previous cases (estimations of
thermophysical properties) authors have only less experimental data for development of
model (about 20 for each of cases). Due to their long names and complex chemical structures
these compounds in this chapter only are presented as their codes taken from original
papers (Kua & Kassa, 2003; Kua et al., 2003a; Kua et al., 2003b; Kua et al., 2003c; Kua &
Patoka, 2004; Kua & Cabal, 2004a; Kua & Cabal, 2004b; Kua et. al., 2006. Data of
reactivation ability for these reactivators were given by the mentioned author team (Kua et
al.). Classical group contribution method includes groups describing some central atom,
central atom with its bonds, or central atom with its nearest surrounding. However these
models commonly used experimental data of hundreds or thousands compounds for
parameters calculation. Due to for much small database in these cases it was necessary to
design new fragments depending on the molecular structures available compounds.
Structural fragments in this work cover larger and more complex part of molecules in
comparison with other papers focused to group contribution methods. Reactivation potency
is given in the group contribution method by the following relation, eq. 7:
n
Rp xi Rpi (7)
i 1
where Rpi is value of individual fragment i presented in molecule by which it contributes to

total value of Rp, x is number of frequency of this fragment i in molecule. Parameters Rpi
were obtained by minimization function SRp, eq. 8:

m
SRp Rpi ,calc Rpi ,exp (8)
i 1
where suffix exp presents experimental data and suffix calc the calculated values of Rp, m is
number of compounds in dataset. The results obtained by this new approach were
compared with experimental data using the following statistical quantities - an absolute
error of individual compounds AE (eq. 9) and the average absolute error of dataset AAE (eq.
10):
AEi Rpi ,calc Rpi ,exp (9)
m R
pi ,calc Rp i ,exp
AAE (10)

i 1 m

Parameters of new model were calculated from the experimental data of the basic dataset.
For model for reactivators AChE inhibited by chloropyrifos the input database included
data of reactivation ability Rp for 24 reactivators (K 135, K 078, TO 096, TO 100, K 076, TO
094, TO 063, TO 097, TO 098, K 347, TO 231, K 117, K 074, K 033, K 106, K 107, K 110, K 114,
HI-6, K 282, K 283, K 285, K 129, K 099) of concentration c=110-3 moldm-3. Values for 17
groups with the AAE of 1.85 % of Rp were calculated. Designed groups with their calculated
values of Rpi are presented in Table 10. These calculated parameters were tested on the test
set of 5 independent compounds (TO 238, K 111, K 113, Methoxime, K 280) of which
experimental data were not applied to group contributions determination. The AAE of Rp
prediction for this test-set was 1.45 %. Table 11 presents experimental data and predicted
values for these 5 independent compounds. Also illustration of usage of this method for two
compounds from this test set is added below.
As it is clear from Table 10 the highest values of contributions are given for fragments P3, P7
for monoaromatic reactivators and P11, P12 and P14 for two aromatic rings in reactivator
molecule. On the other hand the smallest contribution (the negative ones) to total value of
reactivation ability yields fragments P5 a P6 for monoaromatic compounds and P16 and P17
for two aromatic ring reactivators. These values resulted in fact that reactivation ability of
new reactivators for reactivation AChE inhibited by chloropyrifos should be increased by
presence of the following functional groups in molecules: another quarternary nitrogen
atom in aliphatic ring bonded to aromatic quarternary nitrogen atom, the oxime groups in
para- or meta- positions and presence of other aliphatic rings bonded to aromatic ring in
other position than quarternary nitrogen and oxime groups. In all cases it is clear that
reactivation ability decreases with presence of cycle ring, double bond and also in a less
range with the presence of oxygen atoms presented in molecules. Also ortho- position of
oxime group does not contribute positively.
Rpi Rpi
no. Fragment description no. Fragment description
/% /%
two oxime groups in
Oxime group (=NOH) in position o- positions o- due to a
P1 due to a quarternary nitrogen N+ 26.365 P9 quarternary nitrogen atom in 26.580
atom in aromatic ring aromatic ring
two oxime groups in

Oxime group (=NOH) in position p-
positions m- due to a
P2 due to a quarternary nitrogen N+ 15.365 P10 15.737
quarternary nitrogen atom N+
atom in aromatic ring
in aromatic ring
Other quarternary nitrogen atom N+ two oxime groups in
with 4 CHx- groups in molecule, in positions p- due to a
P3 46.792 P11 47.105
aliphatic ring bonded to nitrogen quarternary nitrogen atom N+
atom N in aromatic ring in aromatic ring
two oxime groups, one in
position o-, other in position
Number of members bonded in
P4 -1.047 P12 m- due to a quarternary 52.105
aliphatic ring after the group P3
nitrogen atom N+ in aromatic
ring
position o-, other in position
Cycle ring bonded to nitrogen atom -
P5 P13 p- due to a quarternary 25.842
N in aromatic ring 10.365
ring
position m-, other in position
Oxygen atom O bonded in aliphatic -
P6 P14 p- due to a quarternary 56.105
ring bonded to one aromatic ring 32.437
ring
Oxygen atom O bonded in
Presence of other aliphatic ring
P7 88.073 P15 aliphatic ring between two -5.842
bonded to aromatic one
aromatic rings
Number of members bonded in
aliphatic ring following group N-
Cycle between two aromatic -
P8 CHx- (nitrogen atom N is a part of -2.344 P16
rings 10.474
aromatic ring), (which are not
included in other groups)
Double bond between two -
P17
aromatic rings 22.105
Table 10. List of structural fragments and their values for estimation of reactivation ability of
reactivators for acetylcholinesterase inhibited by chloropyrifos
Reactivator Rp,exp / % Rp,calc / % Deviation / %

TO 238 48.00 49.55 1.55
K 111 8.00 5.26 -2.74
K 113 37.00 36.63 -0.37
Methoxime 45.00 47.11 2.11
K 280 4.00 4.48 0.48
Table 11. Results for estimation of reactivation ability of the test dataset of 5 reactivators of
acetylcholinesterase inhibited by chloropyrifos
Illustration of new method for reactivation ability prediction of two reactivators (TO 238
and K 280) of which experimental data were not used for parameters calculation follows.
TO 238 K 280
Figure 5. Chemical structure of two reactivators of acetylcholinesterase signed as TO 238 and K 280
Example of usage of the new model for reactivation ability prediction for TO 280 reactivator:
Rp,calc(TO 238) = P1 + 2P6 + P7 = 26.365 + 2(-32.437) + 88.073 = 49.546 %

Rp,exp(TO 238) = 48.00 %
AE = Rp,calc(TO 238) - Rp,exp(TO 238) = 1.55 %.
Example of usage of the new model for reactivation ability prediction for K 280 reactivator:
Rp,calc(K 280) = P9 + P17 = 26.580 + (-22.105) = 4.475 %

Rp,exp(K 280) = 4.00 %
AE = Rp,calc(K 280) - Rp,exp(K 280) = 0.48 %.
For model development for reactivators AChE inhibited by sarin the input database
included data of reactivation ability Rp for 18 reactivators (K 127, K 128, K 141, K 276, K 311,
K 277, K 077, K 142, K 131, K 100, K 233, K 194, K 191, K 067, K 119, K 053, Pralidoxime, HI-
6) of concentration c=110-3 moldm-3 were taken. Due to the smaller database in comparison
with the chloropyrifos-inhibited case it was not possible to apply the same structural
fragments. Values for 11 new structural different groups with the AAE of 3.39 % of Rp have
been calculated. Designed groups with their calculated values of Rpi are presented in Table
12. These calculated parameters were tested on the test set of 4 independent compounds (TO
055, TO 058, K 197, Obidoxime) of which experimental data were not applied to group
contributions determination. The AAE of Rp prediction for this test-set was 2.18 %. Table 13
presents experimental data and predicted values for 4 independent compounds.
Rpi Rpi
no. Fragment description no. Fragment description
/% /%
Other member of ring between two
Quarternary nitrogen
quarternary nitrogen atoms N+ or/and
P1 atom N inclusive in 22.50 P7 -6.41
bonded at the last quarternary nitrogen atom
aromatic ring
N of molecule
+
Presence of oxime Presence of oxygen atom O in molecule

P2 -31.21 P8 2.16
group other than mentioned in the following group
ortho- position of
P3 substituent on aromatic 46.03 P9 Presence of group >C=O in molecule 7.88
ring
meta- position of
Presence of group -NHx(x = 0, .., 2) in
P4 substituent on aromatic 14.49 P10 -12.20
molecule
ring
para- position of Presence of a double bond between two
P5 substituent on aromatic 40.01 P11 carbon atoms in a ring between two 1.66
ring quarternary nitrogen atoms N+ in molecule
Presence of cycle in a
P6 -10.03
molecule
Table 12. List of structural fragments and their values for estimation of reactivation ability of
reactivators for acetylcholinesterase inhibited by sarin
As it is shown in Table 12, the highest and the positive values of group contributions are
given for fragments P1, P3-P5, P8 and P9. On the other hand the smallest contribution (the
negative ones) to the total value of reactivation ability yield fragments P6, P7 and P10. Also
the value of fragment P2 for oxime group seems to have a negative effect to the total value
but it should be said, that the oxime group has to be summed up with some group for its
position on aromatic ring. It results in a fact that the oxime group in meta- position has the
negative influence to the total value of reactivation ability, on the other hand the total value
of Rp increases with oxime group in positions of ortho- or para-. These values resulted in fact
that reactivation ability of new reactivators for reactivation AChE inhibited by sarin should
be increased by the presence of the following function groups in molecules: another
quarternary nitrogen atom in aromatic ring, the oxime groups in ortho- or para positions,
presence of oxygen atom or group >C=O in molecule. It is clear that reactivation ability
decreases with presence of cycle ring and also with presence of the group NHx (x = 0, .., 2) in
molecules. Also meta- position of oxime group, as same as the longer ring (CHx)n (x = 0, .., 2)
bonded at quarternary nitrogen atoms, that means group P7, do not contribute positively.
Reactivator Rp,exp / % Rp,calc / % Deviation / %

TO 055 30.00 32.38 2.38
TO 058 25.00 27.63 2.63
K 197 4.00 4.08 0.08
Obidoxime 41.00 44.70 3.70
Table 13. Results for estimation of reactivation ability of the test dataset of 4 reactivators of
acetylcholinesterase inhibited by sarin
Illustration of new method for reactivation ability prediction of two reactivators (TO 055
and TO 058) of which experimental data were not used for parameters calculation follows.
TO 055 TO 058
Figure 6. Chemical structure of two reactivators of acetylcholinesterase signed as TO 055 and TO 058
Rp,calc(TO 055) = 3P1 + 3P2 + 3P5 + 3P6 + 3P7 + P10 = 3(22.50) + 3(-31.21) + 3(40.01) + 3(-10.03)
+ 3(-6.41) + (-12.20) = 32.38 %; Rp,exp(TO 055) = 30.00 %
Rp,calc(TO 058) = 2P1 + 2P2 + 2P5 + 2P6 + 3P7 + 2P8 = 2(22.50) + 2(-31.21) + 2(40.01) + 2(-
10.03) + 3(-6.41) + 2(2.16) = 27.63 %; Rp,exp(TO 058) = 25.00 %
As it is clear, in comparison with the previous cases, these models are applicable only for the
same inhibitors but for new reactivators of ACHE inhibited by the same inhibitors (the first
for chloropyrifos, the second one for sarin). But on the other hand, it can be also used as a
tool for easy prediction of reactivation potency of some newly synthesized reactivators
without any other in vitro standard tests.
3. Conclusion
Most of the industrial applications and products contain a mixture of many components and
for the production it is important to know the properties of individual substance and the
properties of aggregates. The accomplishments of all of these experiments are too expensive
and time-consuming, so the calculation or estimation methods are good way to solve this
problem. The group contribution methods are the important and favourible estimation
method, because they permit to determine value of property of extant or hypothetic
compound. Group contribution methods are the suitable tool for estimation of many
physico-chemical quantities of pure compounds and mixtures too as it was showed and
confirmed above for some cases. It can be used for estimation of pure compounds, as well as
mixtures, for one temperature estimation, as well as for temperature range, etc. The biggest
advantage of these methods is they need knowledge only chemical structure of compounds
without any other input information. The presented models have been developed for
estimation of many variable properties, enthalpy of vaporization, entropy of vaporization,
liquid heat capacity, swelling of Nafion, flash temperature and reactivation ability of
reactivators of acetylcholinesterase inhibited by organophosphate compounds. Proposed
models and their structural fragments, accuracy and reliability depend mainly on frequency
of input data and their accuracy, correctness and reliability. The most of presented models
of group contribution methods, not only in the cases presented in this chapter, can be
applied for the wide variety of organic compounds, when groups describing these
molecules are presented. Some of models can be applied from only limited families of
compounds due to their parameters were calculated only for limited database of
compounds. Group contribution methods can be applied either for estimation or prediction
of properties at one temperature or as a temperature function depending on their
development. The accuracy of developed models is the higher, the input database is more
reliable.
Author details
Zdeka Kolsk
Faculty of Science, J. E. Purkyn University, Usti nad Labem, Czech Republic
Milan Zbransk and Alena Randov

Institute of Chemical Technology, Prague, Czech Republic
Acknowledgement
This work was supported by the GA CR under the project P108/12/G108. Authors also thank
to Ing. Michal Karlk from ICT Prague, Czech Republic, for data for flash temperature
estimation and Prof. Kamil Kua from Department of Toxicology, Faculty of Millitary
Health Science Hradec Kralove, Czech Republic, for data on reactivation ability.
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propane dibromide. Tetrahedron Letters, Vol.44, No.15, pp. 3123-3125, ISSN 0040-4039
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Acetyylcholinesterase Activity by -bis-(4-hydroxyiminomethylpyridinium)alkanes
in vitro. Journal of Applied Biomedicine, Vol.1, No.4, pp. 207-211. ISSN 1214-0287
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Chemistry. Vol.19, No.1, pp. 39-43, ISSN 1475-6366
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5575/06
Chapter 7
Thermodynamic Properties and Applications

of Modified van-der-Waals Equations of State
Ronald J. Bakker
1. Introduction
Physical and chemical properties of natural fluids are used to understand geological
processes in crustal and mantel rock. The fluid phase plays an important role in processes in
diagenesis, metamorphism, deformation, magmatism, and ore formation. The environment
of these processes reaches depths of maximally 5 km in oceanic crusts, and 65 km in
continental crusts, e.g. [1, 2], which corresponds to pressures and temperatures up to 2 GPa
and 1000 C, respectively. Although in deep environments the low porosity in solid rock
does not allow the presence of large amounts of fluid phases, fluids may be entrapped in
crystals as fluid inclusions, i.e. nm to m sized cavities, e.g. [3], and fluid components may
be present within the crystal lattice, e.g. [4]. The properties of the fluid phase can be
approximated with equations of state (Eq. 1), which are mathematical formula that describe
the relation between intensive properties of the fluid phase, such as pressure (p),
temperature (T), composition (x), and molar volume (Vm).
p T , Vm , x (1)
This pressure equation can be transformed according to thermodynamic principles [5], to

calculate a variety of extensive properties, such as entropy, internal energy, enthalpy,
Helmholtz energy, Gibbs energy, et al., as well as liquid-vapour equilibria and
homogenization conditions of fluid inclusions, i.e. dew point curve, bubble point curve, and
critical points, e.g. [6]. The partial derivative of Eq. 1 with respect to temperature is used to
calculate total entropy change (dS in Eq. 2) and total internal energy change (dU in Eq. 3),
according to the Maxwell's relations [5].
p
dS dV (2)
T V , nT
p
dU T p dV (3)
T V , n
T
where nT is the total amount of substance in the system. The enthalpy (H) can be directly
obtained from the internal energy and the product of pressure and volume according to Eq.
4.
H U pV (4)
The Helmholtz energy (A) can be calculated by combining the internal energy and entropy
(Eq. 5), or by a direct integration of pressure (Eq. 1) in terms of total volume (Eq. 6).
A U TS (5)
dA pdV (6)
The Gibbs energy (G) is calculated in a similar procedure according to its definition in Eq. 7.
G U p V T S (7)
The chemical potential (i) of a specific fluid component (i) in a gas mixture or pure gas (Eq.
8) is obtained from the partial derivative of the Helmholtz energy (Eq. 5) with respect to the
amount of substance of this component (ni).
A
i (8)
ni T , V , nj
The fugacity (f) can be directly obtained from chemical potentials (Eq. 9) and from the
definition of the fugacity coefficient (i) with independent variables V and T (Eq. 10).
f
RT ln i0 i i0 (9)
f
i
where i0 and fi0 are the chemical potential and fugacity, respectively, of component i at
standard conditions (0.1 MPa).

p RT
RT ln i n

V
dV RT ln z . (10)
i T , V , n
V
j
where i and z (compressibility factor) are defined according to Eq. 11 and 12, respectively.
fi
i (11)
xi p
Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 165
pV
z (12)
nT RT
2. Two-constant cubic equation of state

The general formulation that summarizes two-constant cubic equations of state according to
van der Waals [7], Redlich and Kwong [8], Soave [9], and Peng and Robinson [10] is
illustrated in Eq. 13 and 14, see also [11]. In the following paragraphs, these equations are
abbreviated with Weos, RKeos, Seos, and PReos.
RT 2
p (13)
Vm 1 Vm Vm 3 4 Vm 4
nT RT nT 2 2
p (14)
V nT 1 V nT 3 V nT 4 V nT 2 4 2
2
where p is pressure (in MPa), T is temperature (in Kelvin), R is the gas constant (8.3144621
Jmol-1K-1), V is volume (in cm3), Vm is molar volume (in cm3mol-1), nT is the total amount of
substance (in mol). The parameters 1, 2, 3, and 4 are defined according to the specific
equations of state (Table 1), and are assigned specific values of the two constants a and b, as
originally designed by Waals [7]. The a parameter reflects attractive forces between
molecules, whereas the b parameter reflects the volume of molecules.
W RK S PR
1 b b b b
2 a aT -0.5 a a
3 - b b b
4 - - - b
Table 1. Definitions of 1, 2, 3, and 4 according to van der Waals (W), Redlich and Kwong (RK), Soave
(S) and Peng and Robinson (PR).
This type of equation of state can be transformed in the form of a cubic equation to define
volume (Eq. 15) and compressibility factor (Eq. 16).
a0 V 3 a1V 2 a2 V a3 0 (15)
b0 z 3 b1z 2 b2 z b3 0 (16)
where a0, a1, a2, and a3 are defined in Eq. 17, 18, 19, and 20, respectively; b0, b1, b2, and b3 are
defined in Eq. 21, 22, 23, and 24, respectively.
a0 p (17)
a1 nT p 3 4 1 nT RT (18)
a2
nT 2 p 4 2 1 3 1 4 nT 2 RT 3 4 nT 2 2 (19)
a3 nT 3 p 1 4 2 nT 3 RT 4 2 nT 3 1 2 (20)
3
RT
b0 (21)
p
2
RT RT
b1 3 4 1 (22)
p p
RT RT 2
4 3 4 1
2
b2 (23)
p p p
RT 1 2
b3 1 4
2
(24)
p p
The advantage of a cubic equation is the possibility to have multiple solutions (maximally
three) for volume at specific temperature and pressure conditions, which may reflect
coexisting liquid and vapour phases. Liquid-vapour equilibria can only be calculated from
the same equation of state if multiple solution of volume can be calculated at the same
temperature and pressure. The calculation of thermodynamic properties with this type of
equation of state is based on splitting Eq. 14 in two parts (Eq. 25), i.e. an ideal pressure (from
the ideal gas law) and a departure (or residual) pressure, see also [6].
p pideal presidual (25)
where
nT RT
pideal (26)
V
The residual pressure (presidual) can be defined as the difference (p, Eq. 27) between ideal
pressure and reel pressure as expressed in Eq. 14 .
nT RT nT RT nT 2 2
p presidual (27)
V V nT 1 V 2 nT 3 V nT 4 V nT 2 4 2
The partial derivative of pressure with respect to temperature (Eq. 28) is the main equation
to estimate the thermodynamic properties of fluids (see Eqs. 2 and 3).
p pideal p
(28)
T T T
where
p n R nT R nT RT (nT 1 )
T
T V V nT 1 V nT 1 T
2
1 ( nT 2 2 )

V nT 3V nT 4 V nT 4
2 2 2 T (29)

nT 22

nT 3V nT 4 V nT 2 4 2
V T
2
2
nT 3V nT 4V nT 2 4 2
The parameters 1, 3, and 4 are usually independent of temperature, compare with the b
parameter (Table 1). This reduces Eq. 29 to Eq. 30.
p n R nT R 1 (nT 2 2 )
T 2 (30)
T V V nT 1 V nT 3V nT 4 V nT 2 4 2 T
Other important equations to calculate thermodynamic properties of fluids are partial

derivatives of pressure with respect to volume (Eq. 31 and 32).
p nT RT nT 2 2
2V nT 3 nT 4 (31)
V V nT 1 V
2 2
2
2p 2nT RT 2nT 2 2
2V nT 3 nT 4
2

V2 V nT 1 V
3 3
2
(32)
2nT 2
2

V
2
2
nT 3V nT 4 V nT 2 4 2
Eqs. 31 and 32 already include the assumption that the parameters 1, 2, 3, and 4 are
independent of volume. Finally, the partial derivative of pressure in respect to the amount
of substance of a specific component in the fluid mixture (ni) is also used to characterize
thermodynamic properties of fluid mixtures (Eq. 33).
p RT nT RT (nT 1 )

ni V nT 1 V nT 1 ni
2
1 ( nT 2 2 )
(33)
V 2 nT 3V nT 4 V nT 2 4 2 ni
nT 2 2 (nT 3 ) (nT 4 ) (nT 4 )
V 2nT 4
V ni ni ni
2
2
3. Thermodynamic parameters
The entropy (S) is obtained from the integration defined in Eq. 2 at constant temperature
(Eqs. 34 and 35).
S1 V1
p
dS T dV (34)
S0 V0 V , nT
V1
pideal p
S1 S0 T
dV
T
(35)
V0
The limits of integration are defined as a reference ideal gas at S0 and V0, and a real gas at S1
and V1. This integration can be split into two parts, according to the ideal pressure and
residual pressure definition (Eqs. 25, 26, and 27). The integral has different solutions
dependent on the values of 3 and 4: Eq. 36 for 3 = 0 and 4 = 0, and Eqs. 37 and 38 for 3 > 0.
V V n V 1 1 (nT 2 2 )
S1 S0 nT R ln 1 nT R ln 1 T 1 0 (36)
V0 V0 nT 1 V1 V1 V0 T
V V n V
S1 S0 nT R ln 1 nT R ln 1 T 1 0
V
0 V0 nT 1 V1
(37)
1 (nT 2 )
2
2V1 nT ( 3 4 ) q 1 (nT 2 2 ) 2V0 nT ( 3 4 ) q
ln ln
q T 2V1 nT ( 3 4 ) q q T 2V0 nT ( 3 4 ) q
where
q nT 4 4 2 ( 3 4 )2 (38)
The RKeos and Seos define q as nT b , whereas in the PReos q is equal to nT b 8 , according to
the values for 3 and 4 listed in Table 1. Eqs. 36 and 37 can be simplified by assuming that
the lower limit of the integration corresponds to a large number of V0. As a consequence,
part of the natural logarithms in Eqs. 36 and 37 can be replaced by the unit value 1 or 0 (Eqs.
39, 40, and 41).
V0
lim 1 (39)
V0 V
0 n
T 1
1
lim 0 (40)
V0
V0
2V nT ( 3 4 ) q
lim 0 1 (41)
V0
2V0 nT ( 3 4 ) q
The entropy change that is caused by a volume change of ideal gases corresponds to the
second term on the right-hand side of Eqs. 36 and 37. This term can be used to express the
behaviour of an ideal mixture of perfected gases. Each individual gas in a mixture expands
from their partial volume (vi) to the total volume at a pressure of 0.1 MPa, which results in a
new expression for this term (Eq. 42)
V V
nT R ln 1 ni R ln v1 (42)
V0 ideal.mix i i
where ni is the amount of substance of component i in the fluid mixture. In addition, the
partial volume of an ideal gas is related to the standard pressure p0 (0.1 MPa) according to
the ideal gas law (Eq. 43, compare with Eq. 26).
ni RT
vi (43)
p0
Finally, the entropy of fluid phases containing gas mixtures at any temperature and total
volume according to the two-constant cubic equation of state is given by Eq. 44 for 3 = 0 and
4 = 0, and Eq. 45 for 3 > 0.
p V V nT 1 1 (nT 2 2 )
S S0 ni R ln n 0RT nT R ln
T
(44)
i i V V
p V V nT 1 1 (nT 2 )
2
2V nT ( 3 4 ) q
S S0 ni R ln n 0RT nT R ln
T
ln (45)
i i V q 2V nT ( 3 4 ) q
The subscripts "1" for the upper limit of integration is eliminated to present a pronounced
equation. The standard state entropy (S0) of a mixture of ideal gases is defined according to
the arithmetic average principle (Eq. 46).
S0 ni si0 (46)
i
where si0 is the molar entropy of a pure component i in an ideal gas mixture at temperature T.
The internal energy (U, see Eq. 3) is obtained from the pressure equation (Eq. 14) and its
partial derivative with respect to temperature (Eqs. 28 and 30):
U1 V1
p
dU T T p dV

(47)
U0 V0
V1
1 (nT 2 2 )
U1 U 0 V 2 n V n V n 2 2 nT 2 2 T
T
dV (48)
V0 T 3 T 4 T 4
Similar to the integral in the entropy definition (see Eqs. 44 and 45), Eq. 48 has different
solutions dependent on the values of 3 and 4: Eq. 49 for 3 = 0 and 4 = 0, and Eq. 50 for 3 > 0.
1 ( nT 2 2 )
U U0 nT 2 2 T (49)
V T

1 2 (nT 2 2 ) 2V nT ( 3 4 ) q
U U0 nT 2 T ln (50)
q T 2V nT ( 3 4 ) q
The definition of q is given in Eq. 38. The standard state internal energy (U0) of a mixture of
ideal gases is defined according to the arithmetic average principle (Eq. 51).
U0 ni ui0 (51)
i
where ui0 is the molar internal energy of a pure component i in an ideal gas mixture at
temperature T.
Enthalpy (Eq. 52 for 3 = 0 and 4 = 0, and Eq. 53 for 3 > 0), Helmholtz energy (Eq. 55 for 3 =
0 and 4 = 0, and Eq. 56 for 3 > 0), and Gibbs energy (Eq. 58 for 3 = 0 and 4 = 0, and Eq. 59
for 3 > 0) can be obtained from the definitions of pressure, entropy and internal energy
according to standard thermodynamic relations, as illustrated in Eq. 4, 5, and 7. Standard
state enthalpy (H0), standard state Helmholtz energy (A0), and standard state Gibbs energy
(G0) of an ideal gas mixture at 0.1 MPa and temperature T are defined in Eqs. 54, 57, and 60,
respectively.
nT RTV 1 (nT 2 2 )
H U0 2nT 2 2 T (52)
V nT 1 V T
nT RTV nT 2 2 V
H U0 2
V nT 1 V nT 3V nT 4 V nT 2 4 2
(53)
1 (nT 2 2 ) 2V nT ( 3 4 ) q
nT 2 2 T ln
q T 2V nT ( 3 4 ) q
H0 U 0 nT RT (54)
p V V nT 1 nT 2 2
A U 0 TS0 ni RT ln n 0RT nT RT ln (55)
i i V V
p V V nT 1
A U0 TS0 ni RT ln n 0RT
nT RT ln
i
i V (56)
n
2
2V nT ( 3 4 ) q
T 2 ln
q 2V nT ( 3 4 ) q
A0 U0 TS0 (57)
p V V nT 1 nT RTV 2nT 2 2
G U0 TS0 RT ni ln 0 nT RT ln (58)
i
ni RT V V nT 1 V
p V V nT 1 nT RTV
G U0 TS0 RT ni ln 0 nT RT ln
i
ni RT V V nT 1
(59)
n
2
2V nT ( 3 4 ) q nT 2V
2
T 2 ln 2
q 2 V nT ( 3 4 ) q V nT 3V nT 4 V nT 2 4 2
G0 U0 TS0 nT RT (60)
The Helmholtz energy equation (Eqs. 55, 56, and 57) is used for the definition of chemical
potential (i) of a component in either vapour or liquid phase gas mixtures (compare with
Eq. 8), Eq. 61 for 3 = 0 and 4 = 0, and Eq. 62 for 3 > 0, calculated with two-constant cubic
equations of state.
U0 S pV V nT 1
i T 0 RT ln 0 RT RT ln
ni ni n
i RT V
(61)
nT RT (nT 1 ) 1 nT 2 2

V nT 1 ni V ni
U0 S pV V nT 1 nT RT (nT 1 )
i T 0 RT ln 0 RT RT ln
ni ni ni RT V V nT 1 ni
n 2 1 n 2 q 2V nT ( 3 4 ) q
T 2 T22 ln
n
i q q n i 2V nT ( 3 4 ) q
(62)
n 2 1 n n q
T 2 T 3 T 4
q 2V nT ( 3 4 ) q ni ni ni
nT 2 2 1 n n q
T 3 T 4
where
q 1 n n n
4nT 4 T 4 nT ( 3 4 ) T 3 T 4 (63)
ni q ni ni ni
The definitions of the partial derivative of q in respect to amount of substance (Eq. 63)
according to 3 = b and 4 = 0 [8, 9] is illustrated in Eq. 64, and 3 = b and 4 = b [10] in Eq. 65.
q (nT b)
(64)
ni ni
q (nT b)
8 (65)
ni ni
The fugacity coefficient (i) is defined according to Eqs. 9 and 10 from the difference
between the chemical potential of a real gas mixture and an ideal gas mixture at standard
conditions (0.1 MPa), see Eq. 66 for 3 = 0 and 4 = 0, and Eq. 67 for 3 > 0. Fugacity coefficient
defined in Eq. 66 is applied to Weos and Eq. 67 is applied to RKeos, Seos, and PReos.
pV V nT 1 nT RT (nT 1 ) 1 nT 2
2
RT ln i RT ln RT ln
(66)
nT RT V V nT 1 ni V ni
pV V nT 1 nT RT (nT 1 )
RT ln i RT ln RT ln
n
T RT V V nT 1 ni
n 1
2
n q
2
2V nT ( 3 4 ) q
T 2 T22 ln
n
i q q ni 2V nT ( 3 4 ) q

(67)
n 2 1 n n q
T 2 T 3 T 4
nT 2 2 1 n n q
T 3 T 4
4. Spinodal
The stability limit of a fluid mixture can be calculated with two-constant cubic
equations of state, e.g. see [6]. This limit is defined by the spinodal line, i.e. the locus of
points on the surface of the Helmholtz energy or Gibbs energy functions that are
inflection points, e.g. see [12] and references therein. The stability limit occurs at
conditions where phase separation into a liquid and vapour phase should take place,
which is defined by the binodal. Metastability is directly related to spinodal conditions,
for example, nucleation of a vapour bubble in a cooling liquid phase within small
constant volume cavities, such as fluid inclusions in minerals (< 100 m diameter)
occurs at conditions well below homogenization conditions of these phases in a heating
experiment. The maximum temperature difference of nucleation and homogenization is
defined by the spinodal. In multi-component fluid systems, the partial derivatives of
the Helmholtz energy with respect to volume and amount of substance of each
component can be arranged in a matrix that has a determinant (Dspin) equal to zero (Eq.
68) at spinodal conditions.
AV V An An
1V 2 V
AV n An An
1 n1 n1
Dspin 1 2
0 (68)
AV n An An
2 1 n2 2 n2
This matrix is square and contains a specific number of columns that is defined by the
number of differentiation variables, i.e. volume and number of components in the fluid
mixture minus 1. The individual components of this matrix are defined according to Eqs. 69,
70, 71, 72, 73, and 74. The exact definition of these components according to two-constant
cubic equations of state can be obtained from the web site http://fluids.unileoben.ac.at (see
also [6]).
2A

V 2
AV V (69)
n1 , n2 ,
2A
An (70)
1 n1 n 2
1 n2 , V ,
2A
An (71)
2 n2 n 2
2 n1 , V ,
2A
An AV n (72)
1V n V 1
1 n2 ,
2A
An AV n (73)
2V n V 2
2 n1 ,
2A
An
n n
An (74)
1 n2 2 n1
1 2 V ,
The determinant in Eq. 68 is calculated with the Laplacian expansion that contains "minors"
and "cofactors", e.g. see [13]. The mathematical computation time increases exponential with
increasing number of components. Therefore, the LU decomposition [14] can be applied in
computer programming to reduce this time.
The spinodal curve, binodal curve and critical point of a binary CO2-CH4 mixture with
x(CO2) = 0.9 are illustrated in Figure 1, which are calculated with the PReos [10]. The
spinodal has a small loop near the critical point, and may reach negative pressures at lower
temperatures. The binodal remains within the positive pressure part at all temperatures. The
binodal is obtained from equality of fugacity (Eq. 66 and 67) of each component in both
liquid and vapour phase, and marks the boundary between a homogeneous fluid mixture
and fluid immiscibility [6, 15].
Figure 1. (a) Temperature-pressure diagram of a binary CO2-CH4 fluid mixture, with x(CO2) = 0.9. The
shaded area illustrates T-p condition of immiscibility of a CO2-rich liquid phase and a CH4-rich vapour
phase (the binodal). The red dashed line is the spinodal. All lines are calculated with the equation of
state according to PReos [10]. The calculated critical point is indicated with cPR. cDK is the interpolated
critical point from experimental data [16]. (b) enlargement of (a) indicated with the square in thin lines.
5. Pseudo critical point

The pseudo critical point is defined according to the first and second partial derivatives of
pressure with respect to volume (Eqs. 31 and 32). This point is defined in a p-V diagram
where the inflection point and extremum coincide at a specific temperature, i.e. Eqs. 31 and
32 are equal to 0. The pseudo critical point is equal to the critical point for pure gas fluids,
however, the critical point in mixtures cannot be obtained from Eqs. 31 and 32. The pseudo
critical point estimation is used to define the two-constants (a and b) for pure gas fluids in
cubic equations of state according to the following procedure. The molar volume of the
pseudo critical point that is derived from Eqs 31 and 32 is presented in the form of a cubic
equation (Eq. 75).
0 Vm3 3 1 Vm2 3 42 3 1 3 4 Vm 1 42 3 4 42 3 4 (75)

2

The solution of this cubic equation can be obtained from its reduced form, see page 9 in [15]:
x3 f x g 0 (76)
where
f 3 4 2 1 1 3 4 (77)

g 2 13 1 2 4 2 3 4 3 4 4 2 3 12
2
(78)

Vm x 1 (79)
The values of f and g in terms of the b parameters for the individual two-constant cubic
equations of state are given in Table 2. The molar volume at pseudo critical conditions is
directly related to the b parameter in each equation of state: Weos Eq. 80; RKeos Eq. 81; Seos
also Eq. 81; and PReos Eq. 82.
Weos : Vm pc 3b (80)
b
RKeos : Vm pc 3.847322 b (81)
3
2 1
PReos : Vm pc 1 Q b 3.951373 b (82)
where Q is defined according to Eq. 83, the superscript "pc" is the abbreviation for "pseudo
critical".
4 8
1 1
Q 4 8
3 3
(83)
Equation of state f g b in Eqs. 80-82 b in Eqs. 94-96 difference

van der Waals [7] -3b2 -2b3 31.3727 42.8453 37 %
Redlich and Kwong [8] -6b2 -6b3 24.4633 29.6971 21 %
Soave [9] -6b2 -6b3 24.4633 29.6971 21 %
Peng and Robinson [10] -6b2 -8b3 23.8191 26.6656 12 %
Table 2. Definitions of f and g according to Eq. 77 and 78, respectively. The values of b are calculated for
the critical conditions of pure CO2: Vm,C = 94.118 cm3mol-1, TC = 304.128 K and pC = 7.3773 MPa [18]. The
last column gives the percentage of difference between the values of b (Eqs. 80-82 and 94-96).
The temperature at pseudo critical conditions is obtained from the combination of Eqs. 80-82
and the first partial derivative of pressure with respect to volume (Eq. 31).
8 2 2
Weos : T pc 0.29629630 (84)
27 bR bR

2 3
RKeos : T pc 3
2 1 2 0.20267686 2 (85)
bR bR
2Q 4 3
PReos : T pc 2 0.17014442 2
2
(86)
Q 4 2 bR bR
Q

where Q is defined according to Eq. 83. The order of equations (84, 85, 86) is according to the
order of equations of state in Eq. 80, 81,and 82. The parameter 2 is used in Eqs. 84, 85 and,
86 instead of the constant a (see Table 1). Eq. 87 illustrates the transformation of Eq. 85 for
the RKeos [8] by substitution of 2 according to its value given in Table 1.
2
3a
4 3
2 1
3
T pc 3
(87)
bR
Any temperature dependency of the a constant has an effect on the definition of the pseudo
critical temperature. The pressure at pseudo critical condition (Eqs. 88-90) is obtained from a
combination of the pressure equation (Eq.14), pseudo critical temperature (Eqs. 84-87) and
pseudo critical molar volume (Eqs. 80-82).
1 2 2
Weos : p pc 0.03703704 (88)
27 b2 b2
2 2

3
RKeos : p pc 3
2 1 0.01755999 (89)
b2 b2
Q2 2 2 2
PReos : p pc 0.01227198 (90)
Q
2 2
2
4Q 2 b b2
where Q is defined according to Eq. 83. The order of equations (88, 89, and 90) is according
to the order of equations of state in Eqs. 80, 81, and 82. These equations define the relation
between the a and b constant in two-constant cubic equations of state and critical conditions,
i.e. temperature, pressure, and molar volume of pure gas fluids. Therefore, knowledge of
these conditions from experimental data can be used to determine the values of a (or 2) and
b, which can be defined as a function of only temperature and pressure (Eqs. 91-93, and 94-
96, respectively).
2 2
27 R TC R2TC 2
Weos : 2 0.421875 (91)
64 pC pC
1 R2TC 2 R2TC 2
RKeos : 2 0.42748024

(92)
9 3
2 1 pC pC
Q Q R T
2
2
4Q 2 2
2 2 2
R2TC 2
PReos : 2 C
0.45723553 (93)
4Q 2 Q 2
2 pC pC
1 RTC RTC
Weos : b 0.125 (94)
8 pC pC
RKeos : b
3
2 1 RT C
0.08664035
RTC
(95)
3 pC pC
PReos : b
Q 2
2
RTC
0.07779607
RTC
(96)
2Q Q 2
2 pC pC
where TC and pC are the critical temperature and critical pressure, and Q is defined
according to Eq. 83. The order of equations (91-93, and 94-96) is according to the order of
equations of state in Eqs. 80-82. Comparison of the value of b calculated with experimental
critical volume (Eqs. 80, 81 and 82) and critical temperature and pressure (Eqs. 94, 95, and
96) is illustrated in Table 2. The difference indicates the ability of a specific equation of state
to reproduce fluid properties of pure gases. A large difference indicates that the geometry or
morphology of the selected equation of state in the p-V-T-x parameter space is not exactly
reproducing fluid properties of pure gases. The empirical modifications of the van-der-
Waals equation of state according to Peng and Robinson [10] result in the most accurate
equation in Table 2 (11% for pure CO2).
6. Critical point and curve

The critical point is the highest temperature and pressure in a pure gas system where
boiling may occur, i.e. where a distinction can be made between a liquid and vapour phase
at constant temperature and pressure. At temperatures and pressures higher than the critical
point the pure fluid is in a homogeneous supercritical state. The critical point of pure gases
and multi-component fluid mixtures can be calculated exactly with the Helmholtz energy
equation (Eqs. 55-57) that is obtained from two-constant cubic equations of state, e.g. see [17,
18], and it marks that part of the surface described with a Helmholtz energy function where
two inflection points of the spinodal coincide. Therefore, the conditions of the spinodal are
also applied to the critical point. In addition, the critical curve is defined by the determinant
(Dcrit) of the matrix illustrated in Eq. 97, see also [6].
AV V An An
1V 2 V
AV n An An
1 n1 n1
Dcrit 1 2
0 (97)

DV Dn Dn
1 2
The number of rows in Eq.97 is defined by the differentiation variables volume and number
of components minus 2. The last row is reserved for the partial derivatives of the
determinant Dspin from Eq. 68:
Dspin
DV (98)
V
Dspin
Dn (99)
1
n1
Dspin
Dn (100)
2
n2
The derivatives of the spinodal determinant (Eqs. 98-100) are calculated from the sum of the
element-by-element products of the matrix of "cofactors" (or adjoint matrix) of the spinodal
(Eq. 101) and the matrix of the third derivatives of the Helmholtz energy function (Eq. 102).
CV V Cn Cn
1V 2 V
CVn Cn Cn
1 n1 n1
1 2
(101)
CV n Cn Cn
2 1 n2 2 n2
AV V K An An
1V K 2 VK
AV n An An
1K 1 n1 K n1 K
2
(102)
AV n K An An
2 1 n2 K 2 n2 K
Figure 2. Calculated critical points of binary CO2-CH4 fluid mixtures in terms of temperature (red line)
and pressure (green line), obtained from the PReos [10]. Solid circles are experimental data [16, 19]. The
open squares are the critical point of pure CO2 [20].
where Cxy are the individual elements in the matrix of "cofactors", as obtained from the
Laplacian expansion. The subscript K refers to the variable that is used in the third
differentiation (volume, amount of substance of the components 1 and 2. To reduce
computation time in software that uses this calculation method, the LU decomposition has
been used to calculate the determinant in Eq. 97. The determinants in Eqs. 68 and 97 are both
used to calculate exactly the critical point of any fluid mixture and pure gases, based on
two-constant cubic equations of state that define the Helmholtz energy function.
An example of a calculated critical curve, i.e. critical points for a variety of compositions in a
binary fluid system, is illustrated in Figure 2. The prediction of critical temperatures of fluid
mixtures corresponds to experimental data [16, 19], whereas calculated critical pressures are
slightly overestimated at higher fraction of CH4. This example illustrates that the PReos [10]
is a favourable modification that can be used to calculate sub-critical conditions of CO2-CH4
fluid mixtures.
7. Mixing rules and definitions of 1 and 2

All modifications of the van-der-Waals two-constant cubic equation of state [7] have an
empirical character. The main modifications are defined by Redlich and Kwong, Soave and
Peng and Robinson (see Table 1), and all modification can by summarized by specific
adaptations of the values of 1, 2, 3, and 4 to fit experimental data. The original definition
[7] of 1 (b) and 2 (a) for pure gases is obtained from the pseudo critical conditions (Eqs. 91-
93, and 94-96). This principle is adapted in most modifications of the van-der-Waals
equation of state, e.g. RKeos [8]. Soave [9] and Peng and Robinson [10] adjusted the
definition of 2 with a temperature dependent correction parameter (Eqs. 103-105).
2 aC (103)
2
T
1 m1 (104)
TC

m mi i (105)
i 0, 1, 2
where ac is defined by the pseudo critical conditions (Eqs. 91-93), and is the acentric factor.
The summation in Eq. 105 does not exceed i = 2 for Soave [9] and Peng and Robinson [10].
The definition of the acentric factor is arbitrary and chosen for convenience [5] and is a
purely empirical modification. These two equations of state have different definitions of
pseudo critical conditions (see Eqs. 91-93 and 94-96), therefore, the values of mi must be
different for each equation (Table 3).
Soave [9] Peng and Robinson [10]

m0 0.480 0.37464
m1 1.574 1.54266
m2 -0.176 -0.26992
Table 3. Values of the constant mi in Eq. 105.
The two-constant cubic equation of state can be applied to determine the properties of fluid
mixtures by using "mixing rules" for the parameters 1 and 2 which are defined for
individual pure gases according to pseudo critical conditions. These mixing rules are based
on simplified molecular behaviour of each component (i and j) in mixtures [21, 22] that
describe the interaction between two molecules:
1mix xi 1(i) (106)

i j
2 mix xi x j 2 (i , j) (107)
i j
where
2 (i , j ) 2 (i) 2 ( j) (108)
These mixing rules have been subject to a variety of modifications, in order to predict fluid
properties of newly available experimental data of mixtures. Soave [9] and Peng and
Robinson [10] modified Eq. 108 by adding an extra correction factor (Eq. 109).
2 (i , j) 1 ij 2 (i) 2 ( j) (109)
where ij has a constant value dependent on the nature of component i and j.
8. Experimental data
As mentioned before, modifications of two-constant cubic equation of state was mainly
performed to obtain a better fit with experimental data for a multitude of possible gas
mixtures and pure gases. Two types of experimental data of fluid properties were used: 1.
homogeneous fluid mixtures at supercritical conditions; and 2. immiscible two-fluid systems
at subcritical conditions (mainly in petroleum fluid research). The experimental data consist
mainly of pressure, temperature, density (or molar volume) and compositional data, but can
also include less parameters. Figure 3 gives an example of the misfit between the first type
of experimental data for binary CO2-CH4 mixtures [19] and calculated fluid properties with
RKeos [8] at a constant temperature (15 C). The RKeos uses the pseudo critical defined
parameters 1 and 2 (Eqs. 92 and 95) and mixing rules according to Eqs. 106-108 and is only
approximately reproducing the fluid properties of CO2-CH4 mixtures at subcritical
conditions
Experimental data of homogeneous supercritical gas mixtures in the ternary CO2-CH4-N2
system [23] are compared with the two-constant cubic equations of state in Table 4. The Weos
[7] clearly overestimates (up to 14.1 %) experimentally determined molar volumes at 100 MPa
and 200 C. The Seos [9] is the most accurate model in Table 4, but still reach deviations of up
to 2.3 % for CO2-rich gas mixtures. The PReos [10] gives highly underestimated molar
volumes at these conditions.
Figure 3. Modelled immiscibility of binary CO2-CH4 gas mixtures (shaded areas) in a pressure - amount
CH4 fraction diagram (a) and amount CH4 fraction - molar volume diagram (b) at 15 C. The solid and
open circles are experimental data [16]. The red squares are the properties of pure CO 2 [20]. The yellow
triangle (Cexp) is the interpolated critical point for experimental data, and the green triangle (CRK) is the
calculated critical point [8]. tie1 and tie 2 in (b) are calculated tie-lines between two phases at constant
pressures 6.891 and 6.036 MPa, respectively.
composition Vm(exp)
W RK S PR
CO2 CH4 N2 cm3mol-1
0.8 0.1 0.1 56.64 64.61 (14.1%) 54.90 (-3.1%) 57.94 (2.3%) 53.59 (-5.4%)
0.8 0.2 0.2 58.92 65.81 (11.7%) 56.61 (-3.9%) 59.61 (1.2%) 56.93 (-6.1%)
0.4 0.3 0.3 61.08 67.08 (9.6%) 58.27 (-4.6%) 61.12 (0.1%) 56.93 (-6.8%)
0.2 0.4 0.4 62.90 68.28 (8.6%) 59.83 (-4.9%) 62.42 (-0.8%) 58.28 (-7.3%)
Table 4. Comparison of supercritical experimental molar volumes [23] at 100 MPa and 200 C with two-
constant cubic equations of state (abbreviations see Table 1). The percentage of deviation from
experimentally obtained molar volumes is indicated in brackets.
Figure 3 and Table 4 illustrate that these modified two-constant cubic equations of state still
need to be modified again to obtain a better model to reproduce fluid properties at sub- and
supercritical conditions.
9. Modifications of modified equations of state

The number of publications that have modified the previously mentioned two-constant
cubic equations of state are numerous, see also [11], and they developed highly complex, but
purely empirical equations to define the parameters 1 and 2. A few examples are
illustrated in the following paragraphs.
9.1. Chueh and Prausnitz [24]

The constant values in the definition of 1 and 2 (Eqs. 92 and 95) are modified for individual
gases by Chueh and Prausnitz [24]. This equation is an arbitrary modification of the RKeos
[8]. Consequently, the calculation of the value of 1 and 2 is not any more defined by
pseudo critical conditions, which give exact mathematical definition of these constants.
Although the prediction of fluid properties of a variety of gas mixtures was improved by
these modifications, the morphology of the Helmholtz energy equation in the p-V-T-x
parameter space is not any more related to observed fluid properties. The theory of pseudo
critical conditions is violated according to these modifications.
The mixing rules in Eqs. 106-108 were further refined by arbitrary definitions of critical
temperature, pressure, volume and compressibility for fluid mixtures.
i j R 2TCij
2
2 (i , j) (110)
2 pCij
i j R2TCij
2.5
aij (111)
2 pCij
where i and j are the newly defined constant values of component i and j, and TCij and pCij
are defined according to complex mixing rules [see 24]. The values of TCij and pCij are not
related to true critical temperatures and pressures of specific binary gas mixtures.
The prediction of the properties of homogeneous fluids at supercritical conditions (Table 5) is

only slightly improved compared to RKeos [10], but it is not exceeding the accuracy of the Seos
[11]. At sub-critical condition (Figure 4), the Chueh-Prausnitz equation is less accurate than the
Redlich-Kwong equation (compare Figure 3) in the binary CO2-CH4 fluid mixture at 15 C.
composition Vm(exp)
CP H B1 B2
CO2 CH4 N2 cm3mol-1
0.8 0.1 0.1 56.64 56.42 (-0.4%) 55.96 (-0.6%) 56.84 (0.4%) 56.53 (-0.2%)
0.8 0.2 0.2 58.92 57.85 (-1.8%) 57.68 (-2.1%) 59.43 (0.9%) 58.81 (-0.2%)
0.4 0.3 0.3 61.08 59.21 (-3.1%) 59.17 (-3.1%) 61.67 (1.0%) 60.79 (-0.5%)
0.2 0.4 0.4 62.90 60.44 (-3.9%) 60.38 (-4.0%) 63.45 (0.9%) 62.40 (-0.8%)
Table 5. The same experimental molar volumes as in Table 4 compared with two-constant equations
of state according to Chueh and Prausnitz [24] (CP), Holloway [25, 26] (H), Bakker [27] [B1], and
Bakker [28] (B2). The percentage of deviation from experimentally obtained molar volumes is
indicated in brackets.
9.2. Holloway [25, 26] and Bakker [27]

The equation of Holloway [25, 26] is another modification of the RKeos [8]. The modification
is mainly based on the improvement of predictions of homogenous fluid properties of H2O
and CO2 mixtures, using calculated experimental data [29]. The value for 1 and 3 (both b)
of H2O is arbitrarily selected at 14.6 cm3mol-1, whereas other pure gases are defined
according to pseudo critical conditions. The definition of 2 (i.e. a) for H2O as a function of
temperature was subjected to a variety of best-fit procedures [25, 26]. The fitting was
improved from four experimental data points [25] to six [26] (Figure 5), but was restricted to
temperatures above 350 C. Bakker [27] improved the best-fit equation by including the
entire data set [29], down to 50 C (Eq. 112).
Figure 4. See Figure 3 for details. The RKeos is indicated by dashed lines in (a) and (b). The shaded
areas are immiscibility conditions calculated with the Chueh-Prausnitz equation. tie1 and tie 2 in (b) are
calculated tie-lines between two phases at constant pressures 6.944 and 5.984 MPa, respectively.
Figure 5. Temperature dependence of the a constant for pure H2O in the modified cubic equation of
state [25, 26]. The open circles are calculated experimental data [29]. fit [25] is the range of fitting in the
definition of Holloway [25], and fit [26] of Holloway [26]. RK illustrates the constant value calculated
from pseudo critical condition [8].
2.0246 10 3 1.4928 106 7.57 108

aH O 9.4654 106 (112)
2 T 2 3
T T
where T is temperature in Kelvin, and the dimension of a is cm6MPaK0.5mol-2. The

properties of homogeneous pure CO2, CH4 and N2 fluids [27] were also used to obtain a
temperature dependent a constant (Eqs. 113, 114, and 115, respectively).
5.9363 10 3 1.4124 10 6 1.1767 10 8

aCO 1.2887 106 (113)
2 T 2 3
T T
3.5216 10 3 1.155 106 1.1767 10 8

aCH 1.1764 10 6 (114)
4 T 2 3
T T
0.20059 10 3 0.15386 106

aN 0.060191 10 6 (115)
2 T 2
T
The aij value of fluid mixtures with a H2O and CO2 component (as in Eqs. 106-108 and 110-
111) is not defined by the value of pure H2O and CO2 (Eqs. 112 and 113), but from a
temperature independent constant value (Eqs. 116 and 117, respectively). In addition, a
correction factor is used only for binary H2O-CO2 mixtures, see [25, 29].
a0 H 2O 3.5464 106 MPa cm6 K 0.5 mol 2 (116)
a0 CO2 4.661 106 MPa cm6 K 0.5 mol 2 (117)
Table 5 illustrates that the equation of Holloway [25] is not improving the accuracy of
predicted properties of supercritical CO2-CH4-N2 fluids, compared to Chueh-Prausnitz [24]
or Seos [9], and it is only a small improvement compared to the RKeos [8]. The accuracy of
this equation is highly improved by using the definitions of a constants according to Bakker
[27] (see Eqs. 112-115), and result in a maximum deviation of only 1% from experimental
data in Table 5.
Experimental data, including molar volumes of binary H2O-CO2 fluid mixtures at

supercritical conditions [30, 31, 32] are used to estimate fugacities of H2O and CO2 according
to Eq. 118 (compare Eq. 10).
Vm , i Vm
ideal
RT ln i dp (118)

0
where Vm,i - Vmideal is the difference between the partial molar volume of component i and the
molar volume of an ideal gas (see also Eq. 43). The difference between Eqs. 118 and 10 is the
mathematical formulation and the use of different independent variables, which are
temperature and pressure in Eq. 118. The integration to calculate the fugacity coefficient can
be graphically obtained by measuring the surface of a diagram of the difference between the
ideal molar volume and the partial molar volume (i.e. Vm,i - Vmideal) as a function of pressure
(Figure 6). The surface obtained from experimental data can be directly compared to
calculated curves from equations of state, according to Eq. 10 (Table 6).
The dashed line in Figure 6 is calculated with another type of equation of state: a
modification of the Lee-Kesler equation of state [33] that is not treated in this manuscript
because it is not a two-constant cubic equation of state. Fugacity estimations of H2O are
similar according to both equations, and reveal only a minor improvement for the two-
constant cubic equation of state [27]. The experimental data to determine fugacity of CO2 in
this fluid mixture is inconsistent at relative low pressures (< 100 MPa). The calculated
fugacity [27] is approximately compatible with the experimental data from [31, 32].
Figure 6. Fugacity estimation in a pressure - dv diagram at 873 K and a composition of x(CO2) = 0.3 in
the binary H2O-CO2 system, where dv is the molar volume difference of an ideal gas and the partial
molar volume of either H2O or CO2 in binary mixtures. Experimental data are illustrated with circles,
triangles and squares (solid for CO2 and open for H2O. The red lines are calculated with Bakker [27],
and the shaded area is a measure for the fugacity coefficient of H2O (Eq. 118).
Pressure (MPa) Exp. fugacity (MPa) B1 fugacity (MPa)

10 6.692 6.659 (-0.5%)
50 27.962 27.3061 (-2.3%)
100 45.341 44.6971 (-1.4%)
200 77.278 75.0515 (-2.9%)
300 114.221 111.072 (-2.8%)
400 160.105 157.145 (-1.8%)
500 219.252 216.817 (-1.1%)
600 295.350 294.216 (-04%)
Table 6. Fugacities of H2O in H2O-CO2 fluid mixtures, x(CO2) = 0.3, at 873.15 K and variable pressures.
B1 fugacity is calculated with Bakker [27]. The deviation (in %) is illustrated in brackets.
9.3. Bowers and Helgeson [34] and Bakker [28]

Most natural occurring fluid phases in rock contain variable amounts of NaCl, which have
an important influence on the fluid properties. Bowers and Helgeson [34] modified the
RKeos [8] to be able to reproduce the properties of homogeneous supercritical fluids in the
H2O-CO2-NaCl system, but only up to 35 mass% NaCl. The model is originally restricted
between 350 and 600 C and pressures above 50 MPa, according to the experimental data
[35] that was used to design this equation. This model was modified by Bakker [28]
including CH4, N2, and additionally any gas with a (2) and b (1) constants defined by the
pseudo critical conditions (Eqs. 91-93 and 94-96). Experimental data in this multi-component
fluid system with NaCl can be accurately reproduced up to 1000 MPa and 1300 K. Table 5
illustrates that this modification results in the best estimated molar volumes in the ternary
CO2-CH4-N2 fluid system at 100 MPa and 673 K. Similar to all modifications of the RKeos [8],
this model cannot be used in and near the immiscibility conditions and critical points (i.e.
sub-critical conditions).
10. Application to fluid inclusion research

Knowledge of the properties of fluid phases is of major importance in geological sciences.
The interaction between rock and a fluid phase plays a role in many geological processes,
such as development of magma [36], metamorphic reactions [37] and ore formation
processes [38]. The fluid that is involved in these processes can be entrapped within single
crystal of many minerals (e.g. quartz), which may be preserved over millions of years. The
information obtained from fluid inclusions includes 1. fluid composition; 2. fluid density; 3.
temperature and pressure condition of entrapment; and 4. a temporal evolution of the rock
can be reconstructed from presence of various generation of fluid inclusions. An equation of
state of fluid phases is the major tool to obtain this information. Microthermometry [39] is an
analytical technique that directly uses equations of state to obtain fluid composition and
density of fluid inclusions. For example, cooling and heating experiment may reveal fluid
phase changes at specific temperatures, such as dissolution and homogenization, which can
be transformed in composition and density by using the proper equations of state.
The calculation method of fluid properties is extensive and is susceptible to errors, which is
obvious from the mathematics presented in the previous paragraphs. The computer package
FLUIDS [6, 40, 41] was developed to facilitate calculations of fluid properties in fluid
inclusions, and fluids in general. This package includes the group "Loners" that handles a
large variety of equations of state according to individual publications. This group allows
researchers to perform mathematical experiments with equations of state and to test the
accuracy by comparison with experimental data.
The equations of state handled in this study can be downloaded from the web site
http://fluids.unileoben.ac.at and include 1. "LonerW" [7]; 2. "LonerRK" [8]; 3. "LonerS" [9]; 4.
"LonerPR" [10]; 5. "LonerCP" [24]; 6. "LonerH" [25, 26, 27]; and 7. "LonerB" [28, 34]. Each
program has to possibility to calculate a variety of fluid properties, including pressure,
temperature, molar volume, fugacity, activity, liquid-vapour equilibria, homogenization
conditions, spinodal, critical point, entropy, internal energy, enthalpy, Helmholtz energy,
Gibbs energy, chemical potentials of pure gases and fluid mixtures. In addition, isochores
can be calculated and exported in a text file. The diagrams and tables presented in this study
are all calculated with these programs.
Author details
Ronald J. Bakker
Department of Applied Geosciences and Geophysics, Resource Mineralogy, Montanuniversitaet,
Leoben, Austria
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Chapter 8
Thermodynamics Simulations Applied to

Gas-Solid Materials Fabrication Processes
1. Introduction
The development and the design of materials and/or the processes of their fabrication are
generally very time consumer and with expensive operations. Various methods of
development can be conceived. Often, "empirical" approaches are adopted: the choice of the
experimental parameters is established either on technological or commercial criteria, the
optimization being the results of a trial and error approach, or on the results of design of
experiments (DOE) approach targeted at a property of a material or a parameter of a very
particular process. Another approach is to use process modeling: to simulate the process by
a more or less simplified model. The modeling of gas-solid materials fabrication processes
brings together several physical and chemical fields with variable complexity, starting from
thermodynamics and\or kinetics studies up to the mass and heat transport coupled with
databases and with thermodynamic and/or kinetics transport properties.
The objective of this chapter is to illustrate the interest areas computer-aided materials
design and of processes optimization based on the thermodynamic simulation and giving
some interesting examples in different domains. Databases as well as their necessary tools
for the implementation of the thermodynamic calculations will be described.
The thermodynamic simulations of multicomponent systems contribute at two important
points: the selection of the material and the optimization of the conditions of fabrication. In
order to obtain a finely targeted product which meet specific functionalities, it is necessary
to answer the following questions:
- what type of composition, quantity, and microstructure of the material allow to obtain
such properties?
- it is possible to elaborate the material? By what process, with which reagent/ species
and which operating conditions?
- is stable this material during a treatment in temperature, and under a given atmosphere?
- does this material react with its environment (substrate, oven, atmosphere)?
These questions are connected because the properties of the material, essentially conditioned
by the microstructure of the final material, are going to depend on its chemical composition, to
the process, to the operating conditions and on dimensions of the fabrication equipment.
The answers to these questions can be provided and shown from calculation of phase
diagrams, evaluation of chemical reactions, calculation of equilibrium pressures, and from
reaction diagrams.
2. Description of the methodologies

To evaluate equilibrium state, two possible approaches exist. The first one is to choose a
priori a limited number of species and the simple chemical reactions which are susceptible to
represent the studied process, and to estimate one or several most favorable reactions. It can
be reminded the very classic use of the diagrams of Ellingham for the synthesis of metals
from their oxides.
The second approach, more complex, is based on the analysis and the consideration of all
the species belonging to the chemical system in the studied process.
The optimization procedure must have the following stages:
a. The analysis of the system with the inventory of all the species reasonably susceptible to
be present during the reactions taking place in the process.
b. The construction of a consistent set of thermodynamic data for these species.
c. The thermodynamic calculations at equilibrium of complex system
d. The best representation of the results for the users
Thus, the thermodynamic calculations often give satisfactory results for processes which use
high temperatures and residence time or reaction but for processes at low temperature, the
kinetic factors must be not neglected. That is why the recent developments of
thermodynamic softwares tend to include descriptions of phenomena of diffusion and
reaction kinetics.
The thermodynamic approach gives the superior limit of possibilities of process

(considering the reaction rates as infinite). It can be the only way of modeling for a complex
system where the mechanisms of reaction and the kinetic data are badly known.
To include some dynamic aspects (mass transport) in the modeling, an approach which
takes into account the evaluation of flows will be presented. It concerns applications where
the total pressure is low (<10 Pa).
2.1. The analysis of the system

The analysis of the system consists in listing the following points: the range of temperature T,
range of pressure P or of volume V, the duration of the process, the list of the reagent species,
Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 193
the inventory of the components of the reactor and the nature of the atmosphere. For these last
points, it means elaborating a list of all the compounds, the gaseous species, the elements and
the solid solutions which result from the combination of the basic elements of the system.
This list is automatically generated thanks to interfaces with databases. However, it is

advisable to make sure that the used database is very complete. As an example, the list
corresponding to the chemical system Si-C-H-Ar (proceeded CVD (Chemical Vapor
Deposition) contains about sixty species excluding the hydrocarbons CxHy where x>3 [1].
2.2. Calculation of a thermochemical equilibrium

In a process reactor, at constant pressure, the balance is reached when the total free Gibbs
energy function of the system is minimal (equation 1). To determine the nature and the
proportion of the present phases at equilibrium, it is necessary to have the description of the
energies of Gibbs of all these phases.
G Ne Gj
qj (1)
RT j 1 RT
where qj the number of moles of the species j, Gj the molar free energy of Gibbs of the
species j, Ne total number of species.
The Gibbs energy can be described from the enthalpy (H) and the entropy (S):
G(T ) H(T ) T S(T )

(2)
with
T
H (T ) H (298 K ) c P (T )dT (3)
298 K

c P (T )
S(T ) S(298 K ) T
dT (4)
298 K
The necessary data are thus: Cp(T), H(298K), S(298K) and the data of possible phases
transitions Ttrans, Htrans(T).
Various formalisms are adopted for the analytical expression of the function Cp (T). Among
them, the formalisms of the SGTE (Scientific Group Thermodata Europe ) [2] (equation 5)
and of the NASA [3](equation 6) are :
d
cP (T ) a bT cT 2 (5)
T2
cP (T ) a bT cT 2 dT 3 eT 4
(6)
where a, b, c, d, e are adjustable parameters.
So, it can be described analytically the Gibbs energy G for a stoichiometric compound
(equation 7), for a gas (equation 8) and a solution phase (equation 9):
F
G(T ) A BT CT ln T DT 2 ET 3 (7)
T
P
G(T , P) G(T ) RT ln (8)
P0
G(T , x) Giref (T ) G id (T , xi ) G excs (T , xi )

i

G (T , xi ) RT ( xi ln xi )
id

i (9)
excs
G (T , xi ) described from a mod el

Besides, as neither the enthalpy nor the entropy can be described in an absolute way, a
reference state must be used for these two functions of state. For the entropy, the adopted
convention consists in taking a zero value at 0 K. In the case of the enthalpy, the most
common convention is to choose the stable structure of the element at T = 298K, as standard
reference state (e.g. Al cfc, Ti hcp, O2 gas ). For the reference state, H(298K)=0 and
S(0K)=0.
As the reliability of the results of the thermodynamics simulation depends widely on the
quality and on the consistence of the necessary data, it is advisable to attach an importance
to the consistence of the available information: thermodynamics measurements, theoretical
calculations, characterizations (X-ray diffraction, Environmental Scanning Microscopy),
balance of phases (diagrams). In the Table 1 are given some experimental and theoretical
techniques usually used to obtain the thermodynamic data.
The thermodynamic information are accessible in compilations of binary phases diagrams

(for example Hansen [5], Elliot [6], Massalski [7]), ternary (Ternary Alloys [8]), or specialized
journals (CALPHAD, Journal of Phase Equilibria, Intermetallics), or tables (JANAF
Thermochemical Tables [9], Barin [10], Gurvich [11]).
Today, most of data are available in international electronic databases. In Europe, the
economic interest group "Scientific Group Thermodata Europe [12]" proposes common data
bases for compounds, pure substances and for solutions. Also let us quote the Coach data
bank ( more than 5000 listed species) proposed by Thermodata [1], well adapted to simulate
gas/solid processes, the FACT bank (oxides/salts) proposed by the company GTT [13] and
the Research Center in Calculation Thermodynamics [14], base TCRAS [15], bases NASA
combustion [16], NIST [17].
Experimental Theory
Ab initio calculations
H(T) Calorimetry (dissolution) Estimations : Miedema [4],
analogy
Temperature measurement at low
Cp(298K), S(298K)
temperature
Estimations : Neumann-Kopp
Cp(T) law(Cp=0 for a condensed
compound)
volume-specific heat capacity
Cp, S(T) Differential Scanning Calorimetry (DSC)
calculations
Electromotive force, Mass Spectrometry
G(T) (activity data, partial pressures at
equilibrium)
Differential Thermal Analysis (DTA)
Ttrans, Htrans (T)
Thermogravimetric analysis (TGA)
Table 1. The classically used techniques to obtain the thermodynamic data
2.3. Calculations of complex equilibrium

The software of complex equilibrium is based on the minimization at constant temperature
T of the Gibbs energy and constant pressure P (equation 1) or Helmholtz energy (equation
10), at constant volume:
F Ne Gj P.V
qj (10)
RT j 1 RT RT
qj the number of moles of the species j .
The constraints of mass equilibrium of each present element in the chemical system
expressed according to the number of atoms on the pure element i (C elements) are
translated by the equation (11 ):
Ne
ni qeTie with i 1 C (11)
e 1
where Tie represents the stoichiometry of the species e for the element i.
These C equations can be translated under the matrix shape (equation 12):
n T * q with Ne C (12)
There are multiple algorithms allowing this minimization. Various classifications were given,
the most exhaustive having been supplied by Smith and Missen [18]. In a simple way, two
groups of algorithms can be distinguished: on one hand the methods of direct minimization,
about zero order for the calculation of the function G, on the other hand, the methods of the
first order based on the equality of the chemical potential which require the calculation of the
function derivatives. These last ones also include the methods of second order, using among
others the algorithm of Newton-Ralphson which is based on the second derivatives. It is
necessary to note that the methods of the first order must be perfectly controlled because they
can lead to a maximum instead of a minimum and consequently to a wrong result.
A method of the first group is described below: the matrix T is decomposed into a regular
square matrix Tp of dimension C and a matrix Td of dimension (C, Ne-C) such as:
n Tp qp Td qd (13)
The C species which constitute the matrix column qp are called the main species because
they are chosen among the most important species and have by definition a linear
independent stoichiometry. The Ne-C remaining species of the matrix Td is called derived
species although they are chosen as variables from the minimization. So the Ne-C values qd
are given by the procedure of minimization, C values qp is calculated by resolving the linear
system:
1 1
qp Tp n Tp Td qd (14)
An iteration of this method is divided into two steps. Firstly, the phase of exploration, every
variable is modified by a value + or - h.
If Xn-1 is the vector representing the variables after n-1 iterations: the species i having a step
hi and Gi the value of the function
Gi G( x1, x 2 ,..., xi 1, xi hi , xi 1`,..., xv) (15)
if Gi+<Gi either,
Gi G( x1, x 2 ,..., xi 1, xi 2hi , xi 1`,..., xv) (16)
or,
Gi G( x1, x 2 ,..., xi 1, xi hi , xi 1`,..., xv) (17)
When the exploration phase is ended, the next step is to move to the second algorithm phase
where from the values of G + and Xn + issued from the exploration phase, we calculate X++ =
Xn-1 + (Xn+-Xn-1) as well as the corresponding value G++ to obtain the optimal set [19]. To
proceed the mimimization procedure, a certain number of more and more friendly
softwares are available commercially. It can be listed as example:
Gemini1/Gemini2 [1]
FactSage [14]
MTDATA [20]
Thermocalc [21]
3. Applications
Thomas [22], Bernard [23] and Pons [24] present few examples on CVD processes to
illustrate the use of an a priori thermodynamic analysis. In the following paragraphs, it was
chosen to show other few examples which evidence the help of thermodynamic modeling in
industrial bottlenecks:
Thermal stability of Metal-Organic Precursors used in CVD and ALD processes.

Stability of SiC in H2 atmosphere
HfO2 plasma etching
SiO2 PVD evaporation-condensation deposition process.
In the last two examples which correspond to processes operating at low pressure (<1 Pa), in
addition to pure thermodynamic approach, a dynamic approach was presented which
includes calculations of the major species flows.
3.1. Microelectronics: Thermal stability of metal-organic precursors used in CVD

and ALD processes
In the pursuit of smaller and faster devices manufacture, microelectronics industry scales
down feature sizes and thus has to develop new materials and processes. Nowadays,
organometallic precursors are widely used in ALD (Atomic Layer Deposition) and CVD
(Chemical Vapor Deposition) deposition processes due to low deposition temperature
(generally below 523 K). The objective of computational modeling for gaseous phase
processes like ALD or CVD is to correlate the as-grown material quality (uniformity, growth
rate, cristallinity, composition, etc) to general parameters such as growth conditions, reactor
geometry, as well as local parameters that are actual flow, thermal fields and chemical
kinetics at the solid/gas interface.
The gaseous precursors compounds used for the transport of the elements to be deposited
by these processes have to meet several physicochemical properties requirements including
relatively high volatility, convenient decomposition behavior and thermal stability. The
tantalum organometallic precursor pentakis dimethylamino tantalum (PDMAT), remains an
attractive solution for tantalum nitride films deposition. Unfortunately, information on
physical and chemical behavior of this kind of precursor is scarce and namely species that
are formed during vaporization and transported to the deposition chamber remain
generally unknown. Thus, the knowledge of thermodynamics of these gaseous compounds
could help in the understanding of the transport and growth mechanisms. Indeed, thanks to
thermodynamics, it is possible to evaluate what evolves at equilibrium in the precursor
source, in the input lines and in the deposition chamber where deposition reactions occur.
To control, optimize and understand any ALD or CVD processes, thermodynamic
simulations are very useful and therefore data should be primarily assessed.
3.1.1. Assessment of PDMAT thermodynamic data by mass spectrometry

In order to deposit thin layers of TaN using PDMAT, ALD experiments evidenced a
cracking of this precursor in the ALD reactor [25].
Cracking reactions of PDMAT can be complex and occur at the same time. A quantitative
interpretation of cracking reactions can be deduced from observed molecules by mass
spectrometry [26, 27] with the condition that all products and reactants of the reaction are
observed and measured by the mass spectrometer at the same time. Without additional
hydrogen contribution, the two following cracking reactions of Ta [N(CH3)2]5(g) could occur:
i. either the Ta- [N(CH3)2] bond breaks with the additional break of H-CH2 to produce
HN(CH3)2 (the so-called substitution):
Ta N CH3 2 g Ta N CH3 2 NCH3CH2 g HN CH3 2 g , (18)

5 3
ii. or the only bond break of Ta- [N(CH3)2],
Ta N CH3 2 g Ta N CH3 2 g N CH3 2 g . (19)

5 4
As no N(CH3)2 (g) radical was detected, the observed HN(CH3)2 (g) molecule could be
formed by the following complete and rapid reaction,

N CH 3 2 g H 2 g ou H g HN CH 3 2 g . (20)
Consequently, it could be assumed that the measured HN(CH3)2 (g) amount is the same as
the initial produced amount of N(CH3)2 (g): this radical spontaneously reacts totally
according to the reaction (20) after being produced by reaction (19). This mechanism could
explain why N(CH3)2 (g) was not detected. So, in this study, the total cracking reaction was
finally considered:

Ta N CH3 2 g
5

H2 g Ta N CH3 2 g
4
HN CH3 2 g (21)
Another cracking reaction could be noticed: OTaN4C8H24 (g) molecule broke down into
OTaN3C6H18 (g) according to the following reaction,
OTaN4 C8 H 24 g H2 g OTaN3C6 H18 g HN CH3 2 g (22)
because the energy of the Ta-N bond is lower than the Ta-O bond.
The experimental study of these two reactions (21) and (22) requires to know or measure
H2(g) pressure. Hydrogen could come from either equilibrium with cracking cell deposits or
either molecules losing one or more hydrogen atoms. In this last case, a new molecule
should be present. In this study, as no hydrogen was detected or introduced intentionally in
the cell, it was assumed that the amino radical is totally consumed and produces HN(CH3)2
(g) with just a sufficient hydrogen amount. So, it can be assumed that the partial pressure of
p(HN(CH3)2) is quite equal to the partial pressure of p(N(CH3)2). That allows us to calculate
the equilibrium constant of reaction (19):
p( N(CH3 )2 ) p(Ta[ N(CH 3 )2 ]4

K p (T ) (23)
p(Ta[ N(CH 3 )2 ]5
Pressure measurements of these three molecules by mass spectrometry lead to the

evaluation of standard enthalpy at 298 K from the third law of thermodynamics:
r H 298
0
K RT ln K p (T ) T r fefT
0
(24)
Measured partial pressures of Ta [N(CH3)2]5 (g), Ta [N(CH3)2]4 (g) and HN(CH3)2 (g) are
elsewhere reported [26, 27].
From this, the average value of rH298 K was evaluated to be equal to (855) kJ/mol.
3.1.2. Thermodynamic simulation of PDMAT (thermal cracking)

Thermodynamic simulations, based on the Gibbs free energy minimization of the Ta-C-N-
H-(O)-(Ar) system were performed using GEMINI software [1] to provide the nature of
the species that should be present at equilibrium under experimental conditions. The sets
of thermodynamic data which have been used come from SGTE 2007 database [28] and
from the mass spectrometry study for Ta [N(CH3)2]5(g), Ta [N(CH3)2]4(g),and NC2H6 (g)
gaseous species [26]. Without any available literature data or any estimates, it cannot be
considered any thermodynamic description of OTaNxCyHz (g) gaseous species and
intermediate TaNxCyHz (g) species such as TaN3C6H16 (g), even though these species are
expected to appear as observed in mass spectrometric measurements and to play a role in
PDMAT cracking and in Ta containing solid formation [26]. Two kinds of simulations
have been performed within a temperature range from 400 to 750 K and at 10 Pa, which is
our typical mass spectrometric total pressure in the cracking cell. First, homogeneous
equilibrium was investigated - no solid phase is allowed to be formed - which
corresponds to no deposition i.e. transport in gas lines held at temperature above the
saturated one (Figure 1).
Second, a heterogeneous equilibrium - the solid phase is allowed to be formed - has also
been simulated, which corresponds to the deposition process occurring in the ALD reactor
and in the cracking cell.
In all these thermodynamic simulations, it appeared that Ta [N(CH3)2]5(g), (PDMAT) is not

stable. In Figure 1 the homogeneous equilibrium calculation show that Ta [N(CH3)2]4(g) is
stable but disappears after 450 K and Ta(g) is the only one main tantalum containing species
after 415 K - but this species will soon be condensed due to large over saturation-. Added to
Ta(g), a lot of cracking gaseous species such as N2 (g), CH4 (g), H2 (g) originate from the
complete amine decomposition and indeed among these species, NC2H7 (g) and NC2H6 (g)
do not appear. The heterogeneous equilibrium calculations shows the formation of C solid
that corresponds to the amine decomposition and this amount of free carbon increases with
increasing temperature. Also, the formation of solid TaN was observed within the whole
investigated temperature range and no gaseous tantalum containing species pertained
contrary to mass spectrometric experiments.
Figure 1. Homogeneous thermodynamic simulations performed starting from 1 mole of the compound
Ta [N(CH3)2]5(g) and 0.001 mol of Ar and for an applied total pressure equal to 10 Pa in order to be
compared with the mass spectrometric experiments.
3.1.3. Conclusions
It is to be concluded that discrepancies exist between thermodynamic simulations and
mass spectrometric experiments. Indeed, thermodynamics predicted total cracking of both
Ta [N(CH3)2]5(g) and amine molecules in the whole investigated temperature ranges, while
in mass spectrometric experiments, Ta [N(CH3)2]5(g) and NC2H7 (g) amine have been
observed only in the low temperature below 623 K [26, 29]. The deviation vs. equilibrium
could be analyzed experimentally by the use of various sizes of cracking cell as well as the
deliberate and controlled introduction of H2(g). However, despite these limitations, these
results indicate the main features of the precursor thermal behavior which can be very
useful in the first stages of the development of any new ALD or CVD (for precursor
transport) processes.
3.2. High power electronics: Stability of SiC in H2 atmosphere

Silicon carbide (SiC) possesses many favorable properties making it interesting for a
multitude of applications, from high temperature to high frequency and high power device.
Among them, its excellent physico-chemical and electronic properties such as wide band
gap and high breakdown field, together with the degree of maturity of technology, makes
SiC a good candidate for mass production of Schottky diodes [30].
SiC device processing is conditioned to the fabrication of large area single crystal wafers
with the lowest defect density associated to deposition of epitaxial thin films which present
good structural quality and controlled doping level [31]. The most common processes used
to develop SiC wafers and SiC thin films are the seeded sublimation growth technique so
called the Modified Lely method and the Chemical Vapor Deposition technique from
propane and silane, respectively.
Huge improvements for both processes have been observed in the last decades. They come
mainly from extensive experimental effort, all over different groups in the world. However,
macroscopic modeling has given valuable information to understand the impact of some
growth parameters and propose new design of experiment to enlarge wafer size and
deposition area.
On both processes [32-35], some modeling trends were largely reported combined with
experimental results obtained in our researchs groups.
Special emphasis is given to chemical related results. To carry out modeling, it was followed
the different levels of complexity procedure described in the earlier paragraphs. Owing to
the similarity of the two systems, studies on species and material databases have been
naturally used for both processes.
CVD- grown SiC films can be obtained from a variety of precursors which are generally
part of the Si-C-H system. However, to obtain high crystal quality of 4H and 6H SiC
layers, which are the most interesting polytypes for the power devices applications,
experimental investigations have demonstrated that silane (SiH4(g)) propane (C3H8(g))
gave the most stable growth, in the typical conditions (temperature higher than 1700K,
pressure between 10 kPa to 100kPa, hydrogen as carrier gas) [36]. Operations are
separated in two steps, first an in situ etching step to prevent epitaxy-induced defects,
then the deposition step.
A great body of literature dealing with both theoretical and experimental results has been
devoted to understanding chemistries relevant to the separate Si-H and C-H systems.
However, it appears that most is unknown about the chemical reactions in which
organosilicon species, that include the three elements, can be involved. This is related to
the difficulty to measure thermochemical properties of such reactive, short life time,
species. Most of the thermodynamic data that have been used for these species come from
ab initio electronic structure calculations combined with empiric bond additivity
corrections [37, 38]. Mass spectrometry measurements have been carried out to estimate
the thermodynamic data of the gaseous species Si2C(g), SiC2(g), SiC(g) and the condensed
SiC(s) phase [39, 40].
With a purely thermodynamic approach, it was examined the preliminary operation of in

situ etching. It was found that the H2(g) etching of SiC(s) at 1700 K under 100 kPa can lead to
the formation of a condensed silicon phase, as shown on Figure 2. Thermodynamic study
was made to understand the impact of the temperature, the pressure and the composition of
the gas mixture [41].
Heterogeneous thermodynamic calculations show that the mixture (H2(g) + condensed

SiC(s)) ends in the formation of gaseous species such as CH4(g) for the C-containing
species and SiH2(g), SiH4(g), SiH(g), Si(g) and Si(s) in condensed phase for the Si-
containing species. With the etching, the amount of the gaseous C-species formed (mainly
CH4(g)) is three times higher than the gaseous Si-species one. So, there is Si in excess
which is condensed at the SiC(s) surface in a solid or liquid phase depending whether the
etching temperature is higher or below the Si melting temperature. When the temperature
is higher than 1800K, at atmospheric pressure, the quantity of formed gaseous Si-species
becomes equal to the quantity of formed gaseous C-species. Consequently, the formation
of liquid silicon is avoided.
3.2.1. Conclusions
Thermodynanic simulations have revealed the main phenomena and indicated some
solutions. Reducing pressure would provide the same beneficial effect, though the etching
rate decreases, as illustrated in Figure 3.
To compensate the formation of gaseous CH4(g), the addition of an hydrocarbon species

such as propane in the initial gaseous mixture would prevent the formation of condensed
silicon.
All these effects have been confirmed with experimental studies (Figure 2).
Si Substrate
70000
Si droplet
60000 SiC-6H
50000
Intensity (a.u.)
40000 SiC-6H
30000
20000
10000
10 m
0
400 500 600 700 800 900 1000 1100

Raman shift (cm-1)
Figure 2. Optical Micrograph of SiC(s) surface etched with H2(g) at 1700 K under 100 kPa, showing
silicon droplets (right). The silicon phase is identified by Raman spectroscopy (left) [41].
1,6E-05
1,4E-05
<SiC> <SiC >+< Si>
Partial pressures (105 Pa)
1,2E-05
CH4
1,0E-05
8,0E-06
6,0E-06
4,0E-06
Siy Hx)
2,0E-06
0,0E+00
0 0,2 0,4 0,6 0,8 1
Pressure (105Pa)
Figure 3. Heterogeneous equilibrium of the SiC(s) - H2(g) system at 1685K. Gaseous species created by
the etching are represented as a function of the pressure [41].
3.3. Thermodynamic analysis of plasma etching processes for microelectronics

With the constant downscaling of Complementary Metal-Oxide-Semiconductor (CMOS)
devices and the consequent replacement of SiO2 many high-k gate materials such as Al2O3,
La2O3, Ta2O5, TiO2, HfO2, ZrO2 and Y2O3 have been investigated. For each high-k material
integration, the etch process has to be revisited.
In the case of the etching of HfO2, one of the main issues is the low volatility of halogenated
based etch by-products [42].
Compared to SiO2 halide based etching process, thermodynamic data shows that, Hf based
etch by-products (HfCl4(g), HfBr4(g), HfF4(g)) are less volatile than Si etch by products
(SiCl4(g), SiBr4(g), SiF4(g)) [43]. Therefore, for HfO2(s) etching, the choice of the halogenated
based chemistry and substrate temperature are crucial parameters. In this work,
thermodynamic studies have been carried out in the pressure (0.5 Pa) and temperature
range (425 K to 625 K) conditions in order to select the most appropriate gas mixture and
temperature leading to the formation of Hf and O based volatile products. Based on
thermodynamic calculations in a closed system, the HfO2(s) etching process has been
simulated.
With this thermodynamic analyses, it is possible to determine an etch chemistry leading to
volatile compounds and to estimate an etch rate under pure chemical etching conditions. It
should be noted that the thermodynamic approach does not take into account the ion
bombardment of the plasma.
3.3.1. Pure thermodynamic calculations of HfO2 etching

For example, lets consider the etching of HfO2(s) in CCl4(g) plasma at 400 K and 0.5Pa. In
such case, the thermodynamic system is composed by four elements Hf, O, C, and Cl. The
thermodynamic calculation inputs are:each element of CCl4(g) (C and Cl atoms) with
HfO2(s) as a solid phase. The main gaseous species are CO2(g) and HfCl4(g) and the main
condensed species are HfCl4(s) on HfO2(s) in a solid phase. There are other gaseous species
in very low amount so that they can be neglected as (CO, Cl2, Cl). These results show that
carbon and chlorine containing chemistries can lead to the etching of HfO2(s) by forming
CO2(g) and HfCl4(g). Similar results have been obtained for the other halide chemistries
CCl3F(g), CCl2F2(g), CCl3F(g), CCl4(g).
3.3.2. Thermodynamic analysis coupled to mass transport: evaluation of etching rate

To point out the more promising chemistry among the usually adopted halogens precursors,
the etch rate has been estimated from the flow calculations of each gaseous and condensed
species under open conditions assuming molecular flow and the validity of the Hertz-
Knudsen relation [44].
For these processes operating at low pressure (<10 Pa), it is possible to associate the incident
and emitted flows from a given surface to the equilibrium partial pressures [45].
These calculations are based on the effusion calculations principles from the gas kinetic
theory.
For a gaseous species e, the total flow e which is emitted from a vaporizing surface can be
calculated according to the Hertz-Knudsen relation:
pe
e mol / s.m2 (25)
2 M e RT
Where pe et Me are the partial pressure and molar mass of the species e, respectively.
For each etched or deposited element i, there is equality between the incident flow and the
emitted or produced from reactions flows:
(incident) (emitted) (condensed) (26)

i i i
on the deposited or etched surface

For example, in the case of HfO2(s) etching by CHCl3(g) with Ar(g), the system is Hf, O, C,
H, Cl, Ar
For the previous thermodynamic calculations (HfO2(s) and CHCl3(g)) the major species at
equilibrium are:
CO2(g), HCl(g), HfCl4(g), Ar(g) in the gaseous phase

C(s), HfO2(s), HfCl4(s) in the solid phase
for a temperature of 300 K and a pressure of 5 Pa.
The flow equations are in this case (principle of mass conservation) :
Flow of incident C = flow of evaporated C + flow of condensed C:

PCO
F C( s) CHCl3 ( g )
1 2
(27)
2 .R.T MCO
2
Flow of incident H = flow of evaporated H :
PHCl
CHCl3 ( g )
1
(28)
2 .R.T M HCl
Flow of incident Cl = flow of evaporated Cl + flow of condensed Cl :
P
1 PHCl 4. HfCl4 F HfCl ( s) 3. CHCl ( g ) (29)
2 .R.T M HCl 4 3
M HfCl
4
0
pCHCl
with F(.(s)) the flow in solid phase species and CHCl3 ( g ) 3
(T0 the
2 .MCHCl .R.T0
3
0
temperature at the gases inlet and pCHCl the inlet partial pressure).
3
So five unknowns are obtained: PCO , F C( s) , PHCl , PHfCl , F HfCl4 ( s)

2 4
To be able to solve this system, five equations are needed. Already, three equations with
these ones of flow exist. For the both missing, its enough to consider:
The equation of total pressure: PCO PHCl PHfCl PAr Ptotale

2 4
And the value of the equilibrium constant for the assessment of mass equation of the
system, the fifth global equation is supplied by:
1 1
HfO2 ( s) 2.CHCl3 ( g) C( s) .HfCl4 ( s) CO2 ( g) 2.HCl( g) .HfCl4 ( g) (30)
2 2
the equilibrium constant of this equation is :
1
2 2
PCO .PHfCl .PHCl
Kp 2
2
4
(31)
PCHCl
3
P x1
CO2
P x
HCl 2
with : PHfCl x3 . (32)

4
F C ( s) x 4

F HfCl4 ( s) x5
The system of five equations and five unknowns is obtained:
x1
x4 CHCl3
1

2 .R.T MCO2

x2
CHCl3
1
2 .R.T M
HCl

1 x2 4. x3 x 3. CHCl
(33)
2 .R.T M HCl M HfCl
5 3
4

x1 x2 x3 PAr PTotale
1
x .x 2 .x 2
1 3 2 K
P2 p
CHCl3

The partial pressures of the main species are obtained. To determine the etch rate, it is
needed to use the calculated values for the pressures of the gases containing the elements of
material to etch.
In our example, the following gases CO2(g) and HfCl4(g) are considered.
The theoretical etch rate ER is given by the lowest value between:
ER = flow HfCl4(g).molar volume HfCl4(g) or flow CO2(g).molar volume CO2(g) (in m/s)
Where:
PCO
FlowCO . 2
(34)
2
2 .R.T MCO
2
and
PHfCl
Flow HfCl . 4
in molecules / s.m (35)
4
2 .R.T M HfCl
4
with PCO and PHfCl determined by the resolution of the mathematical system and N the
2 4
Avogadro number, P in Pa and M in kg.
Figure 4 shows the evolution of the calculated HfO2(s) etch rate as a function of
temperature for different F/Cl ratios in CClxFy(g) based chemistries. The etch rate is lower
when the F/Cl ratio increases in the gas mixture at temperature higher than 400 K. The
decrease in the etch rate is explained by the non volatility of HfF4(g) in the investigated
temperature range.
3.3.3. Conclusions
From these results, thermodynamic studies predict that a chlorocarbon gas mixture -such as
CCl4 -seems to be the most promising chemistry to etch HfO2(s) under pure chemical etching
conditions.
110
CClF3
100
CCl2F2
90 CCl3F
80 CCl4
70
Etch rate (a.u.)
60
50
40
30
20
10
0
300 K 400 K 500 K 600 K 700 K
Temperature ( K)
Figure 4. Evolution of the thermodynamically calculated HfO2(s) etch rate as a function of F-Cl ratio in
CClxFy(g) based chemistries.
3.4. Optics: SiO2 PVD deposition

From optics applications, the example of the evaporation/condensation process to obtain
SiO2 films is chosen. In that process, the surface of the evaporating source is heated by
electronic bombardment, while the substrate is held at low temperature.
The control and the reproducibility of this type of process is based on the following points:
Stability of the source with time (chemical composition, morphology of surface of the
evaporating zone)
Temperature and surface of the evaporated area (what is linked to the parameters of the
electronic bombardment).
The object of this study is to simulate the evaporation of a source of glassy silica with the
aim of depositing SiO2. The heated zone is about 3-7 cm2, the reactor has a volume about 1
m3, the substrate is located at 1 m from the source.
The first paragraph is dedicated to the pure thermodynamic simulations to determine the
major species originated from the evaporation. In the second one, the calculations of the
flows of evaporation at equilibrium as well as exchanged flows between source and

substrate surfaces are presented.
3.4.1. Pure thermodynamic calculations of SiO2 evaporation

The thermodynamic simulations corresponding to the SiO2(s) evaporation are realized by
considering an excess of solid SiO2(s) at a given temperature, in a constant volume. The
range of tested temperature is 1600 - 2500 K. The results of the simulation indicate that the
only solid present at equilibrium is SiO2(s) and that there is no formation of solid silicon.
In the range of selected temperature, the evaporation of the silica is thus congruent (the ratio
of the quantity of silicon and oxygen produced in the gaseous form is equal to 2). Figure 5
presents the nature and the partial pressures of the gaseous species formed at equilibrium.
Figure 5. Calculated partial pressures for SiO2 vaporization.
The major species in this range of temperature are SiO(g), O2(g), O(g) and SiO2(g), with trace
of Si(g). It can be noted that the mainly evaporated species is not SiO2(g) as it could believed
to justify the stoichiometric composition of the deposits. From the results of the molar
fractions calculated for various species, the gas phase reaction which takes place is globally
the following:
SiO2 s SiO g 0.42 O2 g 0.15 O g (36)

These curves show that the evaporated material quantity and consequently the evaporation
rate increases with temperature. That explains the best results obtained with sources carried
beyond their melting point (besides the higher quality of the surface with regard to a solid
source).
The calculated total pressure above silica is represented on the figure 5.

For the temperatures of evaporation above 1600 K, the total pressure over the silica is
superior to 0.1 Pa. If the total pressure is fixed to a lower value, there is then complete
consumption of the quantity of silica carried at the evaporation temperature from a
thermodynamic point of view.
0.8
0.7
0.6
Total pressure (Pa)
0.5
0.4
0.3
0.2
0.1
0
1600 1800 2000 2200 2400 2600
Temperature (K)
Figure 6. Calculated total pressure for SiO2(s) vaporization
3.4.2. Thermodynamic analysis coupled to mass transport: evaluation of deposition rate

The evaporation flows of the gaseous species originating from the SiO2(s) evaporation
should respect the congruent vaporization relation (ratio Si/O in the gaseous phase = 2),
demonstrated by the previous approach.
2 * O SiO O 2 * Si O 2 * SiO Si 2 * SiO O 4 * Si O 2 * SiO (37)

2 2 2 2 2 2 2
where e is the molecular flow of the species e, according to equation (25).
As illustrated by the previous etching case, it is possible to calculate all the species partial
pressures (pe) which verify the equation (37).
From the calculated flows from equation (37), the molar volume of SiO2(s), the reactor
geometry, and the temperature conditions on the surface, it is possible to estimate the
growth rate and the deposition profile (Figure 7). The growth rate on the substrate is given
from the exchanged flows between the two surfaces source and substrate, from basic
assumptions of molecular flows.
With coaxial source and substrate, the exchanged flow between the r0 radius source and r1,
radius substrate, separated by a distance h is given by the relation (38).
e pe
e * * [h2 r02 r12 ( h 2 r02 r12 )2 4 * r02r12 ]mol / s.m2 (38)
2Me RT 2
Figure 7. Deposition profile vs deposition temperature for two evaporation temperatures; Substrate
radius r0= 0.5 m; evaporating source surface= 3cm2, h= 1m
The results of the simulations are the same order as the obtained experimental values.
3.4.3. Conclusions
The simulations of the evaporation of SiO2(s) show that it is congruent and that there is thus
no evolution of the load in time. The mainly produced gaseous species are SiO(g), O2(g), and
O(g). Their proportions remain constant but their quantities increase with the temperature
of evaporation. Simulations of the evaporation/condensation process provide good
estimations of the deposition rate.
4. Conclusions
This review illustrates the interest to operate a priori an thermodynamic approach to
determine the feasibility and optimize a fabrication process, specially gas-solid fabrication
process. Kinetic approaches will give rise to more realistic simulations but are often difficult
to implement, for lack of reliable information. The classic pure thermodynamic can provide
useful information. It can be the only approach in the case of complex chemical systems for
which few kinetic data are available. To take into account the dynamic character of the
processes, the approaches mixing thermodynamics simulations and calculations of
exchanged flows are possible. In every case, the methodology has to contain continuous
comparisons between experimental results and simulations.
Author details
Laboratory Science et Ingnierie des Matriaux et Procds (SIMaP)
Grenoble INP/CNRS/UJF, Saint Martin dHres, France
Acknowledgement
This paper was inspired by the collaborative works with the colleagues of the SIMaP
(Laboratoire de Science et Ingnierie des Matriaux et Procds): Jean-Nol Barbier, Claude
Bernard, Christian Chatillon, Alexander Pisch, Arnaud Mantoux, Raphal Boichot, Michel
Pons.
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Section 4
Material and Products

Chapter 9
Application of Thermodynamics
and Kinetics in Materials Engineering
Lin Li
1. Introduction
1.1. Background
During the last 30 years, there was a surge for coupling thermodynamics and phase
diagrams in the field of material science. Many large programmers as well as the exploring
of versatile solution models, the description of the magnetism energy of elements and
solutions, etc. were developed. Thermo-Calc, as one of the most successful commercial
software package for calculation of phase equilibrium from a broad database, offered
appropriate guidance for the materials study and reduced the amount of experiments. For
example, the slag database in this commercial software package could be used for predicting
the composition of oxide and sulphide inclusion formed during the deoxidation and
solidification process with a specific multiphase equilibrium calculation.
However, there was still far from much work in the field of prediction or estimation based
on the principles of thermodynamics and kinetics for the practical processes in mass
production or the designing of kinds of materials. This chapter aims at introducing some
computational results on the designing of advanced materials.
2. Research and development on Transformation Induced Plasticity

(TRIP) steel
2.1. TRIP steel containing Al
Low carbon low alloy TRIP steel receives significant interest in automobile industry since it
offers excellent combination of high strength and formability for stretch forming or deep
drawing applications. The high formability in this steel is attributed to the transformation
induced plasticity of retained austenite. The amount and stability of retained austenite are
the key factors, which influences the transformation behavior during straining.
As well known high Si content suppresses the formation of cementite during the bainitic
transformation and it leads to an increase of the stability and the amount of retained austenite.
However, high Si content might cause problems in steel production such as strong oxide layer,
poor surface characteristics and low coat-ability. This leads to galvanizing problems.
Therefore, efforts are made to improve the composition concept, say, the substitution of Si
by other elements which might not spoil surface quality. In the first phase, different amount
of Al is added as an alternative to the steel to substitute for Si[1]. In order to understand the
complex effects of Al, Si in TRIP steel, many samples of different composition are prepared.
As an example, the overall compositions of five samples of them are listed in Table 1[2],
where steel no.2, 4, 11 with high Al content are designed as the galvanizing base material
with high requirement on elongation, steel no.5 and 10 are compared materials.
No. C Mn Si Al P Fe
2 0.18 1.56 0.02 1.73 0.017 Bal.
4 0.18 1.65 0.45 1.01 0.015 Bal.
5 0.21 1.41 1.07 0.32 0.017 Bal.
10 0.19 1.47 0.87 0.33 0.024 Bal.
11 0.19 1.47 0.22 0.94 0.024 Bal.
Table 1. Compositions of TRIP steels (in wt-%)[2]
Simulation of the inter-critical annealing at 780C of steels is performed with Thermo-calc

and its database. The Gibbs free energy of an arbitrary phase is listed as:
Gm = PI 0 (Y ) GIO0 + RT N S yiS ln yiS + PIZ (Y ) LIZ (1)

I0 S i Z 0 IZ
The first summation in equation (1) represented the standard energy, the second the mixing
entropy and the third the excess Gibbs energy.
The results[2] (see in Table 2) show steel no.2 and 4 must have good plasticity and fairly good
strength since both have high volume fraction of phase (ferrite), though the phase
(austenite) is less, it can still induce some bainite transformation in the low temperature and
raise the strength of the steels. From Table 2[2], it seems steel no.11 may have good combination
and highest value of strength and plasticity since it possesses much higher phase than steel
no.2 and 4 and also the high phase volume fraction which is favor to ductility.
Simulation of the continuous annealing process in the inter-critical temperature is
performed with Dictra software package[2]. The concentration profiles in the equilibrium
phases are estimated with the number-fixed frame of reference with respect to the
substitutional elements as follows:
jk jk 0 (2)
where j is flux and k was substitutional. For crystalline phases of iron based alloys, the
vacancy exchange mechanism of diffusion was predominant, thus, in the lattice fixed frame
of reference, the diffusion flux of component k could be written as:
Application of Thermodynamics and Kinetics in Materials Engineering 219
Jk xk k k (3)
where xk was the mole fraction of k, k represented mobility and k the gradient of
chemical potential of element k.
Employing a coupled thermodynamic/kinetic method for the solution of the related
equations, the concentration profile of the various elements is obtained. Some of the
obtained diffusion data are used to guide the processes in mill.
Mechanical properties of the produced TRIP steels are shown in Fig.1[2], where all the steels
are inter-critical annealed at 780C for five minutes and then cooled to different
temperatures in the bainite transformation zone.
steel phase C Mn Si Al P % %
no.
2 2.66E-4 1.18E-2 1.96E-4 2.00E-2 2.05E-4 73.4 26.6
6.07E-3 2.61E-2 2.10E-4 9.66E-3 7.19E-5
4 1.71E-4 1.14E-2 4.58E-3 1.24E-2 1.98E-4 63.4 36.6
4.65E-3 2.55E-2 4.36E-3 6.00E-3 6.62E-5
5 1.30E-4 8.57E-3 1.16E-2 4.22E-3 2.52E-4 51.1 48.9
4.18E-3 2.00E-2 9.71E-3 2.12E-3 8.32E-5
10 1.20E-4 9.04E-3 9.40E-3 4.32E-3 3.52E-4 52.4 47.6
3.88E-3 2.10E-2 7.92E-3 2.17E-3 1.16E-4
11 1.65E-4 9.77E-3 2.27E-3 1.21E-2 3.38E-4 54.5 45.5
3.99E-3 2.06E-2 2.12E-3 6.15E-3 1.22E-4
Table 2. Calculated equilibrium compositions (in wt-%) at 780C and corresponding vol.% of and
phases[2]
Figure 1. Mechanical properties of the various TRIP aided steels after different heat treatment[2]
Mechanical properties of steel no.2 and 4 are in accordance with thermodynamic estimation
except steel no.11 which does not show high strength and elongation rate as expected.
Kinetic calculation results in Fig.2-5 explain that phenomena: after inter-critical annealing,
the distribution of C and Mn in steels no.5, 10 and 11 does not exhibit substantial difference.
However, high Si concentrates in the phase of steels no.5 and 10 while high Al in steel
no.11. It follows from that result Al can substitute for Si to induce TRIP effect but its
function is not as strong as Si.
Figure 2. Concentration profile of C at the / interface during inter-critical annealing at 780C of the
steel No.5, No.10 and No.11
Figure 3. Concentration profile of Mn at the / interface during inter-critical annealing at 780C of the
Figure 4. Concentration profile of Al at the / interface during inter-critical annealing at 780C of the
Figure 5. Concentration profile of Si at the / interface during inter-critical annealing at 780C of the
Different from steels no.5 and 10, steels no.2, 4 and 11 therefore possess both super coat-
ability and satisfactory mechanical properties due to their high Al content. These three steels
mentioned above were adopted and produced in ThyssenKrupp stahl and Voest-Alpine
Arcelor and the sheet steels were manufactured as important structural parts, e.g.,
reinforcement A-pillars and reinforcement B-pillars in FIAT and PORSCHE, which are the
pioneers in the organization of ULSAB (Ultra-Light Steel Auto Body).
2.2. TRIP steel containing P

As stated above, in order to replace Si partially and/or totally, efforts were made with Al
instead[1,2]. The substitution was successful but only limited at low Al content. Side effect of
high Al content in the steel is estimated that it may cause clogging during continuous
casting due to precipitation of aluminum oxide[3]. Searching for the other effective element
to substitute for Si was then triggered. In the periodic table of elements, Al, Si, and P are
located nearby in the same period, these elements have similar electronic structures and
may have similar properties. This comes true especially to Si and P since they both are semi-
metals. It is then natural to consider P as another substitute for Si. P can, on one hand,
depress the carbon activity in cementite, prevent cementite precipitation and increase the
stability of austenite. On the other hand, this element has a strong tendency to segregate at
grain boundary and to induce cold brittleness. Segregation formulation was developed by
Guttmann and Mclean in a ternary system (Fe, M, I) [4] based on the sublattice model in melt
salts and stoichiometric phases contributed by Hillert et al[5]. Li et al. extended the
segregation equation into a five-element system[6], and generalized it into a multicomponent
system as[7]:
y Ig / yVg ( y IB / yVB )exp{[ 0GI 1 / c g yigiIg 1 / c B yiBiIB 1 / c g y Jg LgA: JI

i A i A JI
1 / c g
y Jg LgA: JV 1/ c B
y JB LBA: JI 1 / c B
y JB LBA: JV ] / RT } (4)
JI JI J
g
yM / y Ag ( y M
B
/ y AB )exp{[ 0GM 1 / a g yIg MI
g
1 / a B yIBBMI 1 / a g yig Lgi:MV
iM
1 / a B yiB LBi : MV 1 / a B yig LgAi :V 1 / a B yiB LBAi :V ] / RT } (5)

iM iA i A
where variable y indicates site fraction in sublattice, g grain boundary, B matrix, V

vacancy, A base metal, J and I represent impurity, i and M metal element, c and a
fraction of sites available in grain boundary or matrix, 0 GI and 0GM are the intrinsic
segregation Gibbs free energy of impurity I and metal element M , LBA(:gJI) stands for the
interaction energy between J and I in one sublattice when another sublattice is fully
occupied by element A , BMI( g ) means the interaction energy between elements in different
sublattices. Following references [7,8], assuming that interaction energy keeps the same on
grain boundaries and in matrix and omitting the interaction between impurities and
vacancy and between metal element and iron, a series of parameters[7,8] can be listed as
follows: a g c g 0.5 , a B 0.75 , c B 0.25 , 0 GP = 47KJ/mol, 0GMn = 8KJ/mol, MnP = 12.5
KJ/mol, LFe :PC = -9KJ/mol. With all the data stated above and the composition of an assumed
steel with enough high phosphorus (C = 0.15%, Mn = 1.6%, Si = 0.3%, P = 0.07%), the
equilibrium segregation amount of phosphorus on grain boundaries at 400C is calculated
as 32%[9], which is a value high enough to cause temper brittleness.
The soaking temperature at the over-aging process of cold-rolled TRIP steel is set in the
temperature range from 350 to 480C. However, the soaking time is quite short, normally for
3~5 min, being far from equilibrium condition. Thus, the estimated equilibrium segregation
amount of phosphorus is not suitable in describing the over-aging process of TRIP steels.
Based on Mclean contribution with his kinetic approach for a binary system[10], the amount
of segregative element on grain boundaries can be expressed as:
( yi (t ) yi (0)) / ( yi yi (0)) 2( Xi / yid)( Dit / )1/ 2 (6)
where yi (t ) is the grain boundary coverage of element i at time t , yi (0) is its initial
value and yi the equilibrium value. Di is the bulk diffusion coefficient of i , d the grain
boundary thickness and Xi the mole fraction of i in matrix. Taking d 10-7cm as usual, t
5min 300sec and T 673K according to the actual process condition, X P 1.38710-3
(i.e., wt 0.07%), yi (0) 0; according to Sundman et al, DP 3.5310-18[11].
The segregated amount of P at grain boundary after soaking at 400C for 300 s is:
y P (300 sec) 2( X P / d)( DPt / )1/ 2 =0.051%[9] (7)
which is a small amount and would not be of any damage in grain boundary for the TRIP
steel. Mechanical properties of the designed steel were measured at low temperatures (
20C, 60C) and no substantial difference was found between the results obtained at low
temperatures and room temperature[9]. Moreover, cold fracture test was taken with the
structural part assembles of automobiles and no sign of cold brittleness was detected. The
new type TRIP steel containing P was manufactured according to design stated above in
Ansteel company group in China.
2.3. Attractive effect of Al in TRIP steel

Aluminum, however, if the clogging of Al2O3 can be efficiently prohibited through careful
control in the continuous casting process, is also a good promoter of TRIP effect. The reason
has been studied thermodynamically and the authors found that with the existed database
the phase diagram of a steel containing certain a amount of Al can not be described
accurately[12] and must be revised. In their work[12], high purity Fe (99.99 wt%, Source), Al
(99.97wt%, Source) and C (99.99wt%, Source) are used to prepare different composition Fe-
Al-C alloys. Each alloy composition is checked by wet chemical analysis, as given in Table 3.
Additional annealing of encapsulated ingots is carried out at 1100C for 360 h to reach
equilibrium states and to obtain a homogeneous element distribution. To check the
homogeneity of the annealed alloys, an EDX line scanning of Al and C is applied on the
cross-section of the alloys showing the elements are evenly distributed in the Fe matrix. The
DIL experiments are carried out in a Formaster-D dilatometer to investigate the ferrite to
austenite transformation during the heating and cooling cycles and the results are also listed
in Table 3.
Composition (wt%) Experimental T (C) Calculated T (C)

Alloy
C Al Fe A1 A3 A1 A3
C1 0.15 1.57 98.28 731 987 729 1006
C2 0.25 1.51 98.24 708 935 728 918
C3 0.41 1.47 98.12 739 892 727 850
C4 0.54 1.50 97.96 734 861 728 823
C5 0.75 1.53 97.72 732 810 729 796
C6 0.76 1.54 97.70 737 788 729 797
C7 0.91 1.42 97.67 726 827 726 769
C8 1.01 1.54 97.45 734 822 729 793
Al1 0.19 0.91 98.90 735 900 726 889
Al2 0.20 1.13 98.67 745 938 725 900
Al3 0.21 1.30 98.49 745 953 726 920
Table 3. Compositions of the Fe-rich alloys and the transformation temperatures of the alloys obtained
by DIL analysis and thermodynamic calculation[12]
With the new set of experimental data, it is possible to optimize the Fe-Al-C system in Fe-
rich corner. The standard element reference (SER) state of Fe (bcc), Al (fcc) and C (graphite)
is used as the reference state of the Gibbs energy as usual. The molar Gibbs energy of the
ternary liquid phase is described by the Redlich-Kister polynomial [13]:
liquid
Gm xi 0Giliquid RT xi ln xi
i Fe , Al ,C i Fe , Al ,C
xFe x Al LFe , Al xFe xC LFe ,C x Al xC LAl ,C xFe x Al xC LFe , Al ,C (8)
Where xi is the mole fraction of element i and 0 Giliquid is the Gibbs energy of liquid Fe, Al
and C. The binary parameters Li,j are obtained from the thermodynamic evaluation of the
limiting binaries, whereas the LFe,Al,C is a ternary interaction parameter.
The Gibbs energy of solid phases, fcc (austenite), bcc (ferrite) and hcp in the Fe-Al-C system
is described by a compound energy formalism consisting of substitutional and interstitial
sublattices[14]. The Fe and Al substitute each other in the metal sublattice, while C and
vacancies in the interstitial sublattice. The crystal structure is therefore modeled as (Fe, Al)a
(C, Va)c. Symbols a and c denote the numbers of sites which is dependent on the crystal
structure. Here the values of a and c are regarded as a = 1, c = 1, 3, and 0.5 for the fcc, bcc and
hcp phases respectively. The molar Gibbs energy is expressed as:

Gm yi ( oGi:C yC oGi:Va yVa ) aRT yi ln yi cRT ( yC ln yC yVa ln yVa )
i i
yi y j ( yC Li , j :C yVa Li , j :Va ) yC yVa yi Li :C ,Va (9)
i j i
yi y j y k ( yC Li , j:C yVa Li , j :Va ) Gmag

i j k
Where i, j = Fe, Al and K = C or Va. In Eq. 9, the variable yi is the site fraction of component i
in its sublattice. The components in different sublattices are separated by a colon and in one
sublattice by a comma. Gi:Va is the Gibbs energy of pure element i in a relevant non-
magnetic state and Gi:C is the Gibbs energy of a hypothetical non-magnetic state, where all
interstitial sites are occupied by carbon. All G values are given relative to the reference state.
Gmag is the magnetic part of the Gibbs energy.
In the Fe-Al-C system, only one ternary K phase was reported besides the liquid, fcc, bcc
and hcp phases. In this optimization, the description of the K phase is after the
thermodynamic assessment of Kumar et al [15].
Li et al[12] optimized the Fe-Al-C ternary system based on the previous thermodynamic
description of the Fe-C, Fe-Al and Al-C systems[15, 16] as well as the obtained DIL data[12].
Furthermore, Li et al[12] extrapolated the thermodynamic properties of the limiting binary
and ternary systems to higher order systems to construct the self-made database, especially
for TRIP steels containing Mn, Si, Al, C, Nb and V as alloying elements. A calculated vertical
section of the Fe-Mn-Si-Al-C system is presented in Fig.6 for the alloys meeting very well
with the experimental results.
Phase diagram of a steel with the same composition as in Fig.6 but without Al is calculated
with the self-made database and shown in Fig.7. It is obvious that the bcc+fcc field in Fig.6 is
much wider than that in Fig.7. As calculated: when at 800, the carbon content in fcc phase
in Fe-Mn-Si-Al-C steel is 0.476%, while at 802, the carbon content in fcc phase in Fe-Mn-Si-
C steel is only 0.206%. That means if soaking at the same temperature, the former dissolves
much than two times carbon in the fcc phase resulting much higher stability of fcc phase
and much better TRIP effect.
1600
liquid
1400
fcc+liquid
TEMPERATURE_CELSIUS
1200
fcc
1000
fcc+graphite
800 bcc+fcc
fcc+bcc+graphite
600
bcc+graphite
400
0 0.5 1.0 1.5 2.0 2.5
WEIGHT_PERCENT C
Figure 6. Extrapolated vertical section of the Fe-Mn-Si-Al-C steel with 1.60 wt% Mn, 0.37 wt% Si, and
1.31 wt% Al[12].
Figure 7. Phase diagram of the Fe-Mn-Si-Al-C steel with 1.60 wt% Mn, 0.37 wt% Si
This new finding brings substantial improvement for the mechanical properties of TRIP
steel. Following this idea, i.e, keeping reasonably high amount Al in the steel and treating it
in an ordinary Continuous Annealing Line (CAL), a high performance TRIP steel is
manufactured in modern plant, whose strength and ductility product reaches 30,000MPa%.
It is actually the property target of a third generation steel[17].
3. Research and development on large-section pre-hardened mold steel

for plastic
In large-section pre-hardened plastic mold steel, the inclusion of high alumina content is
detrimental to machinability, which is considered as the most important property of mold
steel for plastic. It is known that non-metallic inclusion may appear in molten steel at
various stages of the refining process or during solidification. One could not analyze in situ
the precipitation of inclusions at every period of steel-making by traditional experimental
method. However, the effective composition regulation and suitable heat treatment during
production could influence inclusion precipitation and improve the quality of the mold steel
for plastic. This paragraph is designed to produce a large-section pre-hardened plastic mold
steel relying on the step by step thermodynamic calculation[18].
The SLAG database in Thermo-calc software package contributed by Gaye[19] is a useful tool
which studied the slag mixture of m oxides ( ( Mi )u Ov , i =1, 2, , m) including two kinds of
i i
sub-lattice. One is an anionic sub-lattice filled with oxygen ions and the other is cationic sub-
lattice filled with the cations in the decreasing order of their charge (e.g Si4+Ca2+). The
structure of the melt is described in term of symmetric (i-O-i ) and asymmetric (i-O-j) cells,
in numbers Rii,...2Rij...; the energy parameters consist of parameters for asymmetric cells
formation and parameters of interaction between cells. This simplified melt structure greatly
and made it possible to describe the multi-component system in terms of only a few binary
parameters. Because the formation of melt can be thought as the result of the following bond
respond:
(i-O-i ) + (j-O-j) = 2(i-O-j) (10)
Then the expression for the mixing free energy of the melt can be derived by statistic
thermodynamic method.
This paragraph applies the SLAG database of Thermo-calc, to predict a definite range of the
composition, with which oxide and sulphide inclusion formed during the deoxidation
treatment could be effectively controlled and inhibited.
Since Si and Mn in the steel affect the precipitation of alumina, the inter-relation curve of
Si and Mn contents is calculated and plotted with a macro file which is input to the
software. The calculated result can be used as a guide for the metallurgy engineer to
select suitable composition of mold steel for plastic in a broad range. For Al contents of
100 ppm and 300 ppm at a given temperature of 1800K, the calculation results are shown
in Fig.8 respectively. The curve in Fig.8 is the calculated critical line of alumina
precipitation. When the composition of steel locates at the right side of the curve,
alumina does not precipitate and the main inclusion in molten-steel is manganese-
aluminate. However, if the composition locates at the left side of this curve, the alumina
precipitates in molten steel. Thus, the mentioned results are used in the designing of
mold steel.
Figure 8. Effect of Si and Mn contents on alumina precipitation under 1800K for (a) Al content of
100ppm (b) Al content of 300ppm[18]
As stated above non-metallic inclusions may appear in molten steel at different stages.
Therefore, in addition to the former considerations, the composition of the mold steel is
designed in such a way that the oxide inclusion is fixed to be exogenous inclusion, which
precipitates before solidification of liquid steel and can be eliminated after slag raking and
gas rinsing, or be modified by injecting Ca-Si powder in the ladle. As calculation indicates in
Fig.9a, the solidification temperature of the designed steel is 1760K while the lowest
precipitation temperature of alumina is 1769K, 9K higher than the solidification point
meeting well with the design requirement. The same result is obtained in Fig.9b, where the
equilibrium phase diagram is calculated with another database of Thermo-calc, showing the
solidification point of the steel is 1760K.
Moreover, the composition is carefully designed to let the driving force of the oxide
precipitation be the biggest one following closely by the driving force of MnS. Then, when
cooling, the alumina precipitates firstly and MnS precipitates afterwards to form the desired
structure of good machinability where hard alumina is set in the core and soft MnS outside.
Furthermore, as known, good machining performance connects normally with high

homogeneity of microstructures in the steel which is sometimes dependent on annealing
process. With Thermo-calc, the main type of carbide which exists in the mold steel but can
be dissolved during annealing is designed through the modification of steel composition
considerately. The designed carbide is in the type of M7C3, and this prediction is proved by
TEM detection. Soaking temperature for dissolving this carbide is estimated as 1220C. Then
suitable heat treatment process is taken to ensure the high homogeneity and super
machinability of the steel after the annealing treatment in steel production.
Figure 9. (a) Relationship between the precipitation amount of alumina and temperature in the
designed mold steel, solidification temperature being shown (b) phase diagram of the same steel[18]
Measurement shows the inclusion number in the designed steel is reduced to be less than
one tenth of the steel without composition regulation and its machinability reaches the
world highest level of mold steel for plastic. The carefully designed mold steel is
successfully put into mass production in Baosteel company.
4. Research and development on the high strength TWIP steel

Recently TWIP (TWin Induced Plasticity) steel, as one of the most promising advanced HSS
(High Strength Steel), was developed showing the highest elongation rate (80%) and fairly
good strength (600Mpa) due to the effect of TWIP. However, in practical use such as
automobile anti-crash parts, the strength seems to be too low but ductility too high. With
further consideration of alloy concept, much high strength can be obtained for the steel
which comes from hcp martensite transformation. The equilibrium temperature between fcc
phase and hcp phase in FeMnSi system and FeMnSiC system has been calculated
thermodynamically[20]. It is found that the equilibrium temperature can be adjusted and
controlled to be near to the room temperature through rational coordination of Si, Mn and C
content in the steel. These results make it possible for realization of strain induced
martensite transformation in the steel. However, the (hcp) martensite phase
transformation is related to the stacking-fault energy (SFE) in austenite, which is affected by
the special characteristics of alloy elements and their interactions and is discussed
hereafter[20].
As known, the stacking-fault energy for pure metal can be considered as Gibbs free energy
difference between atoms with two layer of fcc and atoms with two layer of hcp. While
for alloy, its Gibbs free energy difference between fcc and hcp close-packed structure is not
strictly equal to stacking-fault energy, because the element concentration at stacking faults is
different from the average composition of alloy, especially the Suzuki Effect caused by C,N ,
which leads to the obvious difference of concentrations between stacking faults and base
material. So according to the work of Olson and Cohen[21], the thermodynamic model of
stacking-fault energy can be expressed as:
SF 2A G 2 (11)
Where,
4 1
A 2
3 a N
is the bulk density of atomic surface in face-centered cubic, a is the lattice constant of alloy,
N is the avogadros constant N =6.021023. is the binding energy of phase interface,
according to Allain[22], =(515)mJ/m2. For simplicity, an average, i.e., 10mJ/m2 is taken
by Li et al in their calculation[20]. G is the free energy difference between face-centered
cubic ( ) and close-packed hexagonal () . Referring to Dumay[23], this part can be expressed
as:
G GFeMnSu

GFeMnSu/C
Gmg (12)
Where, the first item in the right part of the equation represents the effect of main elements
such as Fe, Mn and Si on transformation free energy, denoted as:

GFeMnSu Gi FeMn [C D( Fe Mn )] Fe Si [ E F(Fe Si )] (13)
i
Where Gi is the transformation free energy difference of in pure components i.

i is the mole fraction of element i, T is temperature in Kelvin, the last two items in
equation (13) represent the interaction between Fe-Mn and Fe-Si, where the interaction
between Fe and other elements as well as the mutual action of alloy elements can be
neglected. The parameters of C, D, E, F in equation (13) were obtained form the

corresponding curve fitting and listed in Table 4 after Dumaya et al[23]. The GFeMnSu/C in
equation (12) represents effect of interaction between all the substitute elements and carbon
on the transformation free energy, which is:
a bX
GFeMnSu/C (1 e C ) cXMn (14)
XC

While in equation (12), Gmg is the mole magnetic free energy difference between phase
and phase, which is:

Gmg

G m Gm (15)
G , G represents respectively the mole magnetic free energy[24-26] of phase and phase,
m m
which is:

Gm RT ln( 1) f ( ) (16)
B
Where:
1 79 1 474 1 3 9 15 T
f ( ) 1 { [ 1][ ]}( 1)
D 140 p 497 p 6 135 600 TC
Or:
1 5 15 25 T 518 11692 1
f ( ) [ ]( 1), butD ( 1)
D 10 315 1500 TC 1125 15975 p
as for fcc and hcp crystal structure, p=0.28, for other structure, p=0.5.
TN 250ln( xMn ) 4750 xC xMn 22 xCu 2.6 xCr 6.2 xSi 720( K )
TN 580 xMn ( K )
GF
e -2243.38+4.309T Jmol-1

GMn -1000.00+1.123T Jmol-1
GF
eMn C=1246 Jmol-1, D=-717 Jmol-1
GF
eMnx C a=1246 Jmol-1, b=24.29 Jmol-1,c=17175 Jmol-1
B 0.7 xFe 0.62 xMn 0.64 xFe xMn 4 xC Jmol-1
B 0.62 x Mn 4 xC Jmol-1
G A
l 2800+5T Jmol-1

GSi -560-8T Jmol-1

GFeSi E=2850 Jmol-1; F=3520 Jmol-1
GV -3500 Jmol-1
Table 4. Parameters used in calculation of stacking-fault energy in Fe-Mn-X-C system(X=Si, Al, V)[23]
Y.K.Lee et al[27] considered that as for Fe-Mn alloy with 16-24% Mn, the phase transformation
driving force of hcp martensite was -68~-120 J/mol. Allain et al[22] thought that for Fe-Mn-C
system, if the stacking-fault energy (SFE) was above 12mJ/m2, the austenite was easy to
induce twins; if the SFE lower than 18 mJ/m2, austenite easy to induce hcp martensite. The
suggestion of Allain et al[22], say, the SFE value between 12~18 mJ/m2 is adopted as the value
which induces martensite transformation in the TWIP steel. The calculation result for a steel
with 18% Mn but different Si and C is shown in Fig.10 where the composition range suitable
for the assigned SFE is pointed.
Steels with different Mn,Si and C content but their SFE ranges between 12~18 mJ/m2 is
calculated and listed in Table 5 [20].
For designing of the test steel, a value of stacking fault energy in the range of 12~18mJ/m2 is
firstly adopted. Besides, the change of carbon content can be used to adjust the size of
stacking fault energy while the content of Mn is to be set as low as possible to be favorable
to the line process. Based on the above calculation the composition of the high strength high
ductility steel is designed as 16~22%Mn, 0.3~0.6%C and 0.2~0.8%Si. The Gibbs free energy
difference between fcc matrix phase (austenite) and hcp martensite in the steels is calculated
with a self-made database[28] and, as an example, the difference of two phases in a steel of
18%Mn-0.528Si-0.35C is shown in Fig. 11. It can be seen that the T0 temperature(at which the
Gibbs energy of fcc phase equals to hcp phase) is 330K, if adding -68 J/mol as driving force[27]
to the difference, the corresponding temperature is 293K, which means hcp martenisite can
be obtained in room temperature.
30 30
28 (a) 28 (b)
26 26
24 24
22 22
20 20
2
18 18
SFE,mJ/m
2
SFE,mJ/m
16 16
14 14
12 12
10 10
8 8
6 6
4 4
2 0.45 0.63 2 0.44
0 0
0.2 0.4 0.6 0.8 1.0 0.2 0.4 0.6 0.8 1.0
Mass fraction of C,% Mass fraction of C,%
32 30
30 (c) 28 (d)
28 26
26 24
24 22
22 20
20 18
18
2
2
SFE,mJ/m
SFE,mJ/m
16
16
14
14
12 12
10 10
8 8
6 6
4 4
2 0.365 0.52 2 0.32 0.47
0 0
0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0
Mass fraction of C,% Mass fraction of C,%
Figure 10. Estimated stacking fault energy(SFE) in Fe-18Mn-YSi-C alloys with Y = 0(a),Y= 0.3(b),Y= 2(c)
and Y = 5(d) [20]
Fe-Mn Si C(SFE=12) C(SFE=18)

Fe-22Mn 0 0.282 0.44
Fe-22Mn 0.3 0.28 0.43
Fe-22Mn 2 0.24 0.38
Fe-22Mn 5 0.23 0.37
Fe-18Mn 0 0.45 0.63
Fe-18Mn 0.3 0.44 0.6
Fe-18Mn 2 0.365 0.52
Fe-18Mn 5 0.32 0.47
Fe-15Mn 0 0.55 0.73
Fe-15Mn 0.3 0.53 0.7
Fe-15Mn 2 0.44 0.6
Fe-15Mn 5 0.37 0.52
Table 5. Chemical compositions with different SFE(mass fraction, %)

Figure 11. Gibbs free energy difference of two phases G in Fe-18Mn-0.528Si-0.35C(mass fraction,
%)steel
The test steel is melt in the 35kg vacuum melting furnace and the measured stacking fault
energy is 20mJ/m2. The ingot is heated up to 1200C and then forged into the stocks with a
thickness of 25mm. The stocks are heated at 1100C for 30min, finally hot rolled into the
plates with a thickness of about 1.5mm and then quenched in oil. The final specimens are
conducted with XRD, metallographic and SEM analyses. XRD spectrum shows weak -
martensite peak in the steel. Optical metallography confirms there exists -martensite in the
steel when the sample is chemical polished and the effect of mechanical grinding is
removed. SEM topography also indicates thin strips with different orientations which is
regarded primarily as -martensite. Therefore, as revealed by calculation, -martensite is
formed in this high-Mn TWIP steels after oil quenching.
In order to raise the mechanical property of the steel, different heat treatment after hot
rolling is applied. Table 6 shows different final rolling temperatures and cooling methods
after hot rolling.
Steel No. Final hot rolling temp./ C Cooling medium

Mn18_1 850 water
Mn18_2 750 water
Mn18_3 850 air
Table 6. Final rolling temperatures and cooling methods after hot rolling
Figure 12 shows the XRD spectrum of the test steels treated with different heat treatment
methods after hot rolling processes. It can be seen that the microstructure is the combination
of austenite and -martensite after hot rolling at 850C and water quenching, but the
microstructures are austenite alone after treatment by other processes. Figure 13 shows the
strain-stress curves of the test steels treated with different processes. It can be seen that air
cooling after hot rolling (as Mn18_3 steel) can lead to the best property such as strength
above 1GPa and elongation rate above 60%. To examine the effect of structure on property,
the fracture of the steels is analyzed with XRD as shown in Fig. 14. It can be found that -
martensite peak is displayed in the fracture of three specimens. Among this peaks, -
martensite peak in Mn18_3 specimen is the weakest. Thus, according to the XRD results
before and after drawing and the result of tensile test, it can be concluded that -martensite
existed before tensile test as well as a great amount of -martensite induced during tensile
test may both raise the strength of the steel, while only a bit of induced -martensite during
tension improves the property much effectively. All those steels exhibit strength higher than
800 MPa caused by martensite transformation.
800
(111)
700
600
500
XRD
400 (101)
(200) (220) (311)

300
(100)
(102) (103) Mn18_3
200
Mn18_2
100
Mn18_1
0
20 30 40 50 60 70 80 90 100
2 theta
Figure 12. XRD spectra of hot rolling steel

1.2
/GPa 0.8
Mn18_1 Mn18_2 Mn18_3

0.6
0.4
0.2
0
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7

Figure 13. Stress-strain curves of hot rolling steels
300
(111)
250
200
XRD
(220)
(101)
150 (200) (311)
(100)
(103)
100 (102)
Mn18_3
50 Mn18_2
Mn18_1
0
20 30 40 50 60 70 80 90 100
2 theta
Figure 14. XRD spectra of hot rolling steel after deformation
Combining with the calculation results and experimental process stated above, new type of
high strength and ductility TWIP steel is successfully produced in Ansteel group.
5. Research on high-tech ceramics

Ceria-doped zirconia ceramics found profound use in automobile emission system recently.
When this ceramics is exposed to an inert atmosphere or low oxygen partial pressure at
elevated temperature, the Ce+4 will be reduced to Ce+3, a nonstoichiometric phase Zr1-zCezO2-
x is then formed and the ZrO2-CeO2 system will convert to a quasi-ternary ZrO2-CeO2-CeO1.5
system. It is therefore very useful to study the effect of oxygen partial pressure on the
stability of the nonstoichiometric fluorite phase Zr1-zCezO2-x in the ZrO2-CeO2-CeO1.5 system,
which is directly connected to the ability to accumulate or release oxygen of a system,
proved to be a guide in producing the high-tech ceramics in the modern industry especially
in automobile manufacturing factory.
In this paragraph, the three limiting binary systems ZrO2-CeO2, ZrO2-CeO1.5 and CeO1.5-CeO2
are evaluated with compound energy model[29-31] and substitutional model[32]respectively
and the calculation results met well with each other proving the substitutional model is still
available to the complex oxide system[33,34].
In ZrO2-CeO1.5 system[33], compound energy model with structure (Zr+4, Ce+3)1(O-2, Va0)2 is
used for css phase. The Gibbs energy of one mole of formula unit can be expressed as
follows:
css
Gm yZr 4 yO2 oGZr 4 :O2 yZr 4 yVa0 oGZr 4 :Va0
yCe 3 yO2 oGCe 3 :O 2 yCe 3 yVa0 oGCe 3 :Va0
(17)
RT[( yZr 4 ln yZr 4 yCe 3 ln yCe 3 )
2( yO2 ln yO2 yVa0 ln yVa0 )] EGm
The excess term EGm is given by an equation of the form:
E
Gm yZr 4 yCe 3 [ L0Zr 4 ,Ce 3 :O2
(18)
( yZr 4 yCe 3 ) L1Zr 4 ,Ce 3 :O2 ]
In the CeO1.5-CeO2 system[33], the nonstoichiometric phase <CeO2-y> is described with

structure (Ce+4, Ce+3)1 (O-2, Va0)2. The Gibbs energy of one mole of formula unit can be
expressed as follows:
css
Gm yCe 4 yO 2 oGCe 4 :O 2 yCe 4 yVa0 oGCe 4 :Va0
yCe 3 yO 2 oGCe 3 :O 2 yCe 3 yVa0 oGCe 3 :Va0
(19)
RT[( yCe 4 ln yCe 4 yCe 3 ln yCe 3 )
2( yO2 ln yO2 yVa0 ln yVa0 )] EGm
The excess term EGm is given as follows:
E
Gm yCe 4 yCe 3 [ L0Ce 4 ,Ce 3 :O2
(20)
( yCe 4 yCe 3 ) L1Ce 4 ,Ce 3 :O2 ]
In the ZrO2-CeO2 system[33], the css phase is modeled with two sublattices, (Zr+4, Ce+4)1(O-2)2.
Because the valence of cations and anions can fit the condition of electroneutrality without
the addition of any defects. All the limiting binaries are optimized and all the parameters
are obtained[33].
When ZrO2-CeO2 system exposed in reduced atmosphere at high temperature, part of CeO2
changes to CeO1.5 in css phase. A new nonstoichiometric phase <Zr1-zCezO2-x> is considered
under the conditions. To describe the ionic characteristics of this phase, the compound
energy model, i.e., (Zr+4, Ce+3, Ce+4)1(O-2, Va0)2 is also applied to this phase. Based on the
parameters of phase css in the three sub-binary oxides system, The Gibbs free energy of one
mole phase is[33]:
css
Gm yZr 4 yO2 oGZr 4 :O 2 yZr 4 yVa0 oGZr 4 :Va0
yCe 3 yO 2 oGCe 3 :O2 yCe 3 yVa0 oGCe 3 :Va0
yCe 4 yO 2 oGCe 4 :O 2 yCe 4 yVa0 oGCe 4 :Va0
(21)
RT[( yZr 4 ln yZr 4 yCe 3 ln yCe 3
yCe 4 ln yCe 4 ) 2( yO2 ln yO2
yVa0 ln yVa0 )] EGm
The excess term EGm is represented by:
E
Gm yZr 4 yCe 3 [ L0Zr 4 ,Ce 3 :O2 ( yZr 4 yCe 3 )
L1Zr 4 ,Ce 3 :O2 ] yCe 4 yCe 3 [ L0Ce 4 ,Ce 3 :O2
(22)
( yCe 4 yCe 3 ) L1Ce 4 ,Ce 3 :O 2 ] yZr 4 yCe 4
[ L0Ce 4 ,Zr 4 :O 2 ( yCe 4 yZr 4 ) L1Ce 4 ,Zr 4 :O2 ]
The calculated phase diagrams and corresponding experimental information of ZrO2-CeO2,

ZrO2-CeO1.5 and CeO1.5-CeO2 systems are shown in Fig.15-17[33], where the little circles
denote experimental data. In Fig.17, only the miscibility gap is considered in CeO1.5-CeO2
system. The calculated results met very well with experiments and keep consistent with
each other.
Figure 15. Calculated and experimental phase diagram of ZrO2-CeO1.5 system, circles showing the
experimental result[33]
Figure 16. Calculated and experimental phase diagram of ZrO2-CeO2 system, cycles showing the
Figure 17. Calculated and experimental miscibility gap in CeO1.5-CeO2 system, circles showing the
In order to understand thermodynamically the degasing of CeO2, additional deduction is

necessary as follows:
The chemical potential of oxygen in phase <CeO2-y> depends on the two mass variables,
undefected species CeO2 and defected CeO1.5. In CeO1.5-CeO2 system, it would be natural to
list the formula
4CeO1.5 O2 4CeO2 (23)

With the evaluated model parameters of phase <CeO2-y> and Thermo-Calc, The authors[33]
get the chemical potential of component CeO2 and CeO1.5 respectively. Therefore, the
chemical potential of oxygen in this phase can be listed as:
O o O RT ln( PO2 ) 4CeO 4CeO (24)

2 2 2 1.5
Under reduced atmosphere, phase css in ZrO2-CeO2 system changes to <Zr1-zCezO2-x>. Since
no defects have been introduced in phase css in ZrO2-CeO2 system, The authors[33] also get
oxygen potential for phase <Zr1-z CezO2-x> from Eq. 24. To get the relation between
nonstoichiometry y in <CeO2-y> and oxygen potential in phase <Zr1-zCezO2-x> in the ternary
system at different temperatures, some manipulation has been made. It is supposed that
phase <Zr1-z CezO2-x> is composed of (1-z) mole ZrO2 and z mole <CeO2-y>. <CeO2-y> is
composed of m2 mole CeO2 and m1 mole CeO1.5. Then the O/Ce ratio is calculated from the
ratio O/(Ce+Zr)
2 y [2 x 2(1 z)] / z (25)
To obtain the ln(y)-T-ln(PO2) relation, one first need to determine the moles, mi, of each
components. These are calculated from the mass-balance for cerium and oxygen, which is
z m2 m1 and z(2 y ) 2 m2 1.5m1 (26)
Which lead to
m1 2 zy , m2 z(1 2 y ) (27)
Where z =1 mole represents a system without component ZrO2.
With the thermodynamic parameters of the three sub-binary systems[33] and Eq. 24, the
relation ln(y)-ln(PO2) in CeO1.5-CeO2 system, as well as in ZrO2-CeO1.5-CeO2 system are
calculated by Thermo-Calc[33].
Fig. 18-20 shows the calculated results. Fig. 18 represents the experiment data and the
calculated relation ln(y)-ln(PO2) at 1773K, 1573K, 1473K, where the little circles denote
experiment data from Lindemer et al.[35]. It is obvious that the assessed parameters from
CeO2-CeO1.5 system with compound energy model can represent the relations very well.
Fig. 19 reveals the relation between CeO1.5 and ln(PO2) in a system without component ZrO2
(z=1) at different temperatures, showing temperature has great effect on oxygen partial
pressure. In Fig. 20, different solid lines represent different z values (0.1, 0.2, 0.3, 1.0)
corresponding to different mole fraction of ZrO2 (0.9, 0.8, 0.7, 0 respectively) in the ternary
system at 1473K. It is obvious that the same nonstoichiometry y corresponds to different
oxygen partial pressure at different z. Also can be found is the significant effect of z value
(the content of ZrO2) on the relation between oxygen partial pressure and nonstoichiometry
value.
Figure 18. Calculated and experimental relationship ln(y)-ln(PO2), circles showing the experimental
result[33]
Figure 19. Relations between the different amounts of CeO1.5 and oxygen partial pressure at different
temperatures[33]
Figure 20. Predicted relations ln(y)-ln(PO2) at 1473K with different z values [33]
A substitutional model was used to describe the quasibinary systems, which estimates the
mixing entropy of complex ceramic systems in a very simple way. Kaufman et al[32] Du et
al,[36] and Li et al.[37-39] already successfully evaluated oxide phase diagrams in this way. Li et
al[40] pointed:
When calculating oxide systems, if there do not exist any short range ordering, shortage of
elements or molecular-like associate in sublattice, the substitutional model is an effective
alternative of sublattice model. Furthermore, if the valence of the cations are the same, the
application of substitutional model can obtain the same formalism of Gibbs free energy and
the same calculated result as that can be obtained by the subblatice model, though the
former is more simple and easy to be extened into higher order symtems.
Then, the Gibbs free energy of one mole solution phase, is described as:
2
m ( x , T ) xi .G f (T ) RT xi ln xi x1x2
i
G
i 1
(28)
1
K n 3
( x1 x2 ) n
n0
The first term on the right side accounts for the mechanical mixture of the pure components.
oG i
f (T ) is the standard Gibbs free energy , i.e., the formation energy of mass parameter
i from the elements in their standard states. The second term refers to an ideal solution, and
the third term is the excess Gibbs free energy function, which is a Redlich-Kister polynomial.
The K n factor in Eq. (29) is a temperature-related polynomial and is expressed as:
K n An BnT C nT ln T DnT 2 En / T F nT 3 (29)
Gibbs free energy of one mole (cation) stoichiometric compound phase with pyrochlore
structure is described as:
Zr 02 CeO1.5
G(1 / 4)Zr2Ce2O7 (1 / 2) Gcss
f (1 / 2)Gcss
f A B*T (30)
Also with the relationship deduced in Eqs.(23-27), one can find in a system without ZrO2
component i.e., z=1 (mole), the mole fraction of CeO1.5 is N1=m1/(m1+m2) and the mole
fraction of CeO2 is N2=m2/(m1+m2). Moreover, y=0.50.5N2.
Based on the thermodynamic information of the limiting quasi-binary systems, which is

evaluated in reference [34,41] the molar Gibbs free energy of the nonstoichiometric phase
Zr1 zCe zO2 x can be written according to Maggianu[42] as:
GZr1 zCezO2 x / ( m1 m2 m3 )
ZrO2 CeO2
N1G css
f N 2 G css
f
ZrO2
N 3 G css
f N1RT ln( N1 ) N 2 RT ln( N 2 )
N 3RT ln( N 3 ) K1,2
3
N1N 2 K1,2
4
N1 N 2 ( N 1 N 2 ) (31)
3
K1,3 N1 N 3 4
K1,3 N1 N 3 ( N1 N3 ) 3
K2,3 N2 N3
4
K2,3 N2 N3 ( N2 N3 )
i
Where oG css
f is the standard Gibbs free energy of formation of mass parameter i from
ZrO2
the elements in their standard states. oG css
f is after the compilation of Pankratz, [43]
CeO1.5
whereas oG css
f is retrieved from the quasi-binary phase diagrams [41] . Kin, j is the
interaction coefficient, where n is the order of the RedlichKister polynomial and the
subscripts i,j represent the components, i.e., CeO1.5=1, CeO2=2, ZrO2=3. Ni(i=1,2,3) is the
molar fraction of CeO1.5, CeO2 and ZrO2 respectively.
The partial molar free energy for mass parameter i equals to,
[G' Zr1 zCe zO2 x ] / mi Gi (32)
With the equation similar to Eq. 24,
RT ln( Po2 ) 4 GCeO2 4 GCeO1.5 (33)
The relationship between ln(y) and ln(PO2) at 1473K is calculated and shown in Fig. 21,
which is exactly the same as shown in Fig. 20 calculated by CEM.
Figure 21. Predicted relationship between ln(y) and ln(PO2) at 1473 K at different CeO2 y molar
fractions in the ZrO2CeO2CeO1.5 system[34]
The research staff members in Exhaust System of MERCEDES CAR GROUP checked
independently the work stated above over years, they followed each of the published papers
and calculated their system with the equations and model parameters in the publications.
They were convinced that the calculation stated above predicted the mechanism in the
automobile emission system and met very well with their detected data in all the gasoline
engines of Mercedes Car.
6. Conclusion
An aspiration of engineers in materials field is to have the possibility to estimate in advance
the composition, properties, processing parameters, etc., while they are planning to develop
a new material. This chapter offers a basic sketch where one could find how
thermodynamics, coupled with accurate experiment results, constructs the entrance for
mass production. In order to limit the chapter length, only less examples were listed and
most of them are stressed at steels, which include developing new type steel, improving the
quality of existed steel and discussing the factors mainly influencing steel property.
Calculation is applied in the light of the existed commercial software package though, in
some cases, suitable derivation to reveal the relationship between thermodynamic
properties of substances and self-made database exhibit also extreme importance in the
designing of materials. Moreover, both compound energy model and substitutional model
are used to describe the complex degassing behavior in the ZrO2-CeO2 system which reveals
how and why the simple model could be successfully applied in complex systems.
Author details
Lin Li
School of Materials, Shanghai University, Shanghai, P.R.China
Acknowledgement
This work is financially supported by National Key Basic Research Development Project of
China (973 Programme, No.2010CB630802), NSFC(No.50934011 and No.50971137) and
School of Materials, Shanghai University.
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CeO1.5CeO2 system, J. Eur. Ceram. Soc., 23 (2003) 99106
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Chapter 10
Thermodynamics of Wool Dyeing
Rza Atav
1. Introduction
The pleasure derived from imparting color to clothing has existed since the time of the
earliest civilizations; a world of fashion without color is impossible to imagine. Coloration
processes produce the most visible results of all the finishing operations carried out
during preparation of textile goods [1]. Dyes are synthetic aromatic compounds which can
bring bright and firm color to other materials. It is reported that over 100,000 commercially
available dyes exist and more than 7x105 metric tons of dyes are produced worldwide
annually [2]. When a textile fiber is immersed in a solution of dye under suitable conditions,
the fiber becomes colored, the color of the solution decreases and dyeing has occurred [3].
The wool fiber is the hair of the sheep and forms the protecting covering of the animal [4].
Structurally, a wool fiber is an assembly of cuticle and cortical cells held together by the cell
membrane complex (See Figure 1). The dyeing and diffusion properties of fibers are known
as governed by this membranous structure, which is formed predominantly by internal
wool lipids [5].
Figure 1. Cross-section diagram of a merino wool fiber [6]

Wool cuticle cells (overlapping cells that surround the cortex) are subdivided into two main
layers, namely the exocuticle and endocuticle [7]. The outer surface of the scale of the cuticle
is covered by a very thin membrane called the epicuticle. Below this hydrophobic epicuticle
is the exocuticle, a cystine-rich part forming about two-thirds of the scale structure. The
exocuticle just below the epicuticle is referred to as the A layer, having a distinctly higher
cystine part than the rest of the exocuticle (known as the B layer). Below the exocuticle,
forming the rest of the scale structure is the endocuticle and then a thin layer of intercellular
cement [6].
For wool, its complexity is illustrated by the different important chemical groups it has and
the intermolecular forces of attraction that are formed. First, there are the polar peptide
groups (i.e., -CO-NH-). Second, the oxygen of the carbonyl groups (-CO-)is slightly
negatively charged and, as a result, will form hydrogen bonds with the slightly positively
charged hydrogen of the imino groups (-NH-) of other peptide groups. Third, cystine, the
sulfur-containing amino acid capable of forming disulfide crosslinking tends towards
greater chemical stability, resulting in less dye absorption [8].
Wool dyeing is a process involving high temperature for long periods in acidic to neutral
pH medium to do good penetration, optimum fastness, and dyebath exhaustion. The shape
of the conventional dye uptake curve is consistent with an initial dwell time (20 to 40C)
when dye is transported 1 through the medium, a primary exhaustion stage (40 to 60C)
when dye levels at the fiber surface and diffuses within, and a secondary stage (60 to 90C
and above) during which time the dye disperses and immobilizes within the fiber. There is
much resistance to dye penetration from the epicuticle layer of the cuticle cell of the wool
[9].
The surface of the cuticle cells is highly hydrophobic due to covalently bound fatty acids.
The covalently bound fatty acids and the high amount of disulphide bridges make the outer
wool surface highly hydrophobic. Especially in the printing and dyeing of wool, the
hydrophobic character of the wool surface is disturbing. Diffusion of the hydrophilic dyes
into the fibers is hindered [10].
Earlier workers identified the epicuticle with the barrier to dye penetration, thinking that
this part forms a continuous membrane around the fiber. The barrier has also been ascribed
to the cuticle and to the highly crosslinked A-layer of the exocuticle. All these suggestions
on the nature of the barrier were based on a common belief that dyes must diffuse through
the cuticle cells to reach the fiber cortex (i.e. the transcellular route shown in Figure 2) [11].
A continuous phase of membrane cells, the cell membrane complex underneath the cuticle,
forms a network of penetrating canals to help mediate the impedance of the lipid barrier to
dye diffusion, thereby facilitating dye penetration into the fiber interior [9].
In the manufacture of the almost infinite variety of wool textures, the dyeing of the wool
itself is one of the series of many operations involved; and whilst of cardinal importance, the
dyeing process must be subordinated to the particular final texture devised by the
manufacturer [13]. For dyeing of wool fibers acid, metal complex 1:1 and 1:2, chrome
Thermodynamics of Wool Dyeing 249
Figure 2. Diffusion pathways for dyes into wool [12]
and reactive dyes can be used [14]. In this chapter knowledge related to the
thermodynamics of wool dyeing will be given.
2. Thermodynamics of wool dyeing

Dyeing systems can be classified as follows;
1. Non-ionic dyes applied to substrates which are non-ionic or ionic

a. Disperse dyes on essentially non-ionic substrates, such as the hydrophobic fibers
produced from polyester, secondary cellulose acetate and cellulose triacetate, and
b. Disperse dyes on ionic substrates such as nylon.
2. Ionic dyes applied to substrates which themselves carry a charge
a. Ionic dyes applied to substrates which carry the same charge as the dye, as exemplified
by anionic dyes on cellulose, and
b. Ionic dyes applied to substrates which carry the opposite charge as the dye, such as
anionic dyes on wool and nylon and cationic dyes on acrylic fibers [3].
From above classification, it can be understood that the wool dyeing is a good example for
dyeing systems described in 2b. In general, wool dyeing process occurs in four basic steps;
- Wetting and swelling of fibers in dyeing liquor

- Adsorption of dye molecules on the fibers
- Diffusion of dye molecules into the fibers
- Fixation of dye molecules in fibers via various physical and chemical forces [15]
Knowledge in detail related to the thermodynamics of wool dyeing such as aggregation and
adsorption of dyes, rate, standard affinity, enthalpy and entropy of dyeing exc. is given below.
2.1. Aggregation of dyes

The nature of the dyeing process requires a complete understanding of the state of the dye
in the dyebath, and many of the problems associated with the dyeing of wool can be
explained in terms of the colloidal or aggregated nature of the dye [16]. Aggregation can be
defined as Clustering of each particle of a substance to give it colloidal properties [1]. A
number of organic dyes form aggregates in solution via weak non-covalent interactions. The
color, physical properties such as the solubility and photophysical behavior of dyes are
affected due to aggregate formation [17]. In dyes, the aggregation principally forms dimers
except at high concentrations in solvents with a high dielectric constant. For coloration of
materials, it is the monomer adsorbed on the surface. There may be next build up of dye
units through aggregation but the first layer must be composed of monomers [18].
Many studies have been carried out on the aggregation of dyes molecules or ions in aqueous
and non aqueous solutions. The interactions between dye molecules and other molecular
entities are of paramount importance in many industrial processes. The forces of attraction
responsible for such interactions are also capable of causing physical interaction between
dye molecules to produce molecular species ranging in size from dimmers to aggregates
containing hundreds of molecules [19].
The dye aggregation is a function of temperature, electrolyte concentration, surfactant type,

and dye concentration [20]. Aggregation is promoted by increasing the concentration of dye
in solution [3]. The addition of electrolyte to a dyebath can increase the degree of
aggregation, but fortunately the aggregation process is reversible and may be decreased by
a rise in temperature. A certain degree of aggregation can be beneficial since it tends to
increase the attraction of the dye for the fiber, but the large size of the dye aggregates can
lead to a drastic reduction in the rate of fiber penetration, or in some cases to the
precipitation (separation) of a dye from solution after prolonged storage [1]. Also chemical
structure of dye molecule has an important effect on aggregation. For example; the
tetrasulphonated dye C.I. Acid Red 41 has been shown to be monodisperse in aqueous
solution by both diffusion-based and light scattering techniques. This result is to be
expected, since the four sulphonate groups confer upon this molecule a high degree of
hydrophilicity. When the number of sulphonate groups is reduced to one, as in C.I. Acid
Red 88, then aggregation is expected to increase. The aggregation of C.I. Acid Red 88 has
been determined by diffusion and by polarography at 25C, and was found to range
between 2 and 5 [16].
So far the changes in absorption spectra have been described qualitatively, yet the
aggregation of dyes in aqueous and non-aqueous solutions may be studied quantitatively.
The Maximum Slope has proved to be the simplest and the most convenient method to
apply for such quantitative study. This method is based on the assumption that a simple
equilibrium model between a monomer (m) and polymer (m)n is operative [19]:
n(m)(m)n
First the following equation is used to estimate the values for degree of aggregation and
aggregation constant:
logC (1- ) = n logC (- n) + log n Kn (1- n)1-n (1)

where n = n / n
1 = molar absorbativity of monomer
= experimentally measured molar absorptivities
n = molar absorbativity of polymer
C = concentration of dye solution in mol/L
n = aggregation number
Kn = aggregation constant
By plotting logC (1- ) against logC (- n), the points should lie on a straight line; the slope
of which gives the degree of aggregation (n), and the aggregation constant (Kn) can be
calculated from the intercept. Reliable results are very difficult to be obtained due to the
assumption one has to make for 1 and n. The above equation is then rearranged in the form
[19]:
1/(n-1) logC (1- ) n/(n-1) n logC (- n) = log C = X (2)
where = (nk)1/(n-1)(1- n)-1
The Maximum Slope Method consists of correlating the curves of vs. logC and vs. X for
different values of n and n until a value of n is reached which gives the best fit between the
experimental results and the theoretical curve [19].
2.2. Adsorption of dyes

Adsorption is a process that occurs when a gas or liquid solute accumulates on the surface
of a solid or a liquid (adsorbent), forming a molecular or atomic film (the adsorbate). It is
different from absorption, in which a substance diffuses into a liquid or solid to form a
solution. The term sorption encompasses both processes, while desorption is the reverse
process [21].
The strength of the adsorption depends on the kind of interactions taking place between the
fiber surface and the dye molecules. Clearly, the highest strength results when a chemical
interaction occurs. Unfortunately, in many fiber/dye systems such surface interaction cannot
be realized. In the case of physical adsorption process, the strength is determined by the
Lifshitz - van der Waals, hydrogen bonding, and electrostatic interactions. The nature of the
process can be evaluated from the thermodynamic functions of the process [22]. As a result
of its chemical structure, wool contains a considerable number of both acidic and basic
groups and hence, it was natural to consider that the adsorption of ions by wool was
directly concerned with the presence of these groups; this is in turn led to the idea that ions
are adsorbed by wool on specific sites in the fiber [3].
Adsorption is usually described through isotherms, that is, functions which connect the
amount of adsorbate on the adsorbent, with its pressure (if gas) or concentration (if liquid)
[21]. The Langmuir isotherm, the Freundlich isotherm, and the Nernst isotherm are all
commonly used to classify dyeing isotherms even though they more correctly apply to the
adsorption of gases on metal surfaces [16]. Their shapes are shown in Figure 3 [23].
Figure 3. Specific isotherms of dye-fiber systems (Ds: Dye concentration in the dyebath, Df: Dye
concentration in the fiber) [23]
The simplest physically plausible isotherm is based on three assumptions:
1. Adsorption cannot proceed beyond monolayer coverage.

2. All sites are equivalent and the surface is uniform
3. There are no interactions between adsorbed molecules, so the ability of a molecule to
adsorb at a given site is independent of the occupation of neighboring sites [24].
The Langmuir isotherm is well suited to describe dye adsorption by certain textile fibers.
Considered in terms of dyeing, the basic postulate is that adsorption of dye takes place on
specific sites in the fiber and that when a dye molecule occupies a site that site is saturated
and incapable of further adsorption [3]. The Langmuir model is valid for monolayer
sorption onto a surface with a finite number of identical sites. Langmuir isotherm theory is
based on the assumption that adsorption on a homogeneous surface [25]. On the bases of
these assumptions Equation 3 can be written [16]:
Cf,a= KCs,m / (1 + KCs,m) (3)
Cf,a: concentration of adsorbed dye molecules on the fiber
Cs,m: concentration of mobile dye molecules in the bath
K: Adsorption constant
In the case of the Freundlich model (Equation 4) the dye is considered as being contained in
an internal phase of volume V of the fiber.
ln[C]f = ln KF + x ln[C]s (4)
where: [C]f represents the dye concentration in the fiber at equilibrium, in mol/kg dry fiber,
and [C]s represents the dye concentration in solution at equilibrium, in mol/L; KF is the
equilibrium constant, and x is a sub-unitary power [26]. The Freundlich isotherm is
commonly used to describe adsorption characteristics for heterogeneous surface [27]. The
Freundlich model assumes a heterogeneous multilayer adsorption surface with sites that
have different energies of adsorption which are not equally available [28].
The Nernst adsorption isotherm (Equation 5) is considered as a limit case of Freundlich and
Langmuir adsorption isotherms [26].
[C]f = KP [C]s (5)
Nernst isotherm equation is a mathematical representation of the distribution law, which

states that a dissolved substance, irrespective of its total amount, distributes itself between
two layers or phases in a constant concentration ratio, at constant temperature; the ratio,
equal to the constant in Equation 5, is referred to as the distribution or partition ratio.
Theoretically the law is limited to describing the behavior of dilute solutions [3].
2.3. Rate of dyeing

Four steps can be envisaged in the process of dye uptake:
a. diffusion to the fiber surface,

b. transfer across that surface,
c. diffusion within the fiber to appropriate sites, and
d. binding at those sites.
In principle, any of these could be the slowest-and hence the rate determining-step. The
theory of the kinetics of wool dyeing has generally been based on the premise that (c) is the
rate determining step (diffusion control). Various algebraic expressions have been derived
from Ficks laws of diffusion in an attempt to describe experimental dyeing rates. The most
common treatment is the parabolic, rate law, which was originally derived by Hill to
explain the diffusion of phosphate and lactate in muscles. If a semi-infinite solid is brought
into contact with a liquid containing a diffusible substance at concentration y0, then the total
amount diffused across a unit area (A) at time t is given by the following equation:
A = 2.y0.(Dt/)1/2 (6)
where D is the diffusion coefficient of the substance in the solid [29]. The calculated
diffusion coefficient appears to be exceedingly small when compared with values for other
simpler ions and molecules. This may, of course, be due merely to the size of the dye anion,
as diffusion within the solid is subject to greater restriction than aqueous diffusion, which
suggests that the diffusing unit must force a path through more or less rigidly held
molecules, so that a high activation energy is required. The apparently very low mobility of
the dye ions may be due to interaction of ions with the fiber in such a way that the majority
of ions within the fibers are held on specific sites; diffusion proceeds by way of a small
fraction of mobile dye ions, thus giving an apparently very low value for diffusion
coefficient [30].
The rate of diffusion of a dye in a fiber increases with increase in dyeing temperature. The
effect of temperature on the rate of diffusion is given numerically by the activation energy of
diffusion (E) according to the relationship shown in Equation 7:
DT=D0e-E/RT (7)
Where DT is the observed diffusion coefficient at absolute temperature T, D0 is a constant

and R is gas constant. Hence, if the logarithm of the observed diffusion coefficient is plotted
against the reciprocal of T, a straight line of slope E/R should be obtained; from which E can
be calculated [23].
Time of half-dyeing (t1/2) is the time taken for a fiber to adsorb 50% of the dye it would
adsorb at equilibrium. It provides an indirect measure of rate of diffusion and is useful for
comparing the behavior of dyes applied under identical conditions. Because of the very
gradual approach to equilibrium, the time taken to reach equilibrium cannot be measured
accurately. However, equilibrium adsorption, C can be estimated readily by dyeing for a
prolonged period and t1/2 is then determined using a graph of exhaustion versus time of
dyeing at Ct=0.5C (Figure 4). In certain cases, it is preferable to plot exhaustion against logt
since then the relevant portion tends to be a straight line and a more accurate estimate of t1/2
can be obtained [23].
Figure 4. Exhaustion of dyes (%C) with time [23]
In practice, the experimental conditions must be chosen with care. If the conditions are such
that the bulk of the dye is adsorbed on to the surface of the fibers quickly this will musk the
effect of diffusion into the fiber [23, 31]. The conditions should be so chosen that the dye-
fiber attraction is low and the final exhaustion is not very high (<80%). The time of half
dyeing is also very dependent on the amount of dye used [23].
If the time of half dyeing is known for two different temperature activation energy of
diffusion (E) can be calculated from the equation given below [31];
log(t1/2)323 log(t1/2)363 = [E/2.3*R] * [(363-323)/(363*323)] (8)

2.4. The standard affinity of dyeing

Thermal activation is only the first stage in the dyeing process. The driving force in the
transfer of dyes from solution to the fiber is the difference in free energy between the two
phases. In other words, the energy needed to compress the dye molecules from their
freedom of movement in the solution to the restricted volume within the fiber. This is more
conveniently expressed in the form of the chemical potential () which is defined as the
difference in free energy between two phases when a very small quantity of dye is added to
the solution, all other variables kept constant. The standard potential is derived from the
basic equation, applicable to ideal solution, namely Equation 9:
= A + RT lnC (9)
where A is a constant, and C is the molar concentration [23].
A numerical parameter is needed to describe the behavior of individual dyes at equilibrium

(thermodynamics) which is independent of variations in the dyeing conditions. Such a
parameter would be standard affinity of the dye. Standard affinity of dyes has been defined
as the difference between the chemical potential of the dye in its standard state on the fiber
and the corresponding chemical potential in its standard state in the dyebath [32].
Affinity (-) is measurable according to the principles of thermodynamics and may be

expressed in energy unit (kjoules/mole). It is the most basic thermodynamic parameter of
the dye in dyeing solution towards fiber substrate. The greater the degree of exhaustion at
equilibrium the greater is the affinity [33].
The standard affinity for the distribution of dye between the fiber and dyebath is
proportional to the logarithm of the ratio of the absolute activities of the dye in the fiber and
dyebath. Since the activity of the dye is assumed to be directly related to its concentration,
one can write equation as follows [16];
0 RT[ In([C ]F / [C ]L )] (10)
: standard affinity (J mol-1)
R: gas constant (8.317 J K-1 mol-1)
T: absolute temperature (K)
[C]F: concentration of dye on the fiber at equilibrium (g/l)
[C]L: concentration of dye remaining in the dyebath at equilibrium (g/l)
It was this point, where values had to be assigned to activities of the ions in the fiber, that a
difference of opinion arose and this led to two different approaches being formulated,
namely the Langmuir or Gilbert-Rideal method and the Donnan method. The differences
between the two are described pictorially in Figure 5 for a simple, monobasic strong acid
HX [3].
Figure 5. Pictorial representation of two approaches to wool dyeing theory: (a) Gilbert-Rideal, (b)
Donnan [3]
a) Gilbert - Rideal theory: In that explanation, the activity coefficients of ions sorbed into the
wool phase are reduced due to specific binding with sites on the wool, that is, the formation
of ion pairs. Wool dyeing generally occurs in the presence of an acid as well as the dye (the
acid is usually applied in a preliminary step). Gilbert and Rideal proposed that dye uptake
is an anion exchange process, in which the dye molecules displace smaller anions [29].
b) Donnan theory: In this theory, the dye was considered to partition between the external
solution and an internal solution phase in the wool. The latter phase is believed to contain a
high concentration of fixed ionic groups, and hence solute molecules have reduced activity
coefficients in that phase due to Coulombic interactions [29].
Derbyshire and Peters, proposed a unified interaction theory for all dye-fiber systems,
postulating that the principal contribution to the standard affinity of the dyes, of all classical
types, to all kinds of fibers arises from the nonpolar Van der Waals forces. They postulated
that non-polar forces are mainly responsible for dye-fiber attachment and that in aqueous
solution they occur between hydrophobic surfaces. The dyeing behavior of each type of
fiber is predicted from the postulate that dye substantivity is due to non-polar forces. They
suggested that the hydrophobic parts of the dye molecules have adequate affinity for the
hydrophobic parts of the fiber. Accordingly the less hydrophobic dye molecules also have
sufficient affinities for the more hydrophobic synthetic fibers, whereas dye molecules with
larger hydrophobic parts will be required to dye a hydrophilic fiber such as wool [34].
Zollinger considered hydrophobic bonding in addition to the two well-known types of dye-
fiber interaction in the adsorption of anionic dyes by wool such as coulombic attraction of
dye anions to cationic groups on the fibers and Van der Waals (London) forces. The
thermodynamic parameters such as standard enthalpies and standard entropies were
measured for the adsorption of three suitable acid dyes on wool, and it was concluded that
aliphatic side-chains contributed to the dye-fiber hydrophobic interaction. However, the
detection of this contribution was difficult, because of the additional effect of dye-dye
aggregation equilibria in solution [35].
Iyer et al. carried out a study using three different related acid dyes (Table 1); they
calculated the heats and entropies of dyeing. They showed that with increasing hydrocarbon
chain length, the affinity of the dye was increased, while the effect of a phenyl group was
greater than that of a straight chain of four carbon atoms. It is surprising that the heat
evolved on dyeing is decreased as the affinity increases. This is unusual, since higher
affinity generally corresponds to larger heat of dyeing [36].
- - H0 S0
R
(kCal mol-1) (kCal mol-1) (Cal k-1 mol-1)
-CH3 5.3 7.6 -7.2
-C4H10 5.8 7.1 -4.1
-C6H6 6.0 5.6 +1.2
Table 1. Thermodynamic parameters of acid dyes on wool (at 50C and pH 4.6) [36]
The results of the study carried out by Ferrini et al. (Table 2) was also indicated that the
phenyl group is more effective in reducing H0 than is the butyl chain [37]. Asquith et al.
claimed that the reason of the effect of a phenyl group to be greater than that of a straight
chain was the effect of the phenyl group on dye aggregation to be greater than that of the
butyl chain [38].
- H0 S0
Temp. (C)
(kCal mol-1) (Cal k-1 mol-1)
41-51 4.8 -2.2
70-79 7.2 -9.3
41-51 7.0 -4.9
70-79 11.3 -17.7
41-51 5.7 -0.8
70-79 8.9 -10.5
Table 2. Heats of dyeing and entropies of acid dyes on wool [37]
2.5. The enthalpy of dyeing

The second thermodynamic quantity which is important in describing a dyeing process is
the heat of dyeing or the change in enthalpy of the system when adsorption takes place [3].
As a result of dye molecules to be adsorbed on the fiber surface, free movement of these
molecules gets restricted. So that entropy decreases when dye molecule is adsorbed.
Adsorption also causes free energy to decrease.
G0 = H0 T.S0 (11)
According to the Equation 11, enthalpy change should be negative, in other words
adsorption is exothermic. For this reason adsorption amount will increase, when
temperature is decreased [15]. Also the affinity of a dye is dependent on temperature. It
decreases as the temperature rises, i.e. the equilibrium shifts in favor of the external phase.
When -/T is plotted against 1/T (T is the absolute temperature for a particular affinity
value), the slope of the straight line obtained gives H0, the heat of dyeing [39]. However,
the numerical value of , obtained from dye absorption, cannot be verified, and S0 is
impossible to measure, while H0 is solely dependent on . Hence, using Equation 5, any
error in will accumulate in H0 and S0. One of the errors in determining may be
due to aggregation of the dye in solution under some conditions. Such an aggregation
equilibrium could explain why a linear plot of - /T against 1/T cannot always be
obtained. In an attempt to clarify the latter point, Asquith et al. carried out a study on two
dyes (C.I. Acid Orange 7 and 10), one known to be non-aggregating under the selected
conditions of dyeing studied. Figure 6 shows the plots of - /T against 1/T for these two
dyes [38].
Figure 6. The relationship between - /T and 1/T for various acid dyes [38]
According to these experimental results Asquith et al. denoted that for Orange 7, the plots
each consist of two straight lines, intersecting at 60C, which clearly indicates that this dye
has two H0 values, corresponding to two temperature ranges-viz, below and above 60C.
The deviation from linearity in the above plots immediately leads to the speculation that the
and H0 values obtained from dyeing with Orange 7 has been influenced by dye
aggregation equilibria in solution [38].
If the values of are available for two absolute temperatures T1 and T2, it is more
convenient to use the Equation 12 [39]:
H0= (T21-T12) / (T2-T1) (12)
where T1 is the initial dyeing temperature in Kelvin; T2, the final dyeing temperature in
Kelvin, 1, the affinity at T1 K, and 2, the affinity at T2 K [40]. The value of H0
represents the difference in heat content between that needed to free one mole of dye from
the solvent, and that required to free the same quantity of adsorbed molecules from the
surface or from the interior of the solid by thermal agitation. It is thus the heat of sorption,
i.e. the increase in heat content (enthalpy) of the system when the dye is sorbed. Large
negative values of H0, therefore, correspond to high potential affinity [23].
2.6. The entropy of dyeing

The third thermodynamic parameter is the standard change in the entropy of the system
(S0) [3]. The standard entropy of dyeing, S0, can be calculated from the Gibbs equation
[26]:
= H0 T.S0 (13)
Because there is no direct experimental means of measuring the entropy change, it is

necessary to calculate its value from measurements of and H0 [3]. According to
Boltzmans conception, the entropy is proportional to the probability of the system [26]. The
change in entropy (S0) represents (on a logarithmic scale) the ratio of probability of
sorption (1) to that of desorption (2) as shown in Equation 14:
S0 = Rln1 - Rln2 = Rln(1/2) (14)

This entropy of sorption is the gain in entropy or disorder of the system when dye is
adsorbed [3]. From the dyeing point of view the entropy change is of practical importance
especially in two cases, in which either two dyes are compared on a common fiber or one
dye is compared on two fibers. Therefore, dyeing entropy can almost be identified with
dye/fiber orientation [26].
The entropy changes due to the dye sorption can be evaluated in a similar way to the
enthalpies from the sorption isotherms determined at different temperatures via the free
energy of adsorption G0.
S0ad=R(T1 lnC1 - T2 lnC2) / (T2 - T1) (15)

The change in entropy upon the sorption process consists of two parts, one of which results
from the dehydration of dye molecules before their adsorption (and dilution of the solution)
and the other is connected with the actual interaction of the molecules with the solid surface.
While the latter part is negative (loss of the molecular freedom), the former is positive.
During a spontaneous adsorption process, the total entropy change is always positive [22].
3. Conclusion
Wool fibers have the most widely usage in the textile sector among the animal fibers and
these fibers are dyed with acid, metal complex 1:1 and 1:2, chrome and reactive dyes. In
order to understand the dyeing mechanism of these fibers better, it is needed to know
thermodynamic and kinetic aspects of the dyeing such as aggregation and adsorption of
dyes, rate, standard affinity of dye, enthalpy (standard heat) and entropy of dyeing exc.
Author details
Rza Atav
Namk Kemal University, Textile Engineering Department, Tekirda, Turkey
4. References
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ISBN 0 901956 56 2 1993
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Chapter 11
Mesomechanics and Thermodynamics of

Nanostructural Transitions in Biological
Membranes Under the Action of Steroid
Hormones
L.E. Panin
1. Introduction
Biological membranes are liquid heterocrystals with low shear stability. The main structure-
forming bonds in biological membranes are covalent and hydrogen bonds, and hydrophobic
and weak electrostatic interactions. These bonds are responsible for high membrane
elasticity a property of particularly importance to erythrocytes, which have to pass
through blood capillaries of diameter equal to the erythrocyte one. Any structural changes
that increase the erythrocyte membrane viscosity hamper the motion of erythrocytes
through capillaries and may result in diffuse hypoxia. In this context, of great interest is the
effect of stress hormones (cortisol, adrenaline, noradrenaline) on the behavior of erythrocyte
membranes.
The nonspecific binding of stress hormones with erythrocyte membranes was studied earlier
in [1]. It was shown that excess of these hormones in blood are capable for nonspecific
binding with blood cells, primarily with erythrocytes, producing changes in rheological
properties of the blood. It was found that CO, OH, and NH active groups incorporated in
the structure of hormones can form hydrogen bonds with similar groups of proteins and
phospholipids of erythrocyte membranes. Hydrophobic rings of hormones can participate
in hydrophobic interactions with residues of phospholipid fatty acids, as a result of which
complex domains arise in the membrane structure, the membrane microviscosity increases,
and the motion of erythrocytes through capillaries becomes difficult. This effect is
particularly dangerous to heart because it can leads to coronary syndrome [2, 3].
Physicians still fail to understand the nature of this phenomenon, which shows up as
exertional angina and ischemic ST segment depression on electrocardiograms with a

normally functioning left ventricle.
Anabolic steroid hormones have been used for many decades, finding their most extensive
use in sports medicine. Nowadays, it is impossible to train as an international class athlete
without anabolic hormones. A coachs aspiration for high sporting results prompts that
coach to use an ever increasing amount of anabolic steroids. Lacking a profound knowledge
of sports medicine, such a coach cannot imagine all of the negative effects of anabolics on
the body of an athlete. Moreover, sports medicine itself has no comprehensive information
on the subject. As a consequence, the number of sudden and unexpected deaths of atheletes
during the competitions has drastically increased in recent years [4].
Physicochemical analysis of the behavior of erythrocyte membranes as liquid heterocrystals

makes it possible to disclose a link between structural changes in erythrocyte membranes
and erythrocyte function. Of particular interest is activity of the Na+, K+-ATPhase that
supports the transmembrane potential of cells and precludes their aggregation. It was
previously supposed that the regulatory action of different ligands can be based on certain
conformational changes of the Na+, K+-Phase [5]; however, the mechanism by which
steroid hormones affect the activity of the Na+, K+-Pase is poorly known.
In this work, the mechanism of testosterone, androsterone, dehydroepiandrosterone

(DHEA), dehydroepiandrosterone sulfate (DHEAS) and cortisol interaction with structural
components of erythrocyte membranes (mesomechanics and termodinamics of
nanostructural transition) changes in their microviscosity and functional characteristics
during the interaction have been studied. The results obtained could also shed light on the
causes of cardiovascular catastrophes, which are often observed in sportsmen taking
anabolic steroid hormones for a long time [6].
2. Materials and methods

The action of five hormones: testosterone, androsterone, dehydroepiandrosterone (DHEA),
dehydroepiandrosterone sulfate (DHEAS) and cortisol (Amersham) is analyzed in the work
(Fig. 1).
For this purpose, the following methods were used.
2.1. Atomic force microscopy (AFM) of erythrocytes

Erythrocytes were obtained from fresh blood after decapitation of Wistar rats under light
nembutal narcosis. Blood was diluted twofold by isotonic phosphate buffer ( 7.35)
containing 0.043 M of 24 and 0.136 M of Na24. After precipitation of cells by
centrifuging at 330 g for 10 min, supernatant liquor was decanted, and the washing
procedure was repeated twice more.
All the procedures were performed at 4 C [1]. The resulting erythrocyte suspension of
20 mcl volume was deposited onto a glass slide as a thin smear. The smear was predried for
Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 265
10 min in air at 24 C and humidity of 40%. After evaporation of excessive surface moisture,
the smear was observed under a Solver Bio atomic force microscope (NT-MDT, Russia) at
24 C using a semi-contact mode. An analogous procedure of obtaining red blood cells for
the AFM examination was employed earlier by other authors [7]. In each experiment first a
control specimen without hormones, and then the experimental one have been tested.
Silicon cantilevers NSG11 (NT-MDT, Russia) with a resonant frequency between 120 and
180 kHz and spring constant ~ 6 N/m were used (all of these probe parameters were offered
by manufacturer). Images of the surface relief of erythrocyte membrane after absorption of
hormones were obtained with the scan size 11 m2 and 1.31.3 m2.
Figure 1. Chemical structure of steroid hormones.

2.2. IR spectroscopy of erythrocyte shadows

Erythrocyte shadows were obtained after their hemolysis in hypotonic phosphate buffer
( 7.35) containing 2.75 mM of KH24 and 8.5 mM of Na24. Shadows were
precipitated by centrifuging at 5500 g, supernatant liquor was decanted. The washing
procedure was repeated four more times [8]. All operations and further storage of shadows
were performed at 4 C.
A film for taking the IR spectra of erythrocyte shadows was prepared in a cuvette with
fluorite backing via slow evaporation of water under weak vacuum at a pressure of ca. 0.1
atm (ca. 0.5104 Pa) and temperature 41 C [8]. Drying lasted 180 min. A suspension of
erythrocyte shadows in a 0.001 M phosphate buffer with pH 7.35 and volume 60 mcl was
introduced into a cuvette. This was supplemented with 30 mcl of the same buffer and
1.0 mcl of the hormone solution with concentration 106 M. Stirring and incubation lasted 10
min at 16-17 C. The cuvette was placed horizontally on a special table of a vacuum unit.
When the film was prepared, the cuvette was transferred into an optical chamber and blown
with dry air for 30 min, then the scanning unit was switched on. IR spectra were taken on a
Specord-M80 spectrometer (Germany, Leipzig), sequentially experiment and control against
the fluorite backing, or experiment and control to obtain a difference spectrum. Integration,
determination of the spectrum band frequency, and mathematical processing were
performed with special programs enclosed to the spectrometer. Erythrocyte suspensions
were examined upon addition of cortisol using UV (Evolution 300, Thermo Scientific, USA).
Merk or Sigma reagents were used in the work.
2.3. Fluorescence analysis of erythrocyte shadows

Fluorescence measurements were performed with a Shimadzu spectrofluorophotometer RF-
5301(PC)SCE. 4 ml of hypotonic phosphate buffer containing 2.75 mM of 24 and
8.5 mM of Na2HP4 ( 7.35), and erythrocyte shadows were poured into a quartz cuvette
of size 1 1 4 cm3. The concentration of shadow proteins was determined by the Warburg
Christian method from changes in the optical density of suspension [9]. On the average, it
varied in the range of 0.100-0.250 mg/ml.
A cuvette with the shadow suspension was placed into a spectrofluorimeter thermostat for 1
hour. Getting a stationary temperature regime in the cuvette was controlled by an electronic
thermometer. In all the experiments, temperature in the cuvette was 36 C. After
establishing a stationary temperature in the cuvette, intensity of the intrinsic fluorescence of
tryptophan residues in protein membranes was measured. The tryptophan emission
spectrum was taken in the range of 300 nm 400 nm at the excitation wavelength
281 nm, with the maximum of emission intensity observed at 332 nm. The average value of
maximum emission intensity was obtained graphically after its continuous measuring for 4
minutes. Intensity of tryptophan fluorescence fluctuated within 1%. The possible reasons
include variation of temperature in the cuvette with suspension, instrumental error in
determination of fluorescence intensity, and photochemical reactions occurring in the
system. Spectral width of the slits was 1.5/10. The tryptophan absorption spectrum was
recorded in the range of 220 nm 300 nm at the emission wavelength = 332 nm.
Testosterone, androsterone, dehydroepiandrosterone (DHEA) and dehydroepiandrosterone
sulfate (DHEAS) were dissolved in a mixture of dimethyl sulfoxide (DMS) and ethanol
(1 : 1, V/V). Concentration of the hormone in the initial mother liquor was 103 M. If
necessary, the solution was diluted with hypotonic phosphate buffer to obtain a desired
concentration.
A solution of hormones with the concentration 106 M was prepared in hypotonic phosphate
buffer. The time of hormone incubation with shadows was one hour. Absorption and
emission spectra were taken, the average value of emission and absorption intensity was
measured. For each hormone (testosterone, androsterone, dehydroepiandrosterone (DHEA)
and dehydroepiandrosterone sulfate (DHEAS)), the binding constant Kb was calculated by
the method [10] as well as the stoichiometric concentration of a bound hormone Bmax and a
change in free energy of the system G . The interaction of hormone and erythrocyte
membrane is described by the equation
B nS Sn B , (1)
where B is a membrane protein, S is the hormone, and n is the number of moles of hormone
per a mole of proteins. The binding constant Kb was calculated by the formula
S B
Kc n , (2)
S B
where Sn B is the concentration of bound protein, B is the concentration of free protein,

and S is the concentration of free hormone. It is supposed that hormone, upon binding to
protein, completely quenches its fluorescence. Thus, the fluorescence intensity F will be
proportional to the concentration of free protein. Lets write C for total concentration of
protein in the cuvette, and x for concentration of the bound protein. Then,
Fmax C
(3)
F C x ,
where F is the intensity of tryptophan fluorescence at = 332 nm (the excitation

wavelength = 228 nm), Fmax is the intensity of tryptophan fluorescence in the absence of
hormone (when the entire protein is free), is the proportionality factor, and AS is the
stoichiometric concentration of hormone. When concentration of hormone exceeds AS , the
fluorescence quenching does not increase. Dividing the first equation of set (2) by the second
one gives
Fmax F
x Q C , where Q (4)
Fmax
A
S A n x A n Q C , where A is the total concentration of hormone; n S ;
C
B C x C(1 Q) . Substitution of (2) and (3) into expression for binding constant (1)
gives
Q
Kc (5)
(1 Q)( A nQC )
In our case, molar mass of membrane proteins is unknown, so the concentration of proteins
in cuvette C is determined in mg/ml, and concentration of hormones A in mol/l. The
constant n is expressed in moles of molecules of hormone per milligram of protein (M/mg)
and is a ratio of the maximum concentration of bound hormone to the concentration of
membrane proteins. This can be written as
AS mole
BMAX (6)
C mg protein
Changes in Gibbs free energy G of the system upon transition of hormone from aqueous
medium to erythrocyte membrane are calculated by the formula
G RT ln( Kc ) J , (7)
mole
J
where R 8.314 , and T is the absolute thermodynamic temperature.
K mole
The measurement errors appeared due to inaccuracy in volumetric dosing of the shadow
suspension specimens and their titration against hormones. Specimens were dosed using
pipette dispensers DPAOF-1000 and DPAOF-50, their relative error at (202)C being 1%
and 2%, respectively. 4 ml of the buffer was taken once with a DPAOF-1000 pipette, and
suspension of erythrocytes and hormones was dosed twice using a DPAOF-50 pipette. The
fluorescence intensity of erythrocyte shadows F is directly proportional to the
concentrations of proteins C and hormones A in the specimen. Relative error EF in
measuring the F value can be estimated by the formula
1% 2% 2%
2 2 2
EF 3%. (8)
Relative measurement errors for Kb and BMAX can be obtained in the same way. They are
equal to 10%.
In calculation, the values of fluorescence intensity F were corrected for dilution of

suspension after the introduction of solution with hormone, for quenching of tryptophan
emission by the solvent (a mixture of DMS and ethanol), for proper fluorescence of
hormones, and evaporation of water from the cuvette.
2.4. Measurement of erythrocyte membrane microviscosity

Membrane microviscosity for translational diffusion of pyrene probe was calculated as a
ratio of fluorescence intensity of the pyrene dimer to fluorescence intensity of the pyrene
monomer. Microviscosity of erythrocyte membranes was measured also on a Shimadzu
RF-5301(PC)SCE spectrofluorimeter. The experimental specimen was prepared as follows:
4 ml of hypotonic phosphate buffer containing 2.75 mM of KH24 and 8.5 mM of
Na24 ( 7.35), a fluorescent pyrene probe, erythrocyte shadows and a specified
amount of hormone were placed in a quartz cuvette of size 1 1 4 cm3. Before use, all
the components were stored at 4 C. The concentration of shadow protein in the cuvette
was 0.100-0.250 mg/ml; that of pyrene, 7.76106 M. Pyrene was diluted in ethanol, its
initial concentration being 1.5103 M. The cuvette was placed into the spectrofluorimeter
thermostat for 10 min, then the fluorescence measurements were performed at 36 C.
Before placing the specimen into the spectrofluorimeter thermostat, it was shaken
vigorously for 1 min. For fluorescence measurements of shadows upon their loading with
a different amount of hormones, each time a new specimen was prepared by the same
procedure. Such a procedure is necessary because pyrene favors fast degradation of
erythrocyte membranes.
To measure microviscosity of a lipid bilayer near proteins (the region of protein-lipid

interaction), we used the excitation wavelength = 281 nm and spectral slit width 1.5/5.
Microviscosity of a lipid bilayer far from proteins (the region of lipid-lipid interaction) was
measured with the excitation wavelength = 337 nm and spectral slit width 1.5/3. At that,
the maxima of emission intensity were observed at = 374 nm and = 393 nm (the vibronic
emission peaks of excited pyrene monomers), and = 468 nm (the emission maximum of
excited pyrene dimer).
The relative microviscosity of membranes was determined as a ratio ( A) / 0 , where

( A) and (0) are microviscosities of membranes, respectively, with and without hormone
added to the shadow suspension. For the region of lipid-lipid interaction, relative
microviscosity was calculated by the formula
A F468 (0) F393 ( A)

(9)
0 F468 ( A) F393 (0)
where F468 ( A) is the fluorescence intensity of pyrene at wavelength = 468 nm in a

specimen at the hormone concentration A in suspension; F468 (0) is the fluorescence intensity
of pyrene at wavelength = 468 nm in a specimen with no hormone in suspension. F393 ( A)
and F393 (0) are the fluorescence intensities of pyrene at wavelength = 393 nm at the
hormone concentration A in suspension and without hormone in suspension, respectively.
The excitation wavelength is 337 nm.
For the region of protein-lipid interaction, relative microviscosity was calculated by the
formula
A F468 (0) I 468 F393 ( A) I 393

(10)
0 F468 ( A) I 468 F393 (0) I 393
where I 393 and I 468 are the fluorescence intensities of tryptophan at wavelength = 393 nm
and = 468 nm, respectively. The excitation wavelength is = 281 nm. A relative
measurement error for relative microviscosity was equal to 6%.
2.5. Change of the Na+, K+-Pase activity

Erythrocytes were extracted from fresh blood of rats. Erythrocyte suspensions with
hormones of differing concentration were analyzed to activity of the Na+, K+-Phase. The
experimental procedures used in these investigations are described in [5].
3. Results
3.1. Atomic force microscopy
Under atomic force microscope, erythrocytes of healthy animals looked as large biconcave
discs ca. 6 m in diameter, which agrees with the results obtained by other authors [7]. At a
higher magnification, their surface showed a slight nonuniformity caused most likely by the
presence of membrane proteins. When the erythrocyte suspension was supplemented with
DMS and ethanol (0.25% of the mixture volume), the surface nonuniformity increased,
probably due to denaturating effect of solvent on the surface structural proteins (Fig. 2).
Domains with the length 200-250 nm and height 2 nm are seen. The pattern changed upon
addition of testosterone to erythrocyte suspension with the final concentration 10-7 M (Fig.
3). The interaction of testosterone with erythrocyte membranes leads to their restructuring.
The surface is tuberous, there are domains of size 400 400 nm and height 20-25 nm, with
smaller domains on the surface of large ones: size 50 50 m2 and height 10 nm. Between
them, there are regions of loosened substance that form hollows. In this case, there are
pronounced distortions in the primary structure of erythrocyte membranes.
Other structural changes of erythrocyte membranes were obtained in our study upon
interaction with androsterone (Fig. 4) with the final concentration 106 M. The surface is flat,
there are domains of size 100 100 nm and height 6-8 nm. In comparison with control
specimens, domains decreased in area, but increased in height.
The surface of rat erythrocyte after adsorption of DHEA is depicted in Fig. 5. Concentration
of the hormone is 107 M. The surface is tuberous, there are domains of size 220 220 nm
and height 20 -25 nm. However, they are not separated into subdomains, as in the case of
testosterone.
Of the four hormones, DHEAS has the weakest effect on the membrane morphology. The
surface of rat erythrocyte after adsorption of DHEAS is shown in Fig. 6. Concentration of the
hormone is 107 M. The surface is flat, there are domains of size 100 100 nm and height 3 - 4
nm. Changes are insignificant in comparison with control. It can be suggested that DHEA
and DHEAS did not affect deep layers of the membranes, so the effect was much less
pronounced. IR spectroscopy allowed us to reveal the nature of these structural
transformations.
Figure 2. Control surface of rat erythrocyte. The erythrocyte suspension was supplemented with DMS
and ethanol (0.25% of the mixture volume): (a) scan size 1 1 m2; (b) center section of the surface.
Figure 3. Surface of rat erythrocyte after adsorption of testosterone.

Concentration of the hormone is 10-7 M: (a) scan size 1.5 1.5 m2; (b) center section of the surface.
3.2. IR spectroscopy of erythrocyte shadows

Analysis of IR spectra of erythrocyte shadows obtained from rats with no hormone
loading (Fig. 7) revealed in membrane-bound proteins not only a disordered structure,
but also -helix at 1650 and 1656 cm1, and -structure at 1686 and 1520 cm1. Besides, we
recorded NH stretching vibrations in proteins (3308 cm1), CH stretching vibrations in
proteins and phospholipids (2948, 2930 and 2848 cm1), and a set of bands corresponding
to phospholipids, in particular, C=O bond (1748 cm1), P=O bond (1236 cm1), 2
deformation vibrations (1460 and 1386 cm1), 44-55 bond (1048 cm1) and C-C bond of
deformation vibrations (978 cm1). It should be noted that = band (1736 cm1) is quite
narrow, which gives grounds to suggest that phospholipids in membranes of normal
erythrocytes are well ordered at a level of ester bonds of higher carboxylic acids and
glycerol.
3.2.1. Effect of testosterone

Under the action of testosterone, intensity of absorption bands 1544, 1656 and 3292 cm1
increased by 30% and more (Fig. 8, Table 1). Absorption band of N bond showed a
3308 3272 cm1 shift ( = 36 cm1). The bands 2852 and 2932 cm1 increased in intensity;
the ratio of band intensities 2852/2932 cm1 changed. The enhancement of integral intensity
of the indicated absorption bands indicates an increased ordering of membrane proteins
and, in particular, an increased fraction of -helices.
The fraction of -helices grows due to structural transition tangle -helix. A 3308 3272 cm
1 band shift of NH bond ( = 36 cm1) is caused by the formation of hydrogen bond
between keto group (C3=O) in testosterone A-ring and NH bond of peptide group in
membrane protein or indole ring in tryptophan. An increased intensity of the 2932 and 2852
cm1 bands together with a growing intensity ratio 2852/2932 cm1 confirm the rising
orderliness of the entire membrane. Absorption band 1740 cm1 (= bond of the ester
group in phospholipids) increased in intensity and shifted to the short-wave region. The
enhanced intensity of = bond reflects an increased ordering of phospholipids within
domains and an increased interdomain ordering. The short-wave shift of this band is caused
by the formation of hydrogen bond between OH group at 17 carbon atom in testosterone D-
ring and = bond in phospholipids. Similar to segnetoelectrics a hysteresis phenomenon
was observed in erythrocyte membranes [11, 12]. The spectrin-actin-ankyrin meshwork,
which is connected both with membrane proteins and phospholipids, also contributes to
the ordering of phospholipids. The 1088 1098 and 1236 1248 cm1 shifts of absorption bands
to the short-wave region result from dehydration of phospholipids due to increase in their
orderliness, since the hydration process shifts these bands to the long-wave region [13] An
increased intensity of bands 1098 and 1247 cm1 (-- and = bonds of phospholipids,
respectively) in comparison with control specimens confirms an enhanced ordering of
phospholipids under the action of the hormone.
Thus, the formation of complex domains in erythrocyte membranes upon their interaction
with testosterone is caused by simultaneous interaction of and OH groups of the
hormone with and N groups both of proteins and phospholipids. In the process, water
is displaced to adjacent regions, which is accompanied by membrane loosening.
Figure 4. Surface of rat erythrocyte after adsorption of androsterone.

Concentration of the hormone is 10-6 M: (a) scan size 1.5 1.5 m2; (b) center section of the surface.
3.2.2. Effect of androsterone

Incubation of rat erythrocyte shadows with androsterone (CC = 2.76 x 108 M) results in
shifting the frequency of NH bonds (stretching vibrations of amide A) to the long-wave
region by 38 cm1 as well as shifting of N bond of amide II ( = 2 cm1) (Table 1). Integral
intensity of absorption bands of (1654 cm1) and N groups (3280 cm1) increased by
30% and more. There appeared a band at 1635 cm1 corresponding to the -structure. An
increase in intensity of stretching vibrations of CH bonds at 2848 and 2930 cm1 was
observed. The frequency shift of NH bond is related with the formation of hydrogen bond
with 17= group of the hormone D-ring. Androsterone has a more flexible structure as
compared to cholesterol: its , and -rings can take a more favorable conformation during
the interaction with membrane proteins. Only D-ring has a flat structure, due to the
presence of carbon 17 with s2 hybridization. Hydrophobic interaction with the membrane
surface should also be taken into account. High conformational mobility of the molecule
creates more advantageous steric conditions for hydrophobic interaction both with
tryptophan, which fluorescence quenching was observed in our study, and hydrophobic
regions on the membrane surface. This increases the constant of their binding to hormone
and leads to more pronounced structural changes in the membranes. An increase in
intensity of -peptide bond is related with the growing fraction of -helices due to
transition tangle -helix. An increase in intensity of absorption band 1620-1635 cm1 is
caused by structural transition tangle -structure. Of interest is a hypothesis stating that
the indicated transitions may take place in contractile proteins, since their removal from the
membrane results in a decrease or disappearance of transitions [12-13].
3.2.3. Effect of dehydroepiandrosterone

Incubation of DHEA with erythrocyte shadows showed that the frequency of stretching
vibrations of N peptide bond shifted by 20 cm1 to the long-wave region (3308 3288 cm1),
whereas halfwidth of amide A decreased. An increase in the integral intensity of absorption
bands at 1546, 1654.9 and 3288 cm1 was observed (Table 1).
A 1236 1247.6 cm1 band shift points to dehydration of phosphate groups in phospholipids.
Shifting of the frequency of = bond in phospholipids (1748 1732 cm1) was observed;
intensity of this band also increased. The 2930 2925.8 and 2848 2851 cm1 shifts (
stretching vibrations) took place, intensity of the bands increased. The intensity ratio
2852/2924 cm1 changed.
3.2.4. Effect of dehydroepiandrosterone sulfate

Incubation of DHEAS with erythrocyte shadows resulted in the band shift 3308 3286 cm1
(N peptide bond) by 22 cm (Table 1). Bands at 1548, 1656 and 3298 cm increased in
1 1
intensity with respect to control specimen; however, this was more pronounced upon
addition of DHEA as compared to DHEAS. Absorption bands 1632 and 1684 cm1 attributed
to -structure were observed. The band shift was recorded: 2930 2928 and 2848 2852 cm1,
which was accompanied by a change in the 2852/2928 cm ratio. The band at 1236 cm1 (=
1
bond) showed a strong splitting and had 3-4 bands in the region of 1236-1256 cm1. Bands at
1084 and 1100 cm1 (P-O- bond) were observed. A 1748-1738 cm1 shift was detected;
however, it was less pronounced than in the case of DHEA addition. The DHEAS hormone
has a stronger binding with hydrophilic heads of phospholipids as compared to DHEA, and
a weaker binding with membrane proteins. This suggests that DHEAS molecules cannot
penetrate deep into the membrane due to their higher hydrophilicity with respect to DHEA.
Figure 5. Surface of rat erythrocyte after adsorption of DHEA.

Concentration of the hormone is 10-7 M; (a) scan size 1 1 m2; (b) center section of the surface.
Figure 6. Surface of rat erythrocyte after adsorption of DHEAS.

Concentration of the hormone is 10-7 M; (a) scan size 1 1 m2; (b) center section of the surface.
Overall, it can be concluded that the interaction of DHEA and DHEAS with erythrocyte
membranes is accompanied by the formation of hydrogen bonds between keto group
(17=) and N group of proteins as well as between group at 3 in the A-ring of the
hormones and C=O group in biomembrane phospholipids. The formation of indicated
hydrogen bonds leads to ordering of membrane proteins (transition tangle -helix) and
phospholipids. Hydrophobic interactions of hormone with the surface of erythrocyte
membranes also contribute to their structural rearrangement; however, they are much less
pronounced for DHEAS as compared to DHEA. The reason is that substitution of group
by SO3 strongly diminishes the energy of hydrogen bond, since in group the unshared
pair of electrons is located on the oxygen atom, whereas in SO3 group it is delocalized over
the entire -conjugated bond.
4. Fluorescence analysis
In the study, absorption intensity (D) and emission intensity (F) of tryptophan were
estimated at different wavelengths. Corrections were made for dilution of erythrocyte
shadow suspension after the introduction of a hormone solution, for tryptophan emission
quenching by a solvent (DMS : ethanol), intrinsic fluorescence of hormones, and evaporation
of water from a cuvette. To obtain a correction for solvent, the erythrocyte shadow
suspension was titrated with solvent.
It was shown that solvent decreases the intensity of tryptophan absorption at = 227.8 nm
by 33% and results in its long-wave shift to = 230.2 nm. Absorption intensity at = 281 nm
changed only by 1.3% without a long-wave shifting. A maximum of emission intensity
differed from control specimen also at = 332 nm. It did not shift upon addition of solvent,
but its intensity decreased by 1.3%.
Upon addition of testosterone with the final concentration 3106 M to erythrocyte shadows,
the absorption intensity at 227 nm diminished by 19 a.u. or by 2.8%; this was accompanied
by an upward shift of to 230.4 nm. As the hormone concentration increased to 6.05106 M,
the absorption intensity at 227 nm decreased by 25 a.u., or 5.0%, which was accompanied by
shifting the absorption maximum to 232 nm. In the region of 280 nm, addition of hormone
caused only minor changes in fluorescence. Considerable changes in the spectrum were
obtained upon addition of androsterone to the shadows. Even at a concentration of 6.92 10
8 M, which is two orders of magnitude lower compared to the case of testosterone, the
absorption intensity at 227 nm decreased by 90 a.u., or 122%. It means that this hormone
penetrates deeper into erythrocyte membranes than testosterone and enhances the tangle
-helix transition in proteins, thus increasing their ordering. When erythrocyte shadows
were supplemented with DHEA or DHEAS, the hypochromic effect was weak or entirely
absent. A decrease in absorption intensity and a long-wave shift observed in our study can
be attributed to the effect of solvent.
Analysis of the tryptophan fluorescence quenching spectra testifies that all four hormones
interact with membrane-bound proteins, although a degree of this interaction differs
(Figs. 9-12). The most pronounced quenching was observed in the case of androsterone (Fig.
9). The maximum fluorescence quenching was observed at a concentration of 2.2108 M.
Testosterone showed a lower fluorescence quenching (Fig. 10). The maximum quenching
was observed at a concentration of 1.2107 M, which is 5.5 times higher as compared to
androsterone. Fluorescence quenching was even less pronounced with DHEA (Fig. 11). In
this case, the maximum quenching occurred at a concentration of 2.4106 M. And finally, the
lowest fluorescence quenching was observed for DHEAS (Fig. 12). The maximum quenching
took place at a concentration of 5.3106 M, which is 2.2 times higher as compared to DHEA.
Figure 7. IR spectra of rat erythrocyte membranes (control) (Cphosph.buff. = 0.01 M, pH 7.35, relative
humidity 0%): (a) = 900-1800 cm-1, (b) = 2600-3700 cm-1.
Figure 8. IR spectra of rat erythrocyte membranes incubated with testosterone (CC = 2.7 10-8 M,
Cphosph.buff. = 0.001 M, pH 7.35, relative humidity 0%): (a) = 900-1800 cm-1, (b) = 2600-3700 cm-1.
According to the results obtained, testosterone and androsterone penetrate deeper into
erythrocyte membrane and have a stronger effect on the structure of membrane-bound
proteins toward their increased ordering. DHEA and DHEAS have some effect on
erythrocyte membranes; these hormones adsorb on the membrane surface, but do not
penetrate deep into hydrophobic layer of the membranes. These hormones have a weaker
binding with proteins via hydrogen bonds.
This conclusion is confirmed by the calculated values of hormone binding constant (b),
total amount of bound hormone (max), and changes in free energy (G) upon hormone
transition from free state to the membrane-bound one (Table 2). The highest values of b
were obtained in our study for testosterone and androsterone, b for androsterone being
higher by a factor of 4. Amount of the bound hormone (max) obeyed an inverse relationship:
it was 2.4 times higher in the case of testosterone as compared to androsterone. Changes in
free energy upon interaction of hormones with erythrocyte membranes were most
pronounced
Compound CO NH C=O P=O P-O-C O54- CH A

stretch. 5O4 stretch.
Shadows 1655.4 3308 1748 1236 1080 1056 2948 1.2150

(control) 1686 2930 10
2848
Shadows + 1656 3270 1260 1098 2958

androsterone 1635 329 1240 1088 2928
(A = 2.76 1620 2 2848
108 )
Shadows + 1657 3272 1739.4 1247 1098 1065 2956.4 2.2433

testosterone 1684 3298 1236 1088 1076 2924 10
(A = 2.7 10 1632 3309 2850
8 )
Shadows + 1654.9 3288.0 1732 1247.6 1088 1070.7 2956.3 2.1266

DHEA 2925.8 10
(A = 2.64 2851.8
108 )
Shadows + 1656.0 3286 1738 1248.0 1084 1070 2952.0 1.2598

DHEAS 1680 3300 1052.7 2926.4 10
( = 1.63 1632.0 3312 2852.0
108 )
Table 1. IR spectroscopy. Frequency parameters of rat erythrocyte shadows after their interaction with
hormones
Figure 9. Q = (Fmax - F)/Fmax versus the concentration A of androsterone hormone introduced into a
cuvette. Concentration of membrane protein C = 0.203 mg/mL.
Figure 10. Q = (Fmax- F)/Fmax versus the concentration A of testosterone hormone introduced into a
cuvette. Concentration of membrane protein C = 0.101 mg/mL.
Figure 11. Q = (Fmax _ F)/Fmax versus the concentration A of dehydroepiandrosterone hormone

introduced into a cuvette. Concentration of membrane protein C = 0.139 mg/mL.
All values for DHEA and DHEAS strongly differed from those listed above. Binding
constants were nearly two orders of magnitude lower. Amount of the bound hormone (max)
was much greater, indicating a low specificity of interaction with the membranes. Changes
in free energy (G) were low for both hormones (Table 2).
Thus, a comparison of two pairs of hormones demonstrated their considerable difference

from each other. The higher is b, the greater is the binding specificity and the lower is the
amount of bound hormone (max). Large negative values of G for testosterone and
androsterone testify that their interaction with erythrocyte membranes increases their
ordering (negentropy). DHEA and DHEAS are characterized by a low specificity of binding
to membranes.
Figure 12. Q = (Fmax - F)/Fmax versus the concentration A of dehydroepiandrosterone sulfate hormone
introduced into a cuvette. Concentration of membrane protein C = 0.139 mg/mL.
It shows up even when hormones are compared with each other. In DHEA, substitution of
group by S3 in the 3rd position of A-ring decreases b by a factor of 3.8 and increases
max by a factor of 2.2. A decrease in G is also pronounced. The reason is that the presence
of group and additionally of two keto groups and an S atom enhances the interaction of
DHEAS with hydrophilic and N groups of the surface proteins. DHEA and DHEAS
cannot bind to the proteins residing in hydrophobic layer of the membrane. These two
hormones do not change the conformational state of spectrin-actin-ankyrin meshwork and
have only a slight effect on the morphology of membrane surface. DHEAS, being most
hydrophilic among the four hormones, has the weakest effect. As hormone hydrophilicity
increases, the amount of membrane-bound hormone rises and b decreases. During the
interaction of testosterone and androsterone with erythrocyte membranes, both hydrogen
bonds and hydrophobic interactions may strongly contribute to the growth of b. This is
explained by a deeper penetration of hormones into hydrophobic layer of erythrocyte
membrane, which increases the specificity of their interaction. The accompanying structural
transitions in membrane proteins, tangle -structure -helix, increase ordering of these
proteins and substantially raise the G value. Results obtained in the study agree well with
changes in microviscosity of erythrocyte membranes.
Amount of bound Changes in free

Binding constant b
Steroid hormone hormone Bmax energy G
(1)
(mol/mg protein) (kJ/mol)
testosterone (2.240.22)x106 (1.090.11)x109 -37.6
androsterone (3.20.32)x10 6 (4.460.45)x1010 -38.5
DHEA (5.990.60)x10 4 (1.800.18)x10 8 -28.3
DHEAS (1.560.16)x10 4 (4.030.40)x10 8 -24.8
Table 2. Parameters of steroid binding to erythrocyte membrane based on tryptophan fluorescence
quenching of membrane proteins
5. Changes in microviscosity
In erythrocyte membrane, a fluorescent pyrene probe is distributed in the lipid phase and
can be a source of information on the state of its deeper layers. The rate of its migration and
the ability to form excimers upon interaction with each other are estimated. This is the way
to determine changes in microviscosity of the membranes.
In our study, an increase in microviscosity was most pronounced at the addition of

androsterone to erythrocyte membranes. Microviscosity started to grow at a hormone
concentration of 108 M, the growth proceeding up to 2.5108 M with subsequent saturation
(Fig. 13). The S-shaped curve points to high cooperativity in changing the conformational
state of the membrane. A microviscosity increment attained 50% with respect to the initial
state. In the region of protein-lipid interactions it appeared earlier and reached a higher
value as compared to the region of lipid-lipid interactions. The absorption intensity (D) and
emission intensity (F) of tryptophan in membrane proteins started to decrease at the same
concentrations and attained a maximum also at the same concentrations (Fig. 9). Thus, our
results revealed a cooperative nature of changes in erythrocyte membranes under the action
of androsterone.
Addition of testosterone produced similar changes in membrane microviscosity. In the

region of protein-lipid interactions, microviscosity increased at lower concentrations of
hormone and attained higher values as compared to the region of lipid-lipid interactions
(Fig. 14). In both cases, the revealed structural changes were initiated in proteins and carried
over to lipids by virtue of cooperativity.
The effect of DHEA and especially DHEAS on erythrocyte membranes is much less
pronounced as compared to testosterone (Figs. 15, 16). DHEA and DHEAS increased
microviscosity by 10% with respect to initial values. In these experiments, the concentration
of DHEAS reached 8106 M. For DHEA, the growth started at a hormone concentration of
5107 M and attained its maximum at 1.5106 M (Fig. 15). Alteration of viscosity was
described by S-curve and correlated with a decrease in fluorescence and absorption of
tryptophan (Fig. 11). The latter processes started at the same hormone concentrations and
reached their minima also at the same concentrations. Microviscosity in the region of
protein-lipid interactions increased earlier, at lower concentrations of hormone, and was
more pronounced than in the region of lipid-lipid interactions. Structural changes were
initiated in proteins and involved lipids due to cooperativity.
Figure 13. Changes in the relative microviscosity of membranes (A)/(0) of erythrocyte shadows at the
concentration A of androsterone hormone. Concentration of shadows C = 0.133 mg protein/mL. Line 1
shows changes of the region of lipid-lipid interaction; line 2 the region of protein-lipid interaction.
concentration A of testosterone hormone. Concentration of shadows C = 0.117 mg protein/mL. 1 - the
region of lipid-lipid interaction; 2 the region of protein-lipid interaction.
The mechanism of changes in membrane microviscosity under the action of a more

hydrophilic hormone DHEAS is quite different. Microviscosity goes to a constant value at a
higher concentration of DHEAS in suspension as compared to that of DHEA (5106 M
versus 1.5106 M for DHEA). First changes of microviscosity appeared in the region of lipid-
lipid interactions (Fig. 16), which was followed by an increase of microviscosity in the
region of protein-lipid interactions. DHEAS interacted with polar heads of phospholipids,
then structural changes carried over to proteins due to cooperativity. Hydrophilic molecules
of DHEAS cannot penetrate deep into hydrophobic layer of the membranes. There are only
minor structural changes in the spectrin-actin-ankyrin meshwork and weak changes in
membrane microviscosity.
concentration A of hormone DHEA. Concentration of shadows C = 0.113 mg protein/mL. 1 - the region
of lipid-lipid interaction; 2 the region of protein-lipid interaction.
concentration A of DHEAS hormone. Concentration of shadows C = 0.290 mg protein/mL. 1 - the region
of lipid-lipid interaction; 2 the region of protein-lipid interaction
6. Change of the membrane microviscosity, and Na+, K+-ATPase activity

Erythrocyte suspensions from fresh blood of rats with hormones of differing concentration
were analyzed. For this purpose cortisol and adrenalin were used.
Under the action of hormones, the microviscosity of erythrocyte membranes increases

following a saturation curve (Fig. 17). This increase depends on the hormone type and
differs greatly for protein-lipid and lipid-lipid interactions. As can be seen from Fig. 17,
protein-lipid interaction makes a decisive contribution to the increase in membrane
microviscosity under the action of hormones. It is due to this contribution that the system of
compaction domains is formed in the membrane, resulting in an increase in erythrocyte
rigidity. The effect depends strongly on the hormone type. Adrenaline, which penetrates the
entire erythrocyte bulk, rapidly increases the erythrocyte microviscosity, and the latter
comes to saturation even at small hormone concentrations of 1710-9 M. Cortisol acts on an
erythrocyte surface layer alone; hence, the microviscosity reaches saturation only at a
cortisol concentration of 60 10-9 M, and the increase in viscosity with cortisol is half as much
as that with adrenaline.
The most important result concerns the influence of hormones on the activity of the Na+, K+-
Pase (Fig. 18). For both hormones analyzed, increasing the hormone concentration causes
the quantity first to increase, reach its maximum, and then to decrease. The maximum of
activity corresponds to the hormone concentration at which the microviscosity reaches
saturation. A good correlation is found between the stages of variation in activity and in
microviscosity with an increase in the concentration of different types of hormones.
Adrenaline, which is responsible for the rapid increase in erythrocyte microviscosity, is

responsible as well for the rapid increase in the Na+, K+-Pase activity and for its
subsequent fast decline following the maximum (Fig. 18a). Increasing the cortisol
concentration (Fig. 18b) causes a slow increase in microviscosity and Na+, K+-Pase activity
(), and then a slow decrease in whose value does remain high at a very high hormone
concentration. At a 20 10-9 hormone concentration, the activity is 0.05 and 0.03 mol/hmg
protein for adrenaline and cortisol, respectively. At the stage of decline in at 60 10-9
hormone concentration, ~ 0.02 and 0.035 mol/hmg protein for adrenaline and cortisol,
respectively.
The maximum activity in the series of adrenaline and cortisol is observed at their
respective concentrations of 3 108 and 5 108 M.
Important information on the nature of structural changes produced in erythrocytes by the

analyzed hormones was obtained with infrared spectroscopy [14]. The increase in the
absorption band intensity of CO- (1655.2 cm1) and NH-bonds (1548 and 3290 cm1) by about
20 % with cortisol points to enhanced ordering of membrane proteins due to the tangle -
helix structural transition [15]. The shift 3308 3280 in stretching vibrations of the peptide
NH-bond and the increase in its intensity owes to the formation of a hydrogen bond
between cortisol and NH-bond of proteins. The increase in the absorption band intensity of
the =-bond of phospholipids and its shift 1748 1740 points to enhancement of ordering
of higher carboxylic acids and to a decrease in phospholipid entropy.
Figure 17. Changes in the relative microviscosity of membranes (L) of erythrocyte shadows at the
concentration A for adrenaline (a) and cortisol (b) hormones added to the shadows suspension.
Concentration of shadows C = 0.128 mg protein/ml. Concentration of pyrene in the suspension is 7.710-6
M, temperature of the specimens 309.10.1 K (36C), pH of the suspension 7.35. The measured value of
L(A) exhibit an error of 6%. 1 - the region of lipid-lipid interaction; 2 the region of protein-lipid
interaction
Figure 18. Changes in the activity of Na+, K+-ATPase of erythrocyte membranes as a function of a
hormone concentration in suspension: a adrenaline; b cortisol.
The concurrent hormone interaction with protein and phospholipids enhances the protein-
lipid interactions resulting in a complex domain structure in erythrocytes. The frequency
shift of the =-bond toward the short-wave range and the increase in its intensity is
associated with dehydration of membranes due to its hormone-induced compressive
deformation. It is the loss of bound water that increases the frequency of the P = O-bond
[16]. The displacement of water dipoles from protein-lipid domains to adjacent regions leads
to the development of mesobands of localized deformation and discontinuities in them.
The obtained experimental results suggest that an important role in the action of hormones
on erythrocytes belongs to two factors:
- collective effect of the increase in erythrocyte elastic modulus due to the formation of
the domain structure in the region of protein-lipid and lipid-lipid interaction
(macroscale);
- hindered structural transitions in mass transfer processes through a membrane
(microscale).
The first factor causes an increase in energy quanta h (phonone) required for structural
transitions in mass transfer through erythrocyte membranes. This factor increases the
activity of the Na+, K+-Pase at the first stage of growth of hormone concentrations.
The second factor retards microscale structural transitions. Once the microviscosity ceases to
increase (the formation of the domain structure is completed), the contribution of the first
factor no longer grows, the contribution of the second factor continues to escalate, and the
activity of the Na+, K+-Pase decreases.
7. Effect of cortisol
Here we try to go beyond the influence of cortisol on the red cell membrane, and consider
the action of the hormone on erythrocyte as a multi-layered liquid crystal system.
The mechanism of erythrocyte deformation and structural transformation of membranes
and hemoglobin by the action of cortisol is still scantily investigated. The interaction of
hemoglobin with contraction proteins and band 3 protein of erythrocytes is reported by
Discher, D.E., Mohandas, N. & Evans, E.A [17]. These works imply that the disturbance and
deformation of erythrocyte membrane caused by cortisol or other external factors can be
transferred to hemoglobin by means of band 3 integral protein or contraction proteins.
According to modern ideas, contraction proteins reside as at the inner as outside of
membrane. Within this concept, a reverse response is also possible, i.e., the disturbance can
be transferred from hemoglobin to the cell membrane.
The addition of cortisol to erythrocyte suspension with the hormone concentration of 108 to
6108 M produced a set of UV spectral curves. A maximum of absorption band at 418 nm
was shown to decrease with increasing the hormone concentration. A decrease in the optical
density was 22% as compared to erythrocyte suspension without hormone (control)
(Fig. 19). The resulting set of curves was used to plot the dependences of optical density for
band 418 nm on the concentration of hormones.
Figure 19. Changes in the optical density of absorption band 418 nm at the addition of cortisol to
human erythrocyte suspensions (C = 10-8 6 10-8 M).
An increase in the optical density in the regions of 600-700 and 310 nm, which points to
increasing diffusion of light has been also observed. In these regions, optical density
changed by ~5.5%, which considerably exceeds the measurement error (0.5%) (Fig. 19). It
should be noted that absorption band at 418 nm may shift spontaneously by 2-3 nm in
different runs, generally to the short-wave region. Shifting of this band occurs either due to
fluctuations in the structure of hemoglobin itself [18] or by the action of fluctuations in the
structure of membrane and cell as a whole [19, 20].
The analysis of IR spectra of rat erythrocyte ghosts not loaded with hormone (control, Fig. 7)
revealed not only a disordered structure, but also the presence of -helix 1650-1656 cm1 and -
structure (1686 and 1520 cm1) in the proteins of rat erythrocyte ghosts [1]. N stretching
vibrations of proteins (3308 cm1), CH stretching vibrations of hydrocarbon chains in proteins
and phospholipids (2948, 2930 and 2848 cm1) as well as some bands typical of phospholipids,
in particular, C=O bond (1748 cm1), = bond (1236 cm1), 2 deformation vibrations (1460
and 1386 cm1) of hydrocarbon chains, 4-4-5-5 bond (1048 cm1) of monosaccharides in
glycolipids and glycoproteins, and - deformation vibrations (978 cm1) have been recorded.
Note that the = band (1736 cm1) is quite narrow; hence it follows that phospholipids are
well ordered at the level of ester bonds in higher carboxylic acids and glycerol.
Analysis of the IR spectra of rat erythrocyte ghosts upon incubation with cortisol at its
concentration of 4.4 . 108 M revealed a ca. 20% increase in intensity of the absorption bands
of CO (1655.2 cm1) and NH bonds (1548 and 3290 cm1), the effect building up with an
increase in the hormone concentration (Table 3, Fig. 20). A growing intensity of the band
1655.2 cm1 testifies an increase in the fraction of -helix [8]. The increasing fraction of -
helices in membrane proteins is related with the structural transition tangle -helix.
A shift of N bond (stretching vibrations of peptide bond, 3308 3280 cm1, = 28 cm1)
was accompanied by a growth of its intensity, which is related with the formation of
hydrogen bond between cortisol and N group. Hydrogen bond is likely to form between
keto group of A-ring (C3=) and N group of the membrane protein. Meanwhile, keto
group (C20=) of D-ring and OH group at 11 in C-ring could also be involved in the
formation of hydrogen bonds. The presence of several hydrophilic groups strongly changes
the biological activity of cortisol and other steroid hormones, in distinction to cholesterol.
Cholesterol binds to phospholipids mainly due to hydrophobic interaction (Van der Waals
forces) with fatty acid residues [19]. Shifting of CH bond stretching vibrations
2848 2852 cm-1 ( = 4 cm-1) and 2930 2925 cm-1 ( = 5 cm-1) were observed. The latter
increased in intensity under the action of hormone. Changes in intensity of this band
confirm the presence of structural transition, but cannot differentiate the place where the
transition occurs in membrane proteins or in phospholipids, as CH bond is present both
in proteins and phospholipids. However, as seen from our experimental data, this band
reflects mainly the changes in phospholipid orderliness.
An increase in intensity of the absorption band of phospholipid C=O bond and its shift 1748
1740 cm1 were observed. This increase of the band intensity indicates a growing
orderliness of higher carboxylic acids and a decreasing entropy in phospholipids. Shift of
the band is related with the formation of hydrogen bond between hormone, for example OH
group at C21, and CO bond of phospholipids. Such interaction of the hormone
simultaneously with protein and phospholipids can occur at the interface between protein
and phospholipids, i.e., in a near-boundary or annular layer of the band 3 integral protein,
glycophorin and other proteins.
P=O bond shifted in frequency by 3 cm1 to the short-wave region and increased in intensity.
Shifting of P=O bond to the short-wave region is attributed to dehydration of membranes
during their deformation under the action of hormone. A loss of bound water increases the
frequency of P=O bond [1]. Deformation (contraction) occurs due to spectrin-actin and
spectrin-ankyrin networks [19], since the extraction of spectrin from membrane relieves the
deformation caused by hormones. It should be noted that 30% of membrane proteins is
represented by spectrin. Overall, contraction proteins constitute 55-60% of all membrane
proteins [21]. Steroids can attack either the spectrin-actin-ankyrin network located both on
internal and external surfaces of the membrane or the integral proteins associated with
contraction proteins [22].
Our FTIR spectroscopy study of the hormone effect on intact erythrocytes revealed
considerable changes of the spectra in absorption regions both of proteins and
phospholipids. In particular, cortisol gave rise to absorption band 1636 cm1 corresponding
to -structure of membrane proteins, which indicates a transformation in the secondary
structure of membrane proteins (tangle -structure transition) involving also the

contraction proteins. Shifting of some other absorption bands attributed both to proteins
and phospholipids was observed too (Fig. 21).
Noteworthy are the shift of absorption band 2870 cm1 corresponding to stretching
vibrations of CH bond in hemoglobin [23], and a more pronounced splitting in the region of
stretching and deformation vibrations of phospholipid CH orderliness in and between the
domains. A stronger splitting of CH bonds testifies the formation of new lipid-protein
clusters as a result of intermolecular interaction, due to compaction of membrane elements
caused by structural transformation of the contraction proteins network. In our earlier
studies of high density lipoproteins (HDL), when calculating the enthalpy of structural
transitions from experimental data, the occurrence of smectic A smectic C transition in
HDL phospholipids [8] has been suggested. Such a transitions may occur here, since it has a
low enthalpy [8, 24].
Of interest is the appearance of the absorption band 2851.8 cm1, which is assigned to
stretching vibrations of CH bond in phospholipids [8]. This band results from structural
transition in membrane phospholipids.
No. The object of CO NH val. C=O P=O P-O-C 05C4-C504 CH val. ACO
measurement
Ghosts 1655,4 3308 1748 1236 1080 1056 2948 1,2150E
(control) 1686 2930 + 01
2848
2 Ghosts + 1655,2 3290,4 1743 1236 1080 1051,2 2924,2 1,5169E
cortisol - 2848,9 + 01
(C= 4,410-8 M) 3308.0
3 Ghosts + 1656,0 3280 1740 1239 1083,7 - 2962 1,5640E
cortisol 1630 3300 2925 + 01
(C= 10-7 M) 2852
4 Erythrocytes 1649,9 3282,1 1245,7 1106,2 2956,8
(control) 3272,0 2935,8
2871,7
3030,2
5 Erythrocytes + 1642,7 3285,3 1741,1 1239,4 1100,0 1060,2 2956,6
cortisol 1627,5 3270,2 1707,5 1201,3 1089,5 2937,5
(C= 10-8 M) 3247,3 2872,3
3028,4
3052,4
Note. ACO is the integral intensity of absorption band CO of the peptide bond in semilogarithmic form.
Table 3. Frequency characteristics of human erythrocytes and rat erythrocyte ghosts before and after
their interaction with hormones
Figure 20. IR spectraof rat erythrocyte ghosts at the addition of cortisol (C = 4.4 10-8 M): a. - = 1000
1800 cm-1, b. - = 2600 3400 cm-1.
Figure 21. FTIR spectra of human erythrocytes at th addition of cortisol (C = 3 10-8 M): a. - = 1000
1800 cm-1, b. - = 2600 3400 cm-1.
Splitting in the region of 1088 ( bond) and 3282 cm1 (NH bond) was observed. Splitting
of these bands indicates an increasing orderliness in phospholipids and membrane proteins,
respectively. An increase in the fraction of -structure points to the tangle -structure

transitions; however, in this case more pronounced is the -helix -structure transition,
due to redistribution of intensity between absorption bands at 1650 and 1638 cm1. The first
band corresponds to -helices, the second one to -structure [19].
Using the fourth derivative of the absorption band 1600-1700 cm-1 the maintenance of elements
of the secondary structure in the erythrocyte membranes has been calculated. The results are
given in Table 4. This table shows the considerable increase of -structure under the action of
adrenaline. In this case we observe the structural transition tangle -structure. However, the
increase of -helices and decrease of tangle under the action of cortisol has been seen. So it can
be concluded the structural transition tangle -helix took place.
A comparison of IR spectra obtained from ghosts and intact erythrocytes revealed some
general regularities: 1) splitting of absorption bands of NH peptide bonds, 2) an increased
intensity of absorption bands corresponding to -structure, 3) splitting of absorption bands
corresponding to CH bonds of phospholipids, 4) a frequency shift of some bands (Table 4).
However, there is also a distinction related with the appearance of absorption bands at 2870
and 1108 cm1 corresponding to hemoglobin [23]. These bands are shifting when
erythrocytes are subjected to the action of hormones.
Conformation Erythrocyte Erythrocyte + cortisol

(control) Ccortis = 3 10-8 M
-helical 25% 48%
-structure 25% 30%
Random coil 25% 22%
Table 4. The quantitative definition of the elements of secondary structure in membrane proteins
Thus, these results suggest that the erythrocyte react to the effect of steroid hormones as a
complex liquid-crystalline co-operative system in which nanostructured transitions are
irreversible and are closely associated with the functional activity of cells.
8. Thermodynamics of nanostructural transitions in erythrocyte as a

liquid crystal system, a relation with the cell function
The application of IR and UV spectroscopy showed that the interaction of steroid hormones
with erythrocytes increases the ordering of both the membranes and hemoglobin, which
means an increase in negentropy.
E. Schrodinger defined it as
S = k lg (1/D), (11)
where S is the negative entropy, or negentropy; k is the Boltzmanns constant equal to

3.2983 1024 cal/deg; D is the quantitative measure of disorderliness of atoms in the system,
lg (1/D) is the negative logarithm of D, and 1/D is the measure of orderliness.
However, of prime importance for us is that increasing negentropy is always supported by

increasing amount of structural information. This can be expressed by the following
equation:
-S = k lg(1/D) + pi log pi (12)
where pi is the probability of individual events in the system. Thus, the informational
component in this equation determines an increase of negentropy in the system and is
related with acquisition of new properties.
Developing the concept about a correspondence between negentropy and structural

information, we can present the following equality:
-S = k lg(1/D) = pi log pi (13)
Hence,
lg (1/D) = (pi log pi)/k, and (14)
( p log p ) / k
1 / D 10 i i , then (15)
( p log p ) / k ( p log p ) / k
D 10 i i or 1 / 10 i i (16)
If in the Helmholtz equation for free energy entropy is replaced by D, this gives the
following expression:
T
F U (17)
p log p / k
10 i i
Thus, F can be considered as a function of the amount of structural information in a system.

This equation is essential for understanding the self-organization processes in living
systems, so as the cell. An increase in the amount of structural information determines the
transition from liquid crystal to crystal. This may incapacitate a cell from its functioning. It
has been already shown that the interaction of steroid hormones increases microviscosity of
erythrocyte membranes in the regions of lipid-lipid and protein-lipid interactions. At low
concentrations of hormones in the incubation medium, the activity of erythrocyte Na+,K+-
Pase even increases, probably due to growing elasticity of the lipid microenvironment of
the enzyme, which facilitates structural transitions in the enzyme itself. At high
concentrations of hormones (the saturation phase), an increase in microviscosity in the
region of lipid-protein interactions makes impossible structural transitions in the enzyme;
so, its activity rapidly drops. This determines a dome shape of the enzyme activity curve.
Since erythrocyte is a liquid crystal cooperative system, changes occur not only in the
activity of Na+,K+-Pase of erythrocyte membranes, but also in the state of cell
hemoglobin, its ordering and ability to bind oxygen.
It seems interesting to compare changes in liquid crystals with those occurring in solid
crystals in the fields of external action.
Destruction of solid and liquid crystals increases the molar volume [24, 25].
A dependence of the Gibbs thermodynamic potential F() on the molar volume taking into
account local zones of different scale stress concentrators is described by the equation:
F() = U TS + p - iCi, (18)
where i chemical potential, Ci concentration (Fig. 22, [26]) .
At critical values of molar volume i = (1,26), the thermodynamic potential F() has local
minima. They reflect local nonequilibrium potentials in the zones of different scale
hydrostatic tension. Critical values of i correspond to different levels of homeostasis in a
deformable solid:
0 is an equilibrium crystal; the initial level of homeostasis;
1 are the zones of stress microconcentrators where dislocation cores are generated; the next
level of homeostasis;
2, 3 are the zones of stress meso- and macroconcentrators where local structural-phase
transitions with the formation of meso- and macrostripes of local plastic deformation take
place; the next levels of homeostasis;
4 corresponds to intersection of curve F() with the abscissa. At a further increase of the
local molar volume, changes of the Gibbs thermodynamic potential proceed under the
conditions of F() 0, and the system becomes unstable. Various forms of material failure
appear; solid crystal starts to behave as a liquid one.
6 the existence of two phases is possible: at = 5 the vacancy phase atom, at 6

different thermodynamic levels of the crystal lattice in a deformable solid, different levels of
its homeostasis.
Thus, plastic deformation of solid and liquid heterocrystals in the fields of external action is
a multilevel process of their destruction, with the corresponding levels of crystal lattice self-
organization and levels of its homeostasis, i.e., the destruction via different phases of
strengthening (self-organization). On solid crystals this decreases the orderliness and
amount of structural information. In liquid crystals this increases the orderliness and
amount of structural information i.e. liquid crystal crystal transition.
Dependence of Gibbs thermodynamic potential on the molar volume and changes in the
structural information (I), taking into account local zones of stress concentrators is
determined by the expression:
( p log p ) / k
F( , I ) U T / 10 i i p C (19)
i i
These quantitative interrelations underlie transition of the system to a new structural level
of homeostasis.
Figure 22. The dependence of the Gibbs thermodynamic potential F (v) from the molar volume v in the
light of local zones of stress concentrators of different scales [26].
In biological membranes as liquid crystals, destruction is related with structural transitions

and is generally accompanied by increasing structural orderliness (the order order
transition). Earlier [1], it was shown that the action of steroid hormones on erythrocyte
membranes disturbs the mechanisms of self-organization that operate in the cells in normal
functional condition. The active CO, NH and OH groups of stress hormones interact with
CO and NH groups both of proteins and phospholipids in biological membranes. This leads
to the formation of complex protein-lipid clusters, where compressive hydrophobic
interactions are reinforced. Molecularly bound water is displaced to adjacent regions. Here,
hydrostatic forces increase the tensile tangential stresses. Mobile nanostructural
boundaries are formed, along which the biological membranes are destructed. This results
in the formation of numerous pores and mesostrips of plastic deformation. In terms of
physical mesomechanics, these transformations resemble those developing in solid crystals
in the fields of external action (Fig. 23). However, in biological membranes such self-
organization may be related even with increasing order and decreasing entropy, but this is
incompatible with conditions that determine cell viability. Structural transitions cover the
membrane-bound enzymes, transmembrane carriers and hormone receptors. It is reasonable
to say that cell membranes go to a new level of homeostasis (self-organization) which is
incompatible with life. The nature of life implies dynamics. The cell dies. Here, one can tell
about thermodynamic features related with changes in the structure and function
(properties) of solid crystals and biological membranes in the fields of external action.
Various structural transitions (phase transitions, nanostructural, etc.) strongly contribute to

the functional activity of a cell. These are the transitions like smectic A smectic C, smectic
cholesteric, and nematic isotropic state; in proteins, the transitions tangle -
structure and tangle -helix. They all affect the vital characteristics of a cell. I. Prigogine
believed that there is a wonderful analogy between instability of nonequilibrium origin
and phase transitions [27]. This problem is of great interest and deserves special
examination.
Thus, on the curve of thermodynamic Gibbs potential versus molar volume F(), solid
crystals fall in the region of strongly negative values, whereas liquid crystals are located
near zero. Structural transformations taking place in the fields of external action draw
together the positions of liquid and solid crystals on the functional curve. Morphologically,
the destruction patterns of crystals are quite similar (Fig. 9a and b).
Thermodynamically, cells as hierarchic multilevel liquid crystal systems can function only
near a zero value of thermodynamic Gibbs potential, i.e. in the region where reversible
nanostructural transitions underlying life processes can occur.
Figure 23. a Atomic force microscopy. The surface of rat erythrocytes after adsorption of cortisol.
Concentration of the hormone is 10-6M. Deep meso-bands with bifurcation are seen; b Formation of
micropore chains along localized-deformation shear-bands. Plate of high-pure aluminum 180 nm thick
glued on flat specimen of commercial Al. Alternative bending, = 293 ; cycle number N = 17.55106 [26].
Biomembranes are of vital importance in the processes of self-organization of cell

metabolism. These processes are transport of organic compounds through cell (plasma)
membranes with delivery of nutrients to the cell and removal of their decay products
(metabolism); diffusion of gases (O2, CO2) through a cell membrane; passive and active ion
transport and production of electrochemical potential on the outer and inner surfaces of
plasma membranes, and many others. All membranes are liquid crystals. Their behavior in
an organism obeys physicochemical laws. The mechanism of their self-organization is the
same as that of multilevel systems.
Multilevel systems mean the hierarchy of scales of shear stability loss of the internal
structure of a loaded material in local regions at the nano-, micro-, meso- and macrolevels
[26]. In liquid crystals, this is associated with lipid-lipid, protein-lipid, and protein-protein
interactions, i.e. with cooperative behavior of a liquid crystal as a system. The ordering of
these crystals as well as the nature of their components is determined by covalent and
hydrogen bonds, weak electrostatic and hydrophobic interactions. Shear stability loss of
natural liquid crystals depends on structural phase transitions such as the formation of
smectic, cholesteric, nematic and isotropic structures and transitions between them. For
membrane-bound proteins, states like - helix, -structure and chaotic coil are of
significance. Structural transitions can be reversible and irreversible. In the latter case,
defects are accumulated in liquid crystals, making some functions of the cell membranes
unrealizable. The cell dies. These transitions, as a rule, arise on the surfaces of cell
membranes and, because of cooperativeness, go deep into their lower levels. They can be
also initiated at the inner membrane or particle interfaces and can be related to lipids and
proteins. Thus, the case in point is different thermodynamic states of liquid crystals. The low
transition enthalpy suggests that the transitions involve low-energy bonds, mainly
hydrogen bonds, weak electrostatic and hydrophobic interactions. The external factors
capable of changing (disrupting) the interactions are also physicochemical in nature. Among
these factors are variations in temperature, pH, electrolyte content, etc. However, they are
all of no fundamental character, and the behavior of liquid crystals under external actions fit
in the same concept as the behavior of solid crystal does. It is very important for medicine.
As indicated in the report of World Health Organization, cardiovascular pathology,

infections and oncological diseases are three main causes of human mortality all over the
world [28]. Cardiovascular diseases stand first in this short list. In 2005 they killed 17.5
million people, which constitutes 30% of all deaths in the world. WHO predicts that in 2015
these diseases may take away the lives of 20 millions people. This will be caused mainly by
infarctions and strokes, i.e. acute tissue hypoxia.
9. Conclusion
Especially dangerous is myocardial ischemia, which is related with the formation of
atherosclerotic plaques within the coronary arteries and a considerable decrease in the blood
flow rate. Such mechanism of tissue hypoxia development is typical of the older age groups.
However, this pathology may develop also by a different mechanism. Nowadays acute
myocardial ischemia and coronary deficiency are often observed in young people. There are
many cases of sudden death that occur in young sportsmen during the competitions [29].
Coronary arteries of sportsmen are free of plaques, nevertheless, acute coronary deficiency
develops somehow. Stress hormones and steroid anabolics may be a possible reason.
Today the world is changing very rapidly, and not everybody can adjust to these changes.
Chronic stress becomes a wide-spread phenomenon [18]. Such reaction may be very
pronounced in anxious persons. This is why cardiac syndrome X is often diagnosed now. Its
clinical characteristics include angina chest pain with exertion and ischemic type ST segment
depression on electrocardiogram, without angiographic signs of coronary artery stenosis
and with normal left ventricle function. It means that acute coronary deficiency of obscure
etiology occurs not only in sportsmen, but also among people at large [30].
Cortisol is the main stress hormone. It is a cholesterol derivative, and cholesterol is the
essential component of all cell membranes. Of special interest is the erythrocyte membrane.
Erythrocyte is a specialized cell that transfers oxygen from lungs to tissues by means of
hemoglobin (b). In capillaries, oxyhemoglobin bO2 decomposes, and O2 diffuses to the
organ and tissue cells. The first obstacle to such diffusion is erythrocyte membrane. Changes
in the properties of erythrocyte membrane determine the rate of oxygen diffusion across the
membrane. Besides, capillary and erythrocyte may have comparable diameters. Sometimes
the erythrocyte diameter happens to be even larger. To go through so small capillary,
erythrocyte should have a high plasticity. Structural transformations in erythrocyte
membrane under the action of stress hormones may be reflected not only in its plasticity,
but also in the mechanism of gas exchange.
In this work, an attempt to elucidate the effect of steroid hormones on the structure of
erythrocyte membranes and their physicochemical properties, i.e. the introduction of
principles and regularities of physical mesomechanics in biology and medicine provides a
deep insight into the mechanism interrelating structure and function of biological
membranes, both in the norm and at systemic membrane pathology (upon variation of
hormone concentration, temperature, pH, electrochemical potential, etc. has been made.
Thus, from a thermodynamic standpoint, life is the ability of cells to undergo reversible
nanostructural transitions near a zero value of thermodynamic Gibbs potential. A loss of
this ability leads to cell death and development of pathology.
Author details
L.E. Panin
Scientific Research Institute of Biochemistry SB RAMS, Russia
Acknowledgement
The author is grateful to Dr. Sci. (med.) V.G. Kunitsyn and Ph. D. (phys.-math.) P.V.
Mokrushnikov for participation in the preparation of experimental material.
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Erythrocyte Membranes and Their Mechanical Properties, Tyumen University, Tyumen.
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Erythrocyte Membranes and Their Mechanical Properties, Tyumen Gos. University:
Tyumen.
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assessment of erythrocyte membrane properties during cold storage. Mol. Membr. Biol.
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structural transitions in liquid crystals under external actions. Physical Mesomechanics,
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solid as a multiscale system. Corpuscular-wave dualism of plastic shear. Physical
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Chapter 12
Thermodynamics of Resulting Complexes

Between Cyclodextrins and Bile Salts
Yu Liu and Kui Wang
1. Introduction
Cyclodextrins (CDs), a class of macrocyclic oligosaccharides consisting of six, seven, or eight
glucose units linked by -1,4-glucose bonds, have been widely used as receptors in
molecular recognition in the field of supramolecular chemistry because they are able to form
inclusion complexes with hydrophobic guests in aqueous solution owing to their
hydrophilic outer surface and their lipophilic cavity [13]. Therefore, much effort has been
devoted to the design and synthesis of a wide variety of cyclodextrin (CD) derivatives to
explore their binding behaviors for model substrates [4]. In order to further explore their
inclusion complexation mechanism, most of these studies have been focused on the binding
modes and complexation thermodynamics based on CDs and their derivatives in recent
years [5]. Among the numerous guests researched, bile salts attracted much more attention
because they are one kind of important surfactant-like biological amphipathic compounds
possessing a steroid skeleton, which have distinctive detergent properties and play an
important role in the metabolism and excretion of cholesterol in mammals [6]. For example:
the thermodynamics and structure of inclusion compounds of glyco- and tauro-conjugated
bile salts with CDs and their derivatives have been studied by Holm et al. during the last
years [711]; the interactions of different kinds of bile salts with -CD dimers linked through
their secondary faces have been investigated by Reinhoudt and Vargas-Berenguel et al. [12
14]. It has been demonstrated that the formation of inclusion complexes between CDs and
guest molecules is cooperatively governed by several weak forces, such as van der Waals
interactions, hydrophobic interactions, hydrogen bonding, electrostatic interactions, and
every weak force does its contribution to the complexation. In this chapter, the related
investigations concerned on the binding modes, binding abilities, molecular selectivities and
their thermodynamic origins of CDs and their derivatives with four typical bile salts
(Cholate (CA), Deoxycholate (DCA), Glycocholate (GCA), and Taurocholate (TCA)) (Figure
1) have been summarized, which will be discussed from the aspect of the types of host
molecules: (1) natural CD series; (2) modified CD series; (3) bridged CD series. This
summary is helpful to improve understanding of the correlation between the structural
features and molecular-recognition mechanism from thermodynamic viewpoints, and
further guide its biological, medicinal and pharmaceutical applications in the future.
Guests R1 R2
Cholate (CA) OH COONa
Deoxycholate (DCA) H COONa
Glycocholate (GCA) OH CONHCH2COONa
Taurocholate (TCA) OH CONHCH2CH2SO3Na
Figure 1. Molecular structures of four typical bile salts
2. Natural CD series
2.1. Binding modes for bile salts and natural CD series
Since two protons located closely in space (the corresponding internuclear distance is
smaller than 34 ) can produce NOE (Nuclear Overhauser Effect) cross-peaks between the
relevant protons in NOESY (Nuclear Overhauser Effect Spectroscopy) or ROESY (Rotating
Frame Overhauser Effect Spectroscopy) spectra, 2D NMR spectroscopy has become an
important method for the investigation of the interaction between different kinds of CDs
and guest molecules. It is well-known that only H3, H5, and H6 of CDs can give cross-peaks
for analyzing hostguest interactions, as H2 and H4 are not facing to the inner cavity and H1
is affected by D2O. For example, the ROESY study on the resulting complex of natural -CD
1 (Figure 2) with CA has been reported by Tato et al. [15,16]. The results successfully
indicated that in the 1:1 complex between 1 and CA the steroid body entered forward into
the inner cavity of 1 by the side of the secondary hydroxyl groups, with the side chain
folded toward the steroid body, i.e., rings D and C are totally and partially included,
respectively. Therefore, the binding modes of bile salts with different kinds of CDs have
been widely deduced by 2D NMR spectroscopy during the last years.
Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 307
Figure 2. Structure of natural -CD
2.2. Complexation thermodynamics for bile salts and natural CD series

The microcalorimetric titrations can be used to simultaneously determine the enthalpy and
equilibrium constant from a single titration curve. Titrations were performed below the
critical micelle concentration of bile salts. In each run, a solution of the host (guest)
molecules in syringe was sequentially injected into the calorimeter sample cell containing a
solution of guests (hosts). Each addition of hosts (guests) into the sample cell gave rise to a
heat of reaction, caused by the formation of inclusion complexes between hosts and guests.
The heats of reaction decrease after each injection because less and less molecules in cell are
available to form inclusion complexes. A control experiment was performed to determine
the heat of dilution by injecting a host (guest) solution into a pure solution containing no
guest (host) molecules. The dilution enthalpy was subtracted from the apparent enthalpy
obtained in each titration run, and the net reaction enthalpy was analyzed by using the one
set of binding sites model. This model will work for any number of sites N if all sites have
the same Ks and H. In this case, the total heat Q was fitted via a nonlinear least-squares
minimization method to the total host concentration in cell (Mt) using the following
equation:
Q = (NXtHVo/2){1 + Mt/(NXt) + 1/(NKSXt) {[1 + Mt/(NXt) + 1/(NKSXt)]2 4Mt/(NXt)}1/2} (1)
where N is the number of binding sites of host, Xt is the total concentration of guests in cell
and Vo is the cell volume. The value of Q above can be calculated (for any designated values
of N, K, and H) at the end of the ith injection and designated Q(i). Then the correct
expression for the heat released, Q(i), from the ith injection is
Q(i) = Q(i) + dVi/(<ital> Vo){[Q(i) + Q(i 1)]/2} Q(i 1) (2)
where dVi is the volume of titrant added to the solution. Along with obtaining of Ks and H
in this fitting program, the N value in eq 1 can also be obtained, which represents the
numbers of guests bound to one host molecule.
The ORIGIN software (Microcal), used for the calculation of the binding constant (Ks) and
standard molar reaction enthalpy (H) from the titration curve, gave the relevant standard
derivation on the basis of the scatter of data points in a single titration experiment. The binding
stoichiometry was also given as a parameter when fitting the binding isotherm. Knowledge of
the binding constant (Ks) and molar reaction enthalpy (H) enabled the calculation of the
standard free energy of binding (G) and entropy change (S) according to
G = RT lnKS = H TS (3)
where R is the gas constant and T is the absolute temperature.
The microcalorimetric experiments of natural -CD 1 with bile salts (CA, DCA, GCA, and
TCA) showed typical titration curves of 1:1 complex formation [17]. The stoichiometric
ratios observed from curve-fitting results of the binding isotherm fell within the range of
0.91.1. This clearly indicated that the majority of the inclusion complexes had a 1:1
stoichiometry of bile salts and 1.
Thermodynamically, the binding behaviors of bile salts by 1 were entirely driven by

favorable enthalpy changes accompanied by small unfavorable entropy changes, which are
attributed to the predominant contribution of the van der Waals interactions arising from
the size/shape fit and geometrical complement between host and guest and to the
accompanying decreases in translational and structural freedoms upon complexation.
As can be seen from Table 1, the enthalpy change for the complexation of 1 with DCA is more
favorable than that with CA, which directly contributes to the increased complex stability. It is
reasonable that DCA possesses a more hydrophobic structure due to the absence of C-7
hydroxyl group as compared with CA, as a result, it is easier to bind into the cavity of 1, which
leads to more favorable hydrophobic and van der Waals interactions and gives larger enthalpy
and entropy changes. However, the enhanced favorable entropy gain by the desolvation effect
may be canceled by the unfavorable entropy change caused by the structural freezing of the
resulting complexes of 1 and DCA. Therefore, the stronger interaction between 1 and DCA
only shows the larger negative enthalpy change, directly contributing the relatively larger
complex stability constant. Meanwhile, 1 shows a lower binding ability upon complexation
with GCA and TCA. Compared with 1 and CA, the complexation of 1 with GCA and TCA
exhibit similar enthalpy changes but much more unfavorable entropy changes. The more polar
side chains of GCA and TCA may be the reason for it.
3. Modified CD series
3.1. Binding modes for bile salts and modified CD series
3.1.1. Aminated -CDs
The ROESY study on the resulting complex of 2 (Figure 3) with CA has been reported by
Tato et al. [15]. The results exhibited different interactions of the side chain of CA with H5
and H6 of 2 from natural -CD 1. The facts indicated that the side chain was unfolded, with
the negative carboxylate group moving toward the positive protonated amino group, and
the side-chain elongation produced a deeper penetration of the steroid body in the inner
cavity of 2.
The ROESY experiments of modified -CD 3 in the presence of CA or DCA have been
performed in D2O by Liu et al. [17]. The results indicate that the D-ring of CA is
accommodated shallowly in the cavity and CA enters 3 from the second side of CD with the
side chain and D-ring. At the same time, the side chain with the negative carboxylate group
of CA moves toward the positive protonated amino group of 3. For the resulting complex of
DCA3, the ROESY spectrum exhibits entirely different NOE cross-peaks and the D-ring of
DCA is included within the cavity of CD from the primary side of CD. Meanwhile, the
ethide protons of chiral tether interact with H6 of CD.
2D ROESY NMR experiment of 5 and CA has also been performed by Liu et al. in D2O to
investigate the binding mode between bile salt and CD [18]. The results show that steroid
body enters the CD cavity from the second side with its tail and D-ring parts.
3.1.2. Nucleobase-modified -CDs

In host 8, the adenine group is deeply inserted into the -CD cavity with an orientation
parallel to the C7 axis of -CD while the thymine and uracil groups are shallowly inserted in
the -CD cavity with an orientation perpendicular to the C7 axis of -CD [19]. As a result,
upon complexation with DCA guest, the deeply included adenine group in host 8 should be
expelled from the cavity upon complexation with DCA guest, however, the shallowly
included thymine and uracil groups in hosts 9 and 10 are hardly influenced by the inclusion
of DCA guest.
3.1.3. Tryptophan- and Tyrosine-modified -CDs

The binding modes of L/D-Trp--CD (11 and 12) with bile salts have been examined by Liu
et al. by 2D ROESY NMR experiments [20]. For L-Trp--CD (11), the results show that in the
absence of guest, L-Trp residue is only shallowly included or perching on the rim of the CD
cavity. However, in the presence of DCA, the D-ring of DCA is close to the wide end of CD
cavity, and the D-ring of DCA and the side chain is co-included in the same cavity from the
primary side of 11. For D-Trp--CD (12), the 2D NMR results indicate that the D-Trp residue
attached to -CD is more deeply self-included than the corresponding L-Trp residue in the
absence of guest. However, in the presence of DCA, the carboxylate side chain and D-ring of
DCA penetrate into the CD cavity from the secondary side shallowly.
The binding modes of L/D-Tyr--CD (13 and 14) with bile salts have further been examined by
Liu et al. by 2D ROESY NMR experiments [21]. The results show that the L-tyrosine moiety
was self-included in the -CD cavity from the narrow opening. The DCA guest entered the -
CD cavity from the wide opening with the tail and the D ring and coexisted with the L-
tyrosine substituent in the -CD cavity to form a cooperative inclusion manner. For D-
tyrosine-modified -CD (14), the D-tyrosine substituent was deeply self-included in the -CD
cavity and might be located in the center of the -CD cavity. Upon complexation with DCA,
the D-tyrosine substituent of 14 would partially move out of the -CD cavity. Compared with
DCA + 13 complex, DCA penetrated into the -CD cavity of 14 more deeply (Figure 4).
Figure 3. Structures of mono-modified -CD derivatives

Figure 4. The possible binding modes of 1114 (11 (c); 12 (d); 13 (a); 14 (b)) with DCA
3.2. Complexation thermodynamics for bile salts and modified CD series

3.2.1. Aminated -CDs
The microcalorimetric experiments of aminated -CDs with bile salts clearly indicate that
the majority of the inclusion complexes had a 1:1 stoichiometry [17]. Thermodynamically,
the binding constants of 4 upon inclusion complexation with DCA, GCA, and TCA are less
than that with natural -CD 1. It is reasonable that modified -CD 4 decreased the
microenvironment hydrophobicity of natural -CD cavity due to the hydrophilic carboxylic
group in the sidearm, and at the same time there is electrostatic repulsion between the
anionic carboxylate at the sidearm of 4 and anionic carboxylate or sulfonate of bile salts.
Unexpectedly, the resulting complex stability of aminated -CD 4 with CA is higher than
that of native -CD 1, which is mainly attributed to the more favorable enthalpy change. The
possible reason may be the enhanced cooperative van der Waals, hydrogen-bonding, and
electrostatic interactions exceeding the decreased hydrophobicity of the interior of -CD 4.
Positively charged monoamino-modified -CD 2 and modified -CD 3 possessing an

additional binding site in the chiral arm evidently enhance the molecular binding ability and
selectivity towards CA and DCA compared to those for native -CD 1, which is mainly
attributed to the more favorable enthalpy change accompanied with unfavorable entropy
change [17]. The more favorable enthalpy change most likely originates from effective
electrostatic interactions and the additional binding site of hydroxyl group. In addition, the
unfavorable entropy change is likely to originate from the conformation fixation of host and
guest and the rigid complex formation upon complexation. -CD derivatives 2 and 3 give a
lower binding ability upon complexation with GCA and TCA as compared to the
complexation with CA and DCA, which is similar to that for the complexation of -CD 1 and
derivative 4. For the same reason, the more polar side chains at C23 for GCA and TCA
remarkably affect their binding thermodynamics.
A study of 13C chemical shifts as a function of concentration at different pH values has been
performed by Tato et al., which shows a different behavior of complexation for CA and
DCA with 5 resulting in 1:1 and 1:2 inclusion complexes [22]. However, the complexation
phenomena do not depend on the pH of the solution. 13C NMR chemical shifts of the host
and guest molecules change on passing from the free to the complexed state. The side chains
in 5 at position C-6 have a significant effect on the complexation process with the bile salts.
The ROESY experiments confirm the overlap of the CA molecule with 5 resulting a 1:1
inclusion complex, while in the case of DCA molecule, the first molecule of 5 encapsulates
the bile salt to a larger extent than the second molecule of 5, resulting a 1:2 inclusion
complex. Hence the most important factors for the formation of a stable inclusion complex
are the relative size of 5 and the bile salt molecules, the nonpolar cavity of 5, the
hydrophobicity of the bile salts, and the presence of an electrostatic environment outside the
toroidal cavity.
3.2.2. Nucleobase-modified -CDs

The nucleobase-modified -CDs 810 exhibit distinguishable binding abilities toward bile
salts compared with parent -CD 1 [19]. Host 10 shows increased binding of TCA/GCA.
Host 9 exhibits increased binding of GCA while hosts 810 show less binding of the other
bile salts. The inclusion complexation of hosts 810 is driven by favorable enthalpy changes,
accompanied with unfavorable entropy changes. The driven forces are hydrogen-bonding
and van der Waals interactions, simultaneously producing marked geometric configuration
change. Host 8 displays weaker binding ability for every bile salt than hosts 9 and 10 owing
to expelling adenine group from -CD cavity to accommodate bile guests in hosts 8, which is
unfavorable to the hostguest complexation.
3.2.3. Tryptophan- and tyrosine-modified -CDs

The microcalorimetric titrations of L/D-Trp-modified -CD (11 and 12) with a series of bile
acids, i.e., CA, DCA, GCA, and TCA, showed typical titration curves, which can be nicely
analyzed by assuming the 1:1 complex stoichiometry [20]. Modified -CDs 11 and 12
exhibited appreciably smaller binding abilities for GCA and TCA guests than those of native
-CD 1 since GCA and TCA, possessing a strongly hydrophilic and hydrated sulfonate tail,
are not expected to deeply penetrate into the CD cavity by removing the originally included
L/D-Trp group out of the hydrophobic cavity. In contrast, DCA and CA, possessing a less
hydrophilic/hydrated carboxylate tail, showed comparable or even stronger binding and
higher selectivities for hosts chirality than TCA and GCA.
The ITC experiments of hosts 13 and 14 with bile salts (CA, DCA, GCA, and TCA) also
showed the typical titration curves of the 1:1 complex formation [21]. The stoichiometric
ratio N observed from the curve-fitting results was within the range 0.9 to 1.1, which
clearly indicated that the majority of the inclusion complexes had a 1:1 binding mode.
Thermodynamically, the binding of all CDs with the bile salts was entirely driven by the
favorable enthalpy changes accompanied by the unfavorable entropy changes. 14 gave the
higher bind ability toward CA and DCA than 1 and 12 due to the introduction of D-tyrosine
substituent and the conformational difference between 12 and 14. In addition, the bind
constant of 14 for DCA was slightly bigger than that for CA. Possessing a more hydrophobic
structure due to the absence of the C-7 hydroxyl group as compared with CA, DCA was
easier to bind to the -CD cavity than CA, which consequently led to the more favorable
hydrophobic interactions between hosts and guests. Host 14 exhibited the obviously smaller
binding abilities for GCA and TCA guests than 1 and 12. Thermodynamically, the decreased
binding affinities of host 14 toward GCA and TCA arose from the entropy change rather
than the enthalpy change due to the weakened hydrophobic interactions and the relatively
poor size-fit between host and guest. Compared with 1 and 11, 13 showed clearly decreased
binding abilities toward all four of the bile salts, especially for GCA and TCA.
Thermodynamically, the inclusion complexation of 13 with four bile salts exhibited the
favorable enthalpy changes and unfavorable entropy changes. The favorable enthalpy gain
of 13 was slightly higher than those of 1 and 11, but the entropy loss of 13 was much more
than those of 1 and 11 toward corresponding guests.
3.2.4. Methyl--CD and 2-hydroxypropyl--CD

The interactions of CA, DCA, GCA, and TCA with 15 and 16 have been studied by Ollila et
al. by means of isothermal titration calorimetry [23]. The results show that both CA and
DCA bound to 15 and 16 with a 1:1 stoichiometry. The binding constant was significantly
higher for DCA to 15 and 16 compared to CA. This difference in binding affinity is likely
explained by the more hydrophobic nature of DCA due to the absence of the C-7 hydroxyl
group, which is present in CA. The binding affinity was somewhat lower for CA binding to
15 compared to 16, while DCA showed a markedly lower affinity for 15 compared to 16.
GCA and TCA have lower affinities to 15 and 16 compared to CA and DCA. TCA bound
with lower affinity to 15 compared to GCA. Both GCA and TCA gave the same 1:1
stoichiometry for binding to 15 and 16 as did CA and DCA.
For 17, all the hydroxyls are methylated, and the loss of hydrogen bonds for the resulting
complexes is inevitable [24]. Therefore, host 17 only shows weak complex stability constants
to bile salts, which are much lower than those of 1 and 16. In addition, the release of higher
energy water molecules in the cavity of -CD upon complexation with guests makes the
inclusion complexation more favorable, which cannot be obtained in the cases of 17 because
almost no water molecule resides in the cavity of 17. Besides that, 17 should need some
conformational adjustment to accommodate bile guests, which is entropy-unfavorable for
the inclusion complexation.
3.3. Binding modes for bile salts and chromophore-modified CD series

3.3.1. Anthryl-modified -CDs
1H ROESY experiment has been performed by Liu et al. to confirm the binding model of
host 19 with CA [25]. The results indicate that CA molecule is included into the hydrophobic
cavity from the secondary side of -CD, with the side chain folded towards the steroid
skeleton, and the anthracene group is excluded outside the cavity of -CD. CA molecule and
the tether of -CD can be co-included into the cavity through the induced-fit interaction
between host and guest.
3.3.2. Quinolinyl- and naphthyl-modified -CDs

2D ROESY NMR experiments accompanied with molecular modeling studies have been
performed by Liu et al. to investigate the binding modes of DCA with 21 and 22 [26]. The
results show that the side chain and D-ring of bile salts were encapsulated in the -CD
cavity from the wide opening (Figure 5).
2D ROESY NMR experiment of complex of 23 with CA has also been performed to

investigate the binding geometry between permethylated -CDs and bile salts [24]. The
results show that CA is deeply included into the cavity of host 23 with its ring A in the
region of the narrow side and ring D in the region of the broad side. However, upon
complexation with CA guest, the appended naphthalene group in 23 is not entirely expelled
out of the cavity of permethylated -CD but is removed from the central cavity to the region
of the narrow torus rim. The cooperative inclusion manner of both guest molecule and
substituent sidearm into the cavity is mainly benefited from the extended framework of
permethylated -CD.
3.4. Complexation thermodynamics for bile salts and chromophore-modified CD

series
3.4.1. Anthryl-modified -CDs
The stoichiometric ratios gotten from curve-fitting results of the binding isotherm fell within
the range of 0.91.1, indicating that the resulting complexes of bile salts and CDs (1820) are
1:1 [25]. As compared with parent -CD 1, modified -CDs 1820 with different chain length
not only enhanced molecular binding ability but also significant molecular selectivity upon
inclusion complexation with homologous steroids, except for resulting complex of 20 with
TCA. The stability constants for the inclusion complexation of hosts and the each steroid
molecule decreased in the following order: DCA > CA > GCA > TCA. The hydroxyl group at
the C7 carbon atom of CA, GCA and TCA guests prevented deeper inclusion of the steroids
in the -CD cavity than that of DCA guest. On the other hand, the tether length of the host
and induced-fit interactions also played crucial roles in the selective molecular binding
process of modified -CD 1820 with guests. Host 19 possessing suitable tether length could
encapsulate more tightly the steroid guests than the other, through the size/shape-matching
and the induced-fit interactions between the host and guest.
Thermodynamically, the inclusion complexation of 1820 with steroid guests is entirely driven
by favorable enthalpy contribution with negative or minor positive entropy change [25]. The
strong interaction between host and guest leads to the more favorable negative enthalpy
change, which is counteracted by the relative more unfavorable negative entropy change. The
introduction of anthracene group with different chain length, and additional binding site to
CD rim can significantly enhance the binding ability of parent CD toward steroid guests.
Figure 5. The possible binding mode of 22 with DCA
3.4.2. Quinolinyl- and naphthyl-modified -CDs

The binding behaviors of two -CD derivatives bearing 8-hydroxyquinolino and
triazolylquinolino groups (21 and 22) with bile salts have been studied in aqueous buffer
solution by means of microcalorimetrical titration [26]. The results showed that the hostguest
binding behaviors were mainly driven by the favorable enthalpy changes, accompanied by the
unfavorable entropy changes, and the hydrogen-bonding interactions and van der Waals
interactions were the main driven forces governing the hostguest binding.
The binding stoichiometry of the permethylated -CD derivatives 23 and 24 with bile salts
has been determined by the Jobs plot method, which showed that hosts and guests formed
1:1 complexes [24]. Thermodynamically, hosts 23 and 24 show much higher binding ability
to bile salts than permethylated -CD 17 when the naphthalene (or quinoline) sidearm is
appended on it. The pronounced enhancement of complex stabilities for hosts 23 and 24 can be
attributed to the cooperative complex interactions of both the cavity of permethylated -CD
and the chromophore sidearms. Furthermore, it should be mentioned that host 24 always
forms more stable complexes with bile guests than host 23, which indicates that the N atom on
the quinoline ring plays a crucial role during the course of recognition of bile guests.
Hosts Guests pH Ks H TS Methods Refs.

1 CA 7.2 (PBS) 4068 22.98 2.38 ITC 17
DCA 7.2 (PBS) 4844 25.79 4.76 ITC 17
GCA 7.2 (PBS) 2394 22.99 3.7 ITC 17
TCA 7.2 (PBS) 2293 23.77 4.59 ITC 17
2 CA 7.2 (PBS) 11160 25.53 2.43 ITC 17
DCA 7.2 (PBS) 7705 32.16 9.98 ITC 17
GCA 7.2 (PBS) 2075 25.90 6.97 ITC 17
TCA 7.2 (PBS) 2309 26.89 7.69 ITC 17
3 CA 7.2 (PBS) 16920 28.11 3.98 ITC 17
DCA 7.2 (PBS) 9382 35.78 13.11 ITC 17
GCA 7.2 (PBS) 3904 24.74 4.24 ITC 17
TCA 7.2 (PBS) 2796 20.37 0.7 ITC 17
4 CA 7.2 (PBS) 4832 24.90 3.87 ITC 17
DCA 7.2 (PBS) 4034 38.91 18.33 ITC 17
GCA 7.2 (PBS) 2221 19.75 0.65 ITC 17
TCA 7.2 (PBS) 1322 32.75 14.93 ITC 17
5 CA 7.2 (PBS) 11060 36.44 13.36 ITC 18
DCA 7.2 (PBS) 11350 41.15 18.01 ITC 18
GCA 7.2 (PBS) 3050 25.48 5.59 ITC 18
TCA 7.2 (PBS) 3061 18.43 1.47 ITC 18
6 CA 7.2 (PBS) 25315 34.26 9.13 ITC 18
DCA 7.2 (PBS) 30300 38.13 12.55 ITC 18
GCA 7.2 (PBS) 3098 25.82 5.89 ITC 18
TCA 7.2 (PBS) 4659 14.86 6.08 ITC 18
7 CA 7.2 (PBS) 25850 23.53 1.65 ITC 18
DCA 7.2 (PBS) 24785 27.59 2.51 ITC 18
GCA 7.2 (PBS) 4722 21.22 0.25 ITC 18
TCA 7.2 (PBS) 3022 24.29 4.43 ITC 18
8 CA 7.2 (PBS) 1726 31.0 13.3 ITC 19
DCA 7.2 (PBS) 2839 34.8 14.9 ITC 19
GCA 7.2 (PBS) 1032 25.7 8.5 ITC 19
TCA 7.2 (PBS) 1003 26.6 9.5 ITC 19
9 CA 7.2 (PBS) 2567 29.3 9.9 ITC 19
DCA 7.2 (PBS) 3137 34.0 14.0 ITC 19
GCA 7.2 (PBS) 2898 31.2 11.4 ITC 19
TCA 7.2 (PBS) 2284 30.0 10.8 ITC 19
10 CA 7.2 (PBS) 2605 28.6 9.1 ITC 19
DCA 7.2 (PBS) 3813 33.7 13.3 ITC 19
GCA 7.2 (PBS) 3140 29.6 9.7 ITC 19
TCA 7.2 (PBS) 2402 28.8 9.5 ITC 19

11 CA 7.2 (PBS) 2020 23.2 4.3 ITC 20
DCA 7.2 (PBS) 2310 32.1 12.9 ITC 20
GCA 7.2 (PBS) 1110 23.4 6.0 ITC 20
TCA 7.2 (PBS) 1060 23.1 5.8 ITC 20
12 CA 7.2 (PBS) 6680 37.9 14.5 ITC 20
DCA 7.2 (PBS) 6770 46.0 24.1 ITC 20
GCA 7.2 (PBS) 1760 24.9 6.4 ITC 20
TCA 7.2 (PBS) 1470 24.3 6.2 ITC 20
13 CA 7.2 (PBS) 871 26.7 9.9 ITC 21
DCA 7.2 (PBS) 1087 33.1 15.8 ITC 21
GCA 7.2 (PBS) 428 28.3 13.3 ITC 21
TCA 7.2 (PBS) 391 25.7 10.9 ITC 21
14 CA 7.2 (PBS) 8689 41.7 19.2 ITC 21
DCA 7.2 (PBS) 9962 50.5 27.9 ITC 21
GCA 7.2 (PBS) 1105 30.5 13.1 ITC 21
TCA 7.2 (PBS) 809 26.7 10.1 ITC 21
7.4
15 CA 2510 7.9 38.6 ITC 23
(TrisNaCl)
7.4
DCA 4429 10.65 34.0 ITC 23
(TrisNaCl)
7.4
GCA 1764 8.2 34.5 ITC 23
(TrisNaCl)
7.4
TCA 1399 8.75 31.0 ITC 23
(TrisNaCl)
7.4
16 CA 2693 5.7 46.6 ITC 23
(TrisNaCl)
7.4
DCA 6276 6.8 49.9 ITC 23
(TrisNaCl)
7.4
GCA 1958 7.9 36.6 ITC 23
(TrisNaCl)
7.4
TCA 2148 7.2 39.6 ITC 23
(TrisNaCl)
17 CA 7.2 (PBS) 61 ITC 24
DCA 7.2 (PBS) 774 ITC 24
GCA 7.2 (PBS) 228 ITC 24
TCA 7.2 (PBS) 162 ITC 24
18 CA 7.2 (PBS) 11760 42.70 19.47 ITC 25
DCA 7.2 (PBS) 15030 42.72 18.87 ITC 25
GCA 7.2 (PBS) 3870 25.23 4.75 ITC 25
TCA 7.2 (PBS) 2647 20.99 1.47 ITC 25

19 CA 7.2 (PBS) 18965 32.37 7.95 ITC 25
DCA 7.2 (PBS) 22485 36.48 11.46 ITC 25
GCA 7.2 (PBS) 4888 21.61 0.56 ITC 25
TCA 7.2 (PBS) 3755 19.15 0.7 ITC 25
20 CA 7.2 (PBS) 11850 33.23 9.98 ITC 25
DCA 7.2 (PBS) 13365 39.57 16.20 ITC 25
GCA 7.2 (PBS) 4254 20.07 0.65 ITC 25
TCA 7.2 (PBS) 1833 26.58 7.96 ITC 25
21 CA 7.2 (PBS) 2216 25.04 5.94 ITC 26
DCA 7.2 (PBS) 2007 51.92 33.07 ITC 26
GCA 7.2 (PBS) 2434 31.07 11.74 ITC 26
TCA 7.2 (PBS) 3478 23.98 3.76 ITC 26
22 CA 7.2 (PBS) 2443 35.60 16.25 ITC 26
DCA 7.2 (PBS) 3177 33.89 13.90 ITC 26
GCA 7.2 (PBS) 2811 34.94 15.24 ITC 26
TCA 7.2 (PBS) 2809 30.37 10.68 ITC 26
7.2
23 CA 910 Fluorescence 24
(TrisHCl)
7.2
DCA 4320 Fluorescence 24
(TrisHCl)
7.2
GCA 4340 Fluorescence 24
(TrisHCl)
7.2
TCA 3820 Fluorescence 24
(TrisHCl)
7.2
(TrisHCl)
7.2
(TrisHCl)
7.2
GCA 10690 Fluorescence 24
(TrisHCl)
7.2
TCA 8710 Fluorescence 24
(TrisHCl)
7.4
25 CA 7400 22.3 0.2 ITC 27
(TrisNaCl)
7.4
DCA 6700 32.1 10.2 ITC 27
(TrisNaCl)
7.4
26 CA 1280 28.3 10.5 ITC 27
(TrisNaCl)
7.4
DCA 2570 33.3 13.8 ITC 27
(TrisNaCl)

27 CA 7.0 (PBS) 1650 Fluorescence 38
DCA 7.0 (PBS) 2660 Fluorescence 38
29 CA 7.0 (PBS) 60.4 Fluorescence 38
30 CA aqueous solution Fluorescence 36
DCA aqueous solution Fluorescence 36
GCA aqueous solution Fluorescence 36
PBS: Phosphate Buffer Solution; ITC: Isothermal Titration Calorimetry;
Tris: Tris(hydroxymethyl)aminomethane;
: The guest-induced variations in the excimer emission are too small for these values to be determined.
Table 1. Complex stability constants (Ks/M1), enthalpy (H/(kJmol1)), and entropy changes
(TS/(kJmol1)) for intermolecular complexation of bile salts with natural -CD and its mono-modified
derivatives in aqueous solution
All the permethylated -CD derivatives (17, 23 and 24) present the weakest binding ability
to CA guest because the cavity of permethylated -CD possesses a broader hydrophobic
region in comparison with 1, and then permethylated -CD is more suitable to include bile
guests with longer tails (GCA and TCA) than 1 [24]. Moreover, there are similar structures
between CA and DCA except for the difference of one hydroxyl in ring B. It is attractive that
DCA can be included more tightly by 17, 23 and 24 than CA. One reasonable explanation is
that the absence of one hydroxyl in ring B makes the whole framework of DCA more
hydrophobic than CA, and thereby DCA is more suitable to be immersed into the cavity of
permethylated -CDs.
4. Bridged CD series
4.1. Binding modes for bile salts and bridged CD series
4.1.1. Diseleno- and bipyridine-bridged -CDs

ROESY experiments for the complexes of CDs (25, 26, 33, and 35) and DCA have been
performed to illustrate the binding modes between the CDs and bile salts [27]. The results
show that the bridge linker does not interact with DCA and the bile salt molecule is not
cooperatively bound by the two cavities of one dimer molecule. DCA is not included in the
cavity of the dimer from the primary side (narrow open), but penetrates slightly into the
cavity from the secondary side (wide open) using the side chain and D-ring moiety. For 33
(Figure 6), the A-ring moiety of DCA is simultaneously shallowly included in one of the
cavities of another CD to form a liner structure. For monomer 25, the D-ring moiety of DCA
penetrates deep into the cavity of 25 from the secondary side. However, for monomer 26,
DCA is included in the cavity of 26 from the secondary side by its A-ring moiety, differing
from other CDs (by D-ring moiety).
To further obtain the information about the binding modes of bile salts with diseleno- and
bipyridine-bridged -CDs, 2D ROESY spectra for typical hostguest pairs have also been
determined by Liu et al. [28]. For dimer 35 and CA, the results indicate that the carboxylate
side chain and D-ring of CA may penetrate into the CD cavity from the secondary side
shallowly and two CA molecules are bound separately into two cavities of 35 from the
secondary side, which is consistent with the 1:2 binding stoichiometry (Figure 7a). For dimer
39 and DCA, the results are quite different and show a 1:1 cooperative binding mode. The
A-ring of DCA penetrates deeply into one CD cavity of 39, attributing to the less steric
hindrance and higher hydrophobicity of the substituent group on the C-7 position of DCA
(Figure 7b). Under the same experiment using DCA as guest, host 38 adopts a different
binding mode from 39. The carboxylate side chain of two DCA molecules deeply penetrates
into the CD cavity of 38 from the secondary side separately.
4.1.2. Oligoethylenediamino-bridged -CDs

To obtain the information about the binding modes between bile salts and
oligoethylenediamino-bridged -CD dimers (4244), 2D ROESY spectra for typical host
guest pairs have been determined by Liu et al. [29]. The results of ROESY experiments
indicated that the D ring and side-chain of bile salt guest enter one -CD cavity from the
wide opening, and the linker group is partially self-included in the other -CD cavity
(Figure 8).
4.1.3. Aromatic diamino- and sulfonyldianiline-bridged -CDs

From ROESY experiments, Zhao et al. found that the D-ring of CA is wholly included in the
CD cavity of 45 from the wide opening, while the side-chain is located near the narrow
opening of CD cavity and folded toward the steroid body and the phenyl moiety is not
driven out of the CD cavity even after the guest inclusion [30]. Similar binding mode is also
observed in other cases of 45/bile salts complexes.
The binding modes between the aromatic diamino-bridged -CDs 4648 and bile salts have
also been investigated by Zhao et al. via 2D ROESY experiments and the results show that the
D-ring of CA is wholly included in the CD cavity with the wide opening, while the side chain
is located near the narrow opening of the CD cavity and is folded toward the steroid body [31].
The phenyl moiety is not driven out of the CD cavity even after the guest inclusion.
Figure 6. Structures of bridged -CDs

To obtain the information about the binding modes between bile salts and sulfonyldianiline-
bridged -CD 49, 2D ROESY spectra for typical hostguest pairs have further been
determined by Zhao et al. [32]. The correlation signals, along with the 1:1 binding
stoichiometry, jointly indicate a host-linker-guest binding mode between 49 and CA. That is,
upon complexation with 49, the carboxylate tail and the D ring of CA penetrate into one CD
cavity of 49 from the wide opening deeply, while the phenyl moiety of the CD linker is
partially self-included in the other -CD cavity. Similar binding modes are also observed in
other cases of 49/bile salt complexes.
4.1.4. Binaphthyl-, biquinoline- and dithio-bridged -CDs

The binding modes of binaphthyl-, biquinoline- and dithio-bridged -CDs (5055) and bile
salts have been investigated by 2D ROESY experiments in aqueous solution [33]. The results
show that CA enters the CD cavity of 53 from the second side of CD with the side chain and
D-ring. The side chain with the negative carboxylate group of CA moves toward the positive
protonated amino group of 53. The other binaphthyl-, biquinoline- and dithio-bridged -
CDs/bile salts complexes show a similar binding mode as the complex 53/CA, with only a
slight degree of difference in the depth of guest insertion.
Figure 7. The possible binding modes of 35 with CA (a) and 39 with DCA (b)
Figure 8. The possible binding mode of 4244 with CA

4.2. Complexation thermodynamics for bile salts and bridged CD series

4.2.1. Diseleno- and bipyridine-bridged -CDs
To elucidate the difference in binding behavior between the CD dimer and monomer, two
CD dimers (33 and 35) and their monomer analogs (25 and 26) have been used for titration
microcalorimetry with CA and DCA [27]. It is interesting that the results of the
thermodynamic measurements show a 1:1 binding stoichiometry for hosts 25, 26 and 33, but
1:2 stoichiometry for host 35. In addition, although the stability constants for the
complexation between dimer 33 and the bile salts are much larger than those for monomer
26, the long-linked dimer 35 unusually displays a lower cavity binding ability than its
corresponding monomer 25 upon complexation with both guests CA and DCA. The
enhancement of the binding ability of dimer 33 compared to monomer 26 could be ascribed
not only to the cooperative binding but also partly to the peculiar self-inclusion
conformation of 26 that leads to more unfavorable entropy changes, especially for the 26
CA pair. For 35, the two guest molecules are separately and independently included in the
two cavities of 35 because the longer linker, especially the ethylenediamino moiety of dimer
35, makes it possess a relatively large conformational freedom. As the considerable entropy
loss cancels the advantage of enthalpy gain, dimer 35 displays relatively weak binding
abilities. Both hosts 35 and 25 show similar binding ability for DCA and CA. The reason is
that either binding with host 35 or host 25, the two guest bile salts are included into the
cavity of CDs by its D-ring and side-chain moiety, which reduces the influence of the
substituent in C7. However, while binding with hosts 33 and 26, the A-ring moiety
participates in the binding process, so the more hydrophobic C7 substituent of DCA makes
it bind more strongly with the host CDs, giving the higher binding constants than with CA,
especially for host 26.
Either for diseleno-bridged -CDs (3437) or for bipyridine-bridged -CDs (3841), the host
guest stoichiometry changes in the same order, that is, from 1:2 to 1:1 with the increase of
spacer length [28]. For diseleno-bridged -CDs, only 36 and 37 adopt the 1:1 binding mode.
However, for bipyridine-bridged -CDs, only host 38 adopts the 1:2 binding mode; the
others all show the 1:1 cooperative binding mode. The thermodynamic results reveal that,
with the longest spacer, 37 gives the largest stability constants in all diseleno-bridged -CDs,
while the largest stability constants of bipyridine-bridged -CDs toward each guest
molecule is obtained by the dimers 39 and 40 with the moderate spacer lengths, which
suggests that only the CD dimers possessing the proper spacer length can give the perfect
cooperative binding toward guests.
For the dimers adopting 1:1 cooperative binding mode, the enthalpy changes are not only
the main contribution to the binding process but also the determining factor for the binding
abilities [28]. Comparing the diseleno-bridged -CDs with bipyridine-bridged -CDs, all of
the bipyridine-bridged -CDs display much stronger binding abilities toward bile salts than
corresponding diseleno-bridged -CDs, which indicate that the presence of rigid spacer
favors formation of a relatively fixed binding mode and results in the close contact between
two CD cavities and guest molecule, leading to the stronger binding abilities. On the other
hand, due to the presence of the bipyridine fragment, the hydrogen bond between the
hydroxyl group of the bile salt and the nitrogen atom of bipyridine might also be taken as a
plausible explanation for the strong binding abilities of bipyridine-bridged -CDs as
compared with diseleno-bridged -CDs. Upon complexation with CA and DCA, all dimer
hosts adopting a 1:1 binding mode show higher binding abilities than native -CD 1 due to
more favorable enthalpy changes, which perfectly confirms the advantage of cooperative
binding of guests by two CD cavities.
4.2.2. Oligoethylenediamino-Bridged -CDs

1:1 binding stoichiometry is observed for all the complexes between bile salts and
oligoethylenediamino-bridged -CDs (4244) [29]. The inclusion complexation of bile salts
with 4244 is driven by favorable enthalpy changes, accompanied by slight to moderate
entropy loss. Interestingly, the enthalpy changes for the inclusion complexation of 4244
increased, while the entropic changes decreased, with the elongation of the linker group,
giving a binding constant 42 > 43 > 44. The stronger binding of bile salts by the short-linked
-CD dimer is not thermodynamically accomplished by an increase of the originally
favorable enthalpy gain, but by a reduction of the unfavorable entropy loss. The short-
linked -CD dimer, with a better size and hydrophobicity match to bile salts, may
experience more extensive desolvation upon complexation, and thus exhibits the less
unfavorable entropy loss. With the elongation of linker group, the protonated amino group
in the linker is located distant from the anionic carboxylate (or sulfonate) tail of bile salt,
which consequently weakens the electrostatic interactions between the linker group and bile
salt. Moreover, the increase of the number of -NH- fragments in the linker group decrease
the hydrophobicity of -CD dimer to some extent, which is also unfavorable to the
hydrophobic interactions between host and guest.
The stability constants of the complexes formed by -CD dimers 4244 with bile salts are
larger than those of the complexes formed by native -CD 1 [29]. These enhanced binding
abilities of -CD dimers may be mainly attributed to the cooperative host-linker-guest
binding mode between host and guest. The electrostatic interactions between the protonated
amino groups in the linker and the anionic carboxylate (or sulfonate) tail of bile salt may
strengthen the inclusion complexations of these -CD dimers with bile salts. Moreover, the
hydrogen bond interactions of the hydroxyl groups of -CD and the -NH- fragments of the
oligo(ethylenediamino) linker with the carboxylate (or sulfonate) tail of bile salt also
contribute to the enhanced binding abilities of -CD dimers 4244.
Compared with CA, GCA and TCA, DCA possesses a more hydrophobic structure due to
the absence of C-7 hydroxyl group, which consequently leads to stronger hydrophobic
interactions between host and guest. Therefore, DCA gives the highest binding abilities
among the bile salts examined upon complexation with most CDs [29]. Possess more polar
side-chains, GCA and TCA show weak binding abilities upon inclusion complexation
complexation with -CD dimers due to the relatively poor hydrophobic interactions
between host and guest.
4.2.3. Aromatic diamino- and sulfonyldianiline-bridged -CDs

The stoichiometry for the inclusion complexation of 45 with bile salts were determined by
the continuous variation method and the results showed a 1:1 inclusion complexation
between 45 and bile salts [30]. The stability constants for the inclusion complexation of 45
with bile salts are much higher than those values for the native -CD 1. These enhanced
binding abilities of 45 may be mainly attributed to the cooperative host-linker-guest binding
mode between host and guest because the linker group provides some additional binding
interactions towards the accommodate guest. Host 45 displays higher binding ability for CA
than for DCA due to the hydrogen bond interactions between the 7-hydroxy group of CA
and the 2- and 3-hydroxy group of CD. Host 45 shows the weaker binding abilities upon
inclusion complexation with GCA and TCA than that of CA and DCA because GCA and
TCA are unfavorable to insert into the cavity from the second side of CD cavity with their D
ring attributing to the more hydrophilic tail attached to the end of the D ring.
The stoichiometries for inclusion complexation of aromatic diamino-bridged -CDs 4648
with bile salts were further determined by the continuous variation method and the results
show that all the hosts and guests form 1:1 complexes [31]. -CD dimers 4648 also show
enhanced binding ability toward bile salts as compared with -CD 1. The enhanced binding
abilities of aromatic diamino-bridged -CDs may be mainly attributed to the cooperative
host-linker-guest binding mode between host and guest. In addition to the association of the
CD cavity with a guest molecule, the linker group provides some additional binding
interactions towards the accommodated guest.
Unlike the -CD 1, the bridged -CDs 4648 show larger binding constants for CA than for
DCA [31]. Among them, the host 47 gave the highest stability constant for inclusion
complexation with CA. One possible reason for the stronger affinity for CA may involve
hydrogen-bond interactions between the 7-hydroxy group of CA and the 2- and 3-hydroxy
groups of CD, which subsequently strengthen the hostguest association. Moreover, all the
hosts show lower binding ability for complexation with GCA and TCA as compared with
complexation with CA and DCA. The highest binding constants towards GCA and TCA are
with host 47. The universally decreased binding ability toward GCA and TCA must be
related to structure differences between CA and DCA. Attributing to the more hydrophilic
tail, which is attached to the end of the D ring, GCA and TCA are unfavorable for insertion
into the cavity from the second side of the -CD cavity with their D ring.
The binding constants for the complexation of each bile salt by hosts 4648 increases in the
following order: 47 > 48 > 46 [31]. That is, host 47 with a tether of moderate length and
rigidity among the -CD dimers studied is the most suitable for inclusion complexation with
bile salts. This may be attributable to the strict size fit between these bile salts and the
moderate length-tethered -CD dimer 47, which consequently exhibits strong van der Waals
and hydrophobic interactions between host and guest.
The stoichiometry for the inclusion complexation of sulfonyldianiline-bridged -CD 49 with

bile salts has also been determined by the continuous variation method and the results
indicate that all the bile salts can form 1:1 complexes with 49 [32]. Thermodynamically, the
binding constants of 49 with bile salts are larger than those of native -CD 1. The enhanced
binding abilities of 49 may be also mainly attributed to the cooperative host-linker-guest
binding mode between host and guest. In addition to the association of the CD cavity with a
guest molecule, the linker group provides some additional binding interactions towards the
accommodate guest. Distinctly, the binding constant is significantly higher for DCA
compared to CA by native -CD 1. However, different from native -CD 1,
sulfonyldianiline-bridged -CD 49 reverses this binding selectivity, showing larger binding
constants for CA than DCA. One possible reason for the stronger affinity for CA may
involve H-bond interactions between CA and CD, which subsequently strengthen the host-
guest association. Moreover, all the hosts show a weaker binding ability upon complexation
with GCA and TCA than with CA and DCA. The universal decreased binding ability
toward GCA and TCA must relate to the structure differences from CA and DCA.
Attributing to the more hydrophilic tail, which is attached to the end of the D ring, GCA and
TCA are unfavorable to insert into the cavity from the second side of -CD cavity with their
D ring. It is worthy to note that the binding ability of 49 is significantly larger for TCA than
for GCA, which leads to a relatively strong molecular selectivity.
4.2.4. Binaphthyl-, biquinoline- and dithio-bridged -CDs

The stoichiometric ratios from the binding patterns for the titrations of steroids with
binaphthyl-, biquinoline- and dithio-bridged -CDs 5055 fell within the range of 1.8-2.1,
which clearly indicates that the majority of the inclusion complexes have a 1:2 stoichiometry
of steroids and bridged -CDs [33]. Thermodynamically, bridged -CD 52, possessing a
relatively short and rigid tether without amino groups, still gives an enhanced binding
ability upon complexation with steroids, except TCA, when compared its one single unit of
cavity with that of native -CD 1. The enthalpy changes for the inclusion complexation of
bridged -CD 52 with DCA and CA are more negative than that of native -CD 1, resulting
in the relatively stronger binding. On the other hand, the enthalpy change for the
complexation of 52 with DCA is higher than that with CA, which directly contributes to the
increased complex stability. It is reasonable that, possessing the more hydrophobic structure
due to the absence of C-7 hydroxyl group as compared with CA, DCA is easier to bind into
the -CD cavity than CA, which should lead to the more favorable van der Waals
interactions.
All the complexation of aminated bridged -CDs (50, 51, and 5355) toward DCA and CA
give more negative enthalpy changes as compared with that of neutral bridged -CD 52,
validating the contribution of the attractive electrostatic interactions between positively
charged protonated amino group of -CD tethers and negatively charged carboxylate group
of DCA and CA [33]. Accompanied with the more exothermic reaction enthalpies, the
inclusion complexation of DCA and CA by aminated bridged -CDs (50, 51, and 5355)
exhibits more unfavorable entropy changes compared to that for neutral bridged bis(-CD)
52, which possibly originates from the conformation fixation of host and guest and the rigid
complex formation upon complexation.
Mostly, bridged -CDs 50, 51, and 5355 give the lower binding ability upon complexation
with GCA and TCA as compared with the complexation with CA and DCA, which is similar
as the complexation of -CD 1 and bridged -CD 52 [33]. The universal decreased binding
ability toward GCA and TCA must relate to the structure differences from CA and DCA.
The more polar side chains at C23 for GCA and TCA remarkably affect their binding
thermodynamics.
4.3. Binding modes for bile salts and metallobridged CD series

4.3.1. Metallobridged -CDs with naphthalenecarboxyl linkers
2D ROESY NMR and circular dichroism spectroscopy experiments for the complexes of bile
salts with bridged and metallobridged CDs with naphthalenecarboxyl linkers have been
performed by Liu et al. to investigate the binding modes between host and guests [34]. The
result of 57/DCA complex showed that the guest DCA was included in the -CD cavity with
the D-ring and the carboxylic tail located near the narrow opening but the B-ring located
near the wide opening and the naphthyl group was excluded from the -CD cavity upon
inclusion complexation. Moreover, the result of 2D ROESY NMR showed that the
ethylenediamino moiety of the linker group was also partially self-included in the -CD
cavity from the narrow opening. Similar results were also found in other ROESY
experiments of hosts 57 and 59 with bile salts.
4.3.2. Metallobridged -CDs with biquinoline linkers

2D NMR experiments in D2O and molecular modeling studies for the complexes of bridged
and metallobridged -CDs with biquinoline linkers and bile salts have been performed by
Liu et al. to deduce the binding modes between the bile salts and -CD dimers [35,36]. The
results show that a cooperative host-tether-guest binding mode is operative in the
association of -CD dimers with a guest molecule; upon complexation with -CD dimers,
the guest steroid is embedded into one hydrophobic -CD cavity from the primary side,
while the tether group is partly self-included in the other cavity. In the metallobridged -
CDs, the tether group is entirely excluded from the -CD cavities as a result of metal
coordination. This arrangement allows two side groups of the guest molecule to be
embedded into the hydrophobic -CD cavities from the primary side of the -CD to form a
sandwich hostguest inclusion complex.
4.3.3. Metallobridged -CDs with oxamidobisbenzoyl linkers

1H ROESY experiments have been performed in D2O to investigate the binding modes
between bridged and metallobridged -CDs with oxamidobisbenzoyl linkers and bile salts
[37]. The results show a host-linker-guest binding mode between 66 and CA. That is, upon
inclusion complexation with -CD dimer, the carboxylate tail and the D-ring of CA enter
into one CD cavity of 66 from the wide opening, while the linker group of 66 is partially self-
included in the other CD cavity (Figure 9a). A similar binding mode is also observed for the
inclusion complexation of 66 with DCA.
Figure 9. The possible binding modes of 66 (a) and 67 (b) with CA, and the possible binding modes of
6972 with bile salts
With a shallowly self-included conformation, -CD dimers 65, 67, and 68 show a binding
mode different from that of 66. For example, for 67/CA complex, the carboxylate tail and D-
ring of CA enter the CD cavity from the wide opening, and the carboxylate tail is located
close to the linker group. On the other hand, the linker group is mostly moved out from the
CD cavity after complexation with CA (Figure 9b). 65/CA, 65/DCA, 67/DCA, 68/CA, and
68/DCA complexes show a similar binding mode to the 67/CA complex.
In the cases of the metallobridged -CDs 6972, the strong electrostatic attraction from the
coordinated CuII ions in the linker group may also favor the penetration of the carboxylate
tail of bile salt into the CD cavity through the wide opening. Moreover, the 1:2 or 2:4
binding stoichiometry indicates that each CD cavity of a metallobridged -CD is occupied
by a bile salt (Figure 9c).
4.4. Complexation thermodynamics for bile salts and metallobridged CD series

4.4.1. Metallobridged -CDs with naphthalenecarboxyl linkers
The interactions between hosts (2729, 5759) and bile salts have been studied by Liu and
Ueno et al. by the method of fluorescence [34,38]. The results show that all the hosts (2729,
5759) can form 1:1 complexes with bile salts CA and DCA. Thermodynamically, bridged -
CDs possess much stronger binding abilities compared with mono-modified -CDs. These
enhanced binding abilities should be attributed to cooperative binding of the -CD cavity
and the linker group towards the guest molecule, leading to greatly strengthened van der
Waals and hydrophobic interactions between host and guest when compared with mono-
modified -CDs. Furthermore, after metal coordination, the metallobridged bis(-CD)s 58
and 59 significantly enhance the original binding ability of native -CD 1, mono-naphthyl-
modified -CDs 2729 and even parent bridged -CD 57. This enhancement may be
subjected to a multiple recognition mechanism of metallobridged -CDs towards model
substrates. On one hand, the coordination of a metal ion to the linker group shortens the
effective distance of two -CD cavities to some extent and thus improves the size-fit degree
between host and guest. On the other hand, the electrostatic attraction between the anionic
carboxyl group of guest bile salt and the coordinated metal ion of metallobridged -CD may
also favour the hostguest binding to some extent.
4.4.2. Metallobridged -CDs with biquinoline linkers

The interactions between host 51 and bile salts have been investigated by Liu et al. by the
method of fluorescence [35]. The results show that all the bile salts can form 1:1 complexes
with 51. Thermodynamically, the binding constants obtained for CA and DCA are much
larger than those reported for mono-modified -CDs by Ueno et al. under practically the
same experimental conditions [38]. This enhancement is probably due to the cooperative
binding of the steroids by 51. The complex stability decreases in the order: DCA > CA >
GCA > TCA. The highest affinity for DCA is likely to arise from its more hydrophobic
steroid skeleton. Host 51 shows comparable affinities toward CA and GCA, whereas TCA,
possessing a highly polar anionic tail gives the lowest binding constant.
The stoichiometry for the inclusion complexation of hosts 6064 with bile salts has also been
determined by Jobs method [36]. The results show that the stoichiometry of the inclusion
complex formed by the 63/CA system is likely to be 2:2, with intramolecular complexation.
Stoichiometries of 1:1 (for bridged -CD) or 2:2 (for metallobridged -CD) were obtained in
other similar cases of hostguest inclusion complexation. Thermodynamically, the stability
constants of the complexes of bridged -CDs 51, 60 and 61 with bile salts are larger than
those of the complexes formed by mono-modified -CDs 2729 by a factor of about 1.1 to
around 200 benefitting from cooperative binding. In addition to inclusion complexation of
the guest molecule within one hydrophobic CD cavity, the tether group located near the
accommodated guest provides some additional interactions with the guest. In control
experiments, the changes in the fluorescence spectra of 3032 upon addition of guest
steroids were too small to allow calculation of the stability constants, which may be
attributed to strong self-inclusion of the substituted group preventing penetration of the
guest into the CD cavity. Except 60, the mono- and bridged--CDs display higher binding
affinities for DCA than for CA. This stronger affinity for DCA is likely to arise from the
more hydrophobic steroid skeleton of this compound compared with that of CA. The
abilities of both the short-tethered compound 60 and the long-tethered host 61 to bind CA
and DCA are unexpectedly limited compared to the binding abilities of mono-modified CDs
2729 due to the self-inclusion of the tether group for the short-tethered -CD dimer 60 and
the steric hinderance from the relatively large 5-amino-3-azapentyl-2-quinoline-4-
carboxyamide fragment on the exterior of the CD cavity for the long-tethered -CD dimer
61, respectively.
The metal-ligated oligomeric -CDs 6264 have significantly enhanced (around 504100
higher) binding affinities for the tested guest molecules compared with those of the mono-
modified -CDs [36]. These results can be explained by considering a mechanism involving
an uncommon multiple recognition behavior of metallobridged -CDs. A metallobridged -
CD affords four hydrophobic binding sites (four CD cavities) and one (or three) metal
coordination center(s), which jointly contribute to the cooperative binding of the oligomeric
host with the guest molecule upon inclusion complexation. In addition, ligation of a CuII ion
shortens the effective length of the tether to some extent and thus improves the size fit of the
host with the guest. The cumulative result of these factors is that the metal-ligated -CD
oligomers have binding abilities around 6200 times higher than those of their parent
bridged -CDs.
4.4.3. Metallobridged -CDs with oxamidobisbenzoyl linkers

The stoichiometry for the inclusion complexation of hosts 6572 with bile salts has been
determined by Jobs method [37]. The results indicate that each of the Jobs plots for the
inclusion complexation of 6568 with bile salts shows a maximum at a -CD dimer molar
fraction of 0.5, confirming the 1:1 binding stoichiometry between host and guest. For the
inclusion complexation of metallobridged -CDs 6972 with bile salts, however, each of
the Jobs plots shows a maximum at a bridged -CD unit molar fraction of 0.33, which
indicates 1:2 stoichiometry between each bridged -CD unit and guest. The
metallobridged -CDs 69 and 70 may only bind two bile salts to form a stoichiometric 1:2
inclusion complex. However, the metallobridged -CDs 71 and 72 may adopt
intramolecular 2:4 stoichiometry upon inclusion complexation with bile salts.
Thermodynamically, the binding constants for the inclusion complexation of CA and
DCA with bridged -CDs 6568 are higher than the KS values reported for the inclusion
complexation of these bile salts with native or mono-modified -CDs [33,38]. These
enhanced binding abilities highlight the inherent advantage of the cooperative host-
linker-guest binding mode of bridged -CDs 6568. In addition to the association of the
CD cavity with a guest molecule, the linker group provides some additional binding
interactions towards the accommodated guest.
The bile salts CA and DCA are better bound by bridged -CD 65, which possesses the
shortest linker group, than by the long-linked bridged -CDs [37]. This may be attributable
to the strict size-fit between these bile salts and the short-linked bridged -CD 65, which
consequently gives strong van der Waals and hydrophobic interactions between host and
guest.
Significantly, metallobridged -CDs 6972 show greatly enhanced binding abilities with
regard to the bridged -CDs 6568 [37]. These significant enhancements in the binding
abilities may be attributable to a more complicated multiple recognition mechanism
involving the cooperative binding of several CD cavities, conformation adjustment by the
metal coordination, and additional binding interactions between the metal-coordinated
linker group and the accommodated guest molecules.
Except for 66, all of the hosts examined display higher binding abilities for CA than for DCA
[37]. One possible reason for the stronger affinities for CA may involve hydrogen bond
interactions between the 7-hydroxy group of CA and the 2- and 3-hydroxy groups of CD.
4.4.4. Metallobridged -CDs with aminated linkers

The microcalorimetric experiments of -CD 1 and modified -CDs 2, 5, 6, 7 with bile acids
showed typical titration curves of 1:1 complex formation [18]. However, metallobridged -
CD 56 displays a 1:2 hostguest binding stoichiometry. Thermodynamically, as compared
with native -CD 1, most oligo(ethylenediamino)--CDs 2, 5 6, and their CuII complexes 7
and 56 show enhanced molecular binding abilities and guest selectivities towards bile acids.
The inclusion complexation of bile acids with native -CD 1 and their derivatives (2, 5, 6, 7,
and 56) is absolutely driven by favorable enthalpy changes accompanying with moderate
unfavorable or slightly favorable entropy changes. The favorable enthalpy change is
attributed to the dominant contribution of the hydrophobic interactions. Meanwhile, the
unfavorable entropy given by most of the complexes is due to the decrease of rotational and
structural freedom upon complex construction.
As compared with native -CD 1, 5 shows increased binding abilities toward negatively
charged bile acids guest molecules, which should be mainly due to the additional
electrostatic interactions between the amino tether moiety of hosts and anionic carboxylate
or sulfonate tail of guests [18]. Moreover, -CD dimer 56 shows a larger binding constant
upon inclusion complexation with CA and DCA than 5. This may be attributed to that the
coordination of copper ion onto the amino tether of CD affords a more positive charged
environment as compared with its precursor 5. Compared with 5, host 6 also shows stronger
binding abilities toward guest molecules. However, the introduction of copper actually
decreases the original binding ability of 6 towards DCA and gives comparable stability
constant upon complexation with CA. All the hosts, including native -CD 1 and modified
-CDs 2, 5, 6, 7, and 56, show the weaker binding abilities upon inclusion complexation with
GCA and TCA than those of CA and DCA. It is also found that complexes stabilities
enhance with the extended length of spacer for the same guest except for 2/CA to 5/CA. It is
reasonable to believe that the increased stability is due to the enlarged hydrogen binding
interactions.

7.4
33 CA 6860 30.5 8.6 ITC 27
(TrisNaCl)
7.4
DCA 9700 37.0 14.3 ITC 27
(TrisNaCl)
7.4
35 CA 2700 27.1 7.5 ITC 27
(TrisNaCl)
7.4
DCA 3300 35.7 15.7 ITC 27
(TrisNaCl)
7.4
36 CA 4100 24.9 4.3 ITC 28
(TrisNaCl)
7.4
DCA 5400 35.0 13.7 ITC 28
(TrisNaCl)
7.4
37 CA 5030 29.1 8.0 ITC 28
(TrisNaCl)
7.4
DCA 6100 40.2 18.6 ITC 28
(TrisNaCl)
7.4
39 CA 12700 32.4 9.0 ITC 28
(TrisNaCl)
7.4
DCA 12400 45.4 22.0 ITC 28
(TrisNaCl)
7.4
40 CA 12400 25.5 2.2 ITC 28
(TrisNaCl)
7.4
DCA 13100 31.9 8.3 ITC 28
(TrisNaCl)
7.4
41 CA 6800 25.4 3.5 ITC 28
(TrisNaCl)
7.4
DCA 7500 35.2 13.1 ITC 28
(TrisNaCl)
42 CA 7.2 (PBS) 21065 32.8 8.1 ITC 29
DCA 7.2 (PBS) 22780 42.7 17.9 ITC 29
GCA 7.2 (PBS) 9707 23.0 0.3 ITC 29
TCA 7.2 (PBS) 6848 22.4 0.5 ITC 29
43 CA 7.2 (PBS) 5868 39.3 17.7 ITC 29
DCA 7.2 (PBS) 7017 47.4 25.5 ITC 29
GCA 7.2 (PBS) 4031 25.8 5.2 ITC 29
TCA 7.2 (PBS) 2947 26.9 7.1 ITC 29
44 CA 7.2 (PBS) 5606 41.0 19.6 ITC 29
DCA 7.2 (PBS) 5511 52.1 30.7 ITC 29
GCA 7.2 (PBS) 2847 26.5 6.9 ITC 29
TCA 7.2 (PBS) 1877 29.0 10.3 ITC 29

GCA 7.2 (PBS) 7200 Fluorescence 30
TCA 7.2 (PBS) 17610 Fluorescence 30
50 CA 7.2 (PBS) 7351 33.0 10.9 ITC 33
DCA 7.2 (PBS) 5504 42.7 21.4 ITC 33
GCA 7.2 (PBS) 5936 15.1 6.4 ITC 33
TCA 7.2 (PBS) 3058 24.5 4.6 ITC 33
51 CA 7.2 (PBS) 5559 49.3 27.9 ITC 33
CA 7.2 (PBS) 11300 Fluorescence 35
DCA 7.2 (PBS) 8372 48.1 25.7 ITC 33
GCA 7.2 (PBS) 2979 18.1 4.2 ITC 33
TCA 7.2 (PBS) 4441 19.7 1.1 ITC 33
52 CA 7.2 (PBS) 5039 28.2 7.1 ITC 33
DCA 7.2 (PBS) 7900 31.6 9.4 ITC 33
GCA 7.2 (PBS) 4262 21.5 0.8 ITC 33
TCA 7.2 (PBS) 1975 22.0 3.2 ITC 33
53 CA 7.2 (PBS) 10700 30.6 7.6 ITC 33
DCA 7.2 (PBS) 8912 38.1 15.6 ITC 33
GCA 7.2 (PBS) 5689 22.7 1.3 ITC 33
TCA 7.2 (PBS) 2762 37.3 17.6 ITC 33
54 CA 7.2 (PBS) 9899 37.5 14.7 ITC 33
DCA 7.2 (PBS) 11150 39.9 16.8 ITC 33
GCA 7.2 (PBS) 4061 23.5 2.9 ITC 33
TCA 7.2 (PBS) 2502 20.2 0.8 ITC 33

55 CA 7.2 (PBS) 6196 39.3 17.6 ITC 33
DCA 7.2 (PBS) 10325 39.4 16.5 ITC 33
GCA 7.2 (PBS) 2891 23.3 3.5 ITC 33
TCA 7.2 (PBS) 2189 20.0 0.9 ITC 33
56 CA 7.2 (PBS) 13330 29.77 6.23 ITC 18
DCA 7.2 (PBS) 12065 34.02 10.72 ITC 18
GCA 7.2 (PBS) 2925 23.36 3.58 ITC 18
TCA 7.2 (PBS) 2478 21.46 2.09 ITC 18
7.4
(TrisHCl)
7.4
(TrisHCl)
7.4
(TrisHCl)
7.4
(TrisHCl)
7.4
(TrisHCl)
7.4
(TrisHCl)
60 CA aqueous solution 5380 Fluorescence 36
DCA aqueous solution 2790 Fluorescence 36
GCA aqueous solution 1745000 Fluorescence 36
7.2
(TrisHCl)
7.2
(TrisHCl)
7.2
(TrisHCl)
DCA 7.2 Fluorescence 37

(TrisHCl)
7.2
(TrisHCl)
7.2
(TrisHCl)
7.2
(TrisHCl)
7.2
(TrisHCl)
7.2
69 CAa 5.73 107 Fluorescence 37
(TrisHCl)
7.2
DCAa 2.03 107 Fluorescence 37
(TrisHCl)
7.2
(TrisHCl)
7.2
(TrisHCl)
7.2
(TrisHCl)
7.2
(TrisHCl)
7.2
(TrisHCl)
7.2
(TrisHCl)
PBS: Phosphate Buffer Solution; ITC: Isothermal Titration Calorimetry;
Tris: Tris(hydroxymethyl)aminomethane;
: The guest-induced variations in the fluorescence intensities are too small for these values to be determined.
a : Unit of Ks is in M2.
Table 2. Complex stability constants (Ks/M1), enthalpy (H/(kJmol1)), and entropy changes
(TS/(kJmol1)) for intermolecular complexation of bile salts with bridged -CDs in aqueous solution
5. Conclusion
In conclusion, the binding modes, binding abilities, and molecular selectivities of four
typical bile salts (CA, DCA, GCA, and TCA) upon complexation with CDs and their
derivatives are summarized in this chapter from thermodynamic viewpoints. Generally,
native and mono-modified CDs display relatively limited binding ability towards guest
molecules, probably because of weak interactions between hosts and guests, which would
result in a relative small negative enthalpy change, and then, a relative weak binding.
However, bridged and metallobridged CDs have greatly enhanced the binding abilities in
relation to the parent CDs, owing to a multiple recognition mechanism, which would lead to
a relative large negative enthalpy change, and then a strong binding. This summary of the
binding modes and thermodynamic data for the complexation of bile salts with CDs and
their derivatives is quite important to improve the understanding of molecular recognition
mechanism in supramolecular systems and further guide the design and synthesis of new
supramolecular systems based on different kinds of CDs in the future.
Author details
Yu Liu* and Kui Wang
Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University,
Tianjin, P. R. China
Acknowledgement
This work was supported by the 973 Program (2011CB932502) and NSFC (20932004), which
are gratefully acknowledged.
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[33] Liu Y, Yang Y.-W, Yang E.-C, Guan X.-D (2004) Molecular Recognition
Thermodynamics and Structural Elucidation of Interactions between Steroids and
Bridged Bis(-Cyclodextrin)s. J. Org. Chem. 69: 65906602.
[34] Liu Y, Wu H.-X, Chen Y, Chen G.-S (2009) Molecular Binding Behaviours of Bile Salts
by Bridged and Metallobridged Bis(-Cyclodextrin)s with Naphthalenecarboxyl
Linkers. Supramol. Chem. 21: 409415.
[35] Liu Y, Song Y, Wang H, Zhang H.-Y, Wada T, Inoue Y (2003) Selective Binding of
Steroids by 2,2-Biquinoline-4,4-dicarboxamide-Bridged Bis(-cyclodextrin):
Fluorescence Enhancement by Guest Inclusion. J. Org. Chem. 68: 36873690.
[36] Liu Y, Song Y, Chen Y, Li X.-Q, Ding F, Zhong R.-Q (2004) Biquinolino-Modified -
Cyclodextrin Dimers and Their Metal Complexes as Efficient Fluorescent Sensors for
the Molecular Recognition of Steroids. Chem. Eur. J. 10: 36853696.
[37] Liu Y, Yu H.-M, Chen Y, Zhao Y.-L (2006) Synthesis of Bridged and Metallobridged
Bis(-cyclodextrin)s Containing Fluorescent Oxamidobisbenzoyl Linkers and Their
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[38] Ikeda H, Nakamura M, Ise N, Oguma N, Nakamura A, Ikeda T, Toda F, Ueno A (1996)
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Cyclodextrins. J. Am. Chem. Soc. 118: 1098010988.
Chapter 13
Thermodynamics of Hydration in Minerals:

How to Predict These Entities
Philippe Vieillard
1. Introduction
1.1. Nature of water in inorganic compounds.
Many papers have suggested that several specific types of H2O exist. These have been
labelled variously as zeolitic, loosely held, structural, crystal, tightly bound and
external [1-3]. These labels suggest both the differing apparent energies of H2O as well as
their differing apparent structural roles. Three useful distinctions can be made about H2O in
compounds:
1. H2O that varies in content as a continuous function of temperature and pressure

2. H2O that changes discontinuously at a unique temperature for a given pressure
3. H2O that is sorbed to external surfaces
The first type (continuously varying H2O) is characteristic of the zeolites and clay minerals
and considers that most of the zeolites and clay minerals lose or gain H2O in response to
small changes in temperature and pressure over an extended temperature, relative humidity
or the nature of cations in exchanged sites.
The second type of H2O is similar in nature to that found in hydrates of salts and considers
that dehydration occurs over narrow temperature intervals in some compounds. Some
zeolites, like analcime and laumontite, do not exchange water at room temperature. This
type can be called hydrate H2O and has a specific position in the crystal structure.
Hydroxides are excluded from this chapter because the H2O molecule is not identified but is
only virtually present as a hydroxyl OH.
The third type of H2O is externally sorbed to the crystal and may be referred to as external.
This type is present in quantities much smaller than the H2O present within the structure of
any zeolite grain size. In the clay minerals, whose specific surfaces are greater than those of
zeolites, the water located in inter-particle spaces, in inter-aggregate spaces and at the surface
of uncharged clays minerals indicates that a special status of H2O may be different in the
regimes of adsorption or of capillary condensation, and this is not considered in this chapter.
2. Definition of thermodynamic entities of hydration

In evaluating the thermodynamic quantities, it is important to define the standard state
chosen for a given constituent. In the present study, the standard state for water is chosen as
pure water at a temperature of 25C with a vapour pressure of Po, and for the minerals, the
dry compound is at a temperature of 25C with a vapour pressure of P=0.
The reaction of hydration may be expressed by the following reaction:
X( c ) n * H 2O( l ) X nH 2O( c ) (1)
If we consider any standard thermodynamic entity of hydration hyd,298 (enthalpy H hyd

,298

free energy Ghyd ,298 , entropy Shyd ,298 , heat capacity Cphyd. and molar volume VHyd.) for a
given mineral having n bounded molecules, the entity of hydration is related to the total
formation entity f ,298 (enthalpy of ,298.15 free energy G of ,298.15 , entropy S298

, heat
capacity Cp298.15 and molar volume V298) of the mineral by the following:
ohyd ,298 of ,298 X nH 2O 0f ,298 X n * of ,298 ( H 2Oliq ) (2)
where of ,298 X nH 2O and 0f ,298 X are the thermodynamic entity of formation of the
mineral in the hydrated and dehydrated states, respectively, and 0f ,298 H 2Oliq stands for
the thermodynamic entity of formation of bulk water. The unit of the entity ohyd,298 is based
per n moles of bound water or per mole of an anhydrous compound X.
The standard thermodynamic parameters of the hydration water can be calculated if the
thermodynamic entities of formation (enthalpy of ,298.15 free energy G of , 298.15 , entropy

S298 , heat capacity Cp298.15 . and molar volume V298.) of the anhydrous and hydrous end
members are available in thermochemical tables or calculated from calorimetric
measurements. However, the thermodynamic properties of the hydration water can be
estimated by considering the hypothetical intra-crystalline reaction:
X( c ) n * H 2O( hydr ) X nH 2O( c ) (3)
where H2O(hyd) represents the hydration water. The thermodynamics of the intra-crystalline
reaction can be written as follows:
ro ,298 of ,298 X nH 2O 0f ,298 X n * of ,298 ( H 2Ohyd. ) (4)
By assuming that the standard thermodynamic entities of the intra-crystalline reaction are
equal to zero, i.e., ro,298 0 , the standard values of the molar thermodynamic entity of the

hydration water, 0f ,298 H 2OHyd , is finally obtained from eqs (2) and (4):
Thermodynamics of Hydration in Minerals: How to Predict These Entities 341

0f ,298 H 2OHyd n * 0f ,298 H 2Oliq 0hyd ,298 n (5)

The aim of this chapter is to determine how the thermodynamic entity 0f ,298 H 2OHyd of
the hydration water varies in all inorganic compounds, such as minerals, salts, zeolites and
clays. There are two main questions: 1) Is the thermodynamic entity of the hydration water
strongly related to the physical-chemical properties of the inorganic compound or does it
remain constant within a structural family of inorganic compounds? and 2) What are the
adequate relationships that can predict the thermodynamic entity of the hydration water in
any mineral?
3. Measurements of thermodynamics of hydration in minerals

Different methods of measurements of thermodynamic entities of hydration are presented
in this section:
- Hydrofluoric acid solution calorimetry. The calorimetric measurements of the heat of

dissolution of anhydrous and hydrated compounds provide the enthalpy of formation
to form elements. The enthalpies of hydration are obtained by measuring the difference
in the enthalpy of the solution in HF acid at approximately 70C, of a hydrated and a
dehydrated zeolite [4-6] or at 25C in a HF - HNO3 solution for clay minerals [7].
- Transposed-temperature drop calorimetry. The enthalpy of hydration data are obtained
by measurements of the heat evolved from a sample dropped at room temperature into
a calorimeter maintained at 700800C [8], [9-12]. One of the difficulties associated with
this measurement includes the enthalpy effects because of the irreversible structural
changes at 700800C.
- Adiabatic low temperature calorimetry. This is performed on the anhydrous and
hydrated compounds to determine the third law of entropy for the zeolites [4-6] and
clay minerals [7, 13].
- Heat of adsorption combined with adsorption-desorption isotherms. This method
provides measurements of integral enthalpies of hydration as a function of the degree
of hydration. Some of the difficult parameters to control include the amount of H2O
adsorbed by the sample (requires knowledge of the amount of H2O in the sample while
immersed in water), the accurate measurement of the initial state of dehydration and
the potential for irreversible change in the zeolite structure during dehydration such
that the sample does not re-adsorb its full capacity of H2O during immersion [14]. For
clays, the measurements of heat of adsorption were performed on eight homoionic
SWy-1 montmorillonites [15-17] [18] [19] [20] and on vermiculites [21]. One advantage
of the method is that it is a direct measurement of the enthalpy of hydration.
- Phase equilibriums. The enthalpy of hydration can be determined from the phase
equilibrium measurements of the isoteric method, which are plotted as Ln P (or Ln K)
versus 1/T at a constant hydration state. The slopes of these lines give the enthalpy of
hydration for zeolites [22], [23] and for montmorillonites [24-26].
- Gas-adsorption calorimetry. The enthalpies of hydration data are obtained by exposing

a bed of zeolite to differing vapour pressures within a calorimeter [27]. One of the
difficulties of this method is the kinetic limitations on attainment of equilibrium (slow
kinetics requires a very sensitive and stable calorimeter). An advantage of the method is
the capacity to measure partial molar enthalpies of hydration directly.
- Adsorption-desorption isotherms measured at different temperatures. With the
Clausius-Clapeyron relationships, the ability to extract the integral and partial
thermodynamic entities of hydration from isotherms at any two temperatures was
developed by [28, 29] and applied on montmorillonite in [30] and [31]
- Thermochemistry and Raman spectroscopy. A combined study of thermochemistry and
raman spectroscopy has been tested on zeolites [32] and clays [33] [34].
4. Inventory of different values from prediction methods of

thermodynamic entities of hydration water
The thermodynamic data of liquid water and ice are displayed in Table 1. The formation
properties of the hydration water may vary depending on the nature of the physical-
chemical properties of the anhydrous compound [35]. In any case, when the minerals
exist as hydrated phases, the presence of water molecules stabilises them.
Thermodynamically, this corresponds to G0hyd < 0 kJ mol-1 or G0f,(H2OHyd) < -237.14 kJ
mol-1, the value for bulk water at 250C and 1 bar [36]. Additionally, the maximum entropy
is for bulk water and implies that S0(H2OHyd) < 69.95 J K-1 mol-1 [36]. The minimum entropy
may be assessed by considering the entropy of Ih ice, as refined by Tardy et al. [37] (44.77
J K-1 mol-1). To give a minimum value for G0f(H2OHyd) is more complicated. Ice cannot be
of use, for example, because it is not stable at room temperature, and on the contrary,
G0f(Ice Ih) > G0f (bulk water), with 236.59 kJ mol-1. For the enthalpy term H0f(H2OHyd),
because G0hyd < 0 kJ.mol-1 and S0(H2OHyd) < S0(bulk H2O) for hydrated minerals, then
H0hyd must be negative or H0f(H2OHyd) < H0f(bulk H2O) with -285.83 kJ mol-1 [36]. For
the heat capacity of hydration water, very few measurements have been actually
performed so far.
Families Ref. Hf Gf S Cp V
(kJ mol-1) (kJ mol-1) (J K-1 mol-1) (J K-1 mol-1) cm3 mol-1
Liquid water 1 -285.840.04 -237.180.05 69.9230.03 75.576 18.064
Ice 2,3 -292.750.1 -236.590.1 44.7710.05 42.008 19.228
References: 1 [36]; 2 [37]; 3 [35].
Table 1. Average thermodynamic entities (Hf, Gf, S, Cp and V) of liquid water and ice.
Among the numerous methods of prediction of thermodynamics entities of compounds

(salts, and minerals), only twelve are retained and exhibit different values of the
thermodynamic entities of ice-like water obtained from the statistical results from the
anhydrous and hydrated compounds (Table 2).
Families Ref. Nb. Hf Gf S Cp V

comp (kJ/mole) (kJ/mole) (J/K/mole) (J/K/mole) cm3/mole
Sulphates &
1 41 -301.47.7 -244.47.9 41.56.0 395.2 14.51.2
sulphites
Chlorates &
1 34 -308.38.6 -251.88.5 43.75.9 422.7 14.12.3
Chlorides
Zeolites 2 15 59.1
Hydrates 3 342 -298.620.5 -242.4 40.9 42.8 14.75
Silicates 4 ? 39.34.2 13.70.5
Silicates 5 3 54.123
Hydrates 6 ? -297.06
RE chlorides 7 8 -297 46.4
Binary comp. of Na 8 42 -2978.3
Silicates 9 7 43.5 14
Silicates 10 7 -306.9912.8 44.12.0 14.60.09
Silicates 11 6 -292.374.6 -239.915.7
Borates 12 23 -290.42 -237.28 54.86
U bearing minerals 13 14 -295.58 -241.1
References: 1 - [35]; 2 - [38]; 3 - [39]; 4 - [40]; 5 - [41]; 6 - [42]; 7 - [43]; 8 - [44]; 9 - [45]; 10 - [46]; 11 - [47]; 12 - [48]; 13 - [49].
Table 2. Average thermodynamic entities (Hf, Gf, S, Cp and V) of hydration water obtained in
different prediction models.
All of these models of predictions are built on a simple additive scheme and require
knowledge of the thermodynamic entity of the anhydrous compound, the number of water
molecules and the thermodynamic entity of formation of ice-like water or of hydration
water obtained by statistical regressions. For each thermodynamic entity (enthalpy, free
energy, entropy, heat capacity and molar volume), the values are significantly different
within the nature of the compounds or minerals. For each prediction model, the nature of
family, number of compounds and statistical errors are provided to check the extent and the
validity of the model. There appear to be few models of prediction of free energies of
hydration, which is the most useful parameter in geochemical modelling. The best way to
reach this target is to combine the enthalpy and entropy of hydration. Despite the great
diversity of the enthalpy of formation of the hydration water and its great error within
different families of compounds, some recent and accurate models of prediction of the
enthalpy of hydration are important to introduce for compounds such as salts, zeolites and
clays minerals.
To improve the accuracy of prediction, the next section develops several models of
prediction based on different kinds of minerals displaying recent measurements of the
thermodynamic entities of the hydration water closely related either to the environmental
conditions and or to the nature and chemical formulas of the anhydrous compounds.
5. Recommended models of prediction of thermodynamic entities

5.1. Enthalpy of formation
Salts A model of the prediction of hydration enthalpy has been developed and tested on 349
different hydrates salts [50-52]. By considering the following reaction defining the hydration
of a salt Ax Bx :
1 2
Ax Bx n * H 2O( c ) Ax Bx n H 2O (6)
1 2 1 2
the enthalpy of hydration of the reaction (6) becomes
H hyd
o

,298 H f ,298 Ax Bx nH 2O H f ,298 Ax Bx
o
1
o
2
1 2
n * H o
f ,298 ( H 2O( c ) ) (7)
where n is the number of molecules of crystalline water contained in the hydrate under
consideration and H f ,298 (H2O)(c) represents the enthalpy of formation of ice. A parameter

H ( B z2 ) A z1 characterising the anhydrous salt Ax Bx , was defined as follows [50-52]:
1 2

H ( B z2 ) A z1
1
z1 * z2
H o

f ,298 Ax1 Bx2 x1 * H f ,298 A
o z1

x2 * H of ,298 ( B z2 )

(8)
This parameter is analogous to the enthalpy of dissolution of an anhydrous salt per

equivalent (characterised by the product of charges of the cation and anion). The
relationships of the enthalpy of hydration of a salt to the number of the molecules of water
and to the nature of the salt is:
H hyd ,298.15 Az * n * H ( Bz2 ) A z1 b

a
(9)

where A z and are constants that depend on the nature of the cation A z1 present in the
hydrate, n is the number of molecules of the water of crystallisation in the hydrate, and a
and b are constants for all hydrates and respectively equal to 0.791 and -80.0 kJ mol-1 [50-52].
Eq. (9) shows that the enthalpy of hydration is closely related to the nature of the cation in
the anhydrous salt, to the number of water molecules in the chemical formula and to the
nature of the anhydrous salt.
The enthalpy of the formation of ice used in Eq. (7) [50-52] comes from Robie & Waldbaum
[53] and is equal to -279.8 kJ mol-1. As this value is very different from those given in table 1,
the values of coefficients ( A z , a and b) of Eq. (9) need to be determined with H f ,298
H2O(ice)=-292.75 kJ mol-1 by a minimisation technique of the square difference between the
measured and calculated heat of hydration. The values of a and b are assumed constants for
all hydrated salts and are a= 0.612 and b= 17.07; Eq (9) becomes:
H hyd ,298.15 A z * n
0.612

* B z2 A z1 17.07

(10)

The values of A z and for the different salts of cation A z1 are given in table 3 with the
respective standard deviations and % errors of the predicted enthalpy of formation of the
hydrated salts.
An example is given by considering the data of all of the sodium salts displayed in Figure
1A and shows the great variation of the enthalpy of hydration having the same number as
the crystalline water. The different str aight lines are obtained from Eq. (10) with values of
A z and for Na+ and are plotted for the different values of the number of crystalline water

molecules and the nature of the crystalline salts ( H ( B z2 ) A z1 ). For a given anhydrous salt

(same value of H ( B z2 ) A z1 ), the enthalpy of hydration per mole of water appears to not be
constant but decreases when the number of molecules of the crystalline water increases.
Figure 1B displays the enthalpy of crystalline water versus the nature of the anhydrous salt
showing the great disparity and shows that the enthalpy of the crystalline water in all of the
sodic salts is more negative than those of the hexagonal ice. When the number of crystalline
water molecules of any salt increases, the enthalpy of formation of the crystalline water
decreases from large values (NaOH. H2O; H f ,298 H2O= -309.25 kJ mol-1) to values close to
those of ice (Na2Se. 16 H2O; H f ,298 = -297.22 kJ mol-1) and are different from the average
value for 61 Na salts ( H f ,298 = -297.74 kJ mol-1).
Cations A z Nb. of data % error1 Std dev.

(kJ/mol H2O)
Li+ -0.277 -0.341 19 0.34 3.58
Na+ -0.294 1.759 61 0.29 3.44
K+ -0.115 -9.168 15 0.66 10.70
Rb+ -0.360 -6.769 6 0.29 3.38
Cs+ -0.577 18.954 4 0.48 6.35
Be+2 -0.485 -3.068 7 0.25 3.48
Mg+2 -0.312 -10.708 21 0.43 5.39
Ca+2 -0.270 -3.892 25 0.44 4.64
Sr+2 -0.349 -1.894 20 0.32 5.93
Ba+2 -0.327 -4.637 19 0.80 5.31
Zn2+ -0.211 -16.461 12 0.44 6.57
Cd2+ -0.322 2.266 8 0.33 4.29
Cu+2 -0.433 -1.791 11 0.65 4.22
Ni2+ -0.176 -18.056 10 0.46 2.81
Co2+ -0.260 -2.296 11 0.36 3.60
Fe2+ -0.136 -17.806 6 0.18 1.58
Mn2+ -0.238 -5.144 15 0.25 6.14
Cr+2 -0.478 31.459 3 0.28 1.77
UO2+2 -0.247 -7.945 18 0.35 4.80
1: the % error weighs the difference (in %) between the measured and predicted enthalpy of the formation of the
hydrated salts.
Table 3. Values of A z , number of data, % error and statistical error per moles of crystalline water.
z z1
Figure 1. A Hydration enthalpy of sodium salts versus the parameter H ( B 2 ) A ; B Enthalpy of
z z
the formation of the crystalline water versus the parameter H ( B 2 ) A 1 .
Zeolites. The anhydrous compound X (reaction 1) is a zeolite with the following formula:
i nc
i 1 Al Fe Si

Ai Aln Fen Sin ON , in which Al, Fe and Si represent the framework with different

channels occupied by various exchangeable cations present, which are represented by Az+. A
compilation of the average hydration enthalpies per mole of water of 145 diversely
originating zeolites measured using different technical methods [54] provided 76 data points
from the transposed-temperature drop calorimetry (TTDC), 57 data points from the
immersion calorimetry (IC), 6 data points from the phase equilibriums (PE), 5 data points
from the gas-adsorption calorimetry (GAC) and 3 data points from the hydrofluoric acid
calorimetry (HF).
From the selected average enthalpies of hydration of the different zeolites with their
chemical formulas (145 data points), a regression equation for the enthalpy of hydration per
mole of water is proposed [54]:
H Hyd W Al Si * e a b * WP (11)
where coefficients a and b are

a 4.664 2.787 * Al Al Si 0.056 * FDanh. 0.003 * H O site A (12)
b 1.52 0.0047 * H O site A * Al Si (13)

Coefficients of Eqs. (11) (12) and (13), such as the ratio Al/Si, Al/(Al+Si), FDanh.,
H O (site A)(aq) and WP, represent the extra-framework charge, the ratio of tetrahedral
substitution, the framework density of the anhydrous zeolite, the average cation
electronegativity in the exchange site and the intracrystalline water porosity, respectively.
All of these parameters can be calculated from the chemical formula and the unit cell
volume for any zeolite.
The framework density (FD) [55, 56] represents the number of tetrahedral atoms per 1000 3
and are obtained as:
FDanh. nAl nFe nSi / Unit cell Vol * 1000 (14)
The electronegativity of site Az+, defined by HO= (site A), represents the weighed average
of HO= Mz+(aq) of nc different cations in the exchanged site A:
i nc
ni *xi . HO Maqz i
i 1
HO (site.A) (15)
xA
The number of oxygens balancing site Mz+ (in extra-framework sites) is then:
i nc
xA ni *xi (16)
i 1
The parameter HO= Mz+ (aq) characterises the electronegativity for a given cation Mz+ and
is defined as the difference between the enthalpy of formation of the corresponding oxides

H f MiOx
i
(c)
and the enthalpy of formation of the corresponding aqueous cation

H f Mizi ( aq )
:
zi
H O Maq 1

xi
H f MiOx
i
(c)

-H f Mizi

( aq )
(17)
where z is the charge of the cation Mz+ and x is the number of oxygen atoms combined with
one atom of M in the oxide (x = z/2), such that the difference in Eq. (17) refers to one oxygen
atom. A set of internally consistent values was presented by Vieillard & Mathieu [54] and is
given in Table 4.
The total intracrystalline pore volume, WP, was introduced by Barrer [57] for determining the
volume of liquid water that can be recovered thorough the outgassing of the fully hydrated
zeolite. Assuming that the unit cell volume of zeolitic water is the same as that of liquid water (
Vu.c . H O = 29.89 3), during the hydration-dehydration processes, the water porosity (WP) can
2
be calculated as the volume of liquid water in 13 of crystal and is expressed as follows:
29.89 * nH
2O
WP (18)
V u.c . hydr .
where Vu.c. hyd. represents the unit cell volume of a hydrated zeolite containing nH2O water
molecules. Assuming that the number of water molecules nH2O varies from 0 to nH2O max, the
unit cell volume of a zeolite can be directly related to the number of water molecules.
Although such variations in the unit -cell volume do occur, let us assume a linear variation
in the unit-cell volume as a function of the number of water molecules:
Vu.c. hyd Vu.c . anh. k * nH (19)

2O
where Vu.c. anh. represents the unit-cell volume of the anhydrous zeolite. Parameter k weights
the variation in the unit-cell volume between an anhydrous zeolite and a fully hydrated
zeolite per one water molecule. This parameter can be calculated from the available unit-cell
volumes of anhydrous and fully hydrated zeolites. Thus, knowledge of the number of water
molecules and the unit-cell volume of anhydrous and hydrated zeolites is required for the
calculation of the water porosity:
29.89 * nH
2O
WP (20)
Vu.c. anh. k * nH
2O

Ions HO=Mz+(aq) Ions HO=Mz+(aq)
(kJ mol-1) (kJ mol-1)
Li+(aq) -40.90 Ca+2(aq) -92.1

Na+(aq) 65.80 Mg+2(aq) -134.6
K+(aq) 141.00 Fe+2(aq) -181.58
Rb+(aq) 163.24 Mn+2(aq) -164.4
Cs+(aq) 170.0 Zn+2(aq) -197.07
Ba+2(aq) -15.6 La+3(aq) -124.8
Sr+2(aq) -40.4 H+(aq) -285.83
Table 4. Parameter HO=Mz+ (aq) of selected cations [54].
By eliminating 9 erroneous data points [54], the regression coefficient for 136 data is R2= 0.880,
with a standard error of 3.46 kJ mol-1 for all data, regardless of the nature of the
experimental data. Figure 2 displays the predicted enthalpy of hydration of zeolitic water
calculated from Eqs. (11) (12) and (13) versus the experimental enthalpy of hydration coming
from the different technical measurements. Regression coefficients and standard errors are
different within the two main groups: R2= 0.88 and std. err. = 3.41 kJ mol-1 for TTDC data (67
data points), R2= 0.658 and std err. = 2.66 kJ mol-1 for the IC data (57 data points).
When Al/Si and Al/(Al+Si) = 0, the hypothetical integral enthalpy of water in zeolites
obtained by the extrapolation of Eq. (11) is 0, which corresponds to the enthalpy of
hydration of water in cordierite (2.2 1.6 kJ mol-1 from Carey [58]). Unlike zeolites, the water
in cordierite is not coordinated by cations, so the molecular environment of H2O in
cordierite is similar to that of H2O in water.
Figure 2. Predicted enthalpy of the hydration of zeolitic water calculated from Eq. (11) versus the
experimental enthalpy of hydration using different technical measurements.
A detailed computation of the enthalpy of hydration is given as an example for three natural
clinoptilolites (-Ca, -Na and K) with the following chemical formula given by [22]:
- Clinoptilolite-Na: (Ca0.12Mg0.29K0.75Na5.21)(Al6.78Fe0.06Si29.2)O72.05-21.3H2O
- Clinoptilolite-K: (Ca0.13Mg0.25K5.84Na0.27)(Al6.85Fe0.1Si29)O71..9-18.5H2O
- Clinoptilolite-Ca: (Ca2.34Mg0.57K0.9Na0.18)(Al6.7Fe0.017Si29)O71..8-21.9H2O
The values of the ratio Al/Si yield a constant value of 0.235. The electronegativity of the
exchangeable site Az+ for clinoptilolite-Na is, for example, the average electronegativity of
four cations (Na+, K+, Ca2+ and Mg2+ (table 4)) as follows:
HO (site.A)

2.607* HO Naaq

0.375 * HO Kaq

0.12* HOCaaq
2

0.29 * HO Mgaq
2
(21)
3.39
i.e., H O (site.A) =51.42 kJ mol-1.
The unit-cell volume of the anhydrous clinoptiloliteK (V u.c.) is 2019.51 3 [59]. This means
that there are 35.95 tetrahedral atoms (6.95+0.1+29) in 2019.51 3; which indicates that
FDanh.= 17.8 tetrahedral atoms in 10003. The unit-cell volume of the hydrated clinoptilolite-
K (at saturation or fully hydrated) with 18.5 moles of zeolitic waters is 2089.50 3 [54], which
is slightly greater than the anhydrous form and allows the setting of the relationship of
water porosity versus the number of hydration water moles:
29.89 * nH
2O
WP (22)
2019.51 3.78 * n H2O
From these previous examples, the parameters requested for the prediction of the enthalpy
of hydration are displayed in table 5 for the three clinoptilolites (-Na, -K and Ca).
Zeolite minerals V u.c. anh. Vu.c. hydr. k HO= FD. WP Al/Si

(3) (3) Site A Anh.
kJmol-1
Clinoptilolite -Na 2000.00 1 2140.00 1 6.35 51.39 18.02 0.31 0.23
Clinoptilolite -K 2019.51 2 2089.50 2 3.78 109.16 17.80 0.26 0.24
Clinoptilolite -Ca 2019.51 2 2089.50 2 3.20 -64.60 17.78 0.31 0.23
1 - [60]; 2 - [59]
Table 5. Unit-cell volume of hydrated and anhydrous clinoptilolite, factor k (eq. 20), mean HO=Az+ (site
A), framework density and ratio Al/Si for 3 clinoptilolites (-Na, K and Ca).
From the values given in table 5, the enthalpy of hydration of the zeolitic water, H Hyd W ,
can be computed with Eqs. (11), (12) and (13) and are close to experimental values from [22]
(Table 6).
The model of the computation of the enthalpy of hydration of the hydration water
represents a very useful tool and contributes to the knowledge of enthalpies of formation of
hydrated zeolites from anhydrous ones [61].
A useful method for avoiding complications at the outset of a thermodynamic analysis is to

emphasise the H2O rather than the zeolite structure. Using such an approach, the
equilibriums can be considered as the equilibrium between the H2O in the fluid-vapour
phase and the H2O in the zeolite. According to the definition of equilibrium, the chemical
potential of H2O in the vapour phase must equal the chemical potential of the H2O
component in the zeolite. Any series of measurements of the amount of H2O in zeolite at a
known fugacity (or partial pressure of H2O under ideal gas conditions) provides the basis
for the thermodynamic description of the system. The most elegant approach to develop a
thermodynamic formulation is to know the partial molar enthalpy of hydration, H , and
the partial molar entropy S . A constant partial molar enthalpy of hydration indicates an
ideal mixing of the H2O.
Zeolite minerals H Hyd W H Hyd W

predicted (kJ mol-1 H2O) measured (kJmol-1 H2O) References
-22.20
Clinoptilolite.-Na -30.17 [22]
-22.20
Clinoptilolite -K -20.24 -23.97 [22]
Clinoptilolite-Ca -29.03 -32.87 [22]
Table 6. Predicted and experimental enthalpy of hydration, H Hyd W of clinoptilolites Na, -K and Ca.
The bulk enthalpy of hydration or the integral enthalpy of hydration can be used as the
product of the enthalpy of hydration of the water times the number of zeolitic water:
a b * WP * n

H
Hyd Z H Hyd W * nH 2O

Al

Si
*e H2O

(23)
As the integral hydration enthalpy H

Hyd Z is the integral function of the partial molar
enthalpy hydration from nH O = 0 (corresponding to an anhydrous zeolite) to a maximum
2
value of nH O max (corresponding to the fully hydrated zeolite), the partial molar enthalpy of
2
hydration relative to the liquid water, H , which is the derivative function of H
Hyd Z ,
becomes:
1 n nH2O
nH O n 0
H Hyd Z H * dn (24)
2

29.89 * nH O
a b* 2

Vu.c.anh. k * nH O

H Al * e 2 * 1 29.89 * b * Vu.c. anh. * nH 2O
(25)
Si

2
Vu.c. anh. k * nH O
2

The fractional water content can be obtained if the maximum number of zeolitic waters is
known at the saturation state and is equal to:
nH
2O
(26)
nH
2 O ,max.
From values of table 5, the partial molar enthalpy of clinoptilolites K, Na and Ca can be
calculated versus the fractional water content and plotted in Figure 3 with the experimental
partial molar enthalpies measured from immersion calorimetry [62] and from
thermogravimetry [22]. The modelled values of the partial molar enthalpy for the three
clinoptilolites appear to be closer to the data from the immersion calorimetry than from
thermogravimetry. The second important point is the fact that the calculated and
experimental partial molar enthalpy of hydration has a similar behaviour.
The partial molar enthalpy of hydration per mole of H2O increases smoothly from low water
content to high and indicates that the H2O in clinoptilolites occupies a continuum of
energetic states. This is not the case for chabazite-Ca [23], which exhibits three energetically
distinct types of H2O.
This shows that, within different zeolites with the same exchangeable cation, the partial
molar enthalpy as a function of the hydration degree may display different functions. This is
the reason why the fundamental relationship verifying the enthalpy of hydration by means
of the chemical composition and the accurate knowledge of the unit-cell parameters of
anhydrous and hydrated zeolites needs to be improved with new data of hydration
enthalpy of the partially hydrated zeolites on the one hand and a better fit of the effective
water porosity as a function of the hydration degree on the other hand. Then, the
thermodynamic description of the hydration-dehydration process can be modelled as a
function of pressure and temperature with the contribution of predicted enthalpies of
hydration and entropies of hydration.
Figure 3. Partial molar enthalpy of hydration of K-, Na- and Ca- clinoptilolites derived from a model in
[54], immersion calorimetry [62] and thermogravimetry results [22]
Clay minerals:
Unlike zeolites, smectites are clearly not inert phases, as the particles size increases with the
relative humidity [15]. Adsorbed water is distributed throughout the interlayer space, the
outer surfaces of particles and the open pores space in the sample. [15-17] provided
measured values of the surface covering waters for both the hydration and dehydration
reactions of a set of eight homo-ionic SWy-1 montmorillonites saturated by alkali and
alkaline-earth cations from their BET specific surface area (Table 1) and their basal spacing
variations with relative humidity. To quantify the effective amount of water involved in the
hydration reaction, the amount of poral H2O must be quantified and subtracted from the
total amount of H2O taken up by the clay sample. The number of external surface water
molecules (expressed in mmol/g dry clay) can be expressed as a function of relative
humidity [63]. There are numerous papers about the adsorption-desorption isotherms
performed on various clays minerals, but few are devoted to the acquisition of enthalpy of
hydration-dehydration on SWy-1 [15-17, 64] [18, 19, 30] [20] [34] [24, 26, 65] [25] and on
vermiculites [21].
All recent predictive models of the hydration of smectites are based on an approach that
uses the solid solution initiated by Ransom & Helgeson [66]. The hydration of a smectite is
considered through the following reaction between hydrated and dehydrated end-members:
Smectite nm * H 2O( l ) Smectite nm * H 2O( i ) (27)
where nm represents the maximal number of moles of water that can be included in the
smectite on the basis of a half-cell (i.e., O10(OH)2). One considers the interlayer water H2O(i)
(where subscript i stands for interlayer) as a variable weighing the hydration ratio. The
amount of interlayer water in a smectite is proportional to the mole fraction of hydrated
end-member: x*H2O= nm*xhs=(1-nm)*xas; to the mole fraction of the hydrous end-member, xhs
or to the anhydrous end-members xas. Ransom & Helgeson [66] considered the system
hydrated smectite anhydrous smectite + bulk water as a strictly regular binary solid
solution by considering the free energy only. Thus, the excess free energy of mixing can be
expressed as follows:
Gxs xas * 1 xas * WG (28)
where WG is an excess mixing constant. The integral Gibbs free energy of hydration is:
G Hyd xhs * GHyd ,298 xhs * 1 xhs * WG

(29)

in which GHyd ,298 is the standard free energy of hydration. The previous parameter and WG
are determined only from adsorption isotherms by assuming a maximal number of moles of
interlayer water fixed to 4.5 moles. As there are no experimental measurements of heat of

adsorption, the standard enthalpy of hydration, H Hyd ,298 , is determined from GHyd ,298 by

assuming a constant value of S298 H2O(i) equal to 55.02 J K-1 mol-1 [67]. From calculated
H Hyd ,298 , the standard enthalpy of formation of the interlayer water, H f ,298 ( H 2O )i , is

given in table 7.
Vidal et al. [68-69] have assumed that a smectite could be considered strictly regular solid
solutions between four end-members with 0.7 H2O, 2 H2O, 4 H2O, and 7 H2O. Those
compositions correspond to four different hydrated states (with 0, 1, 2, and 3 water sheets,
respectively). For any strictly regular solid solution, the integral enthalpy of hydration is
expressed as the following:
Hyd xhs * H Hyd ,298 xhs * 1 xhs * WH

H
(30)
with
H hyd
0 0 0

,298 nm * H f ,298 H 2O( i ) H f ,298 H 2Oliq (31)
The hydration enthalpy is retrieved from data of [24] for montmorillonite Na and K and
derived from differential heats of adsorption obtained from the measurements of the heat of
immersion [18, 20] for Na-, Ca- and Mg- montmorillonite. Thus, an integral enthalpy of
hydration H f ,298 ( H 2O )i is provided for each of the four solid solutions with nm equal to 0.7,
2, 4 and 7 and is given in table 7. Vieillard et al. [63] consider the hydration of a smectite to
be an asymmetrical regular solid solution between anhydrous and hydrated smectite.
Units (kJ mol-1) H2 O Cs Rb K Na Ba Sr Ca Mg

H f ,298 ( H 2O)i 1
4.5 -289.93 -290.23 -290.45 -291.25 -294.14 -294.57 -294.86 -295.71
H f ,298 ( H 2O )i 2
0-0.7 -295.50 -299.71 -301.43 -302.86
W H2 0. 0. 0. 0.
H f ,298 ( H 2O)i 2 0-2 -293.58 -295.90 -298.60 -300.05
WH 2 -10. -10. -10. -10.
H f ,298 ( H 2O)i 2
0-4 -291.96 -293.83 -296.25 -297.62
W H2 -10. -10. -10. -10.
H f ,298 ( H 2O )i 2
0-7 -291.05 -292.33 -293.86 -294.69
WH 2 -10. -10. -10. -10.
H f ,298 ( H 2O)i 3
5.5 -287.47 -288.01 -288.16 -290.01 -292.10 -292.65 -294.72 -296.56
WH 3
16.0 19.0 15.0 8.0 -60.0 -55.0 -60.0 -49.0
1
WH 3
-90.0 -95.0 -68.0 -33.0 -75.0 -90.0 -100.0 -129.0
2
1 [66]; 2 [68]; 3 - [63].
Table 7. Standard thermodynamic enthalpy H f ,298 ( H 2O)i (in kJ mol-1) of interlayer water and
Margules interaction parameters for the system H2O smectite.
The integral hydration enthalpy is obtained by the following relationships:
,298 xhs * 1 xhs * WH1 * xhs WH 2 * 1 xhs

H Hyd xhs * H Hyd
(32)

in which H Hyd ,298 and Margules parameters WH and WH are determined by a
1 2
minimisation procedure applied to the difference between computed and calorimetric
integral enthalpies on eight homoionic montmorillonite SWy-1 [15-17] and given in table 7.
The maximum number of moles of interlayer water was set to 5.5 moles. Figure 4A displays
the comparison of integral enthalpy of hydration of a smectite- Na computed from the three
models developed previously with different experimental values.
The curve 1 in Figure 4A (yellow dotted line) comes from model of Ransom & Helgeson
[66], is linear and is obtained from the following equation of integral enthalpy of hydration:

H Hyd ,298 24.39 * xhs (33)
where the coefficient -24.39 is computed from H f ,298 ( H 2O )i given in Table 7. The curves
2b, 2c and 2d (green dotted lines) displayed in Figure 4A come together from the model of
Vidal et al. [68] and are graphically represented by four truncated lines with their respective
equations:
0 layer 0 x hs 0.7 : H

Hyd ,298 9.716 * xhs (34)
1 layer 0<x hs <2.0 : H

Hyd ,298 20.14 * xhs xhs * 1 xhs * 10.0 (35)
2 layers 0 x hs 4.0 : H

Hyd ,298 32.0 * xhs xhs * 1 xhs * 10.0 (36)
Figure 4. A Integral enthalpy of hydration versus the number of interlayer cation; B Standard
enthalpy of formation of interlayer water versus the nature of the interlayer cation.
3 layers 0 xhs 7.0 : H

Hyd ,298 45.5 * xhs xhs * 1 xhs * 10.0 (37)
The curve 3 (black line) in Figure 4A comes from the model of Vieillard et al. [63] and is
represented by the following equation:
H Hyd 23.0 * xhs xhs * 1 xhs * 8.0 * xhs 33.0 * 1 xhs (38)
It appears that integral enthalpy of hydration modelled by Vieillard et al. [63] (black line)
based on experimental measurements of heat of adsorption from [15-17] encompasses nearly
all experimental data. As the standard entropy of hydration is assumed constant in [66] and
[68] models, the integral hydration enthalpies provided by these two previous models are
nearly linear. Those obtained by [68] exhibit three sections of curves corresponding to the
three states of hydration (1, 2 and 3 water layers).
In Figure 4B, a relationship between the standard state enthalpy of interlayer water with the
nature of the interlayer cation located in the SWy-1 montmorillonite with a constant layer
charge of 0.38, characterised by its electronegativity (HO=Mz+ (aq), Table 4) is proposed [63]
and given as follows:
H f ,298 ( H 2O )i H f ,298 ( H 2O )( l ) 0.02784 * H O M z 6.275 (39)
Lowering the electronegativity of cation in the interlayer sites stabilises the enthalpy of
formation of the interlayer water. It should be kept in mind that Eq. (39) has been settled for
the same support, i.e., a constant layer charge. For natural montmorillonite-Na, most
enthalpies of hydration of the interlayer water are consistent within a narrow range of
interlayer charge, IC (0.31<IC<0.38) [63]. Due to the lack of calorimetric measurements of
enthalpy of hydration for high charge (IC>0.5) and low charge (IC<0.3) montmorillonites,
the variation of the standard hydration enthalpy as a function of the layer charge remains
highly questionable. An important remaining matter of discussion is the extent to which the
model is able to predict hydration properties of dioctahedral and trioctahedral smectites
with different layer charges and compositions.
5.2. Entropy
Salts - Average values of the entropy of hydration water were obtained [39] and [35] within
chlorides, sulphates and salts (table 2). These average values of salts appear very similar to
the value of entropy for crystalline water, S=40.17 J/K-1 Mol-1 [70]. To improve the accuracy
of prediction, statistical relationships between entropy and the molar volume of hydration
should be investigated.
Zeolites: Initially, an average value of entropy of zeolitic water was proposed by Helgeson
et al. [70] and was equal to SH2O (zeol) = 58.99 J/K-1 Mol-1. From very few available
calorimetric measurements of anhydrous and hydrated zeolites [4, 6, 71], it has been shown
that the entropy of hydration water, at saturation, remains constant at approximately 52.0
J/K-1 Mol-1 [72]. Some authors provide slight deviations of entropy of hydration depending
of the nature of cations in clinoptilolite [22].
Clays minerals: Entropies of interlayer water in clay minerals have never been
measured directly, but have been evaluated from indirect measurements such as a
contribution of experimental enthalpies of immersion and adsorption-desorption isotherms
[63] [34] or from the Clausius-Clapeyron rules with adsorption isotherms performed at
different temperatures [31], [30]. A constant value 55.0 J/K-1 Mol-1 for the entropy of
interlayer water has been chosen [67] and [68] regardless of the nature of the interlayer
water and the numbers of interlayer waters layers. By considering the hydration of a
smectite always as a symmetrical regular solid solution, the integral entropy is expressed as
in [63]:
S Hyd xhs * SHyd

R xhs * ln xhs 1 xhs * ln 1 xhs
(40)
xhs * 1 xhs * WS * xhs WS * 1 xhs
1 2
with Shyd
0 0
,298 nm * S298 H 2O( i ) S298 H 2Oliq
0
(41)

where SHyd , WS , and WS represent the standard entropy of hydration and Margules
1 2
parameters of the excess entropy of mixing, respectively. The integral entropy is expressed
in J K-1 mol-1 of smectite based on O10(OH)2. The determination of these parameters is

retrieved from values of H Hyd , WH , and WH obtained previously in the minimisation
1 2
procedure of integral hydration enthalpy and from the experimental adsorption-desorption
isotherm interlayer water versus relative humidity. This minimisation procedure uses a least

square method and provides SHyd , WS and WS (Table 8).
1 2

S298 H 2O( i ) 1 WS
1
1
WS
2
1
SHyd M z ( aq ) 2
J/K/mole J/K/mole J/K/mole J/K/mole
Cs+ 64.6 163.5 -348.0 -78.
Rb+ 63.8 142.0 -355.0 -84.
K+ 63.7 104.0 -267.5 -93.
Na+ 59.8 49.1 -94.0 -130.
Ba2+ 55.7 -116.0 -211.5 -224.
Sr2+ 54.3 -117.8 -244.5 -261.
Ca2+ 51.5 -93.5 -270.5 -271.
Mg2+ 45.4 -42.8 -380.0 -350.
1 [63]; 2 - [73].

Table 8. Standard thermodynamic enthalpy SHyd of interlayer water, Margules interactions
parameters and hydration entropy of the ion under its hydrated aqueous state for the eight cations.
Figure 5A displays the comparison of the integral entropy of hydration of a smectite- Na

computed from the three models [67] [68] and [63] developed previously with different
experimental values.
As indicated in the enthalpy section, integral hydration entropies modelled by [66] (yellow
dotted line, N1) and [68] (green dotted line, N2a, 2b and 2c corresponding to 1st, 2nd and 3rd
layer) are linear and merge together. In the model proposed by Vieillard et al. [63], three
calculated integral entropies of SWy1-Na water system were plotted in Figure 5A and
correspond to the adsorption (red line), the desorption (blue line) and the theoretical
equilibrium water Swy1-Na (black line, N 3), whose equation is given:
S Hyd 55.8 * xhs R xhs * ln xhs 1 xhs * ln 1 xhs

(42)
xhs * 1 xhs * 49.05 * xhs 94.0 * 1 xhs
The comparison of hydration-dehydration curves calculated by [63] with those provided by

Fu et al. [34] show an opposite interpretation. The data from [34] show that integral
entropies during adsorption are less negative than those during desorption. Data from our
model show the opposite. This difference is explained by the fact that from experimental
works of [34], adsorption follows desorption, while with our data, desorption follows
adsorption. Thus, a maximum entropy difference between hydration and dehydration
functions can be depicted and is equal to 18 J/K/mole. These observations show the
importance of movement of exchangeable cations from ditrigonal cavities and the rotation
of tetrahedrals in the tetrahedral sheets when dry collapsed layers are progressively exposed
to water vapour.
Figure 5. A Integral entropy of hydration versus the number of interlayer cation; B Standard
entropy of formation of interlayer water versus the nature of the interlayer cation.

A correlation between the entropy of interlayer cation S298 ( H 2O )i with the theoretical
hydration entropy, Shyd Mz+ [73] (Table 8), of the interlayer cation [63] is displayed in
Figure 5B with the following equation:

S298 ( H 2O)i S298 ( H 2O)( l ) 0.06542 * S hyd M z 0.413 (43)
Negative values of the hydration entropy of the hydrated ion lower the hydration entropy
of the interlayer water.
5.3. Heat capacity

Salts: An acceptable average heat capacity ranging from 39.05.3 J/K-1mol-1 for sulphates and
sulphites to 42.02.7 J/K-1mol-1for chlorates and chlorides has been proposed [35] and seems
to be close to the average value of heat capacity for crystalline water Cp=40.04 J/K-1mol-1 [70].
Only the average heat capacity function of crystalline water was proposed [70]:
Cp( H 2O )salts 29.75 3.448 * 10 2 * T (44)
Zeolites: Three equations of heat capacities ([41], [74] [45] ) were proposed for a set of
silicate minerals, including analcime and natrolite, and are displayed in table 9.
Heat capacity function (298.15- 500 K)

Eq. A Cp( H 2O )sil 56.61 2.64 * 10 2 * T 0.5 [41]
Eq. B Cp( H 2O )sil 87.62 7.58 * 10 2 * T 0.5 0.53 * 107 * T 3 [74]
Eq. C Cp( H 2O )sil 39.65 32.5 * 10 3 * T 4.694 * 10 5 * T 2 [45]
Eq. D Cp( H 2O ) zeol. 23.999 66.295 * 10 3 * T 0.3948 * 10 5 * T 2 [72]
Table 9. Heat capacity functions for zeolites minerals
Heat capacities of the hydration in zeolites have been performed by Neuhoff & Wang [75]
on three zeolites (analcime, natrolite and wairakite) and exhibit marked variations in the
heat capacity of hydration with temperature. Four zeolites (mordenite, wairakite and two
different values from different sources for analcime and natrolite) for which the heat
capacity of zeolitic water can be obtained by a difference between the heat capacities
measured on both the anhydrous and the hydrated phases [72] are represented in Figure 6A.
Also displayed are the heat capacity values of water in all its states (ice, liquid and vapour)
for comparison [35]. The heat capacity values of zeolitic water obtained by minimisation
techniques (Eq. D of table 9, turquish line) matches with the heat capacity function
equations of [74] and [45].
Figure 6. Heat capacity of zeolitic water versus temperature: A Heat capacities of zeolitic water in
zeolites, in different prediction models and of water in its various states (l for liquid, c for ice and g for
vapour); B Experimental heat capacities of zeolitic waters in natural zeolites and predicted heat
capacities from Eq. (46).
Eq. D of table 9 provides a statistical error of 4.51%, 2.35% and 4.18% for hydrated zeolites at
298.15 K, 400 K and 500 K, respectively. To improve the accuracy of the prediction of the
heat capacity of hydrated zeolites, one considers the normalised hydration volume, which is
the difference of unit-cell volume (Vu.c.) between the hydrated and dehydrated forms for any
zeolite per zeolitic water molecule [72]:
VHy Deh
Vu.c . hydr . Vu.c.dehyd. (45)
nH O
2
Cp( H 2O)zeol. 55.85 13.073 *

VHy Deh 0.0062 0.0305 * V Hy Deh * T
(46)
0.008 0.0048 *

V Hy Deh * T
2
The heat capacities of hydration water given in Figure 6B have been calculated for the four
hydrated zeolites (mordenite, analcime, wairakite and natrolite) from the unit-cell volumes
of their dehydrated and hydrated forms [72]. It can be observed that the heat capacities of
hydration water calculated in this way are much better than those obtained by Eq. D of table
9 (indicated in Fig. 6B as a turquish full line). With this improvement, the errors made on
hydrated zeolites decrease to 3.5%, 2.35% and 3.89% at 298.15 K, 400 K and 500 K,
respectively.
Clays. The heat capacity function comes initially from [67] and is assumed to be
independent of the nature of the interlayer cations:
Cp( H 2O)clays 37.84 51.631 * 10 3 * T 4.0959 * 10 5 * T 2 (47)
This heat capacity equation has also been used by [68] and by [63] in the behaviour of
thermodynamic entities versus temperature.
5.4. Molar volume

Salts: Only [35] provided an average value for different salts: 14.51.2 cm3/mole for sulphates
and sulphites and 14.12.3 cm3/mole for chlorides and chlorates. These average values appear
to be similar to the molar volume of crystalline water (V(H2O)(salts)= 13.7 cm3/mole [76]).
Zeolites: No study on the variation of the molar volumes of the zeolitic water has been
performed. Numerous values of molar volumes of hydrated and anhydrous zeolites have
been provided and gathered in such calculations for enthalpy and entropy of hydration [77],
[61], [72]. In the study of the relationship between entropy and molar volume within zeolites
[72], an average value of the molar volume of hydration water has been calculated and is
V(H2O)(zeol)=2.06 cm3/mole, which is not significantly different from those proposed by
Helgeson (V(H2O)(zeol)= 8 cm3/mole) estimated from standard molal volumes of zeolites. The
weak value of the molar volume of the hydration water is explained by the fact that the
anhydrous zeolites exhibit a rigid (Si, Al) framework with different channels or cavities
occupied by exchangeable cations. During the hydration process, the water molecules are
bound to cations inside the cavities, do not affect the framework and have a weak impact on
lattice parameters.
Clays: The molar volume of the interlayer water was initially determined by Ransom [67]
and also used by [68] and by [63] in thermochemical calculation. Its value is V (H2O)I = 17.22
cm3/mole. This value, greater than those of salts, is explained by the fact that, during
hydration, the molar volume of clay minerals increases in one dimension characterised by
basal spacing (Miller index 001).
6. Discussion of the Gibbs free energy of the formation Behaviour of the

hydration water in environmental conditions.
The relationships among the free energy change, enthalpy of reaction and entropy for an
isothermal process is:
G H T * S (48)
where G stands for free energy change, H for enthalpy of reaction, S for the change in
entropy and T for the absolute temperature. This relationship holds true for both the
integral entities that are represented by G , H
and S and for the partial quantities that
are represented by G , H and S .
Salts: The free energy of formation of the hydration water of hydrated salts can be
calculated from the enthalpy and entropy of hydration given previously. A relationship has
been demonstrated by the statistical regressions [35] between the enthalpy and Gibbs free
energy of crystalline water in the following relation:
G f ,298 H 2Osalts 1.008*H f ,298 H 2Osalts 59.406 (49)
The predicted values contribute to the variations of solubility products and the cation
selectivity constants among the series of salts. An example is given in [78] for two series of
hydrated salts of MgCl2 and SrCl2.
For zeolites and clays, the adsorbent (a single smectite or zeolite phase) is supposed to be
inert so that the derived enthalpy and entropy functions formally represent the energy
variations between the adsorbed and the bulk water.
The integral free energy of hydration G hyd may be determined from the gravimetric
isotherms of adsorption of the water vapour by the following expression [79]:
n nw
P
G hyd R*T* Ln *dn (50)
n0 P0
where R = 8.314 J.mol-1K-1 is the ideal gas constant, n is the amount of adsorbed water, P is
the partial water vapour pressure, and P0 is the saturated water vapour pressure at
temperature T (P/P0 = Relative Humidity/100). This value can be determined by plotting
R*T*Ln(P/Po) versus the water content n (adsorbed or desorbed) and determining the area
under the curve from 0 to nw. When nw approaches 0, R*T*Ln(P/Po) approaches infinity,
making integration somewhat difficult.
Among the zeolites, Eq. (50) has been used on three clinoptilolites (-Na, -K and -Ca) [22] and
show a good correlation between the Gibbs free energies calculated from the adsorption-
desorption isotherms and from the contribution of the enthalpy of hydration and the
entropy of hydration extracted from the equilibrium at high temperature. The model
described by Carey & Bish [62] used a solution solid model between anhydrous and
hydrated zeolite, and the variation of the integral Gibbs free energies of hydration is
expressed as a function of a parameter characterising the ratio of H2O/(maximum H2O).
The main difficulty in these calculations is the determination of the maximal amount of
hydration water at the saturation state (p/p=1).
Among the numerous measurements of adsorption-desorption isotherms on various clays,

very few works provided a consistent Gibbs free energy of adsorption-desorption due to the
difficulty of measurements in the low relative humidity domains. By choosing the system of
water SWy-1-Na, Figure 7 displays the desorption isotherms (Figure 7A), the variation of
the integral free energy of hydration versus the number of moles of the interlayer water
(Figure 7B) and versus the relative humidity (Figure 7C) and the variation of the free energy
of formation of the interlayer water versus the relative humidity.
Figure 7. A - Adsorption-desorption isotherms; B - Integral free energy of hydration versus the number
of moles of interlayer water; C - Integral free energy of hydration versus the relative humidity; D - Free
energy of formation of the interlayer water versus the relative humidity.
In each figure, the data of the free energy of hydration (Eq. 50) from the experimental
isotherms [15, 16] (blue square for adsorption and red square for desorption) and the free
energy of hydration are computed and are reported for comparison of three different works:
the Vieillard et al. model [63] (blue, red and black lines for adsorption, desorption and
theoretical equilibrium, respectively), the Ransom & helgeson model [66] (dotted yellow
line), and the Vidal & Dubacq model [68] (dotted green line). For the adsorption and
desorption reactions, the modelled isotherm calculated by the Vieillard et al. model [63]
(blue and red lines, respectively) agrees well with the experimental data acquired by [15, 16]
in high relative humidity.
At low relative humidity, the uncertainty appears very important between the experimental
desorption data and the desorption curve from the model in [63] (3 kJ/mol for integral free
energy, Fig C) due to the analytical limits and mathematical constraints.
The theoretical equilibrium (black line) suggests that the hydration of a Na-SWy-1 begins
at only R.H.= 0.15 (Figure 7A), which correlates well with the experimental adsorption but
not with the desorption. The integral Gibbs free energy of hydration (figure 7B and 7C)
and the Gibbs free energy of the interlayer water (Figure 7D) of the theoretical
equilibrium between the water and Na-Smectite (black line) are plotted and correspond to
the average values of calculated adsorption-desorption isotherms. The theoretical curve of
equilibrium between the water and Na-smectite provided by Ransom & Helgeson [66]
displays a small number of moles of the interlayer water close to saturation, while those
of Vidal & Dubacq [68] reproduce this stepwise behaviour fairly well because it assumes
three solid solutions with 3 end-members (0.7 H2O, 2 H2O, 4.5 H2O). However, it does not
match the behaviour of water adsorption versus relative humidity, which is not a step
function. The advantage of this approach is that it allows reproducing the observed
stepwise evolution of the smectite volume and water content with varying T and relative
humidity. At low relative humidity, as the hydration of a Na-SWy-1 begins at only R.H.=
0.15, the computations from [68] and [66] (green and yellow dotted lines) do not match the
observed isotherms because there is a strong hydration in the RH= 0.0- 0.18 range. During
the interval of R.H.=0.0-0.2, the adsorption of water molecules occurs predominantly on
the external surface of tactoids (basal external faces and edges of tactoids). This explains
why we observe a very negative integral free energy in the low relative humidity domain
for these two models (green dotted line and in a less extent, yellow dotted lines). The
necessity to take into account only the hydration water, sensu-stricto, is justified. This
procedure has been incompletely performed by Ransom & Helgeson [66] with the external
surface of a kaolinite to estimate the amount of surface covering water, while Vidal &
Dubacq [68] made no correction on the gravimetric waters. At high relative humidity,
Vidal & Dubacq [68] proposed a third step of hydration, with the number of water
molecules increasing up to 7 moles per O10(OH)2. All of the experimental isotherms
performed by [15, 16] exhibit an increase in the water contents beyond RH = 0.9, identified
as osmotic water. The osmotic swelling of the sodium montmorillonite corresponds to an
iso-enthalpic effect, with the heat of adsorption being constant. The theoretical
equilibrium between water and Na-SWy-1 (black line) matches the experimental
dehydration near saturation.
The cationic exchange and hydration reactions are intimately related, and the cationic
exchange reactions not only modify the interlayer composition but also imply changes in the
interlayer water content. These changes can be quite significant and can be evaluated using
the Vieillard et al. model [63], which provides a theoretical number of moles of interlayer
water and integral thermodynamic properties (H, S and G) for the SWy-1 montmorillonites.
Thus, the cationic exchange reactions may depend on an external parameter, such as the
relative humidity.
7. Conclusions and perspectives

This chapter demonstrated some useful relationships in the prediction of thermodynamic
entities. Some important areas are still lacking and deserve further study.
Among the anhydrous and hydrated salts, the relationships between the entropy and molar
volume may exist and will improve the prediction of the entropy of hydration. The function
of the average heat capacities for the hydration water is lacking and will help in
characterising the behaviour of the crystalline water versus temperature.
In the zeolite field, the relationships among the molar volume, water content and relative
humidity may exist within zeolites families with a reversibility in the hydration-dehydration
processes. These relationships will contribute to a better understanding of the behaviour of
partial molar enthalpy versus the degree of saturation or versus the relative humidity.
In the clay Minerals, three following recommendations are needed: 1) to dissociate the
hydration water from the gravimetric water; 2) to measure the heat of hydration among the
dioctahedral and trioctahedral clays; and 3) to find a relationship between the hysteresis and
the entropy of the hydration-dehydration by the molecular modellings. With these three
aims, the knowledge of mechanisms of the hydration within clay minerals will advance our
understanding of cationic exchange in soils under various physical and chemical
constraints.
Author details
Philippe Vieillard
CNRS IC2MP, UMR 7285, Hydrasa, France
Acknowledgement
Financial support from the French National Radioactive Waste Management
Agency (ANDRA), from the french Geological Survy (BRGM) and from the national council
for scientific Research (CNRS) is gratefully aknowledged. Special thanks to Ph. Blanc,
H. Gailhanou and Cl. Fialips for their effective and decisive contribution to this
document.
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Chapter 14
Thermodynamics and Kinetics in the Synthesis of

Monodisperse Nanoparticles
Nong-Moon Hwang, Jae-Soo Jung and Dong-Kwon Lee
1. Introduction
The preparation of monodisperse nanoparticles with uniform size, shape and composition
has been intensively pursed because of their scientific and technological interests [1-4]. The
major advantage of monodisperse particles may be attributed to the uniform properties of
individual particles, which makes the property of whole particles strictly controllable. They
have been widely used in industries such as pharmacy, catalysts, sensors, film precursors,
and information storage. The property of nanoparticles is much more sensitive to their size
than that of micro-particles. For example, the florescence of monodisperse CdSe/ZnS
core/shell nanoparticles depends strongly on their size [5]. The superparamagnetism also
depends strongly on the size of nanoparticles [6]. The properties of these particular size
nanoparticles show great potentials in the field of bio-medicals and electronics.
In general, to prepare the monodisperse nanoparticles in solution, the size had to be selected
after somewhat polydisperse nanoparticles were produced. The separation procedures are
very laborious and expensive because the size of nanoparticles is too small to be sorted.
Moreover, the production yield of monodisperse nanoparticles decreases markedly due to the
loss of nanoparticles during the separation procedures. Therefore, many efforts have been
made to synthesize directly monodisperse nanoparticles without size selection procedures.
Recently, several methods have been developed successfully to synthesize gram quantity
monodisperse nanoparticles directly without size selection procedures. One of them is a
slow heating method developed by Hyeon et al. [6,7], which utilizes the burst nucleation
followed by sustained growth of particles. Although nanoparticles have some size
distribution in the nucleation stage, they became gradually monodisperse during growth. In
this case, the principle for the direct synthesis of monodisperse nanoparticles could be
approached by sustained growth of nuclei formed by burst nucleation with some initial size
distribution [8].
The digestive ripening developed by Klabunde et al. [9-12] is another fascinating method for
the direct synthesis of monodisperse nanoparticles. During digestive ripening, nanoparticles
initially ranging from 2 to 40 nm were spontaneously transformed into particles with nearly
uniform sizes of 4~5 nm. Lee et al. [13,14] could explain the digestive ripening process by
considering the charge effect in the Gibbs-Thomson equation.
The purpose of this article is to provide the thermodynamic and kinetic basis to slow
heating method and digestive ripening, which are two successful processes to synthesize
the monodisperse nanoparticles.
2. Evolution mechanism of monodisperse particles

To understand intuitively the underlying principle for the evolution of monodispersed
particles, lets compare the growth of two spherical particles of different diamters of 1 nm
and 5 nm as shown in Fig. 1(a). The problem could be simple under the assumption that all
the particles grow at the same rate regardless of the size, which is valid for interface-
controlled growth. The size ratio of two particles is 5, which is far from the monodisperse
state. If the two particles grow by 1 nm after some time, their diameters become 2 nm and 6
nm, respectively, as shown in Fig. 1(b). Now the size ratio of the two particles is 3. If the two
initial particles grow by 99 nm after an appreciable amount of time, their diameters become
100 nm and 104 nm, respectively, as shown in Fig. 1(c). Now their size ratio is 1.04, which is
in the monodisperse state with the size being within 5% difference. The time evolution of
the two particles in Fig. 1(a)-(c) shows that just the growth induces the monodispersity. It
should be noted that the initial size difference between the two particles, which is 4 nm, is
maintained throughout the growth but the size ratio continues to decrease with growth,
approaching unity. This tendency to approach the monodisperse distribution by growth is
often called focusing effect [15].
Figure 1. Initially, two spherical particles have the diameters of (a) 1 nm and 5 nm with the size ratio of
5. After growth by 1 nm, the respective particle becomes (b) 2 nm and 6 nm with the size ratio of 3.
After growth by 99 nm, the respective particle becomes (c) 100 nm and 104 nm with the size ratio of
1.04, which has the monodispersity with size difference less than 5%.
Thermodynamics and Kinetics in the Synthesis of Monodisperse Nanoparticles 373
If a colloidal particle grows in supersaturated solution, the solute may diffuse from the bulk
liquid phase containing a uniform concentration of solute Cb to the particle surface through
a diffusion layer with some concentration gradient where Cr is the solubility of the particle.
In this condition the growth rate is described by
D r
1+ Vm Cb - Cr
dr r
= (1)
dt D r
1+ 1+
kr
where D is the diffusion coefficient of the solute, r is the particle radius, is the diffusion
radius around a particle and k is the rate constant of the interface reaction of a solute at the
particle interface.
If D is much larger than kr (D >> kr), the interface reaction process becomes a rate-
determining step and Eq. (1) is reduced to
dr
= kVm Cb - Cr
dt (2)
In this case of the interface-controlled growth, the growth rate does not depend on the
particle size. If D is much smaller than kr (D << kr), however, the diffusion process of a
solute becomes a rate-determining step and thus Eq. (1) is reduced to
dr DVm
= (Cb - Cr )
dt r (3)
In this case of the diffusion-controlled growth, the growth rate is inversely proportional to
the radius of each particle. This means that large particles grow more slowly than small
ones, which is in contrast with the interface-controlled growth, where the growth rate was
the same regardless of the size. Therefore, the diffusion-controlled growth has a stronger
tendency to approach the monodisperse distribution than the interface-controlled growth.
The narrowing of the size distribution was first theoretically studied in the diffusion-
controlled process by Reiss [16]. The variation of the radius distribution 2 during growth
changes with time as follows.
= 2DV
d 2 1
Cb - Cr 1 - r r (4)
m
dt
In Eq. (4), r and 1 r are the mean values of r and 1/r, respectively. Since the arithmetic
mean is larger than the harmonic mean, 1 r is greater than 1/ r . Therefore, in the
supersaturated state, where Cb Cr , Eq. (4) is negative. This means that the variation of the
radius distribution 2 decreases with time as the growth continues.
3. Interface-controlled growth
The tendency to approach the monodisperse distribution by growth can be examined by
computer simulation. Consider the case of interface-controlled growth. As a starting
condition of simulation, it could be assumed that the number of particles is 1000 with the
average size of 0.5 nm and particles have a spherical shape. It can also be assumed that the size
distribution follows the Gaussian function. Since the Gaussian distribution spreads infinitely,
the size distribution is cut off when its probability is less than 0.01. The width of the Gaussian
distribution, which is defined as the difference between the maximum and minimum size with
the probability of 0.01, was 2 nm. The center of the distribution was 0.5 nm. The radius ratio of
the largest to the average-size particle was used as a criterion for the monodispersity. If this
ratio is less than 1.05, the size distribution is regarded as being monodisperse. In the
simulation, the growth rate, which is the same for all particles, was arbitrarily chosen to be
0.025 nm/s. It can further be assumed that there is no additional nucleation during growth, no
coagulation between particles and no Ostwald ripening among particles.
Figs. 2 (a)-(c) show the particle size distribution, respectively, after 0 sec, 100 sec and 800 sec
of growth. For visual representation of the result, the three-dimensional particles are
projected on the two-dimensional plane. The location of the particles was randomly chosen
within the square of the designated area but overlapping between particles was avoided.
The broad size distribution in the initial state becomes narrower with particle growth,
finally being monodisperse after 800 sec. The initial size ratio of 2.70 was decreased to 1.05
after the particle grew from the initial average radius of 0.5 nm to 21.49 nm. It should be
noted that the broad size distribution in the initial state would be changed to the
monodisperse state as far as the average size of particles grows from 0.5 nm to 21.49 nm
regardless of the growth rate. Additional simulation was performed with the initial average
radii of 1 nm and 2 nm. The final average particle radii reaching the monodisperse state
were 41.18 nm and 81.02 nm, respectively.
These results can explain the natural evolution of monodisperse distribution of particles
with growth. However, the results indicate that the minimum average radius for the
monodisperse distribution should be about 20 nm when starting from the average radius of
0.5 nm, which is implicitly assumed to be the critical nucleus size. In the direct synthesis of
monodisperse nanoparticles such as iron oxide reported by Hyeon et al. [6], however, the
average radius is often as small as 4 nm. The average particle size to reach the monodisperse
state shown in Fig. 2 is much larger than that observed experimentally in the direct
synthesis of monodisperse nanoparticles.
Therefore, although the interface-controlled growth can explain the monodisperse evolution for
particles larger than at least a few tens of nanometers, it cannot explain the evolution of
monodisperse nanoparticles less than 10 nm, which requires that the monodisperse state should
be reached at a much smaller particle size than that predicted by the interface-controlled
growth. On the other hand, in the diffusion-controlled growth, the growth rate is inversely
proportional to the particle radius as described by Eq. (3). Therefore, smaller particles would
grow faster than larger ones, whose condition is more favorable in reaching the monodisperse
state at smaller particle size. For this reason, the diffusion-controlled growth might be more
suitable in explaining the evolution of the monodisperse nanoparticles less than 10 nm.
Figure 2. The numerical analysis of the particle growth under the condition of interface-controlled
growth. (a) The initial size distribution: the average radius of the initial particles was set to 0.5 nm with
1 nm width between the maximum and average size. (b) The size distribution of particles in the
intermediate stage after 100 s. (c) The monodisperse state evolved after 800 s with the average particle
radius of 21.49 nm.
Figure 3. The numerical analysis of the particle growth under the condition of diffusion-controlled
growth. (a) The initial size distribution: the average raidius of particles was set to 0.5 nm with 1 nm width
between maximum and average size. (b) The size distribution of particles in the intermediate stage after
100 s. (c) The monodisperse state evolved after 1200 s with the average particle radius of 4.5 nm.
4. Diffusion-controlled growth
The diffusion-controlled growth could also be investigated using the computer
simulation. The initial particle size distribution was identical to the previous case: the
average radius of 0.5 nm and the width of 2 nm for Gauss distribution. The time step for
calculation was 1 sec. The concentration gradient was given a constant value of 0.75
mol/cm3 without the Gibbs-Thompson effect being considered, which results in removing
the Ostwald ripening effect.
Figs. 3(a)-(c) show the two-dimensional display of particles, respectively, after 0 sec, 100 sec
and 1200 sec by diffusion-controlled growth. The initial ratio of 2.70 was decreased to 1.05
after the particle grew from the initial average radius of 0.5 nm to 4.50 nm. It should be
noted that the initial particle size distribution would become monodisperse with the size
ratio of 1.05 as far as the average radius of the particles increases from 0.5 nm to 4.5 nm
regardless of the growth rate if the growth is controlled by diffusion.
Comparison between Figs. 2 and 3 indicates that the monodisperse state is reached much
faster and in a much smaller particle size by the diffusion-controlled growth than by the
interface-controlled growth. Therefore, the direct synthesis of monodisperse nanoparticles
by Hyeon et al. [6] can be explained by the diffusion-controlled growth. The present analysis
indicates that even if there is a broad size distribution in the nucleation stage, it becomes
narrower with growth, eventually leading to a monodisperse state. Because of this focusing
effect, the evolution of the monodisperse nanoparticles seems to be a rule rather than an
exception. Then, a question arises as to why people have difficulty in producing the
monodisperse nanoparticles. Which factor would be critical in the successful synthesis of
highly monodisperse nanoparticles?
5. Factors unfavorable for monodisperse distribution

There are factors which are unfavorable for monodispersity. These are additional
nucleation, random coagulation and Ostwald ripening. It is well established that
coagulation among particles can be inhibited by a suitable choice of surfactants. Therefore,
coagulation is not a critical factor. The effect of Ostwald ripening becomes significant when
the supersaturation is small. More precisely, if the supersaturation made by the capillarity
or the Gibbs-Thompson effect of particles is higher than the supersaturation for growth in
the bulk, Ostward ripening would occur extensively. Then, the size distribution would
deviate from monodispersity and approach the well-established distribution predicted by
the Lifshitz, Slyozov and Wagner (LSW) theory. [17, 18] Therefore, to inhibit Ostwald
ripening, the supersaturation for growth should be maintained much higher than that by the
Gibbs-Thompson effect. This aspect was studied in detail by Kwon et al. [8].
The most critical factor unfavorable for monodisperse distribution is the additional
nucleation during growth. Therefore, growth should be separated from nucleation. The
thermodynamics and kinetics of nucleation are relatively well established. The rate of
nucleation is negligibly low at low supersaturation and becomes very high above certain
supersaturation, varying like a step function. The supersaturation for the onset of nucleation
has a special meaning and is called the critical supersaturation for nucleation, which is
defined as the supersaturation to produce the nucleation rate of 1/cm3sec.
Consequently, to inhibit the additional nucleation during growth, the supersaturation

should be maintained below the critical supersaturation for nucleation. Normally, the
critical supersaturation for homogeneous nucleation is high enough but that for
heterogeneous nucleation is relatively low and can be easily achieved. Therefore, a special
care must be taken to prepare the reactor for the synthesis of monodisperse nanoparticles
free from the site for heterogeneous nucleation.
One attempt to separate growth from nucleation is the seed-mediated growth, where the
preformed nanoparticles are used as seed nuclei [7, 19]. Another attempt to separate growth
from nucleation is the initial burst of nucleation, where an appreciable amount of
supersaturation is consumed during the burst of nucleation and the relatively low
supersaturation is maintained during growth. The hot-injection method [20-22] is an
example of this attempt.
Rapid injection of reagents into a hot surfactant solution raises the precursor concentration
above the nucleation threshold. A burst of nucleation during a short period of time partially
relieves the supersaturation. If the rate of the precursor consumption by the growing
colloidal nanoparticles is not exceeded by the rate of precursor addition to solution, no new
nuclei would form. This process typically produces the nanoparticles with the size
distribution of 10 < < 15% in diameter, which are then narrowed to < 5% through
additional size-selective processing.
The heating-up method [6, 23-25] is a new attempt to separate growth from nucleation.
This process is a batch process and very simple. Metal-oleate precursors are prepared from
metal chloride and sodium oleate. If the metal-oleate precursors are heated in a high-boiling
point solvent, they are thermally decomposed and produce monodisperse nanocrystals. This
method proved to be advantageous for large-scale production. Park et al. [6] showed that as
large as 40g of monodispese magnetite nanocrystals with a yield of >95% could be produced
in a batch. The size uniformity of the nanoparticles is usually better than that by the hot-
injection method. Since this is a batch process, the precursors are not added during growth
to supplement the supersaturation.
The supersaturation that has been consumed during growth can be indirectly estimated
from the final size of the nanoparticles. The highly monodisperse nanoparticles were
reported to grow as large as 22 nm in the heating up process. Considering that the critical
nucleus size is ~ 0.5 nm, the diameter increases by more than 20 nm, which implies that a
considerable supersaturation must have been consumed. Since an appreciable amount of
supersaturation is consumed in the initial nucleation process, the remaining supersaturation
is usually not so high. Therefore, it is highly unlikely that the nuclei should grow as large as
10 nm by remaining supersaturation without precursors being supplied additionally. It

should be reminded that in the hot-injection method the additional precursors should be
supplied to produce nanoparticles larger than 10 nm.
Then, a question arises as to why additional nucleation does not occur during such
extensive growth. It appears that all the supersaturation, which should be consumed to
produce the final size of nanoparticles, is not built up simultaneously but only a very small
fraction of supersaturation, which is too small to trigger the nucleation, is maintained
throughout the growth. This is an ideal situation where growth is separated from
nucleation. One possibility to realize such an ideal situation is that the decomposition of the
metal orleate complex into metal does not occur in the solution but occurs only at the
surface of nanoparticles. In other words, the surface of nanoparticles acts as the catalytic site
for decomposition of the metal orleate. This type of reaction is called self-catalytic.
Therefore, if a system is self catalytic, growth can be separated ideally from nucleation and
monodisperse nanoparticles can be easily synthesized.
6. Digestive ripening
As mentioned earlier, the coarsening kinetics of Ostwald ripening has been well established
by LSW theory [17, 18]. During Ostwald ripening, large particles with a low chemical
potential grow at the expense of small particles with a high chemical potential and, as a
consequence, the average size increases and the total number of particles decreases during
coarsening. Eventually, only one large particle remains, which corresponds to a final
equilibrium state.
However, Klabunde and co-workers reported a series of articles on the synthesis of

monodisperse gold or silver nanocrystals by a digestive-ripening process of polydisperse
nanocrystals. [9-12, 26, 27] Gram quantities of monodisperse gold or silver nanoparticles
could be produced through digestive ripening, where colloidal particles from 2 to 40 nm are
transformed to nearly monodisperse particles of 45 nm diameters.
Digestive ripening is the reverse process of Ostwald ripening. It is interesting and also
puzzling in that small particles grow at the expense of large ones. Clearly, digestive ripening
cannot be understood with the usual GibbsThomson equation solely based on a curvature
effect. According to the theory of diffusion-controlled coarsening [28], the growth rate of a
particle with radius, r, is given by
dr D f Vg Co
= (r)* -(r) (5)
dt rRT
where R is the gas constant, T the absolute temperature, and Df and Co are the diffusivity
and solubility of atoms in the solution, respectively. Eq. (5) is valid when the diffusion field
does not overlap. (r)* is the chemical potential of a particle of critical size, which neither
grows nor shrinks at the given instant.
Since the phenomenon of digestive ripening runs counter to the decrease of interfacial free
energy, a different type of free energy must be involved. The driving force for digestive
ripening must compete against the reduction of the interface free energy. There are two such
free energies. One is strain energy and the other is electrostatic energy. Since solid particles
dispersed in liquid do not have any appreciable strain energy, the electrostatic energy is a
possible candidate. In fact, Klabunde et al, who have developed the digestive ripening
process, reported that their nanoparticles were negatively charged [9, 10]. If nanoparticles
are electrically charged, they have an electrostatic energy inversely proportional to the
radius of the particles. Since electrostatic energy increases with decreasing particle size,
charged particles cannot shrink away completely. Therefore, the presence of charge can
drastically change the Ostwald ripening behavior. The chemical potential change arising
from the presence of charge can be treated by modifying the Gibbs-Thomson equation in
consideration of the electrostatic energy.
To analyze the effect of charge on the coarsening behavior of nanoparticles, it is assumed

that each particle is singly charged, electrically-conducting, and spherical with isotropic
interface free energy, dispersed in a matrix phase with a dielectric constant of 1. According
to this assumption, ions are regarded as the primary embryos of charged nanoparticles. It is
further assumed that the charged nanoparticles do not coagulate with each other and that
the atomic transfer between particles is diffusion-controlled. The Gibbs free energy of a
spherical conducting particle with radius r and charge e (corresponding to the unit charge of
an electron) is expressed as
e2
G = 4r 2 + k , (6)
2r
where is the interface free energy of the particle and k is defined by 1/(4), where is the
vacuum permittivity [29]. ke2 is 2.306810-28 Nm2. It should be noted that with decreasing r,
the interface free energy term decreases but the electrostatic energy term increases.
From Eq. (6), the modified Gibbs-Thomson equation is derived as
Cr 2 q2
= r - o = RTln = Vm -k , (7)
Co r 8r 4

where Co is the solute concentration in the matrix without capillary effect. If the difference
between Cr and Co is small, the equation can be approximated as
C C -C V 2 q2
ln r r o = m -k . (8)
Co Co RT r 8r 4
The coarsening behavior can be analyzed quantitatively by solving Eqs. (5) and (8)
simultaneously under the constraint of mass conservation for a total number of particles Np,
and is expressed as
Np
drn
4rn 2 dt
= 0. (9)
n
Substituting Eq. (5) into Eq. (9) yields
Np
rn D f Vm C* - C0 - Cr,n - C0 = 0. (10)
n
From Eqs. (5), (9) and (10), the following equation can be derived:

N
drn D f Vm2C0 p rn 2 q 2 2 q2
= N p -k - -k . (11)
dt RTrn n rn 8rn4 rn 8rn4
rn
n
If the growth rate of each particle is determined by Eq. (11), the new radius after dt is given
by
dr
rn (t + dt)= rn (t)+ n dt. (12)
dt
Once the initial size distribution of particles is given, the time-dependent size distribution
can be obtained by solving equations (11) and (12) simultaneously by iteration.
To demonstrate that this approach reproduces simple digestive ripening, one large charged
nanoparticle of 15 nm radius and 600 ions of 0.2 nm radius were chosen as an initial state. A
diffusivity, Df, of 10-9 m-1sec-1 and a temperature of 393 K were chosen for calculation.[11]
Besides, the interface energy of = 1 mJm-2, C0 = 0.01 molm-3, and Vm =1.0210-5 m3 mol-1,
which is the molar volume of gold, were chosen. Here, the interface free energy of 1mJm-2 is
chosen, simply because it produces monodisperse nanoparticles of the 1.5 ~ 2 nm size after
digestive ripening. Experimentally, the surfactant, dodecanethiol, which is expected to
diminish the interface free energy between gold and solution, appears to play a critical role
in inducing digestive ripening. [30, 31] As the interface free energy decreases and the electric
charge density increases, the size of finally-evolved monodisperse nanoparticles increases.
Fig. 4 shows the size evolution of charged nanoparticles with time. a1 and a2 in Fig. 4(a)
represent the radius of charged embryos at 200 s and 600 s, respectively. Likewise, b1 and b2
in Fig. 4(a) represent the radius of the 15 nm particle at 200 sec and 600 sec, respectively. The
size of the small charged embryos increases, whereas the size of the large charged particles
decreases. Figs 4(b)-(d) show a display of the size distribution of nanoparticles at 200 s, 600 s
and 900 s, respectively. Finally, the radius of every nanoparticle becomes 1.78 nm at 900 s, as
shown in Fig. 4(d), which corresponds to F in Fig. 4(a), producing perfect monodisperse
nanoparticles. This calculation reproduces the experimentally observed digestive ripening

behavior.
Figure 4. Coarsening behavior of one big particle of 30 nm and 300 embryos of 0.4 nm. (a) a1 and a2
indicate the size of embryos at 200 s and 500 s, respectively. Likewise b1 and b2 indicate the size of the
large nanoparticle at 200 s and 500 s, respectively. Finally, the size of every nanoparticle becomes the
same on F at 900s. The size distribution of nanoparticles at (b) 200 s, (c) 500 s and (d) 900 s, respectively.
In (b), the size of small nanoparticles is 4 nm and that of a large nanoparticle is 19.9 nm. In (c), the size
of small nanoparticles is 4.3 nm and that of a large nanoparticle is 14.9 nm. In (d), the size of every
nanoparticle becomes 4.5 nm. Reprinted with permission from [13]. Copyright 2007 Elsevier.
7. Digestive ripening in a binary system

Smetana et al. [26] reported digestive ripening in a binary system, where separately
prepared monodisperse Au and Ag nanoparticles with a radius of ~3.3 nm, mixed in a
colloid solution, were transformed into monodisperse Au/Ag alloy nanoparticles with a
radius of ~2.8 nm. The final monodisperse nanoparticles did not have a coreshell structure
but had uniform composition distribution. The size of the final monodisperse nanoparticles
was reduced in comparison to that of the initial unalloyed monodisperse nanoparticles,
which implied that additional nucleation had occurred during digestive ripening.
To analyze the coarsening behavior of a binary system of Au and Ag nanoparticles, the

chemical potential of a binary system needs to be derived. According to the phase diagram
of an Au/Ag binary system [31], Au and Ag, which have the same face-centered cubic (FCC)
structure and a small difference in atomic size, have a complete solid solution. Therefore, it
is assumed that Au and Ag nanoparticles behave like an ideal binary solid solution, and
then, the Gibbs-free energy is expressed in the whole composition range as follows [32]:
G = X Au G Au + X Ag G Ag + RT(X Au lnX Au + X Ag lnX Ag )

(13)
From Eq. (13), the chemical potentials of Au and Ag for the alloy are given, respectively, by
Au = G Au + RTlnX Au
(14)
Ag = G Ag + RTlnX Ag
where GAu and GAg are the molar free energies of pure Au and Ag, respectively; and XAu and
XAg are the mole fractions of Au and Ag, respectively. From Eqs. (7) and (14), the chemical
potentials of spherically charged nanoparticles of Au and Ag with radius r can be derived as
2 kz 2 q 2
Au (r) = G Au + RTlnX Au +VSS SS -
r 8r 4
(15)
2 kz 2 q 2
Ag (r) = G Ag + RTlnX Ag +VSS SS -
r 8r 4
where SS and VSS are the interface free energy and the molar volume of the Au/Ag solid
solution, respectively. To investigate the time evolution of the coarsening behavior of the
mixed Au and Ag nanoparticles, the growth rate of particles should be calculated.
Substituting Eq. (5) for dr/dt in Eq. (9) and rearranging the result yield
Np Np
(r)* = rn (rn ) / rn (16)
n=1
n=1
Expressing (r)* in terms of dri/dt and using Eq. (15) for (r) in Eq. (16), the growth rate of
the ith particle by diffusion of Au and Ag atoms is obtained as
-1
2 SS kz 2 q 2 p p RT
2 N N
dri D f VSS Co RT 2 SS kz 2 q 2
= - lnX Au - + + rn rn
lnX Au + - ,
dt ri RT VSS ri 8ri4 n=1 n=1 VSS rn 8rn4

i = 1,2,... for Au
(17)
-1
2 SS kz 2 q 2 p p RT
2 N N
dri D f VSS Co RT 2 SS kz 2 q 2
dt
=
ri RT VSS
- lnX Ag -
ri
+ + n n
r r
8ri4 n=1 n=1 VSS
lnX Ag +
rn
- ,
8rn4

i = 1,2,... for Ag
With Eq. (17), the radius of the ith particle can be calculated at a time, t +t, by
dri
ri (t + t)= ri (t)+ t, i = 1,2,... (18)
dt
The analytic expression for the composition change of nanoparticles cannot be derived.
Therefore, the composition change of nanoparticles should be computed from the mass
change of each element, which is determined from the size change by Eq. (18) for each
iteration.
To check whether these schemes reproduce the experimental result of alloy digestive
ripening, a simple system of 500 Au charged nanoparticles of RAu = 3.3 nm, 500 Ag charged
nanoparticles of RAg = 3.3 nm and 500 charged nuclei of Rnuclei = 0.5 nm was considered. This
system is chosen to represent the experimental condition of as-prepared Au and Ag
nanoparticles mixed for digestive ripening [14]. The 500 nuclei were added because the
experimental fact that the number of final nanoparticles increases after digestive ripening
indicates that additional nucleation occurs. The capital letter Ri indicates an initial radius
with the suffix i implying the ith group of particles with identical radius. The initial mole
fraction of Au nanoparticles, XAu, is set at 0.99 instead of 1 to avoid the infinity in
calculation. In the same manner, XAu of Ag nanoparticles and the size of nuclei are set at 0.01
and 0.5, respectively. The parameters used are Df = 0.5 1014 m2/s, VSS = 1.02 105 m3/mol,
Co = 0.01 mol/m3, kq2 = 2.3068 1028 Jm, T = 393 K, SS = 0.3 J/m2, and z = 30. It should be
noted that if the particles are assumed to be singly charged with z = 1, the interface energy
SS should have a much smaller value than 0.3 J/m2 to reproduce the experimentally-
observed digestive ripening.
For the simplification, the diffusivities of Au or Ag atoms in the nanoparticles are assumed
to be high enough to be homogenized immediately because the final structure of Au/Ag
alloy nanoparticles was reported not to have a core-shell structure but to have a
homogeneous solid solution.
In Fig. 5, the coarsening behavior of nanoparticles with time is schematically displayed. The
time evolution of the microstructure is shown in Figs. 5(a), (b), (c) and (d) at t1 = 0, t2 = 1, t3 =
2 and t4 = 16 h, respectively. Fig. 5(a) shows the initial size distribution and the composition
of nanoparticles, which is represented by the gray scale from black for Au to white for Ag as
shown by the gray scale bar in Fig. 5. Therefore, black, white and gray nanoparticles
represent Au-rich, Ag-rich and Au/Ag alloy nanoparticles, respectively. After 1 h, the radii
of both Au and Ag nanoparticles decrease to 3.07 nm and the mole fractions, XAu, of Au and
Figure 5. Display of the nanoparticles evolved through coarsening at four different times in the system
of 500 Au nanoparticles, 500 Ag nanoparticles and 500 nuclei. Composition is represented by the gray
scale from Au as black to Ag as white. (a) At t1 = 0 h, RAu = 3.3 nm with XAu = 0.99, RAg = 3.3 nm with XAu
= 0.01 and Rnuclei = 0.5 nm with XAu = 0.5. (b) At t2 = 1 h, rAu = 3.07 nm with XAu = 0.64, rAg = 3.07 nm with
XAu = 0.36 and rnuclei = 2.4 nm with XAu = 0.5. (c) At t3 = 2 h, rAu = 3 nm with XAu = 0.54, rAg = 3 nm with XAu
= 0.46 and rnuclei = 2.6 nm with XAu = 0.5. (d) At t4 = 16 h, all the particles become monodisperse at 2.88 nm
with the same composition of XAu = 0.5. Reprinted with permission from [14]. Copyright 2009 Elsevier.
Ag nanoparticles become 0.64 and 0.36, respectively, as shown in Fig. 5(b). The radii of the
nuclei increase to 2.4 nm with their mole fraction, XAu, maintained as 0.5. After 2 h, the size
distribution becomes much narrower approaching a monodisperse state and the
composition becomes more homogenized as shown in Fig. 5(c). The radii of initial Au and
Ag nanoparticles decrease to 3 nm, and the radii of the nuclei increase to 2.6 nm. The mole
fractions of Au and Ag nanoparticles become 0.54 and 0.46, respectively. After 16 h, all the
nanoparticles eventually have the same radius of 2.88 nm and the same composition of XAu =
0.5, as shown in Fig. 5(d). By considering both the electrostatic energy and ideal solid
solution, the coarsening behavior of the digestive ripening process, where the separated Au
and Ag nanoparticles were transformed into monodisperse Au/Ag alloy nanoparticles, was
successfully reproduced.
8. Conclusions
The evolution mechanism of monodisperse nanoparticles is approached thermodynamically
and kinetically. Both interface-controlled and diffusion-controlled growth of particles can
induce monodisperse distribution of particles if coagulation, additional nucleation and
Ostwald ripening are inhibited. The diffusion-controlled growth reaches the monodisperse
state at much smaller size than the interface-controlled growth. The evolution mechanism of
monodisperse nanoparticles by digestive ripening is approached using the modified Gibbs-
Thompson equation considering electrostatic energy. The digestive ripening behavior of
both pure metal and alloy which is contrary to conventional Ostwald ripening, is well
explained assuming that nanoparticles are electrically charged.
Author details
Nong-Moon Hwang and Jae-Soo Jung
Department of Materials Science and Engineering, Seoul National University, Seoul, Korea
Dong-Kwon Lee
LG Chem. Ltd, Research Park, Yoseong-gu, Daejon, Korea
Acknowledgement
This work was supported by the National Research Foundation of Korea (NRF) grant
funded by the Korea government (MEST) (No. M10600000159-06J0000-15910).
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[31] H. Okamoto, T. B. Massalski, Phase Diagrams of Binary Gold Alloys, (ASM

International, Metals Park OH, 1987).
[32] D. A. Porter, K. E. Easterling, Phase Transformations in Metals and Alloys, (Chapman &
Hall, London, 1992).
Chapter 15
Statistical Thermodynamics of Lattice Gas

Models of Multisite Adsorption
Vasiliy Fefelov, Vitaly Gorbunov,

Alexander Myshlyavtsev and Marta Myshlyavtseva
1. Introduction
The lattice models naturally arise in different fields of physics, chemistry and other sciences.
First, it is physics of the solid state and physicochemistry of the surface. Among the many
well-known lattice models the magnetic, alloys, liquid mixture, adsorption models are
usually mentioned. The lattice models can be both classical and quantum. In this chapter
only the classical lattice models focusing on models arising in physicochemistry of the
surface will be considered. For the beginning lets give the most common formal definition
of the classical lattice model.
Let there be given some finite or countable set M. Its elements will be called sites
or nodes of
the lattice and numbered index i. Each site is associated with the vector ( ci ) having ki
components. Each of the components can take a finite countable or uncountable number of
values, i.e. without loss of generality, it can assume that the components of this vector take
either integer or real values in some finite or infinite interval. The specific values of the ci
vector components determine the i-th site state. The M set state uniquely determines the
state of all its elements. The system states
can be divided into allowable andunallowable

ones. Each allowable state of the M ci set is match to the real number EM ci called the
energy per lattice site. (Formally, unallowable state can be assigned value EM ).
Accepting the Boltzmann probability distribution of the system states as an additional
postulate, one can receive object called a classical lattice model. All the models considered
below are particular cases of the introduced generalized lattice model.
Determination of the lattice model dimension may be connected with the number of sites
where can be the particle performing a random walk on the lattice in n steps. For d-
dimensional regular lattice the number N is proportional to the volume of a box with an
edge n, where N ~ nd , i.e. the higher the dimension, the closer neighboring sites are located.
Following this approach 1,2,3,, d-dimensional lattice models (for example, d-dimensional
hypercubic lattices with interaction between the nearest-sites) are naturally obtained. 1,2
and 3-dimensional lattice models are of most importance for specific applications to the
natural sciences. However, besides models whose dimension is equal to some natural
number models which dimension defined the same way as above is fractional or infinite are
of great interest. The simplest example of a model with a fractional dimension is the Ising
model on the diamond-like lattice.
Concluding the general description of lattice models it is worth to introduce the concept of a
homogeneous lattice model. Models properties of all their sites are identical are called
homogeneous lattice models. It follows the obtained lattice model has a geometric
realization possessing the property of translational invariance. As it is mentioned above, the
models relating to physicochemistry of the surface are of main interest, respectively, these
are primarily two-dimensional ones. It is readily to conclude that all the two-dimensional
homogeneous models can be divided to three classes having in the basis the geometric
realizations: the square, triangular and hexagonal lattice. Note that the lattice models having
different types of sites but whose geometric realizations possess translational invariance can
serve the generalization of concept of lattice model homogeneity. From the computational
point of view these models are very similar to homogeneous ones. Thus, the most common
definition of the classical lattice model, its dimension, homogeneity and translational
invariance have been introduced.
Lattice gas model and its various generalizations are one of the most important lattice
models of modern statistical physics. Despite its relative simplicity these shows fantastic
variety of non-trivial physical phenomena. First, this refers to the phase transitions of
various types whose study is of great interest from the standpoint of the general theory.
Note that the adlayers on the monocrystal faces represent the physical realization of many
interesting and important models for d = 2, in particular, these admitting exact solutions.
The fact causes an increased interest of theorists to such systems.
Usually the lattice gas means the molecular system which differs from the continual gas
following feature: molecules of such a system can occupy only such places in the space in
which their centers are located at the sites of one-, two- or three-dimensional geometric
lattice. The interaction energies of molecules located in different configurations respect to
each other are the parameters of the model. In the general case, these parameters also
depend on the relative orientation of the molecules. These interactions called lateral
naturally can be divided to pairs and many-particle. Pair interactions are additive while
many-particle ones are nonadditive.
It is easy to see from the standpoint of common definition of classical lattice model the
lattice gas model (LGM) stated above refers to the same class of models as the Ising model.
Indeed, considering the dependences of the energy of lateral interaction of molecules
on
their relative orientation one can obtain the lattice model in which the vector ci is a scalar
accepting two values (when all the molecules are the same type). From the above it
immediately follows that the simplest LGM is isomorphic to the classical Ising model in the
Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption 391
sense of the common definition. The latter statement is a very important because the
property of one model can be obtained that of another one.
One of the simplest examples of the system for which LGM is quite adequate model is the
monomolecular adsorption model. It is well known that chemisorption has localized
character as in this case there occurs chemical bond between the adsorbed molecule and the
substrate. For substrate being face of monocrystal chemisorbed molecules are located in well
defined places of the periodic lattice formed by the surface atoms. Therefore, the simplest
LGM introduced above is completely adequate model of monomolecular chemisorption on
monocrystal face.
The thermodynamic Hamiltonian of the simplest LGM with one type of particles on regular
lattice (for example, hypercubic) has the form:
H ninj ni , (1)
n ,n i
where is the lateral interaction energies of the nearest neighbors; is the chemical
potential; the occupation number ni is equal to unity if the adsorption site is occupied and
zero in the case of a vacant site. The Hamiltonian (1) for d = 2 in the first approximation
describes the monomolecular (one-center) adsorption on a monocrystal face.
In some cases this description corresponds to reality but in most cases it does not [1]. It is
known that even at adsorption of the most simple gases such as Ar, Kr, Xe, nitrogen, carbon
monoxide, oxygen and others the adsorbate molecule size is usually larger than the distance
between neighboring active centers of adsorption [2-6]. In this connection at the adsorbate
molecule adsorption on one active center it simultaneously occupies one or several
neighboring active centers.
The assumption of one-center adsorption becomes even more inadequate at the description of
adsorption of linear and quasilinear molecules such as the simple saturated and unsaturated
hydrocarbons [7,8]. In the paper complete review of the experimental results on the
adsorption of simple hydrocarbons on the surface of metal monocrystals (Pt, Pd) was given
and, particularly, the adsorption of such molecules was shown to occur parallel to the solid
surface in connection with which multicenter nature of the adsorption becomes apparent.
In addition in this review some types of ordered structures of adsorption monolayer 4 8

alkanes experimentally observed at low temperatyres on the surface of monocrystalline
platinum are discussed. The necessity of describing of the n-alkane adsorption in the
framework of the models with multisite adsorption is also supported by the fact that at the
interpretation of experimental adsorption isotherms by using the known multisite Langmuir
model and other analytical models there exists good correlation between the model
parameter k (the number of active sites occupied by adsorbate molecule) and the real
number of segments in the molecule of the adsorbate [7,8,10-12]. It should be noted that the
above analytical models of multisite adsorption are used to determine the specific surface of
porous solids and its topography (in the case of energetically heterogeneous surfaces).
Obviously that the adsorption of more complex (in regard geometry, the chemical structure
the presence of double/triple bonds or several functional groups) of molecules is even
more nontrivial [14-25]. First of all this is manifested in that complex organic molecules
(cyclic hydrocarbons, aromatic systems etc.) depending on their geometry and chemical
structure can form set of different ordered structures on the solid surface.
Along with the possibility of multisite adsorption that of different orientations of molecules
with respect to the interface is one of the most interesting features of these systems. Indeed,
over the past ten years series of experimental works devoted to the study of organic self-
assembled monolayers on metal surfaces has been published. The general conclusion of
these studies is that the molecule orientation in the adlayer is a function of external
parameters such as concentration, pressure, temperature, electrode potential and others[14-
25]. Moreover, very interesting ordered structures have been experimentally found in some
of similar systems. Those are structures which simultaneously contain the molecules with
different orientations in the adlayer. For example, in [18] the authors investigated behavior
of the adsorption monolayer of molecules p-Sexiphenil on the Au(111) surface in ultrahigh
vacuum using the method of scanning tunneling microscopy. It was shown that five various
ordered structures two of which contain molecules with different orientations in the adlayer
molecules oriented parallel to the surface and tilted to the surface at an angle can be
formed. In [24] phase transitions in the adlayer of acid trimezin molecules on the Au(111)
surface have been investigated using the method of scanning tunneling microscopy, and one
of them proved to lead to formation of the ordered structure containing the acid trimezin
molecules oriented both parallel and perpendicular to the surface. Another striking example
of the adsorption system in which the adsorbate molecules can have different orientations
with respect to the surface is the adsorption of cyclic unsaturated hydrocarbons on the
reconstructed semiconductor surface especially on the reconstructed face of the Si(001) [25-
27]. This is connected to the fact that cycloaddition reaction [2+2] with formation of di-
bond Si-C with the silicon surface atoms results from chemisorption of unsaturated organic
molecules on the silicon surface. In chemisorptions of more complex hydrocarbons
containing several unsaturated bonds the particle adsorbed on the surface can have several
configurations depending on the number of di- bonds Si-C [28]. Moreover, the stable -
complex being resulted from interaction between unsaturated hydrocarbon molecule and
silicon atom has been experimentally discovered recently [29,30]. In light of the above it is
clear that all specified features of the behavior arising at detail studying of adsorption of
simple or complex molecules can be investigated only in the framework of models taking
into account the multisite character of adsorption and the possibility of different orientation
of molecules both with respect to each other and with respect to the solid surface.
Practically, theoretical study of organic self-assembled adsorption monolayers or thin

organic films is of great interest generally in connection to the set of possible applications in
which thin organic films are used anyway [31]. The potential field of application of such
systems is an organic optoelectronics, in particular, electroluminescent devices [32],
photovoltaics [33], organic field-effect transistors [34]. Similar systems are used as coatings
on computer hard drives to provide protection against corrosion and low friction [35].
It is difficult to overestimate the applied significance of considered systems in the field of

chemistry and biochemistry where they are used as active elements of chemical and
biological sensors [36], in heterogeneous catalysis [37] and as coatings for biomedical
implants [38]. Polymorphism of organic thin films and the ability of molecules to constitute
different crystalline forms leads to is it is very difficult to control growth and properties of
such systems. Moreover, it was recently shown that the structure of the organic film
significantly affects epitaxial growth of crystals on the film [39]. This fact can be used to
control the morphology of nanocrystalline systems.
In all these cases location of the molecules on the surfaces is a decisive factor that determines
process of growth of the film and its physical properties. Therefore, a detailed
understanding of elementary phisical and chemical processes occurring in such systems is
the primary motivator at the investigation of molecular self-organization on the solid
surface. The development of realistic models of such systems can allow completely to
control the process of self-assembly of organic and other molecules on the solid surface and
to come nearer to dream of nanotechnology to gather material possessing the necessary
properties with atomic precision. Based on the above it is clear why the interest of
researchers specified both practical and theoretical considerations is now shifting towards
more complex lattice models some of which will be discussed in this review.
Lets consider the class of lattice models describing the so-called multisite adsorption. The
simplest LGM considered above in the two-dimensional case is a model of monosite
adsorption (active centers of adsorption, generally speaking, do not coincide with the
surface atoms). However, as noted above at the description of many adsorption systems one
is forced to abandon from idea about the monosite adsorption. In the framework of the LGM
multisite adsorption is described as a system of prohibitions on certain configurations. At
the same time a relatively simple lattice geometrically equivalent to the crystal lattice of the
surface is persisted but the number of possible states of the site determining which part of
the complex molecule is located above this site and how adsorbed molecule is oriented is
increased. Further, the main results obtained in the framework of the models with multisite
adsorption will be presented.
2. The models of dimer and k-mer adsorption

The simplest model of multisite adsorption is a dimer adsorption model. In the first
approximation the dimer model described adsorption of molecules consisted of two the
same atoms, for example H2, N2, O2 etc. when temperature is relatively low and molecules
cannot dissociate.
Statistical thermodynamics of the dimers lattice models has a long history. This is one of the
earliest lattice models which take into account the own size of molecules in the frame of the
lattice gas model. Apparently, the first model of the dimer has been studied in the context of
the entropy of the adlayer in 1937 [40]. As it turned out, the dimer model has deep
connections with the Ising model and many other important models in statistical physics. In
the early sixties of the twentieth century an exact solution of the dimer model on a square
lattice was obtained in the case of the so-called "close-packed limit", i.e. all lattice sites
belong to one and only one of the dimers [41-43]. In particular, the entropy per one lattice
site was calculated. Interest in the dimer model persists to this day. Exact solutions for the
dimer model were recently obtained with close-packed limit in the case of the two-
dimensional non-orientable surfaces, such as the Mbius strip and Klein bottle [44,45]. The
problem of the packing of dimers in the presence of vacancies is much more complicated
and largely solved numerically [46,47].This is mainly due to three factors: 1) there are no
statistical equivalence between the particle and the vacancy, and 2) any occupied site
indicates that at least one of the neighboring sites occupied too and 3) it is impossible to
determine exactly whether there will be adsorption on the isolated vacancy. Exact solutions
for the dimer model on lattices of dimension greater than two is currently unknown. For
three- and more than three dimensional lattice models it is the overall situation
characteristic not only for the dimer model, but also for the simpler one-centered model
such as the classical Ising model and its many generalizations.
The dimer model in the framework of the lattice gas model can be described as follows. Let
consider the lattice (for simplicity, a square) of the active sites. Each lattice site can be
occupied by one of the segments of a dimer, or be empty. In addition, the orientation of the
dimer should be specified. The last stage of building the lattice gas model is a complete
listing of prohibited configurations. In this case, the system of prohibitions describes the
continuity of the dimer. Just as in the simplest of the lattice gas model, different lateral
interactions can be considered in the constructed model of dimer adsorption too. The dimer
model is actively studied for decades because it is the simplest model of multisite adsorption
and is of theoretical and practical interest.
A natural generalization of the dimer adsorption model is an adsorption model of rigid or

flexible linear k-mers of having no thickness. The only difference from the dimer adsorption
model is the assumption that the adsorbed molecule occupies now k lattice sites forming a
certain configuration. Thus, k-mer is called the model of the adsorbate molecule, consisting of
k equal-sized segments, and the bond length between the segments is equal to the lattice
constant and does not change, and not broken in the process of modeling. In the case of
dimers, k is equal to two. Thus, from a formal point of view the lattice gas model for the
dimer adsorption does not differ from the lattice gas model for k-mers, so it makes sense to
discuss the results obtained in the framework of these models together. Next, referring to
the k-mers reader should keep in mind the dimers adsorption model, except where
otherwise noted.
Depending on whether the same or different properties are segments of the molecule, k-
mers differ by homonuclear and heteronuclear, respectively. Works devoted to the study of
k-mers can be divided into two groups according to the shape of the molecule (flexibility),
the first group is works devoted to the study of flexible k-mers [48-51], the second group is
works studying the adsorption properties of rigid linear k-mers (rigid rods) [49,51,52].
Theoretical analysis of a multisite adsorption of linear molecules in the general case is rather
complicated, and the exact solution for k-mers found only in the simplest one-dimensional
case [52,53]. In these studies were obtained exact expressions for the free energy per active
site as a function of temperature and surface coverage. In this case, the most interesting is
the dependence of the diffusion coefficient on the k-mer length and the surface coverage.
Thus, with increasing size of the molecule the diffusion coefficient for noninteracting or
attracting k-mers increases too, as in the case of repulsive interactions, the diffusion
coefficient can either decrease or increase with the molecule length increasing, depending on
the degree of coverage [52-54]. For more complex cases for the two-dimensional systems
only approximate analytical expressions were obtained. The most well-known analytical
approximation is: 1) the theory of Flory-Huggins [48,55-58], which is a generalization of the
theory of binary solutions of polymer molecules in a monomolecular solvent for the two-
dimensional case. The fact that in the framework of lattice gas model the problem of k-mer
adsorption on homogeneous surfaces is isomorphic to the problem of binary solutions of
polymer in a monomolecular solvent, 2) Guggenheim-DiMarzio approximation [59,60],
which is based on calculating the number of possible ways of packaging rigid k-mers on
lattices with different coordination numbers 3) the approximation based on the extension of
the exact solution for a one-dimensional case [52,53] to higher dimensions [49,61], 4) well
known quasichemical approximation [62] and mean-field approximation [63], 5) fractional
statistical theory (FSTA) for the adsorption of polyatomic molecules, based on Holdan
statistics [64], 6) semi-empirical model [61,65], etc. Unfortunately, none of these
approximations is universal, and each shows quite good results, depending on the
parameters of the model a flexible or rigid k-mer, the length of k-mer, the presence or
absence of lateral interactions between adsorbed molecules, etc. A brief description of the
approximations and compare them with each other can be found in [49,65]. Generally, more
recent analytical approximations for the k-mers adsorption include earlier ones as special
cases. In this regard, lets consider the best of them FSTA and semi-empirical
approximation.
In ref. [51] the authors, by comparing experimental data with results obtained by means of
analytical approximations and a Monte Carlo simulation, studied the adsorption of linear
and flexible polyatomic molecules on honeycomb, square and triangular lattices. Data
obtained by the FSTA model in the case of a square lattice are almost identical to the data
obtained by the Monte-Carlo simulation. A similar analytical calculation by FSTA for the k-
mers adsorption on triangular lattice gives an inaccurate result, because there are a larger
number of possible configurations of a single k-mer on the surface.
In order to verify the accuracy of the proposed approach (FSTA) the authors have
constructed and analytically calculated the two models of real processes. The first is a model
of oxygen adsorption on 5A zeolite and the second one a model of adsorption of propane
on the 13X zeolite. The results of analytical calculations were almost identical to the
experimental data. The principal difference FSTA from earlier models of multisite
adsorption is that in addition to the size of molecules, it also takes into account their shape
and surface geometry. Thereby FSTA can describe the adsorption of both rigid and flexible
molecules.
Analyzing the results deviations for various approximations from the results of Monte
Carlo, it was shown that the most accurate approximation is the semi-empirical model,
developed by Roma et al. Semi-empirical model is a combination of the exact solution for
one-dimensional approximation and Guggenheim-DiMarzio approximation [65]. A new
theoretical approach is significantly better than other existing approximations and allows
fairly simple explaining the experimental data.
When comparing the adsorption isotherms of monomers and k-mers, it was found that in
the second case the symmetry of the "particle-vacancy" is broken. The isotherms are shifted
toward lower coverage with increasing coordination number of the lattice. In other words,
for a given value of the chemical potential the surface coverage increases with the lattice
coordination number.
As can be seen in most works devoted to the development of new analytical methods, the
results are compared not only with the experimental data, but also with the results obtained
by the Monte-Carlo, as the reference.
The Monte Carlo method has proved to be a very powerful tool in the study of k-mers
adsorption. Using this method with different techniques (reweighing, finite-size scaling, and
others [66,67]) many important parameters of the phase behavior for different k-mers
adsorption systems were identified, such as the types of ordered phase structures, the points
of phase transitions and critical indexes of phase transitions, etc. [68,69]. The appearance of
ordered phases for the model k-mers in the presence of lateral interactions has its own
specifics, this is due to the presence of orientation in the arrangement of the adsorbed
molecules relative to each other.
In ref. [70] the authors, using the transfer-matrix method, investigated the ordered
structures of the adsorption layer consisting of interacting dimers adsorbed on a square
lattice. Analysis of the changes of the adlayer entropy and the surface diffusion coefficient
showed that there is a finite number of ordered phases in case of repulsion lateral
interactions between the nearest neighboring molecules.
Later in ref. [71] Ramirez-Pastor et al. using the Monte Carlo method have considered both
attractive and repulsive interactions between adsorbed dimers on a square lattice. It was
shown that in the case of attractive interactions, the phase diagram is similar to the diagram
for a monoatomic gas, but the critical temperature is shifted to higher values. The most
interesting case is repulsive interactions when a variety of ordered structures take place. In
the case of dimers the symmetry of the "particle-vacancy", typical of monatomic particles,
disturbed, that leads to the asymmetry of the adsorption isotherm with respect to the line
= 0.5, on the isotherm two steps take place. When = 0.5 c 2 4 structure formed, which is
characterized by the alternation of the adsorbed dimer and two adjacent vacancies. When
the chemical potential increases and close to = 2/3, adsorbed dimers form parallel
zigzag rows (ZZ phase) [71.72]. A similar phase behavior of adsorbed layer of dimers is
observed in the case of triangular and honeycomb lattices [73] (Fig. 1). In addition, the
scientific group of Ramirez-Pastor, using Monte Carlo method and finite-size scaling
techniques, calculated the critical exponents and critical temperatures, and calculated a
phase diagram for dimers with repulsive lateral interactions on a square [71] and triangular
[74] lattices. It was shown that the system does not belong to the universality class of two-
dimensional Ising model.
Figure 1. Adsorption isotherms of dimers on square, triangular and honeycomb lattices and
corresponding ordered phases [71,73].
The study of the adsorption monolayers consisting of heteronuclear dimers showed that the
phase diagram of the system greatly influenced by the quantity of energy of lateral
interactions between the different types of segments (it is about two different molecules). In
the study of phase diagrams of these films interesting phenomena were found. In particular,
the coexistence of three phases and a variety of structural transitions, and ordered linear
type structure exists even at high temperatures [75].
Similar calculations were performed for the adsorption of homonuclear dimers on

heterogeneous surfaces [1,10,76-79]. In the case where the surface is represented by
heterogeneous clusters of active sites of one kind and another, the approximate solution is
relatively simple (the solution for multisite adsorption on a homogeneous surface can be
used). In describing the adsorption of dimers on heterogeneous surfaces, created at random,
the task becomes more complicated. Slightly more than twenty years ago an approximate
solution was suggested for this model [1,10,79]. However, the original approach of Nitta et al.
could only be applied to surfaces with a discrete distribution of adsorption energy. Later on
the basis of this approximation Rudzinski and Everett [1] obtained a solution for a model
with continuous distribution of adsorption energy on the surface. However, the usable area
of this and other approximations [78] is limited. For example, in [77], the authors investigated
an analytical approximation by Monte Carlo method to describe the adsorption of
homonuclear dimers on heterogeneous surfaces, created randomly (random heterogeneous
surface). The calculation shows that this approximation yields accurate results when the
difference between the energies of adsorption on active sites of one and other kind is small.
There are papers devoted to the description of the first order phase transition such as
"surface gas surface liquid" [75,76,80]. The most important conclusion from all these
studies is that with increasing molecular size the critical temperature shifts to higher values.
On the other hand, increasing of the molecule flexibility leads to decreasing of critical
temperature. A very interesting phenomenon was observed in the study of phase transition
"surface gas surfacee liquid" in the adlayer consisting of heteronuclear trimers namely,
the coexistence of three phases (there is a second phase transition "liquid liquid"). In this
case, the phase diagram is asymmetric there are a shift of the critical density to the unit
and an increasing the critical temperature.
The findings in the study of dimers adsorption on heterogeneous surfaces with a sufficient
degree of accuracy can be extended to the adsorption systems of k-mers [10,78,79]. However,
as was shown in ref. [81], the calculation accuracy of the approximations developed for the
adsorption of dimers on heterogeneous surfaces decreases with increasing molecular size.
Summarizing the results obtained in these works, one can conclude that the phase behavior
of adlayer of dimers on heterogeneous surfaces defined by the following factors: 1) the
distribution of the various active sites of adsorption, and 2) the relation between the k-mer
length and the size of the local heterogeneity, 3) adsorption energy on different active sites.
It should be noted about the theoretical studies of percolation threshold in systems with
multisite adsorption. Information on transitions "percolate region" "nonpercolate area" on
the surface is of great interest both from the point of view of phase transitions science, as
well as from the applied point of view, in particular the appearance of surface conductivity.
In the case of the two-dimensional lattice gas model the percolation threshold is so
minimum value of the coverage on an infinite surface, as infinitely large cluster of
adsorbed molecules is formed. In ref. [82,83] it is shown that in addition to the dimension of
the system and the lattice coordination number on the percolation threshold a size of k-mers
has a significant effect. Influence of temperature on percolation in adsorption systems with
flexible k-mers studied in ref. [50] by the Monte Carlo method. There was found an
interesting phenomenon a nonmonotonic behavior of the percolation threshold as function
of temperature, i.e. there exists a temperature at which the percolation threshold is a
minimum, and the position of the minimum does not depend on the length of k-mers.
Thus, all existing works on the k-mers adsorption, as in the case of dimers, are concentrated
in four main areas: (1) study of the influence of the chemical structure of noninteracting
adsorbed molecules on the behavior of their adsorption, (2) study of the influence of surface
heterogeneity on the k-mers adsorption, (3) description of first order phase transition in the
adlayer in the case of mutual attraction of the adsorbate adsorbate. Only a small number of
papers devoted to the study of phase transition "order-disorder, which takes places in the
case of repulsive intermolecular interactions [69,70]. In particular, in ref. [69], using Monte
Carlo simulation, two important characteristics of the critical properties of repulsive k-mers
were identified: (1) the minimum critical temperature have on the value of k equal to 2
(dimers) and (2) for k > 2 the critical temperature increases monotonically with increasing k.
Similar results (qualitatively) have been obtained from the analytical calculation of the mean
field approximation and the principle of minimum free energy.
Additionally it should be noted that long before the above works, the study of the multisite
adsorption was engaged by Soviet scientists in Temkin (1938 [84]), and Snagovski(1972 [85-
87]). In ref. [84-87] the adsorption isotherms were analytically obtained in the case of
multisite adsorption of two-center (k = 2), square (k = 4) and hexagonal (k = 7) complexes.
Today's papers on multicenter adsorption are essentially the development, and sometimes
repeating, of the works of Temkin and Snagovski.
As one can see, at present the theory of adsorption of k-mers are actively developing
adsorption isotherms are calculated, phase diagrams are constructed, percolation thresholds
are determined, etc. This is due primarily to a large applied importance of such research.
Already, it can be concluded that the behavior of adlayers consisting of molecules that
occupy more than one active site of the surface is significantly different from the behavior of
systems with monosite adsorption. However, it should be noted that in all these considered
works the adsorbate molecule can adsorb only one way to the surface is planar.
3. Multisite adsorption of orientable molecules

Today there is a small number of papers devoted to theoretical investigation of the behavior
of adsorption monolayer consisting of molecules that can have a different orientation with
respect to the surface [88-92]. Lets examine them in detail.
The earliest papers on theoretical study of molecular reorientation in the adsorption

monolayer were carried out at MSU by Gorshtein and Lopatkin in 1971 [88,89]. They
investigated one- and two-dimensional lattice models of diatomic molecules adsorption. It
was assumed that the molecule can adsorb in two different ways with respect to the surface:
vertically and horizontally. Each type of adsorption had its heat of adsorption, and
adsorption energy of vertically oriented molecule was approximately two times smaller. The
lateral interactions between adsorbed molecules were not taken into account. The authors
derived an exact analytical expression for the adsorption isotherms in one-dimensional case
and the approximate equation for two-dimensional lattice. It is shown that for the large
values of adsorption heats at low pressures, most of the molecules adsorbed horizontally,
and the number of vertically orientated molecules is very small. When coverage increasing
the horizontally adsorbed molecules change the orientation, and the number of molecules
adsorbed vertically grows fast. In addition, the authors had obtained expressions for
isosteric heats of adsorption. Having analyzed calculated thermodynamic functions they
concluded that the system exhibits two modes of adsorption: on two neighbor sites in the
region of low pressure and on one site at high pressures.
The authors of [90] studied the adsorption of heteronuclear dimers (A-B) on a homogeneous
surface with a mean-field approximation. In this case the dimer can be adsorbed on the
surface in three different ways: horizontal adsorption with two segments at the same time
and vertical adsorption with the A segment or vertical adsorption with the B segment. It was
assumed that all three types of adsorption differed in the adsorption heat, and the interaction
between adsorbed molecules were absent. The authors derived analytical expressions for the
adsorption isotherms and isobars. In fact, the physical results obtained in this work are in
qualitatively agreement with Gorshteyn and Lopatkins ones and partially duplicate it.
There is the quite interesting model of spin-1 type, which can describe the adsorption of
heteronuclear dimers on different lattices [91,92]. It is assumed in the model that all
adsorbed molecules are oriented vertically to the surface only, and the energy of adsorption
depends on what segment, A or B, molecule adsorb with. The authors of [91,92] considered
the various sets of lateral interactions between dimers, in particular, they took into account
not only interactions between nearest neighbors, but also between next-nearest neighbors.
Such complex lateral interactions in the system led to the set of ordered surface structures
and phase transitions. It had been shown that if the lattice is completely filled the "order-
disorder" transition may occure via a continuous phase transition as well as the first-order
phase transition depending on the model parameters. Moreover, the continuous phase
transition is nonuniversal. It should be noted that the model does not take into account the
possibility of horizontal orientation of the dimer and generally speaking this model can be
attributed to the well-known Blume-Emery-Griffiths model [66].
In [93] authors proposed the general lattice gas model describing the adsorption of complex
molecules. The model can be formulate by following: the molecule can be adsorbed on the
surface by the k ways occupying the m1 , m2 , , mk active sites located in the corresponding
configurations on homogeneous or heterogeneous lattice, respectively. The simplest model of
this type is the model of homonuclear dimers adsorption. In this model it is assumed that
dimer may have two different orientations in the adlayer parallel (adsorption on two active
sites) or perpendicular (adsorption on one active site) to the surface. In the language of this
general model homonuclear dimers adsorption model belongs to the class of models with
k 2, m1 1, m2 2, and heteronuclear dimers adsorption model [90] to the class with
k 3, m1 1, m2 1, m3 2. The model studied in [91,92] belongs to the class of
k 2, m1 1, m2 1. It should be noted that all these simple classes of models have a single
representative and the set of numbers k , m1 , m2 , , mk uniquely identifies the type of model.
Figure 2. Phase diagrams for dimers on square and triangular lattices. Ordered structures: black circles are
site occupied by dimers adsorbed on two sites; gray circles are sites occupied by dimers adsorbed on one site.
As it noted in [90], the results obtained for adsorption of complex molecules can be extended
also to the gas mixtures. In other words, the general model can be considered as a special
case of gas mixtures adsorption model. In this case the number of mixture components will
be characterized by a number k and the molecule kind by value m . So if one consider the
simplest representative of the general model dimer adsorbed on two or one active site, it
would be analogous to a binary mixture of dimers and monomers. These systems will be
equivalent to each other if the model of binary mixture has the fixed difference between the
chemical potentials of the components. From a physical point of view this means that the
adsorbed molecules of one kind, and the behavior of the system is very similar to the
adsorption of the gas mixture. Indeed, when the adsorption properties of complex
molecules [93-97] was studed, it was discovered the phenomenon of non-monotonic
changes in surface coverage with the chemical potential increasing, and a similar
phenomenon was observed in the study of adsorption of binary mixtures [98,99].
In order to evaluate the influence of surface geometry on the phase behavior of adsorbed
monolayer the model of orientable dimers on the square and triangular lattice was studied
[100,101]. It was shown that the influence of the coordination number (the number of
nearest neighbors) plays an important role in the phase formation process. Namely, in the
case of square lattice only two ordered structures consisting of dimers adsorbed only
vertically or only horizontally can form, in the case of triangular lattice except for the phases
of this type another phase consisting of differently oriented molecules appears. Phase
diagrams are presented in Fig.2.
The simplest special case of the general model of adsorption of molecules with different
orientations in the adsorbed monolayer is the lattice model of dimers adsorption discussed
in detail above. Extending the model of dimers adsorption on molecules with more complex
form (cyclic hydrocarbons, aromatic systems, etc.) one can get the lattice model of complex
organic molecules adsorption, which takes into account, firstly, the possibility of different
orientations with respect to the solid surface and, secondly, the diversity and complicated
structure of surface complexes (non-linear shape of the adsorbate molecules). Further, a
special case of the generalized model, which allows to study the effect of varying the
orientation of the complex organic molecules on the behavior of the adsorbed layer in pure
form will be considered. The fact is the model of dimers adsorption along with the
possibility of different orientations of the molecules with respect to the surface takes into
account the ability to the different orientation of molecules relative to each other a priori.
Indeed, in the case of square lattice, the dimer adsorbed parallel to the surface can have two
different orientations which does not allow us, in the framework of this model, to focus on
studying the effect of varying the orientation of the molecule with respect to the solid
surface on the structure and thermodynamic properties of the adlayer.
As model of solid surface homogeneous square lattice is considered and it is assumed that
the molecule can be adsorbed in two different ways: 1) on four active sites (Fig. 3a) and 2) on
one active site (Fig. 3b). In the first case the four active sites involved in adsorption process
form the square. Thus, for the constructed model one have k=2, m1=1, m2=4. In addition, an
Figure 3. Possible configurations of the adsorbed molecules. The small circles represent molecules
adsorbed on one active site, and the large ones molecule adsorbed on the four active sites. The
numbers from 0 to 5 correspond to all possible states of the active site (cell).
infinitely strong repulsion between the nearest neighboring molecules in the model (a nearest
neighborhood between two adsorbed molecules independently of the adsorption way is
prohibited as well) are assumed, which in a first approximation, take into account the complex
structure of the molecule. Active sites prohibited for the adsorption, in the case of two different
orientations of the adsorbed molecules are indicated on Fig. 3 by the cross. It is seen that the
proposed model of multisite adsorption eliminates the effect of varying the orientation of
molecules relative to each other on the structure and thermodynamic properties of the
adsorbed layer, since all possible orientations of the molecules in the plane parallel to the
interface are taken into account simultaneously (Fig. 3). Thus, this model is the simplest model,
which allows to study the effect of varying the orientation of complex organic molecules
relative to the interface on the structure and properties of the adsorbed layer regardless of
other factors. To reduce the dimensionality of the model the value q2 q1 is introduced as
the difference between the heats of adsorption of the four-site location and the mono-site one.
The effective Hamiltonian of the model under consideration can be written as
1
H n 4 ni ci
4 i i
(2)
i i
where the occupation numbers ci and ni are equal to unity for occupied by molecule
adsorbed on one and four sites respectively and zero for empty sites; is the chemical
potential of the adsorbed particles.
The thermodynamic properties of the model have been investigated with standard
importance sampling Monte Carlo method [93]. The calculations of the isotherms and the
surface coverage as the function of the gas phase pressure (chemical potential) are carried
out with the linear size of the lattice L 96 and L 24, 36, 48, 60 used for finite-size scaling
procedures. The linear lattice size was chosen for the adlayer structures to be not perturbed.
Thermodynamic equilibrium is reached by spin-flip (Glauber) dynamics [102] and diffusion

relaxation (Kawasaki dynamics) [103]. To calculate thermodynamic functions successive
configurations of the adlayer are generated using Metropolis transition probabilities [104] in
the grand canonical ensemble.
Analysis of the ground state (T = 0K) of the model allowed to conclude that in the adlayer
due to the infinitely strong repulsive interactions between nearest-neighbor molecules the
set of chessboard type ordered structures forms: c(44)4, c(33)4-1 and c(22).The structures
are schematically shown in Fig. 4. In addition, the lattice gas phase (LG) with zero coverage
exists in the ground state of the system. The corresponding phase diagram of the adsorption
monolayer in the ground state of the system shown in Fig. 5.
Figure 4. Ordered structure of the adlayer. Gray circle denotes a molecule adsorbed on the four active
sites, and the black circle molecule adsorbed on one active site. The structures are shown in order of
their formation with the chemical potential increasing.
Figure 5. Phase diagram of the adlayer in the ground state. The solid line separates the stability region
of the LG phase and stability region of phase c(44)4, while the dashed and dotted lines separate the
stability region of phases c(44)4 c(33)4-1 and phases c(33)4-1 c(22), respectively.
The adsorption isotherms calculated for different values of the ratio /RT are shown in Fig.
6. It is seen that for sufficiently large values of /RT there are three distinct plateaus on the
isotherms, which correspond to thermodynamically stable phases of the adsorption
monolayer at =0,125, =0,22(2) =0,5, where is density of the adlayer (the amount of
adsorbed molecules per site). Based on the values of corresponded to each horizontal
plateau one can conclude that the first plateau determines the existence region of the
ordered phase c(44)4, the second plateau the existence region of the phase c(33)4-1, and
the third the existence region of the phase c(22). In addition, according to the shape of the
adsorption isotherms it can be assumed that the ordered structure c(44)4 is formed from
disordered lattice gas phase via second-order phase transition, which associated with the
origin of a new symmetry element in the system. On the other hand, the phase transitions
c(44)4 c(33)4-1 and c(33)4-1 c(22) are the first-order phase transitions which associated
with sharp changing in the first derivatives of the free energy of the system, in this case it is
expressed by the sharp changing in the number of adsorbed molecules in the system. It is
worth to note that along with an abrupt changing in the number of adsorbed molecules in
the system, phase transitions c(44)4 c(33)4-1 and c(33)4-1 c(22) are also attended by the
reorientation of the adsorbed molecules with respect to the solid surface.
Figure 6. Adsorption isotherms (left) and the dependencies of surface coverage on reduced chemical
potential (right) calculated for different values of /RT.
The dependencies of surface coverage on reduced chemical potential /RT demonstrate the
same phase behavior of adsorbed monolayer (Fig. 6). Namely, there are three horizontal
plateaus on the surface coverage curves at =0,5, =0,55(5) and =0,5 for sufficiently large
values of the ratio /RT. These values of surface coverage, as in the case of the adsorption
isotherms, coincide with the values of surface coverage for the above mentioned phases
c(44)4, c(33)4-1 and c(22), respectively . However, there is one significant difference
between the adsorption isotherms and the dependencies of surface coverage on reduced
chemical potential: the isotherm is not only coincides with the curve of surface coverage, but
even out of proportion to it. Indeed, the dependencies of surface coverage on the reduced
chemical potential are non-monotonic function for sufficiently large values of /RT. While
the adsorption isotherms in accordance with the general conditions of stability of
thermodynamic systems
G(T , p , N ) 1 2G
()Tp G N N
2
Tp
N
N 2! N 2

1 3G 1 4G 1 mG 1 nG
N 0,
3 4 m n
N N ... N
3! N 3 4! N 4 m ! N m n m n ! N n (3)
G(T , p , N )
, 0,
N N T
are monotonically increasing functions for all values of /RT, where grand potential, G
Gibbs free energy, chemical potential, N amount of adsorbed molecules, T
temperature and p pressure in gas phase. The same effect is observed in the dimer
adsorption models on square and triangular lattices. Apparently, this effect takes a place in
any adsorption monolayer of molecules with different orientations with respect to the
interface.
In order to uniquely identify the ordered structures appearing in the adsorption

monolayer the authors of [93] calculated the curves of partial surface coverage by
molecules adsorbed on one and four active sites as functions of the reduced chemical
potential /RT (Fig. 7). It is seen the phase with coverage = 0,5 formed at low values of
/RT consists only of molecules adsorbed on four active sites, so it is obvious that it has
the structure of c(44)4. Then, with increasing chemical potential (gas phase pressure) or
decreasing in temperature of the substrate, the system undergoes the phase transition
from phase c(44)4 to the phase with coverage =0,55(5). It is clear from Fig. 7 that this
phase consists of both molecules adsorbed on four active sites and on one active site.
Therefore, this phase has the structure of c(33)4-1. With further increase of the chemical
potential or when the temperature decreases the system undergoes the phase transition
from phase c(33)4-1 to the phase c(22) with =0,5 and =0,5 which is formed only by
molecules adsorbed on one active site.
Recently, a similar phase behavior of adlayer of complex organic molecules was observed
experimentally (Fig. 8). In [24] the authors investigated the behavior of the adsorption
monolayer of trimesic acid on Au (111) with electrochemical scanning tunneling
microscopy. It was shown that with increasing electrode potential the ordered structure of
the adlayer consisting only of molecules oriented parallel to the surface changes into the
ordered phase, which contains molecules adsorbed both parallel and perpendicular to the
electrode surface. Further increasing in the electrode potential leads to the surface phase
which is formed only by molecules oriented perpendicular to the surface.
Figure 7. The curves of partial surface coverage calculated at /RT = 12. 1 partial coverage of the
surface by molecules adsorbed on one active site; 4 partial coverage of the surface by molecules
adsorbed on four active sites; total surface coverage; density of the adlayer (adsorption
isotherm).
Figure 8. Ordered structure of the trimesic acid adsorption monolayer on Au (111) [21] and the
corresponding structures calculated in the framework of the proposed model.
Analogous sequence of the ordered structures was also observed in other systems, in
particular, in p-sexiphenyl [18] and pyridine adsorption monolayers [23] on Au (111). Thus,
the phase behavior of monolayer adsorption which is realized in the model under
consideration is qualitatively the same as the phase behavior of real adsorption monolayers
of complex organic molecules on homogeneous surfaces. Therefore, a detailed study of the
model and models similar to that is very useful for deeper understanding of the
thermodynamics of self-assembled monolayers of complex organic molecules.
In the framework of the model under consideration, the modern methods of theoretical
physics such as the multiple-histogram reweighting and finite-size scaling techniques (the
fourth-order cumulant of the order parameter) have been used to estimate the phase
diagram (T, ) of complicated organic molecules adsorbed on the homogenous square
lattice (Fig. 9) [93].
Figure 9. Phase diagram of adsorption monolayer of complex organic molecules on homogenous

square lattice.
The phase diagram shown in Fig. 9 differs from the phase diagrams of dimers adsorption
monolayer on square and triangular lattices that: 1) there is the phase consisting of molecules
oriented in both ways (parallel and perpendicular to the solid surface) simultaneously, and 2)
the critical temperature of this phase (c(33)4-1) is higher than the critical temperature of the
ordered phase formed only by molecules adsorbed parallel to the surface. Indeed, the phase
diagram of dimers adsorption on square lattice contains only two regions corresponding to
the ordered phases due to the fact that when dimers adsorb on square lattice the ordered
phase consisting of both dimers adsorbed parallel and perpendicular to the surface does not
appear. In contrast, when dimers adsorb on triangular lattice that ordered phase is formed,
but its critical temperature is lower than the critical temperature of the ordered structure
formed only by dimers adsorbed parallel to the surface.
Thus, the numerical analysis of the thermodynamic properties of the lattice models which
take into account the possibility of varying the orientation of the adsorbate molecules both
with respect to each other and with respect to the solid surface showed that:
1. The phenomenon of non-monotonic changes of the surface coverage as function of the

chemical potential is a general property of the systems under consideration and is not
observed in models of single-site or multisite single-component gas adsorption which
exclude different orientations in the adsorption monolayer.
2. There are ordered structures in the adsorption monolayer of complex organic molecules
consisting of the molecules with different orientations relative to the solid surface,
simultaneously.
3. The transition between the ordered structures of the adsorption monolayer occurs
abruptly through the first-order phase transition.
4. The phase behavior of adsorption monolayer of complex organic molecules strongly
depends on two factors: a) the geometry and chemical structure of the adsorbed
molecule, and b) the geometry of the surface.
It is worth to note that the adsorption of single-component gas consisting of molecules with
complex shape can exhibit the features which typical for the adsorption of multicomponent
gas mixtures [90]. In particular, the model of adsorption of a gas mixture A (adsorb on m1
active sites) and B (adsorb on m2 active sites) is equivalent to the considered models (with k =
2) when the chemical potentials of the gas mixture components are the same, A = B.
4. Conclusion
Lattice gas model and its various generalizations are one of the most important models of
modern statistical thermodynamics and are currently experiencing a new stage of
development. On the one hand, it is related to the solution of some fundamental issues
concerning the limiting behavior of two-dimensional lattice models, and, on the other hand,
it is related to successful attempts to describe with the help of this model complex systems,
in particular, multisite adsorption of various molecules on the solid surface.
Lattice models of multisite adsorption can take into account the number of characteristic
features of complex adsorption systems, the most important of which is the possibility of the
orientation varying of the adsorbate molecules, both with respect to each other and relative
to the solid surface. Analysis of the thermodynamic properties of models of this type
showed that despite its relative simplicity they exhibit a fantastic variety of non-trivial
physical phenomena. First of all, it refers to the processes of self-assembly and phase
transitions of various types, whose study is of considerable interest from the standpoint of
the general thermodynamic theory. In addition, referring to the results of the experimental
data, it can be argued that discussed in this chapter multisite adsorption model is firstly
qualitatively, and in some cases quantitatively, reproduce the behavior of real systems and
secondly have considerable predictive power. The results of study of multisite adsorption
models can be summarized in following conclusions:
1. The adlayer of complex organic and inorganic molecules can form ordered structures
consisting of molecules with different orientations simultaneously (both with respect to
each other and relative to the solid surface).
2. The phase diagram of such systems is asymmetric. Its shape depends essentially firstly
on the size and shape of the adsorbate molecules and secondly on the coordination
number and type of heterogeneity of the substrate surface.
3. The critical temperature of the ordered phases of the adlayer on the one hand increases
with the size of the molecule and on the other hand decreases with increasing
coordination number of the lattice (entropy factor).
4. In models that take into account the possibility of the orientation varying of molecules
adsorbed on the solid surface one can see the phenomenon of non-monotonic change in
the coverage with increasing chemical potential, and the transition between the ordered
structures of the monolayer adsorption occurs abruptly, through first order phase
transition.
From applied point of view a theoretical study of such systems in general is of great interest
because of the many possible applications in which used the adsorption monolayers one
way or another (self-assembled monolayers adsorbed, thin organic films). The potential
application range of such systems is an organic optoelectronics, the development of active
elements of chemical and biological sensors, biomedical materials, heterogeneous catalysis.
In this paper it is shown that the development of lattice models of these systems and study
of its thermodynamic properties allows ones to understand and generalize laws of physical
and chemical processes occurring in such systems, and brings the scientists closer to being
able to fully control the phase behavior of monolayers of organic and other molecules on
solid surfaces.
Author details
Vasiliy Fefelov, Vitaly Gorbunov and Marta Myshlyavtseva
Omsk State Technical University, Russia
Alexander Myshlyavtsev
Omsk State Technical University, Russia
Institute of Hydrocarbons Processing SB RAS, Russia
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Section 5
Non-Equilibrium Thermodynamics
Chapter 16
Influence of Simulation Parameters

on the Excitable Media Behaviour
The Case of Turbulent Mixing
Adela Ionescu
1. Introduction
Although the turbulence is often associated with fluid dynamics, it is in fact a basic feature
for most systems with few or infinity freedom degrees. It can be defined as chaotic behavior
of the systems with few freedom degrees and which are far from the thermodynamic
equilibrium. In this area two important zones are distinguished:
- The theory of transition from laminar smooth motions to irregular motions,

characteristic to turbulence;
- Characteristic studies of completely developed turbulent systems.
In hydrodynamics, the transition problem lays back to the end of last century, at the
pioneering works of Osborne Reynolds and Lord Rayleigh. Since the beginnings, it was
pointed out the fruitful investigation method of considering the linear stability of basic
laminar flow until infinitesimal turbulences. Nonlinearity can act in the sense of stabilizing
the flow and therefore the primary state is replaced with another stable motion which is
considered as secondary flow. This one can be further replaced with a tertiary stable flow,
and so on. It is in fact about a bifurcations sequence, and Couette-Taylor flow is maybe the
most widespread example in this sense.
The situation becomes hard to approach if the non-linearity is acting in the sense of
increasing the rate of growing the unstable linear modes. Although it was anticipated that
the flows can be stable according to the linear theory, in experiments it was concluded that
they are unstable. It must be noticed that Reynolds himself understood this possibility, and
suggested that for the transition from laminar to turbulence for a pipe flow, the condition
must be of instability at certain size perturbations and stability at smaller perturbations.
The issue of transition in flows such Poiseuille flow until Reynolds numbers under the
critical value, must be due to instabilities at finite amplitude perturbations. For these flows
there was nothing relevant found concerning the eventual secondary stable motions,
moreover it seems that turbulence issue directly from primary flow, at a fixed Reynolds
number. These strong turbulence problems are quite difficult to approach and this gives
evidence that still is to be added more substance to the original Reynolds suggestion, after
one hundred years of stability studies. For this quite new theory, unifying with the classic
turbulence is far from being solving, but the recent challenges could open new research
directions.
Generally, the statistical idea of a flow is represented by a map:
x t X , X t 0 X (1)
That means X is mapped in x after a time t. In the continuum mechanics the relation (1) is
named flow, and it is a diffeomorphism of class Ck. Moreover, the relation (1) must satisfy
the following equation:
x

J det D t X det i
X j
(2)

where D denotes the derivation with respect to the reference configuration, in this case X.
The equation (2) implies two particles, X1 and X2, which occupy the same position x at a
moment. Non-topological behavior (like break up, for example) is not allowed.
With respect to X there is defined the basic measure of deformation, the deformation gradient,
F, namely the equation (3):
x

F X t X
T
, Fij i (3)
Xj

where X denotes differentiation with respect to X. According to equation (2), F is non

singular. The basic measure for the deformation with respect to x is the velocity gradient.
After defining the basic deformation of a material filament and the corresponding relation
for the area of an infinitesimal material surface, there can be defined the basic deformation
measures: the length deformation and surface deformation , with the following relations
(Ottino, 1989):
C : MM
, det F C 1 : NN
1/ 2 1/2
(4)
where C (=FTF) is the Cauchy-Green deformation tensor, and the vectors M,N - the orientation
versors in length and surface respectively, are defined by:
Influence of Simulation Parameters on the Excitable Media Behaviour The Case of Turbulent Mixing 421
dX dA
M , N (5)
dX dA
Very often, in practice is used the scalar form of (4), namely the following relation:
2 Cij Mi N j , 2 det F Cij 1 Mi N j (6)
where D is the deformation tensor, obtained by decomposing the velocity gradient in its
symmetric and non-symmetric part.
The flow x=t(X) has a good mixing if the mean values D(ln)/Dt and D(ln)/Dt are not
decreasing to zero, for any initial position P and any initial orientations M and N. As the
above two quantities are bounded, the deformation efficiency can be naturally quantified.
Thus, there is defined (Otino, 1989) the deformation efficiency in length, e = e (X,M,t) of the
material element dX, as follows:
D ln / Dt
e 1 (7)
D : D
1/ 2
Similarly, there is defined the deformation efficiency in surface, , e= e (X,N,t) of the area
element dA: in the case of an isochoric flow (the jacobian equal 1), there exists the equation
(8):
D ln / Dt
e 1 (8)
D : D
1/2
The deformation tensor F and the associated tensors C, C-1, form the fundamental
quantities for the analysis of deformation of infinitesimal elements. In most cases the flow
x t X is unknown and has to be obtained by integration from the Eulerian velocity
field. If this can be done analytically, then F can be obtained by differentiation of the flow
with respect to the material coordinates X. The flows of interest belong to two classes: i)
flows with a special form of v and ii) flows with a special form of F. The second class is
what we are interested for, as it contains the so-called Constant Stretch History Motion
CSHM.
2. Issues on turbulent mixing. Results and challenges

The central problem exhibited in this chapter is the challenge of unifying the theory of
turbulent mixing. This implies few levels: analytical, computational and experimental. The
specific literature is rich in works both on analytical and experimental models. There were
realized few comparative analysis, both for analytical and computational standpoint, for 2D
and 3D models of different flow types.
2.1. Recent issues in the literature

The recent discussions and works (Dimotakis, 1983) on the empirical evidence and
theoretical ansatz on turbulence support the notion that fullydeveloped turbulence
requires a minimum Reynolds of order of 104 to be sustained. This value must be viewed as
a necessary, but not sufficient condition for the flow to be fully developed. Presently
available evidence suggests that both the fact that the phenomenon occures and the range of
values of Reynolds number where it occures are universal, i.e. independent of the flow
geometry.
On the other hand, how sharp this transition is does appear to depend on the details of the
flow. In particular, it is considerable sharp, as a function of Reynolds number, in the
(Couette- Taylor) flow between concentric rotative cylinders. It is less well defined for a
shear layer and, among the flows considered, the least well defined for turbulent jets.
Perhaps an explanation for this variation lies in the definition of the Reynolds number itself
and the manner in which the various factors that enter are specified for each flow. In the
case of the Couette-Taylor flow, for example, both the the velocity UCT a and the
spatial scale CT b a ., where is the differential rotation rate, with a and b - the inner
and outer cylinder radii, are well-defined by the flow-boundary conditions.
In the case of a zero streamwise pressure gradient shear layer, the velocity
US U U1 U 2 is a constant, reasonably well specified by the flow boundary conditions
at a particular station. The length scale s s x must be regarded as a stochastic variable
1
1 1
in a given flow with a relatively large variance. The Reynolds number for the shear layer is
then the product of a well-defined variable and a less well-defined, stochastic, variable.
In the case of a turbulent jet, both the local velocity Uj and the scale j must be regarded as
stochastic flow variables, each with its own large variance. The Reynolds number for the jet
is then the product of two stochastic variables, and, as a consequence, its local,
instantaneous value is the least well-defined of the three.
As regards fully-developed turbulent flow, the presently available evidence does not
support the notion of Reynolds number independent mixing dynamics, at least in the
case of gas phase shear layers for which the investigations span a large enough range. In
the case of gas phase turbulent jets, presently available evidence admits a flame length
stoichiometric coefficient tending to a Reynolds number independent behaviour. It must
be noticed, however, that the range of Reynolds numbers spanned by experiments may not
be large enough to provide us with a definitive statement, at least as evidenced by the range
required in the case of shear layers.
In comparing shear layer with turbulent - jet mixing behavior, the more important
conclusion may be that they appear to respond in the opposite way to Schmidt number
effects, i.e. gas- vs liquid phase behavior. Specifically, there are high Schmidt number
(liquid phase) shear layers that exhibit a low Reynolds number dependence in chemical
product formation, if any. In contrast, there are gas- phase turbulent jets that exhibit an
almost Reynolds number independent normalized variance of the jet-fluid concentration

on the jet axis, with a strong Reynolds number dependence found in liquid phase jets, in
the same Reynolds number range.
To summarize, recent data on turbulent mixing suppport the notion that the fully -
developed turbulent flow requires a minimum Reynolds number of 104, or a Taylor
Reynolds number of ReT102 to be sustained. Conversely, turbulent flow below this
Reynolds number cannot be regarded as fully developed and can be expected to be
qualitatively different (Dimotakis 1983).
The manifestation of the transition to this state may depend on the particular flow
geometry, e.g. the appearance of streamwise vortices and three dimensionality in shear
layers. Neverless, the fact that such a transition occurs, as well as the approximate Reynolds
number where it is expected, appears to be a universal property of turbulence. It is observed
in a wide variety of flows and turbulent flow phenomena. (Dimotakis, 1983)
2.2. Recent results from experimental and computational / analytical standpoint

Recently, it was realized (Ionescu, 2002, 2010) the analysis of the length and surface
deformations efficiency for a mathematical 3D model associated to a vortexation
phenomena. The biological material used is the aquatic algae Spirulina Platensis.
The mathematical study was done in association with the experiments realized in a special
vortexation tube, closed at one end. Locally, there is produced a high intensity annular
vorticity zone, which is acting like a tornado. The small scale at which the turbulence issues
allows retaining the solid particles, mixing the textile fibbers or breaking up the multi-
cellular filaments of aquatic algae.
The special vortex tube used for achieving the breaking up of filaments is a modified
version at low pressure of a Ranque-Hilsch tube (Savulescu, 1998). Completely closing an
end of the tube, there is obtained in this region a high intensity swirl. The flow in the tube is
generally like a swirl, with a rate tangential velocity / axial velocity maxim near the closed
end, where is also created the annular vortex structure.
The approaching aerodynamic circuit is made from: a pressure source, the box of tangential
inputs, the diffusion zone, the tube where there is produced the swirl with additional
pollutants inputs, and the closing end with a rotating end.
It must be noticed that this torrential flow is concentrating and intensifying the vorticity, in
contrast with the usual cyclone-type flow or other flows generators. If in the installation is
introduced a pollutant, there issues a turbulent mixing in the annular vorticity zone. The
spatial and temporal scales revealed the existence of different domains, starting with
laboratory ones and until dissipative domains or others - corresponding to fine structure
wave numbers. Thus, the applications area is very large, including collecting, aggregating,
separating and fragmenting the various pollutants.
From physical standpoint (Savulescu, 1998), the vortex produced in the installation implies
four mechanisms:
- Convection (scalar transport), due to streamlines which are directed towards the ending
lid near the tube walls, with the pressure source near the tube centre line;
- Turbulent diffusion due to the pressure and velocity variation;
- Stratification effects due to pressure and temperature gradients;
- Turbulent mixing due to the velocity concentration in annular structures.
The convection keeps in the transport and deposit of the powder pollutant when the
graining diameter is greater than 5m. However, the graining spectra domain under 5m
undergoes a turbulent diffusion and stratification effects which are generally out of control.
For revealing the local concentration of the streamlines, 2D simplified models were tested.
The multiphase 3D flows simulation is still in study.
The turbulent mixing in multiphase flow reveals the following experiment components:
- The topological limit of the multiphase flow when the pollutant enters in the
aggregation state or remains fragmented, in the host fluid;
- The rheological behaviour of non-Newtonian compositions, under macroscopic effects
of the air velocity.
The installation was realized in two versions: a small scale vortex tube (10-20mm diameter)
and a large scale one (100-300mm). They correspond generally at two particles processing
classes, although in most cases the classes can be superposed.
The first category refers to collecting and separating various powders, from gaseous
emissions to ceramic powders. The parameters which must be taken into account are the
graining spectra, the atmosphere nature and concentration. The vorticity concentration can
be used for processing the deposit of different particles in powder or cement form by an
adequate closing lid.
The second category contains the processing on small scale, including deformation and
breaking up mechanisms for various particles in a host fluid. It is studied the vorticity
concentration near the closing lid.
During such an experiment (Ionescu, 2002), it was processed the aquatic algae Spirulina
Platensis in the host fluid water. After the processing, the long chains of cellular filaments
were fragmented, producing isolated cell units or sometimes there was recorded the
breaking up of some cellular membranes (with less than 100 Angstrom thickness). The initial
and final observations (after the vortexation) are exhibited in figure 1 below. It has been
t Q
used the non-dimensional parameter a 3 , where t represents the time (in seconds), Q
D
the installation debit (m3/sec) and D the diameter (m3). As it can be seen from the picture,
the fragmentation degree starts to increase as a grows. There can also be observed the algae
form before and after the fragmentation.
Following the opinion of the specialists in cellular biology, this new technological method of
processing the flows is more efficient than the classical centrifugation method.
Figure 1. The fragmentation degree variation of Spirulina Platensis
Three specific applications were performed as fluid waste management:
the agglomeration of short fibers (aerodynamic spinning);

the retention of particles under 5m without any material filter;
the breakout of cell membranes of the phytoplankton from polluted waters and the
providing of a cell content solution with important bio-stimulating features.
The mathematical modeling and analytically testing of the above experiment confirmed the
experimental study. Concerning the phenomenon scale, there were taken into account
medium helicoidally streamlines with approximating 10m width. There were not gone further
to molecular level. Also, it is important to notice that for this moment of the analytical testing
of the model, there has not been studied the influence of strictly biological parameters (such
as pH, the temperature, the humidity, etc).
The complex multiphase flow necessarily implies a theoretical approach for discovering the
ways of optimization, developing and control of the installation. Numeric simulation of 3D
multiphase flows is currently in study. In the mathematical framework, the flow complexity
implies the following three stages:
modeling the global swirling streamlines;

local modeling of the concentrated vorticity structure;
introducing the elements of chaotic turbulence.
The mathematical model associated to the vortex phenomena is, basically, the 3D version of
the widespread isochoric two-dimensional flow (Ottino, 1989):
.
x1 G x2
. (9)
x K G x , 1 K 1, G 0
2 1
Namely, the following vortex flow model is in study:
.
x1 G x2
.

x2 K G x1 , 1 K 1, c const. (10)
.
x c
3
In the first stage, the flow model (10) was studied from the analytical standpoint. Namely,
the solution of the Cauchy problem associated to (10) was found. In order to analyze the
length and surface deformations of algae filaments in certain vortex conditions, the Cauchy-
Green deformation tensor was calculated. There were obtained quite complex formulas for
e , e (Ionescu 2002, 2010).
The second stage has been a computational / simulation standpoint. It has been realized a
computational analysis of the length and surface deformation efficiency, in some specific
vortexation conditions. With the numeric soft MAPLE11, the analysis has been two parts.
Firstly, the following Cauchy problems has been solved:
e t 0, x 0 0
(11)
e t 0, x 0 0
using a discrete numeric calculus procedure (Abell, 2005). The output of the procedure is a

listing of the form ti , x ti , i 0..25 . In the second part there have been realized discrete
time plots, in 25 time units, following the listings obtained in the first part. The plots
represent in fact the image of the length and surface deformations, in the established scale time.
Very few irrational value sets were chosen for the length, respectively surface versors, taking
into account the versor condition:
Mi 1, N j 1 (12)
The studied cases are in fact represented by the events associated to different values of
length and surface orientation versors: M1 , M2 , M3 and N1 , N 2 , N 3 for length and
surface respectively. The events were very few, about 60. Their statistical interpretation is
synthesized in (Ionescu 2010), including also the two-dimensional case.
The graphical events are illustrating the analysis of the deformations for Spirulina Platensis,
in 25 time units vortexation. According to (Ionescu 2001, Ottino 1989), the algae filaments
represent Lagrange markers. The special spiral form of the algae gives the answer to the
computational context that the surface deformation e is significant, since it brings more cases
of filaments break up. It was called rare event the event of very sudden breaking up of the
algae filaments, this corresponding from mathematical standpoint to the break out of the
program (because of impossibility of maintaining the required accuracy). Thus, a very
important fact happened: the mathematical simulations matched the experimental analysis.
Sumarising these basic stages in the behavior analysis of the turbulent mixing flow, is
important to notice that the filaments breaking up is due to alternating loadings that the
filament undergoes, in a space-time with random events, available to the break phenomena.
The modeling has been the following basic stages:
Associating known streamlines to the medium flow (that means helical flow in a
cylinder);
Determining the linear and surface deformations from continuum fluid mechanics;
Associating a sequence of random values to the (vectorial) length and surface
orientations.
In fact, there were found four types of processes, all of which were matched by the
simulations
1. Processes with relative linear behavior;

2. Linear-negative processes, which correspond to alternate tasks of stretching and folding
of filaments and are the most;
3. Mixing phenomena where there issue smaller or larger deviations or strong
discontinuities; these concern the situations when some pieces are suddenly coming
off from the whole filament, followed by the restarting of vortexation for the rest of
algae;
4. Rare events these correspond to the turbulent mixing and represent the sudden break
up of spirulina filaments.
The validity of the model is confirmed by two aspects:
the statistic increment in time of the breaking cases, according to the experiments;
the relative singularity of the events which could produce the breaking, fact which is
confirmed by the quite long duration of the experiments which led to the filaments
break up; in very rare cases, the cellular membrane could be broken, and the cellular
content collected.
Crossing over from 2D to 3D case, it is easy to deduce the requirement of a special analysis
of the influence of parameters on the behavior of this complex mixing flow. This would
include more paramater analysis types for some perturbation models in 2D and 3D case, but
also another mathematical analysis types, for example spectral analysis.
2.3. New influence of simulation parameters

The analysis recently has been continued with more computational simulations, for 2D
model, both in periodic and non periodic case, and for 3D model, too. A lot of
comparisons between periodic and non- periodic case, 2D and 3D case were realized
(Ionescu 2008, 2009). In the same time, the computational appliances were varied. If
innitialy, the model was studied from the standpoint of mixing efficiency, in the works that
come after, new appliances of the MAPLE11 soft were tested (Abell 2005, Ionescu 2011), in
order to collect more statistical data for the turbulent mixing theory. In what follows, few of
these appliances are described.
2.3.1. Few MAPLE11 apliances used in simulations

For the purpose of this chapter, there are presented only the recent used appliances of
MAPLE11 soft. There have been used two graphical appliances of this soft, namely DePlot
and Phaseportrait tools, from DETools package. Both of them are based on numeric
methods in producing trajectories of differential equations systems. The most used numeric
method is Fehlberg fourth-fifth order Runge-Kutta method - the so-called rkf45 method - with
degree four interpolant (Abell 2005).
DETools[DePlot] this tool plots solutions to a system of differential equations. The calling
sequences are as follows:
DEplot(deqns, vars, trange, options)
DEplot(deqns, vars, trange, inits, options)
DEplot(deqns, vars, trange, xrange, yrange, options)
DEplot(deqns, vars, trange, inits, xrange, yrange, options)
DEplot(dproc, vars, trange, number, xrange, yrange, options)
Parameters:
deqns - list or set of first order ordinary differential equations, or a single differential
equation of any order;
dproc - a Maple procedure representation for first order ordinary differential equations,
or a single differential equation of any order;
vars - dependent variable, or list or set of dependent variables;
trange - range of the independent variable;
number - equation of the form 'number'=integer indicating the number of differential

equations when deqns is given as a function (dproc) instead of expressions;
inits - set or list of lists; initial conditions for solution curves;
xrange - range of the first dependent variable;
yrange - range of the second dependent variable;
options - (optional) equations of the form keyword=value;

Description:
Given a set or list of initial conditions (see below), and a system of first order
differential equations or a single higher order differential equation, DEplot plots
solution curves, by numerical methods. This means that the initial conditions of the
problem must be given in standard form, that is, the function values and all
derivatives up to one less than the differential order of the differential equation at the
same point.
A system of two first order differential equations produces a direction field plot,
provided the system is determined to be autonomous. In addition, a single first order
differential equation produces a direction field (as it can always be mapped to a system
of two first order autonomous differential equations). A system is determined to be
autonomous when all terms and factors, other than the differential, are free of the
independent variable. For systems not meeting these criteria, no direction field is
produced (only solution curves are possible in such instances). There can be only one
independent variable
The default method of integration is method=rkf45. Other methods can be specified in
the optional equations. Note that because numerical methods are used to generate plots,
the output is subject to the characteristics of the numerical method in use. In particular,
unusual output may occur when dealing with asymptotes.
The direction field presented consists of either a grid of arrows or a set of randomly
generated arrows. In either case, the arrows are tangential to solution curves. For each
grid point, the arrow centered at (x,y) has slope dy/dx. This slope is computed using
(dy/dt)/(dx/dt), where these two derivatives are specified in the first argument to
DEplot. The curved arrow types (curves and comet) require additional data for the
curvature of the direction field, which is computed by moving an epsilon in the
direction of the slope dy/dx, and computing dy/dx, then moving an epsilon in the
direction opposite the slope, and computing dy/dx. This data is then sufficient to draw a
small portion of the direction field lines local to the point, which is then used to draw
the curved arrows.
By default, the two dependent variables are plotted, unless otherwise specified in the
scene option.
The deqns parameter can be given as a procedure, but must conform to the
specification as given in dsolve/numeric, and the number option must be included
before the initial conditions. In this instance, deqns must be of the form:
proc( N, ivar, Y, YP )
...
YP[1] := f1(ivar,Y);
YP[2] := f2(ivar,Y);
...
end proc
where N represents the number of first order equations, ivar is the independent variable, Y
is a vector of length N, and YP is a vector of derivatives which is updated by the procedure
(for the equivalent first order system), also of length N.
The inits parameter must be specified as:

[ [x(t0)=x0,y(t0)=y0], [x(t1)=x1,y(t1)=y1], ... ]
[ [y(t0)=y0], [y(t1)=y1], ... ]
[ y(t0)=y0, y(t1)=y1, ... ]
where, in the above, sets can be used in place of lists, or
[ [t0,x0,y0], [t1,x1,y1], ... ]
{ [t0,x0,y0], [t1,x1,y1], ... }
[ [t0,x0], [t1,x1], ... ]
where the above is a list or set of lists, each sublist specifying one group of initial conditions.
The xrange and yrange parameters must be specified as follows.
x(t) = x1..x2, y(t) = y1..y2 or
x = x1..x2, y = y1..y2
More details about the parameters can be found in (Abell 2005).
DETools[Phaseportrait]. This tool has the following parameters:
deqns - list or set of first order ordinary differential equations, or a single differential
equation of any order;
vars - dependent variable, or list or set of dependent variables;
trange - range of the independent variable;
inits - set or list of lists; initial conditions for solution curves;
options - (optional) equations of the form keyword=value;
Description
Given a list (or set) of initial conditions (see below), and a system of first order
differential equations or a single higher order differential equation, phaseportrait plots
solution curves, by numerical methods. This means that the initial conditions of the
problem must be given in standard form, that is, the function values and all derivatives
up to one less than the differential order of the differential equation at the same point.
A system of two first order differential equations also produces a direction field plot,
provided the system is determined to be autonomous. In addition, a single first order
differential equation also produces a direction field (as it can always be mapped to a
system of two first order autonomous differential equations). For systems not meeting
these criteria, no direction field is produced (only solution curves are possible in such
instances). There can be ONLY one independent variable.
All of the properties and options available in phaseportrait are also found in Deplot .
inits should be specified as
[ [x(t0)=x0,y(t0)=y0], [x(t1)=x1,y(t1)=y1], ... ]
where the above is a list (or set) of lists, each sublist specifying one group of initial
conditions.
2.3.2. Comparative computational analysis

In what follows there is presented the comparative analysis for 2D and 3D mixing flow
models. There are followed two main leves of comparison:
i. The 2D (non-periodic) mixing flow, namely the differential system (9):
.
x1 G x2
.

x2 K G x1 , 1 K 1, G 0
in comparison with a perturbed version of it, the system (13):
.
x1 G x2 x1
. (13)
x K G x G x x
2 1 2 1
ii. The 3D mixing flow model (10)
.
x1 G x2
.

x2 K G x1 , 1 K 1, c const.
.
x c
3
For all models it is used the same set of parameter values (G, KG) as used in (Ionescu 2008),
containing three simulation cases:
- case1: G 0.25, K G 0.035 ;

- case2: G 0.755, K G 0.65 ;
- case3: G 0.85, K G 0.25
Each simulation case is labelled on the figure. The time units number was succesively
increased, in order to better analyse the solution behavior for each model and corresponding
case. The stepsize option for the rkf45 numeric method, on which the Phaseportrait
procedure is based, is implicitely assigned to 0.05. Also, it must be noticed that the above
choice of parameters (one positive and another negative) is optimal for analyzing the
direction field associated to the models solutions.
The scene parameter of the graphic procedure was set to {x(t), y(t)], the same in 2D and in 3D
case.
Figure 2. Case1 of simulation for the model (9). Time units number: t= 0..40
Figure 3. Case1 of simulation for the model (9) with t=0..100. The movement is realized on the same
trajectory
Figure 4. Case2 of simulation for the model (9). The time units number t=0..40
Figure 5. Case2 of simulation for the model (9) with t=0..100. The trajectory tends to aggregate
towards the origin.
Figure 6. Case3 of simulation for the model (9). Time units number t=0.40
Figure 7. Case3 of simulation for the model (9) with t=0..100. The trajectory multiplies but does not
draw near the origin
Figure 8. Case1 of simulation for the model (13). The trajectory changes, it seems to be no longer
periodic, but tends to infinity
Figure 9. Case2 of simulation for the model (13). The time units number t=0..40. The trajectory changes
again and becomes negative
Figure 10. Case2 of simulation for the model (13), with t=0..100.
Figure 11. Case2 of simulation for the model (13) with t=0..200
Figure 12. Case3 of simulation for the model (13), t=0..40. The trajectory becomes positive
Figure 14. Case3 of simulation for the model (13) with t=0..200. The program does not show the field
arrows anymore.
Figure 15. Case1 of simulation for the model (10). Time units number t=0..25
Figure 17. Case2 of simulation for the model (10), t=0..25. A periodic behaviour of the trajectory
Figure 18. Case2 of simulation for the model (10), t=0..75
Figure 19. Case3 of simulation for the model (10), time t=0..25
Figure 20. Case3 of simulation for the model (10), time t=0..75. The circular loops are fewer than in
the case2, for the same simulation time.
Figure 21. Case3 of simulation for the model (10) with t=0..100.
3. Remarks on the simulations and Maple appliances importance

Looking above to the figures, it is important to notice some special features.
It must be pointed out the advance of the phaseportrait appliance of Maple soft, and
generally of the plots package. The possibility of increasing step by step the
simulation time units offers important features of the analysis and consequently of the
model behaviour. For example in fig.3, when time increases, the trajectory moves on
the same line. Comparing to this, in fig.4 the trajectory has some tracks which
overcrowd towards the origin. In case 3, for the same simulation time, the trajectory
only multiplies and does not came toward the origin. Also, figures 8-10 illustrate in a
good manner the influence of time increasing on the trajectory behaviour: this can be
seen from the values variation of x(t) and y(t) on the axes.
All the simulations for 2D case model have been realized in the same initial conditions:
(x(t), y(t)) = (1,1). This gives more accuracy for the graphical comparisons. Applying this
procedure step by step gives the possibility to have a total parameter control at every
stage of simulation. In 3D case the initial conditions were a little modified: (x(t, y(t),
z(t))=(1,0,0). It was taken into account the fact that on the z axis is represented the
velocity and is natural that the mixing process starts from a zero velocity
Also, the scene parameter was the same: [x(t), y(t)] both in 2D and 3D case. That
means in 3D case, the trajectory is studied by watching it from the z axis. The field
arrows are an important appliance of this plot tool, as they are very suggestive
concerning the trajectory features. In this context it is extremely important to notice the
figure 13. In this model (simulation case3), when increasing the time, the field arrows
disappear, the program doesnt show them anymore. This can be glossed like a lose of
equilibrium for the 2D model, in certain parameter context, and this fact can be easily
observed from the great values for x(t) and y(t) on the axis
In figures 8-13 it must be noticed a similarity with the pictures obtained in (Ionescu,
2008), where the origin becomes an unstable focus. It is observed here that when
increasing the time, e.g. in Fig. 10, the trajectory does not go periodic, it changes only
the positivity.
A special attention must be paid for the figure 17, 3D simulation case. For t=0..75 units,
and looking to the trajectory from above, from the z axis, it is obvious that the vorticity
of the flow appears. It is very important to notice that if in (Ionescu 2002, 2010), when
searching for the mixing efficiency, there were necessary small time units for get the
special events of losing the equilibrium of the model, in this case, searching for the
phaseportrait needs some more time units, in order to get visible vorticity of the flow.
The vorticity allure is also visible in the figures 18-20, with some changes in the loops
number and their nearness to the origin.
4. Conclusion
Looking on the above computational analysis, some conclusions issue: regarding the above
comparative analysis, on one hand, and, concerning the general context of random events that
go with the mixing flow phenomena, on the other hand.
Looking at the above pictures, we see that each simulation case brings significant
differences:
For the modified (perturbed) 2D model, just from the case1 of simulation we see that
the trajectory has a great change. It is not periodic anymore like in the initial 2D model,
but is more evident its trend to infinity, just from the beginning of the simulation. The
parameters have a great influence in this sense
Concerning the 3D model, it is obvious that the field arrows could not appear, since
there is a 3D simulation. Instead, the scene parameter was chosen to [x(t), y(t)], like in
2D case model. This is optimal for studying the trajectory behaviour, since it is like we
look at the trajectory from above. The scene parameter is important in analysis, and a
further aim would be to change it in the simulations and make some other comparative
graphical analysis
Concerning the general context of random events that go with the mixing flow phenomena,
the above analysis just brings at that some important conclusions:
It is obvious that the above analysis confirms the fact that the mixing flow model is
a far from equilibrium model. This is confirmed by the number of parameter / time
units analysis. Using different appliances mixing efficiency and computational /
graphical appliances, the conclusion is the same: the model becomes far from
equilibrium, in certain simulation conditions. It must be noticed that the units of
time can be of any type, sufficiently small or large. It depends to the target of the
analysis. Enlarging the set of parameter values would bring another important data
for completing the panel of repetitive events. This would be a next aim. All this
space-time context present in all these analysis, consolidates the basic statement
that the turbulent mixing flows must be approached as chaotic systems. This is in fact
regaining the idea of a system / model high sensitive to initial conditions (Ionescu
2009).
Testing step by step each of the three models above was possible due to the flexible
structure of the MAPLE11 graphical / computational appliances. In the same time this
shows that these repetitive simulations are relatively easy to perform. Maybe useful
comments would produce if sharing some of these files.
Also the step by step analysis guides the reader by successive steps, to the so- called
far from equilibrium model, by the possibility of sensitive modifying the model
parameters and the time at each step of simulation.
The issues of repetitive phenomena, both in 2D and 3D case, give rises to achieve some
appliances of chaotic dynamical systems, whose numeric models would give new
research directions on the behavior in excitable media. This would be a next aim
Author details
Adela Ionescu
University of Craiova, Romania
Acknowledgement
The basic part of my work in turbulent mixing was done in the period of my Ph. D. thesis at
the Polytechnic University of Bucarest Romania. Fruitful experiments and special
discussions were done togheter with the scientific team of the Institute of Applied Ecology,
Bucarest. I am grateful to them.
But my entire acknowledgement points to Ph. D. Prof. Eng. Stefan Savulescu, from
Politechnic University of Bucarest. Without the special vortexation installation constructed
by him, the mixing flow experiments could not be possible. Due to his great experience in
the turbulence field, and his fundamental observations, advices and suggestions, my work
in turbulent mixing have an important sense and the great challenge of unifying the
turbulence theory takes shape.
5. References
Abell, L. Martha.& Braselton, P. James. (2005). Maple by Example. 3rd edition. Elsevier
Academic Press, ISBN 0-12- 088526-3, San Diego, California
Dimotakis, P. E., Miake-Lye, R. C., and Papantoniou, D. A. (1983). Structure and Dynamics
of Round Turbulent Jets. Phys. Fluids 26, ISSN 3185-3192
Ionescu, A. (2002). The structural stability of biological oscillators. Analytical contributions,
InTech, Ph.D. thesis, Politechnic University of Bucarest, Romania
Ionescu, A. (2010). Recent trends in computational modeling of excitable media dynamics. New
computational challengs in fluid dynamics analysis, Lambert Academic Press , ISBN 978-3-
8383-9316-2 Saarbrucken, Germany
Ionescu, A. & Costescu, M. (2008). The influence of parameters on the phaseportrait in the
mixing model. Int. J. of Computers, Communications and Control, vol III, Suppl. issue:
Proceedings of IJCCCC2008, pp. 333-337, ISSN 1841-9836
Ionescu, A. (2009). Recent challenges in turbulence: computational features of turbulent
mixing. Recent advances in Continuum Mechanics. Proceedings of the 4th IASME/WSEAS
International Conference, (Mathematics and Computers in Science and Engineering). ISSN
1790-2769, Cambridge U.K., 24-26 feb 2009
Ionescu, A. & Coman, D. (2011). New approaches in computational dynamics of mixing
flow. In http://dx.doi.org/10.1016/j.amc.2011.03.142
Ottino, J.M. (1989). The kinematics of mixing: stretching, chaos and transport, Cambridge
University Press. ISBN .0-521-36878-2, UK
Savulescu, St. N. (1998) Applications of multiple flows in a vortex tube closed at one end,
Internal Reports, CCTE, IAE (Institute of Applied Ecology) Bucarest, Romania
Chapter 17
ECOP Criterion for Irreversible

Three-Heat-Source Absorption Refrigerators
Paiguy Armand Ngouateu Wouagfack and Rn Tchinda
1. Introduction
In this chapter, the optimization analysis based on the new thermo-ecological criterion
(ECOP) first performed by Ust et al. [1] for the heat engines is extended to an irreversible
three-heat-source absorption refrigerator. The thermo-ecological objective function ECOP
is optimized with respect to the temperatures of the working fluid. The maximum ECOP
and the corresponding optimal temperatures of the working fluid, coefficient of
performance, specific cooling load, specific entropy generation rate and heat-transfer
surface areas in the exchangers are then derived analytically. Comparative analysis with
the COP criterion is carried out to prove the utility of the ecological coefficient of
performance criterion.
2. Thermodynamics analysis
The main components of an absorption refrigeration system are a generator, an absorber,
a. condenser and an evaporator as shown schematically in Fig. 1 [2]. In the shown model, .
QH is. the rate of absorbed heat from the heat source at temperature TH to generator, QC
and Q A are, respectively, the heat rejection rates
.
from the condenser and absorber to the
heat sinks at temperatures TC and TA and Q L is the heat input rate from the cooling
space at temperature TL to the evaporator. In absorption refrigeration systems, usually
NH3/H2O and LiBr/H2O are used as the working substances, and these substances abide
by ozone depletion regulations, since they do not consist of chlorofluorocarbons. In Fig. 1,
the liquid rich solution at state 1 is pressurized to state 1 with a pump. In the generator,
the working
.
fluid is concentrated to state 3 by evaporating the working medium by means
of QH heat rate input. The weak solution at state 2 passes through the expansion valve
into the absorber with a pressure reduction (22). In the condenser, the working fluid at
.
state 3 is condensed to state 4 by removing QC heat rate. The condensed working fluid at
state 4 is then throttled by a valve and enters the evaporator
.
at state 4. The liquid
working fluid is evaporated due to heat transfer rate Q L from the cooling space to the
working fluid (45). Finally, the vaporized.
working fluid is absorbed by the weak
solution in the absorber, and by means of Q A heat rate release in the absorber, state 1 is
reached.
Work input required by the solution pump in the system is negligible relative to the energy
input to the generator and is often neglected for the purpose of analysis. Under such
assumption, the equation for the first law of thermodynamics is written as:
. . . .
Q H + Q L - QC - Q A = 0 (1)
Absorption refrigeration systems operate between three temperature levels, if TA = TC , or

four temperature levels when TA TC . In this chapter, by taking TA = TC , the cycle of the
working fluid consists of three irreversible isothermal and three irreversible adiabatic
processes. The temperatures of the working fluid in the three isothermal processes are
different from those of the external heat reservoirs so that heat is transferred under a finite
temperature difference, as shown in Fig. 2 where
. . .
QO = QC + Q A (2)
T1 and T2 are, respectively, the temperatures of the working fluid in the generator and
evaporator. It is assumed
.
that the working fluid in the condenser and absorber has the same
temperature T3 [2]. Q LC is the heat leak from the heat sink to the cooled space.
The heat exchanges between the working fluid and heat reservoirs obey a linear heat
transfer law, so that the heat-transfer equations in the generator, evaporator, condenser and
absorber are, respectively, expressed as follows:
.
Q H = U H AH (TH - T1 ) (3)
.
Q L = U L AL (TL - T2 ) (4)
.
QO = UO ( AA + AC )(T3 - TO ) (5)
where AH , AL , AC and AA are, respectively, the heat-transfer areas of the generator,

evaporator, condenser and absorber, UH and U L are, respectively, the overall heat-transfer
coefficients of the generator and evaporator, and it is assumed that the condenser and
absorber have the same overall heat-transfer coefficient UO [2].
ECOP Criterion for Irreversible Three-Heat-Source Absorption Refrigerators 447
Figure 1. Schematic diagram of absorption refrigeration system [2]
Figure 2. Considered irreversible absorption refrigeration model and its TS diagram.

The absorption refrigeration system does not exchange heat with other external reservoirs
except for the three heat reservoirs at temperatures TH , TL and TO , so the total heat-transfer
area between the cycle system and the external heat reservoirs is given by the relationships:
A = AH + AL + AO (6)
where
AO = AC + AA . (7)
.
The rate of heat leakage Q LC from the heat sink at temperature TO to the cold reservoir at
temperature TL was first provided by Bejan [3] and it is given as:
.
Q LC = K LC (TO - TL ) (8)
where K LC is the heat leak coefficient.
Real absorption refrigerators are complex devices and suffer from a series of irreversibilities.
Besides the irreversibility of finite rate heat transfer which is considered in the
endoreversible cycle models and the heat leak from the heat sink to the cooled space, there
also exist other sources of irreversibility. The internal irreversibilities that result from
friction, mass transfer and other working fluid dissipations are an another main source of
irreversibility, which can decrease the coefficient of performance and the cooling load of
absorption refrigerators. The total eect of the internal irreversibilities on the working fluid
can be characterized in terms of entropy production. An irreversibility factor is introduced
to describe these internal irreversibilities:
DS3
I= (9)
DS1 + DS2
On the basis of the second law of thermodynamics, DS3 > DS1 + DS2 for an internally
irreversible cycle, so that I > 1 . If the internal irreversibility is neglected, the cycle is
endoreversible and so I = 1 . The second law of thermodynamics for an irreversible three-
heat-source cycle requires that:
. . . .
d Q Q H Q L QO
T
=
T1
+
T2
-
T3
0 (10)
From Eq. (9), the inequality in Eq. (10) is written as:
. . .
QH Q L QO
+ - =0 (11)
T1 T2 IT3
The coefficient of performance of the irreversible three-heat-source absorption refrigerator is:
. . . .

Q L - Q LC Q L Q LC
COP = = . 1 - . (12)
.

QH Q H Q L
From Eq. (6), it is expressed as:
A
AL = (13)
AH A
1+ + O
AL AL
Using Eqs. (3)-(5), Eq. (13) is rewritten as:
A
AL = . .
(14)
QH U L (TL - T2 ) QO U L (TL - T2 )
1+ +
.
U H (TH - T1 ) .
UO (T3 - TO )
QL QL
Combining Eqs. (1) and (11), the following ratios are derived:
.
QL T2 (T1 - IT3 )
= (15)
.
T1 ( IT3 - T2 )
QH
.
QO IT3 (T1 - T2 )
= (16)
.
QL
(T1 - IT3 )T2
The first is the coefficient of performance of the irreversible three-heat-source absorption
refrigeration cycle without heat leak losses.
Substituting Eqs. (15) and (16) into Eq. (14), the heat-transfer area of the evaporator is
expressed as a function of T1 , T2 and T3 for a given total heat-transfer areas :
A
AL = (17)
U LT1 ( IT3 - T2 )(TL - T2 ) U L IT3 (T1 - T2 )(TL - T2 )
1+ +
U H (TH - T1 )(T1 - IT3 )T2 UO (T3 - TO )(T1 - IT3 )T2
By investigating similar reasoning, the heat-transfer areas of the generator and of condenser
and absorber are given respectively by:
A
AH = (18)
U HT2 (T1 - IT3 )(TH - T1 ) U H IT3 (T1 - T2 )(TH - T1 )
1+ +
U LT1 ( IT3 - T2 )(TL - T2 ) UOT1 ( IT3 - T2 )(T3 - TO )
and
A
AO = (19)
UOT1 ( IT3 - T2 )(T3 - TO ) UOT2 (T1 - IT3 )(T3 - TO )
1+ +
U H IT3 (T1 - T2 )(TH - T1 ) U L IT3 (T1 - T2 )(TL - T2 )
Substituting Eq. (17) into Eq. (4):
.
A
QL = (20)
1 T1 ( IT3 - T2 ) IT3 (T1 - T2 )
+ +
U L (TL - T2 ) U H (TH - T1 )(T1 - IT3 )T2 UO (T3 - TO )(T1 - IT3 )T2
Combining Eqs. (8), (12), (15) and (20), the coefficient of performance of the irreversible
three-heat-source refrigerator as a function of the temperatures T1 , T2 and T3 of the
working fluid in the generator, evaporator, condenser and absorber is obtained:
T2 (T1 - IT3 ) T1 ( IT3 - T2 ) IT3 (T1 - T2 )

COP = 1 - x (T - T ) 1
+ +

T1 ( IT3 - T2 )
U L (TL - T2 ) U H (TH - T1 )(T1 - IT3 )T2 UO (T3 - TO )(T1 - IT3 )T2
O L

(21)
where the parameter
K LC
x= (22)
A
represents the heat leakage coefficient and its dimension is w/(Km2)
The specific cooling load of the irreversible three-heat-source refrigerator is deduced as:
-1
. .
Q - Q LC 1 T1 ( IT3 - T2 ) IT3 (T1 - T2 ) - x T -T
r= L = + + ( O L)
A U L (TL - T2 ) U H (TH - T1 )(T1 - IT3 )T2 UO (T3 - TO )(T1 - IT3 )T2
(23)
The specific entropy production rate of the irreversible three-heat-source absorption

refrigerator is:
. . . . .
QO - Q LC Q H Q L - Q LC
. - -
s TO TH TL
s= = (24)
A A
Using Eq. (1) s is rewritten as:

. . . .
1 1 Q 1 1 Q H Q L 1 1 Q
s = - LC + - . + - L (25)

TL TO A TO TH A TO TL A
QL
or
. . .
1 1 Q H 1 1 Q - Q LC
s = - + - L (26)
TO TH A TO TL A
Substituting Eqs.(8), (15) and (20) into Eq. (25), the specific entropy production rate as a
function of T1 , T2 and T3 is given by :
erT1 ( IT3 - T2 ) T1 ( IT3 - T2 ) IT3 (T1 - T2 ) -1

1 1
s = -
1
x (TO - TL ) - 1 - + +
TL TO T2 (T1 - IT3 ) U L (TL - T2 ) U H (TH - T1 )(T1 - IT3 )T2 U O (T3 - TO )(T1 - IT3 )T2

(27)
where

1 - TO

TH
er = (28)
T
O - 1
T
L
is the coefficient of performance for reversible three-heat-source refrigerator.
According to the definition of the general thermo-ecological criterion function for different
heat engine models [4-9], a two-heat-source refrigerator [10, 11] and three-heat-source
absorption refrigerator [2], the new thermo-ecological objective function called ecological
coefficient of performance (ECOP) of an absorption refrigerator is defined as:
. . . .
Q L - Q LC Q - Q LC
ECOP = .
= L (29)
ATenv s
Tenv s
Putting Eq.(26) into Eq. (29):
1
ECOP = (30)
1 1 1 1 1
Tenv - + -
TO TH TO TL COP
When Eq. (21) is put in Eq. (30), the ecological coefficient of performance of the irreversible
three-heat-source absorption refrigerator as a function of T1 , T2 and T3 is derived as :
ECOP =
(
Tenv TO-1 - TL-1 )
-1
erT1 ( IT3 - T2 )
1 T1 ( IT3 - T2 ) IT3 (T1 - T2 )

1- 1 - x (TO - TL ) + +
T2 (T1 - IT3 ) U L (TL - T2 ) U H (TH - T1 )(T1 - IT3 )T2 UO (T3 - TO )(T1 - IT3 )T2

(31)
where Tenv is the temperature in the environment conditions.
3. Performance optimization for a three-heat-source irreversible

absorption refrigerator based on ECOP criterion
The ECOP function given in Eq. (31) is plotted with respect to the working fluid temperatures
( T1 , T2 and T3 ) for different internal irreversibility parameters as shown in Fig. 3(a), (b) and
(c). As it can be seen from the figure, there exists a specific T1 , T2 and T3 that maximize the
ECOP function for given I and x values. Therefore, Eq. (31) can be maximized (or optimized)
with respect to T1 , T2 and T3 . The optimization is carried out analytically.
Figure 3. Variation of the ECOP objective function with respect to T1 (a), T2 (b) and T3 (c) for
different I values ( TG = 403K , TL = 273K , TO = 303K , Tenv = 290 K , UG = 1163 W / m 2 K ,
U E = 2326 W / m 2 K , UO = 4650 W / m 2 K , K L = 1082 W / K , A = 1100 m2 )
For the sake of convenience, let
IT3
x= (32)
T1
IT3
y= (33)
T2
z = IT3 (34)
Then Eq. (31) is rewritten as:
ECOP =
(
Tenv TO -1
- TL-1 )
-1
er ( y - 1)
y x ( y - 1) y-x

1- 1 - x (TO - TE ) + +
1 - x U L (TL y - z) U H (TH x - z)(1 - x) U ( z - T )(1 - x)

(35)
where
T = ITO (36)
and
UO
U= . (37)
I
Starting from Eq. (35), the extremal conditions:
ECOP
=0 (38)
x
ECOP
=0 (39)
y
ECOP
=0 (40)
z
give respectively:
1 y 1 z ( y - 1)
- - - =0 (41)
x (TO - TE ) U L (TL y - z) U ( z - T ) U (T x - z)2
H H
1 y 1 z ( y - 1)
- - - =0 (42)
x (TO - TE ) U L (TL y - z) U ( z - T ) U (T y - z)2
L L
y (1 - x) x ( y - 1) y-x
+ - =0 (43)
U L (TL y - z) U H (TH x - z) U (z - T )
2 2 2
Combining Eqs (41)-(43), the following general relation is found:
U H (TH x - z) = U L (TL y - z) = U ( z - T ) (44)
From Eqs (44), it is derived as:
(1 + b1 ) z b1T
x= - (45)
TH TH
(1 + b2 ) z b2T
y= - (46)
TL TL
where
U
b1 = (47)
UH
U
b2 = (48)
UL
When Eqs. (45) and (46) are substituted into Eq. (43):
D + b2
z =T (49)
1 + b2
where
T (1 - d1 )
1 + d1 1 - L
T
D= (50)
1 - d1
(1 + b2 )
2
T
d1 = x O - 1
T (51)
U L
Therefore Eqs. (45) and (46) are rewritten as:
T
x= B ( D + B) (52)
TH 1
T
y= D (53)
TL
where
b2 - b1
B= (54)
1 + b1
1 + b1
B1 = (55)
1 + b2
Using Eqs. (49), (52) and (53) with Eqs.(32)-(34), the corresponding optimal temperatures of
the working fluid in the three isothermal processes when the ecological coefficient of
performance is a maximum, are, respectively, determined by:
D + b2
T1* = TH (56)
(1 + b1 )(D + B)
D + b2
T2 * = TL (57)
D (1 + b2 )
D + b2
T3 * = TO (58)
1 + b2
Substituting Eqs. (56)-(58) into Eqs. (21), (23), (27) and (31) the maximum ECOP function and
the corresponding optimal coefficient of performance, optimal specific cooling load and
optimal specific entropy generation rate are derived, respectively, as:
1
ECOPmax =
(
Tenv TO-1 - TL-1 )
1
(59)
-1
erTH (TD - TL )
TH D - B12 ( D + B)(TL + BDT )

1- 1 - x (TO - TL ) * 2
T - B ( D + B)T T
1 ( ) H 1 ( ) L
- - +
H 1 L

U B D 1 T B D B T T

TH - B1 ( D + B)T TL
TH D - B12 ( D + B)(TL + BDT )

1 - x (TO - TL ) * 2
*
COP = (60)
TH (TD - TL ) U B1 ( D - 1) TH - B1 ( D + B)T TL

U * B12 ( D - 1) TH - B1 ( D + B)T TH
r* = - x (TO - TL ) (61)
TH D - B12 ( D + B)(TL + BDT )
* 2
1
1 erTH (TD - TL ) U B1 ( D - 1) TH - B1 ( D + B)T TL
s* = - x (T - T ) - 1 - (62)
TL TO O L
T - B ( D + B)T T T D - B 2 ( D + B)(T + BDT )

H 1 L H 1 L

where
U
U* = (63)
(1 + b1 )
2
From Eqs. (17)-(19) and (56)-(58), it is found that , when the three-heat-source absorption
refrigerator is operated in the state of maximum ecological coefficient of performance, the
relations between the heat-transfer areas of the heat exchangers and the total heat-transfer
area are determined by:
b1 B12 ( D + B)(TD - TL )
AH * = A (64)
1 + b1 TH D - B12 ( D + B)(TL + BDT )
b2 DB1 TH - B1T ( D + B)
AL * = A
(65)
1 + b1 TH D - B12 ( D + B)(TL + BDT )
1 B1 TH D - B1TL ( D + B)
AO * = A
(66)
1 + b1 TH D - B12 ( D + B)(TL + BDT )
From Equations (64)-(66), a concise optimum relation for the distribution of the heat-transfer
areas is obtained as:
UH AH * + U L AL* = U AO* (67)

Obviously, this relation is independent of the heat leak and the temperatures of the external
heat reservoirs.
4. Comparison with COP criterion

ECOP
In Fig.4, the variation of the normalized ECOP ( ECOP ), normalized COP (
ECOPmax
COP
COP ) and the specific cooling load (r) with respect to the specific entropy
COPmax
generation rate (s) are demonstrated. One interesting observation from this figure is that
maximum of the ECOP and COP coincides although their functional forms are different:
the coefficient of performance gives information about the necessary heat rate input in
order to produce certain amount of cooling load and the ecological coefficient of
performance gives information about the entropy generation rate or loss rate of
availability in order to produce certain amount of cooling load. The maximum ECOP and
COP conditions give the same amount of cooling load and entropy generation rate. It is
also seen analytically that the performance parameters T1* , T2* , T3 * , A1* , A2 * , A3* , r * ,
s* and COP* = COPmax at the maximum ECOP and maximum COP are same. Getting the
same performance at maximum ECOP and COP conditions is an expected and logical
result. Since, for a certain cooling load the maximum COP results from minimum heat
consumption so that minimum environmental pollution. The minimum environmental
pollution is also achieved by maximizing the ECOP . Although the optimal performance
conditions ECOP and COP criteria are same, their impact on the system design
performance is different. The coefficient of performance is used to evaluate the
performance and the efficiency of systems. This method only takes into account the first
law of thermodynamics which is concerned only with the conversion of energy, and
therefore, can not show how or where irreversibilities in a system or process occur. Also,
when different sources and forms of energy are involved within a system, the COP
criterion of a system doesnt describe its performance from the view point of the energy
quality involved. This factor is taken into account by the second law of thermodynamics
characterized by the entropy production which appears in the ecological coefficient of
performance criterion ( ECOP ). This aspect is of major importance today since that with
the requirement of a rigorous management of our energy resources, one should have
brought to be interested more and more in the second principle of thermodynamics,
because degradations of energy, in other words the entropy productions, are equivalent to
consumption of energy resources. For this important reason, the ECOP criterion can
enhance the system performance of the absorption refrigerators by reducing the
irreversible losses in the system. A better understanding of the second law of
thermodynamics reveals that the ecological coefficient of performance optimization is an
important technique in achieving better operating conditions.
Figure 4. Variation of the normalized ECOP , normalized COP and the specific cooling load with respect
to the specific entropy generation rate ( TG = 403K , TL = 273K , TO = 303K , Tenv = 290 K ,
UG = 1163 W / m 2 K , U E = 2326 W / m 2 K , UO = 4650 W / m 2 K , K L = 1082 W / K , A = 1100

m2 )
5. Conclusion
This chapter presented an analytical method developed to achieve the performance
optimization of irreversible three-heat-source absorption refrigeration models having finite-
rate of heat transfer, heat leakage and internal irreversibility based on an objective function
named ecological coefficient of performance (ECOP). The optimization procedure consists in
defining the objective function ECOP in term of the temperatures of the working fluid in the
generator, evaporator, condenser and absorber and using extremal conditions to determine
analytically the maximum ECOP and the corresponding optimal design parameters. It also
established comparative analyses with the COP criterion and shown that the performance
parameters at the maximum ECOP and maximum COP are same. The three-heat-source
absorption refrigerator cycles are the simplified models of the absorption refrigerators, but
the four-heat-source absorption refrigerators cycles are closer to the real absorption
refrigerators.
Author details
Paiguy Armand Ngouateu Wouagfack
L2MSP, Department of Physics, University of Dschang, Dschang , Cameroon
Rn Tchinda
LISIE, University Institute of Technology Fotso Victor, University of Dschang, Bandjoun, Cameroon
6. References
[1] Ust, Y.: Ecological performance analysis and optimization of power-
generation systems, Ph.D. Thesis Progress Report, Yildiz Technical University,
Istanbul. (2004).
[2] Ngouateu, Wouagfack, P. A., Tchinda, R.: Performance optimization of three-heat-
source irreversible refrigerator based on a new thermo-ecological criterion.
International Journal of Refrigeration. 34, 1008-1015 (2011).
[3] Bejan, A.: Theory of heat transfer-irreversible refrigeration plant. International Journal
of Heat Transfer. 32, 1631-1639 (1989).
[4] Ust, Y., Sahin, B., Sogut, O. S.: Performance analysis and optimization of an irreversible
Dual cycle based on ecological coecient of performance (ECOP) criterion. Applied
Energy. 82 (1), 2339 (2005).
[5] Ust, Y., Sahin, Kodal, A.: Ecological coecient of performance (ECOP) optimization for
generalized irreversible Carnot heat engines. Journal of the Energy Institute. 78 (3), 145
151 (2005).
[6] Ust, Y., Sahin,B., Kodal, A.: Performance analysis of an irreversible Brayton heat engine
based on ecological coecient of performance criterion. International Journal of
Thermal Science. 45 (1), 94101 (2006).
[7] Ust, Y., Sogut, O. S., Sahin, B., Durmayaz, A.: Ecological coecient of performance
(ECOP) optimization for an irreversible Brayton heat engine with variable-temperature
thermal reservoirs. Journal of the Energy Institute. 79 (1), 4752 (2006).
[8] Ust, Y., Sahin, B., Kodal, A., Akcay, I. H.: Ecological coecient of performance analysis
and optimization of an irreversible regenerative Brayton heat engine. Applied Energy.
83 (6), 558572 (2006).
[9] Sogut, O. S., Ust, Y., Sahin, B.: The eects of intercooling and regeneration on the
thermo-ecological performance analysis of an irreversible-closed Brayton heat engine
with variable-temperature thermal reservoirs. Journal of Physics D: Applied Physics. 39,
47134721 (2006).
[10] Ust, Y., Sahin, B.: Performance optimization of irreversible refrigerators based on a
new thermo-ecological criterion. International Journal of Refrigeration. 30, 527534
(2007).
[11] Ust, Y.: Performance analysis and optimization of irreversible air refrigeration cycles
based on ecological coecient of performance criterion. Applied Thermal Engineering.
29, 4755 (2009).
Section 6
Thermodynamics in Diverse Areas

Chapter 18
Thermodynamics of Microarray Hybridization
Raul Mluan and Pedro Gmez Vilda
1. Introduction
Microarrays make the use of hybridization properties of nucleic acids to monitor
Deoxyribonucleic acid (DNA) or Ribonucleic acid (RNA) abundance on a genomic scale in
different types of cells. The hybridization process takes place between surface-bound DNA
sequences - the probes, and the DNA or RNA sequences in solution - the targets.
Hybridization is the process of combining complementary, single-stranded nucleic acids
into a single molecule. Nucleotides will bind to their complement under normal conditions,
so two perfectly complementary strands will bind to each other readily. Conversely, due to
the different geometries of the nucleotides, a single inconsistency between the two strands
will prevent them from binding.
In oligonucleotide microarrays hundreds of thousands of oligonucleotides are synthesized

in situ by means of photochemical reaction and mask technology. Probe design in these
microarrays is based on complementarity to the selected gene or an expressed sequence tag
(EST) reference sequence. An important component in designing an oligonucleotide array is
ensuring that each probe binds to its target with high specificity.
The dynamics of the hybridization process underlying genomic expression is complex as

thermodynamic factors influencing molecular interaction are still fields of important
research [1] and their effects are not taken into account in the estimation of genetic
expression by the algorithms currently in use.
2. State of the art

Many techniques have been developed to identify trends in the expression levels inferred
from DNA microarray data, and recently the attention was devoted to methods to obtain
accurate expression levels from raw data on the underlying principles of the
thermodynamics and hybridization kinetics. The development of DNA chips for rapidly
screening and sequencing unknown DNA segments mainly relies on the ability to predict
the thermodynamic stability of the complexes formed by the oligonucleotide probes.
The thermodynamics of nucleic acids have been studied from different points of view. Wu et
al. [2] analyze the temperature-independent and temperature-dependent thermodynamic
parameters of DNA/DNA and RNA/DNA oligonucleotide duplexes. The differences
between DNA polymer and oligonucleotide nearest-neighbour thermodynamic trends, and
the salt dependence of nucleic acid denaturation allowed to SantaLucia [3] to show that
there is length dependence to salt effects but not to the nearest-neighbour propagation
energies.
An early study on DNA microarray hybridization [4] found that it was strongly dependent
on the rate constants for DNA adsorption/desorption in the non-probe covered regions of
the surface, the two-dimensional diffusion coefficient, and the size of probes and targets and
also suggested that sparse probe coverage may provide results equal to or better than those
obtained with a surface totally covered with DNA probes. A theoretical analysis of the
kinetics of DNA hybridization demonstrated that diffusion was important in determining
the time required to reach equilibrium and was proportional to the equilibrium binding
constant and to the concentration of binding sites [5].
Newer studies on hybridization kinetics and thermodynamics reveal that perfect match
sequences require less time to reach saturation than mismatches. The experimental results of
Dai et al. [6] exhibit inverse temporal behaviour, resulting that surface-bound oligos
hybridizing primarily with their perfect complement sequence tend to equilibrate more
slowly than do those whose binding is dominated by mismatch duplexes. Considering the
assumptions, it has been demonstrated [7] that the hybridization time can in fact increase
the accuracy of expression ratios, and that this effect may be more dramatic for larger fold
changes. Separation between specific and nonspecific binding events can avoid the
confusion about what RNA hybridizes the probes. In this case analysis of the perfect match
and mismatch intensities in terms of simple single-base related parameters indicates that the
intensity of complementary MM introduces a systematic source of variation compared with
the intensity of the respective PM probe [8].
The hybridization of nucleic acids was modelled [9] according with the supposition that the
process of hybridization goes through an intermediate state in which an initial short contact
region has a single-stranded conformation prior to binding.
The hybridization theory gave the possibility of developing models that can be used to
obtain improved measures of expression useful for data analysis. Naef and Magnasco [10]
propose a simpler model to describe the probe effect that considers only the sequence
composition of the probes. They demonstrate that the interactions between nearest
neighbours add much predictive power for specific signal probe effects. The stochastic
model proposed by Wu and Irizarry [11] can be used to improve the expression measure or
in the normalization and summarization of the data.
Thermodynamics of Microarray Hybridization 465
3. DNA hybridization
DNA is a nucleic acid that contains the genetic instructions monitoring the biological
development of all cellular forms of life, and many viruses. DNA is a long polymer of
nucleotides and encodes the sequence of the amino-acid residues in proteins using the
genetic code, a triplet code of nucleotides. DNA it is organized as two complementary
strands, head-to-toe, with the hydrogen bonds between them. Each strand of DNA is a chain
of chemical building blocks, called nucleotides, of which there are four types: adenine (A),
cytosine (C), guanine (G) and thymine (T). Between the two strands, each base can only
bond with one single predetermined other base: A with T, T with A, C with G, and G with
C, being the only possible combination.
Hybridization refers to the annealing of two nucleic acid strands following the base pairing
rule. As shown in Figure 1, at high temperatures approximately 90C to 100C the
complementary strands of DNA separate, denature, yielding single-stranded molecules.
Two single strands under appropriate conditions of time and temperature e.g. 65C, will re-
naturate to form the double stranded molecule. Nucleic acid hybrids can be formed between
two strands of DNA, two strands of RNA or one strand of DNA and one of RNA. Nucleic
acids hybridization is useful in detecting DNA or RNA sequences that are complementary
to any isolated nucleic acid.
Figure 1. DNA-RNA hybridization. Hybridization is the process of combining complementary, single-

stranded nucleic acids into a single molecule. (from [12])
Finding the location of a gene or gene product by adding specific radioactive or chemically
tagged probes for the gene and detecting the location of the radioactivity or chemical on the
chromosome or in the cell after hybridization is called in-situ hybridization.
In the same way, in microarray technology, hybridization is used in comparing mRNA

abundance in two samples, or in one sample and a control. RNA from the sample and
control are extracted and labeled with two different fluorescent labels, e.g. a red dye for the
RNA from the sample population and green dye for that from the control population. Both
extracts are washed over the microarray and gene sequences from the extracts hybridized to
their complementary single-strand DNA molecule previously attached to the microarray.
Then, to measure the abundance of the hybridized RNA, the array is excited by a laser.
In the oligonucleotide microarrays the hybridization process occurs in the same way, the
only difference here is that the sequences to be laid over the chip are sequences of 25
nucleotides length, perfect complementary to same length sequence of the gene, PM
perfect match, and sequences of 25 nucleotides length, designed to correspond to PM, but
having the middle base - the 13th one, changed by its complementary base, MM mismatch,
as in Figure 2. The MM probes give some estimates of the random hybridization and cross
hybridization signals. One principle to be followed in the design of oligonucleotide arrays is
ensuring that the probes bind to their target with high accuracy. When the two strands are
completely complementary they will bind by a specific hybridization, as it can be seen in
Figure 3. On the contrary if there are mismatches between the nucleotides of the strands and
they bind, a process called non-specific hybridization or cross-hybridization occurs.
5 3
mRNA reference sequence
x x x x x x x x x x x
TGTGATGGTGGAATGGTCAGAAGGACTCCTATGATACACCCACGCA
CAGTCTTCCTGAGGATACTATGTGG Perfect Match
CAGTCTTCCTGACGATACTATGTGG Mismatch
Perfect Match probe cells

Probesets of PM and MM
Mismatch probe cells
Figure 2. Perfect Match Mismtach probeset strategy. Sequence of 25-mer length complementary to the
selected part of mRNA sequence form a Perfect Match probe, while the Mismatch probe is artificially
created by changing middle base with its complementary. In an oligonucleotide array a gene is
represented by 11 to 20 probes. (modified from [13])
The hybridization process has been studied from point of view of interaction between base
pairs, the interaction with unintended targets and also from its kinetics processes. Because
in practice the DNA chips are immersed in the target solution for a relatively short time, the
arrival to equilibrium is not guaranteed. Yet full analysis of the reaction kinetics requires
knowledge of the equilibrium state. An understanding of the equilibrium state is also

necessary to identify the relative importance of kinetic controls of the performance of the
DNA microarrays. The effect of the cross-hybridization on probe intensity is predictable in
the oligonucleotide microarrays, and models for avoiding this have been developed [14],
[15], [16] some aspects of it going to be described in the following section.
Figure 3. Cross-hybridization on a nucleotide probe. In specific hybridization the sequences are

completely complementary, while in non-specific or cross hybridization the sequences contain
mismatches. (from [17])
4. Technical factors affecting gene expression

4.1. Thermodynamics parameters
Black and Hartley [18] define enthalpy as the sum of the internal energy of a
thermodynamic system plus the energy associated with work done by the system on the
atmosphere, which is the product of the pressure times the volume, as in equation (1)
H U pV (1)
Because enthalpy is a property, its value can be determined for a simple compressible
substance once two independent, intensive thermodynamic properties of the substance are
known, and the change in enthalpy is independent of the path followed between two
equilibrium states
In [18] the entropy, S, was defined using the following equation:
Q
dS (2)
T
where Q is an amount of heat introduced to the system and T is a constant absolute

temperature. Since this definition involves only differences in entropy, the entropy itself is
only defined up to an arbitrary additive constant.
The following models to be described use the state function parameters, enthalpy and entropy.
State functions define the properties of a thermodynamic state. In a change between two
thermodynamic states, the change in value of the state function is given by the symbol .
The standard enthalpy change, H , is the difference in the standard enthalpies of

formation between the products and the reactants. This state function is associated with
changes in bonding between reactants and products. Changes in enthalpy during reactions
are measured by calorimetry experiments.
The standard entropy change, S , is the difference in standard entropies between reactants
and products. Entropy is a measure of the degree of order in a chemical system due to bond
rotations, other molecular motions, and aggregation. The more random a system (disorder),
the greater the entropy is. The larger a structure, the more degrees of freedom it has, and the
greater its entropy.
4.2. Interaction between pairs

The nucleic acid duplex stability can be endangered by the interaction between the
nucleotide bases. Thermodynamics for double helix formation of DNA/DNA, RNA/RNA or
DNA/RNA can be estimated with nearest neighbour parameters. Enthalpy change, H ,
entropy change, S , free energy change, G , and melting temperature, Tm, were obtained
on the basis of the nearest-neighbour model.
The nearest-neighbour model for nucleic acids, known as the NN model, assumes that the
stability of a given base pair depends on the identity and orientation of neighbouring base
pairs [3]. Previous studies in NN model parameters were brought forth in [15] and [19].
In the NN model, sequence dependent stability is considered in terms of nearest-neighbour

doublets. In duplex DNA there are 10 such unique internal nearest-neighbour doublets. Listed
in the 5-3 direction, these are AT/AT TA/TA AA/TT AC/GT CA/TG TC/GA CT/AG CG/CG
GC/GC and GG/CC. Dimmer duplexes are represented with a slash separating strands in
antiparallel orientation e.g. AC/TG means 5-AC-3 WatsonCrick base-paired with 3-TG-5.
The total difference in the free energy of the folded and unfolded states of a DNA duplex
can be approximated at 37o, with a nearest-neighbour model:
G o total i ni G o i G o init w/term G C

(3)
G o init w/term A T G o sym
where G i are the standard free-energy changes for 10 possible Watson-Crick nearest
neighbours, e.g. G o 1 G37
o
AA/TT . , G o 2 G37o TA/AT . , ni is the number of
occurrences of each nearest neighbour, i, and G o sym equals +0.43 kcal/mol if the duplex
is self complementary and zero if it is not self-complementary. The total difference in the
free energy at 37o, G37
o
, can be computed from H o and So parameters using the
equation:
G37
o
H o T S o (4)
For a specific temperature one can compute the total free energy using the values from Table
1. As described in [19] the melting temperature Tm is defined as the temperature at which
half of the strands are in double helical and half are in the random-coil state. A random-coil
state is a polymer conformation where the monomer subunits are oriented randomly while
still being bonded to adjacent units.
For self-complementary oligonucleotides, the Tm for individual melting curves was

calculated from the fitted parameters using the following equation:

Tm H o / S o R ln CT (5)
where R is the general gas constant, i.e. 1.987cal/K mol, the CT is the total strand
concentration, and Tm is given in K. For non-self-complementary molecules, CT in equation
(5) was replaced by CT/4.
Sequence H S
kcal/mol kcal/mol
AA/TT -7.9 -22.2
AT/TA -7.2 -20.4
TA/AT -7.2 -21.3
CA/GT -8.5 -22.7
GT/CA -8.4 -22.4
CT/GA -7.8 -21.0
GA/CT -8.2 -22.2
CG/GC -10.6 -27.2
GC/CG -9.8 -24.4
GG/CC -8.0 -19.9
Init. w/term GC 0.1 -2.8
Init. w/term AT 2.3 4.1
Symmetry correction 0 -1.4

Table 1. Unified oligonucleotide H and S nearest neighbour parameters in 1M NaCl. The table
shows the values of the total enthalpy and entropy for the dimmer duplexes as used in [3].
The nearest-neighbour parameters of Delcourt et al. (1991) [20], SantaLucia et al. (1996) [19],
Sugimoto et al. (1996) [15] and Allawi et al. (1997) [21] were evaluated from the analysis of
optical melting curves of a variety of short synthetic DNA duplexes in 1 M Na+.
The observed trend in nearest-neighbor stabilities at 37C is GC/CG = CG/GC > GG/CC >
CA/GT = GT/CA = GA/CT = CT/GA > AA/TT > AT/TA > TA/AT, as in Table 2. This trend
suggests that both sequence and base composition are important determinants of DNA
duplex stability. It has long been recognized that DNA stability depends of the percent G-C
content.
G 37 (kcal/mol)
Sequence Delcourt et al. SantaLucia et al. Sugimoto et al. Allawi et al.
AA/TT -0.67 -1.02 -1.20 -1.00
AT/TA 0.62 -0.73 -0.90 -0.88
TA/AT -0.70 -0.60 -0.90 -0.58
CA/GT -1.19 -1.38 -1.70 -1.45
GT/CA -1.28 -1.43 -1.50 -1.44
CT/GA -1.17 -1.16 -1.50 -1.28
GA/CT -1.12 -1.46 -1.50 -1.30
CG/GC -1.87 -2.09 -2.80 -2.17
GC/CG -1.85 -2.28 -2.30 -2.24
GG/CC -1.55 -1.77 -2.10 -1.84
Average -1.20 -1.39 -1.64 -1.42
Init. w/term GC NA 0.91 1.70 0.98
Init. w/term AT NA 1.11 1.70 1.03
Table 2. Comparison of computed NN free energy parameters at 37oC
On the other hand, the nearest neighbour H parameters from Table 1, do not follow this
trend. This suggests that stacking, hydrogen bonding, and other contributions to the H
present a complicated sequence dependence.
4.3. Interaction with unintended targets

As seen in previous sections the major issue in microarray oligonucleotide technology is the
selection of probe sequences with high sensitivity and specificity. It has been shown [22] that
the use of MM probes for assessment of non-specific binding is unreliable. Since the duplex
formation in solution has been studied using the nearest neighbour model [3], [15] the
microarray design in terms of probe selection has been achieved by using a model based on
the previously mentioned nearest neighbour model [16]. The model of Zhang et al. presents
some modification to the nearest neighbour model, firstly to assign different weight factors
at each nucleotide position on a probe with the scope of reflecting that the binding parts of a
probe may contribute differently to the stability of bindings, and secondly to take into
account two different modes of binding the probes: gene specific binding, i.e. formation of
DNA-RNA duplexes with exact complementary sequences, and non-specific binding, i.e.
formation of duplexes with many mismatches between the probe and the attached RNA
molecule. They called their model, the positional-dependent-nearest-neighbour model.
According with their method, the observed signal Iij for probe i in the probe set for gene j is
modelled as:
Nj N*
I ij B (6)
Eij Eij*
1 e 1 e
where B is the background intensity, Nj is the number of expressed mRNA molecules

contributing to gene specific binding, N* represents the number of RNA molecule
contributing to nonspecific binding, E and E* are the binding energies for gene specific and
respectively nonspecific binding. These energies are calculated as the weighted sum of
stacking energies:
Eij k bk , bk 1 (7)
Eij* k* * bk , bk 1 (8)
where k and k* are the weight factors that depend on the position along the probe from
the 5 to 3 end, and bk , bk 1 is the same as the stacking energy used in nearest neighbour
model [15].
The positional-dependent-nearest-neighbour model appears to indicate that the two ends of
a probe contribute less to binding stability according to their weight factors, see Figure 4. a).
It also can be observed that there is a dip in the gene specific binding weight factors of MM
probes around the mismatch position, probably due the mismatch which destabilizes the
duplex structure. In Figure 4. b) it can be noted that stacking energies in the positional-
dependent-nearest-neighbour model can give an explanation for the presence of negative
probe pair signals.
This model, together with the nearest neighbour model solves the problem of binding on
microarrays, but still there are factors that affect the gene expression measuring. One of
them affects the process of competing adsorption and desorption of target RNA to from
probe-target duplexes at the chip surface.
Figure 4. a) weight factors; b) nearest-neighbour stacking energy. (from [16])

4.4. Kinetic processes in hybridization thermodynamics

4.4.1. Derivation of the Langmuir isotherm
For molecules in contact with a solid surface at a fixed temperature, the Langmuir Isotherm,
developed by Irving Langmuir in 1916, describes the partitioning between the gas phase and
adsorbed species as a function of applied pressure.
The adsorption process between gas phase molecules, A, vacant surface sites, S, and
occupied surface sites, SA, can be represented by the following chemical equation, assuming
that there are a fixed number of surface sites present on the surface, as in Figure 5.
S A SA (9)

When considering adsorption isotherms it is conventional to adopt a definition of surface

coverage ( ) which defines the maximum (saturation) surface coverage of a particular
adsorbate on a given surface always to be unity, i.e. max = 1.
4.4.2. Thermodynamic derivation

An equilibrium constant k can be written in terms of the concentrations of reactants and
products:
SA
k (10)
S A
where:
[SA] is proportional to the surface coverage of adsorbed molecules, or proportional to ;
[S] is proportional to the number of vacant sites, (1 );
[A] is proportional to the pressure of gas, P.
Thus it is possible to define another equilibrium constant, b:

b (11)
1 P
Figure 5. Absorption process.

Rearranging the equations (10) and (11) one can obtain the expression for surface coverage:
bP
(12)
1 bP
4.4.3. Kinetic derivation

The equilibrium that may exist between gas adsorbed on a surface and molecules in the gas
phase is a dynamic state, i.e. the equilibrium represents a state in which the rate of
adsorption of molecules onto the surface is exactly counterbalanced by the rate of
desorption of molecules back into the gas phase. It should therefore be possible to derive an
isotherm for the adsorption process simply by considering and equating the rates for these
two processes.
The rate of adsorption will be proportional to the pressure of the gas and the number of
vacant sites for adsorption. If the total number of sites on the surface is N, then the rate of
change of the surface coverage due to adsorption is:
d
k a pN 1 (13)
dt
The rate of change of the coverage due to the adsorbate leaving the surface (desorption) is
proportional to the number of adsorbed species:
d
kd N (14)
dt
In these equations, ka and kd are the rate constants for adsorption and desorption
respectively, and p is the pressure of the adsorbate gas. At equilibrium, the coverage is
independent of time and thus the adsorption and desorption rates are equal. The solution to
this condition gives us a relation for , equation (12), where b ka kd . Here b is only a
constant if the enthalpy of adsorption is independent of coverage.
4.4.4. Dynamic absorption model

Burden et al. [14] develop a dynamic adsorption model based on Langmuir isotherm. If x is
the concentration of mRNA target and t is the fraction of sites occupied by probe-target
duplex, then in the forward absorption, target mRNA attaches to probe at a rate k f x 1 t
proportional to the concentration of specific target mRNA and the fraction 1 t of
unoccupied probes; and in the backward desorption reaction, target mRNA detaches from
probes at a rate kb t proportional to the fractions of occupied probes. The fraction of probe
sites occupied by probe-target duplexes is then given by the differential equation:
d t
dt

k f x 1 t k b t (15)
For the initial condition 0 0 , equation (15) has the following solution:
x x K k f t
t 1 e (16)
x K
where K kb k f .
Using equation (16) Burden et al. estimate the measured fluorescence intensity I, with I0 as
the background intensity at zero concentration, to be:
bx x K k f t
I x , t I0 1 e (17)
x K
At equilibrium, the intensity I(x) at target concentration x follows Langmuir Isotherm (12):
I x I0
bx
(18)
xK
Figure 6. Hyperbolic response function for the intensity I(x) according to the Langmuir isotherm.
5. Hybridization dynamics compensation

5.1. Modelling hybridization by thermodynamics
It is well known that hybridization processes may be seen under the point of view of general
thermodynamic conditions [23], meaning that the hybridization probability of a given test
segment will be defined by its thermodynamic conditions, i.e. by its hybridization temperature.
Regarding this, one can state that hybridization process will respond to the dynamic equation:
Kf

P T

C (19)
Kb
where P represents the number of oligonucleotides available for hybridization, T the

concentration of free RNA target, C the number of bound complexes, kf and kb are the
respective forward and backwards rate constants for the reaction. This equation has as a
natural solution the following expression in the time domain:
C t 1 exp t
T
TK (20)
where K defined as in equation (16) is an equilibrium dissociation constant, and

1
denoting a characteristic time over which the system reaches equilibrium.
k f T K
Recent studies [24], [25] confirm the hypothesis that the hybridization process for the each of
the probe pairs follows a time model according to the one from Figure 7. This model of
evolution predicts that the probability of hybridization will be almost zero if not enough
time interval is provided for the experiment to take place, and that in the limit, if enough
time is allowed saturation will take place.
A practical solution to the different hybridization dynamics can be solved by using multiple
regressions to convey PM-MM probe pairs to equivalent thermodynamic conditions by
processing diachronic hybridization experiments [26].
The last procedure will be explained in more detail in the following paragraphs.
Figure 7. Theoretical model for perfect match hybridization. Intensity of perfect match versus
hybridization time. (adapted from [24])
5.2. Exponential regression model

From equation (20) one can assume that a model to solve the multiple regression problem
implicit in this study will have the following form:

y a 1 e bx (21)
where a and b are parameters to be estimated adaptively using least square fitting and the
gradient method.
Vertical least square fitting proceeds by finding the sum of the squares of the vertical
deviations R2 of parameters a and b:

2
R 2 yi a 1 e
bxi (22)

i
where:

i yi a 1 e bxi (23)
is the estimation error incurred for each component.
With this notation equation (22) will became:
R 2 i2 (24)
i
The condition of R2 to be at a minimum is that
0
R2
(25)
a
0
R2
(26)
b
From equations (24), (25) and (26) one will obtain:

R2
a
i
i
i
a i

i 1 e bxi 0 (27)

R2 i
b
i b
i axi e bxi 0 (28)
i i
A solution for equations (27) and (28) can be found using the gradient method. In this case
the parameters are going to be computed adaptively:
R2 a
ak 1 ak a
a k
i

a i , k 1 e bk xi (29)
bk 1 bk b
b
R2
b i , k ak e bk xi (30)
b k
i
where i , k is defined as in equation (23) and is a parameter used as an adjust step.
5.3. Application for experimental data

The experimental part has been complemented with artificially simulated test probes used
for algorithmic validation. A diachronic database was also being produced to estimate
hybridization time constants for different gene segments.
Considering these assumptions data records have been created from experimental data
fitted by the above mentioned models. The time dynamics of hybridization for both probe
sets and their profiles were evaluated at certain time intervals.
Firstly, the diachronic data distribution for an evolution from 0 to 30 minutes is shown in
Figure 8 in both cases, for the PM probe set and the MM probe set, and in the following
figures, i.e. Figure 9 and Figure 10, show this time evolution for 60 and 120 minutes is also
shown following the model in equation (20).
Figure 8. Time dynamics of hybridization corresponding to perfect and mismatch probes, for a
maximum of 30 minutes.
The next step on data analysis was to look at the probe profiles, at certain times. Figure 11
shows the regression parameters obtained for time constants. The profiles of the perfect and
mismatch were extracted for two different time values underlining the fact that if enough
time is allowed to some probes, the mismatches will also hybridize completely.
Considering this and applying the regression algorithm, we observed that this algorithm
searches for the matching values of expression levels of probes sets and for estimated values
of perfect and mismatch probes. One of the steps of this iterative algorithm can be seen in
Figure 12.
Figure 11. Profiles corresponding to perfect and mismatch probes for time constants, at 30 and 100
minutes.
Once the iterative process was complete, certain probes have reached their target. In the
expression level estimation most of the perfect match probes obtained the expected values,
while some of the mismatch probes did not reach their target, Figure 13. Similar results were
obtained in the case of matching hybridization for time constants.
Figure 12. Top template shows the iterative matching for hidden expression levels. Bottom template
shows the iterative matching for perfect and mismatch hybridization.
Figure 13. Results for the iterative process of matching.
6. Conclusions
The thermodynamics of oligonucleotide hybridization processes where PM-MM results do
not show the expected behaviour, thus affecting to the reliability of expression estimation,
was studied in this chapter and the following conclusions were emphasized:
Modelling the hybridization process through thermodynamical principles reproduces

exponential-like behaviour for each P-T segment pair.
The hybridization process should be confined to the time interval where linear growth
is granted, this is, at the beginning of the exponential curve shown in Figure 6.
Adaptive fitting may be used to predict and regress expression levels on a specific test
probe to common thermodynamic conditions. Time constants may be inferred from the
regression parameters adaptively.
The main features of the PM-MM probe sets may be reproduced from probabilistic
modelling.
It may be expected that more precise and robust estimations could be produced using
this technique with diachronically expressed hybridization experiments.
Author details
Raul Mluan*
Communications Department, Technical University of Cluj Napoca, Cluj Napoca, Romania
Pedro Gmez Vilda

DATSI, Universidad Politcnica de Madrid, Madrid, Spain
Acknowledgement
This work was supported by the project "Development and support of multidisciplinary
postdoctoral programmes in major technical areas of national strategy of Research -
Development - Innovation" 4D-POSTDOC, contract no. POSDRU/89/1.5/S/52603, project co-
funded by the European Social Fund through Sectoral Operational Programme Human
Resources Development 2007-2013.
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to predict stability of DNA duplexes. Nucleic Acids Research. 24:4501 4505
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model for cross-hybridization compensation in high-density genome-wide microarray
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[19] SantaLucia Jr J, Allawi H T, Seneviratne P A (1996) Improved Nearest-Neighbor
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[20] Delcourt S G, Blake R D (1991) Stacking Energies in DNA. The Journal of Biological
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[21] Allawi H T, SantaLucia Jr J. Thermodynamics and NMR of Internal GT Mismatches in
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[22] Li C, Wong W H (2001) Model-based analysis of oligonucleotide arrays: Expression
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kinetics for differentiating specific from non-specific binding to oligonucleotide
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Estimating Oligonucleotide Microarray Expression by Hybridization Process
Modelling. Proc. of IEEE/NLM Life Science Systems and Applications Workshop. 1 2
Chapter 19
Probing the Thermodynamics of Photosystem I

by Spectroscopic and Mutagenic Methods
Xuejing Hou and Harvey J.M. Hou
1. Introduction
Thermodynamics of a chemical reaction is a fundamental and vital issue for complete
understanding of the reaction at the molecular level and involves the elucidation of the
energy level of reactant and products, direction of reaction, and driving force or spontaneity
of the reaction (Tadashi, 2011). Most the chemical reactions are enthalpy driven and are
determined by chemical bonding energy of the reactants and products. However, some of
the chemical reaction or process is entropy driven and are largely due the probability or
disorder of the system during the reaction. Protein denaturation and dissolution of
potassium iodide in water are such examples. In chemistry and biology, especially electron
transfer reaction, the entropy changes are often assumes small and negligible. The
understanding of thermodynamics of electron transfer reactions is relatively limited
(Mauzerall, 2006).
To study the thermodynamics of reaction in chemistry and biology, photosynthetic reaction
is an excellent model system. The photosynthesis involves multiple electron transfer
reaction driven by sunlight under room temperature and neutral pH (Blankenship, 2002;
Diner and Rappaport, 2002; Golbeck, 2006). The understanding of light-induced electron
transfer reaction in photosynthesis will provide fundamental knowledge of chemical
reactions and guide the design and fabrication in artificial photosynthetic system in address
the global energy and environmental crisis in the 21st century (Lewis and Nocera, 2006). In
particular the solar energy storage of solar energy using water splitting reaction mimicking
photosynthesis might solved energy and pure water problems at the same time (Kanan and
Nocera, 2008; Cook et al., 2010; Hou, 2010, 2011). The electron transfer reactions in
photosynthesis involves four major chlorophyll binding protein complexes: Photosystem II,
cytochrome b6f, photosystem I, and ATP synthase (Figure 1). Photosystem I and
photosystem II are belong to two types of different reaction centers in nature, respectively.
Type I reaction centers incorporate a phylloquinone or menaquinone as secondary electron
acceptor, A1, and three tertiary iron-sulfur cluster electron acceptors, FA, FB, and FX. Type II
centers use two quinone acceptors: QA undergoes one-electron reduction, and QB undergoes
a two-electron reduction with concomitant protonation.
Figure 1. Four protein complexes, including photosystem II, cytochrome b6f, photosystem I, and ATP
synthase, are responsible for the electron transfer reactions in photosynthesis. (from
http://www.answersingenesis.org/articles/tj/v17/n3/photosynthesis).
Photosystem I is a pigment-protein complex consisting of more than 11 polypeptides

embedded in the photosynthetic membrane and catalyzes light-induced electron transfer
from reduced plastocyanin (or cytochrome c6) to oxidized ferredoxin (or flavodoxin). The
electron transfer pathway and the electron transfer cofactors in photosystem I is shown as a
black arrows in Figure 1. The primary electron donor is P700, a pair of chlorophyll a
molecules. After absorbing light photon energy, P700 becomes excited species P700* and
delivers one electron to the primary electron acceptor A0, a chlorophyll a molecule. The
reduced A0 anion donates its electron to the secondary acceptor A1, a phylloquione or
vitamin K1 molecule. The reduced A1 anion transfer the electron to FX, FA, FB, and finally to
ferrodoxin for producing NADPH+.
The three-dimensional structure of cyanobacterial PS I at 2.5 A resolution has been obtained

and revealed much of the detailed orientation and binding site of electron transfer cofactors.
These structural details offer a solid basis for structure and function studies at an atomic
level (Figure 2). The almost complete symmetric arrangement of cofactors in PS I suggested
the electron transfer might involve two electron transfer branches (A side and B side). This is
different from the electron transfer mechanism in type II centers. For example, in bacterial
and PS II, only one electron transfer branch (L side or D1 side) is active. The M-side (or D2
side) electron transfer is inactive and may provide protective role in the reaction center in
regulating excess light energy.
Probing the Thermodynamics of Photosystem I by Spectroscopic and Mutagenic Methods 485
Figure 2. X-ray crystallographic structure (upper panel) and the arrangment of the cofactors (lower
pahnel) in photosystem I from cyanobacterium Synechococcus elongatus (Jordan et al., 2001)
(Reproduced with permission from Nature publishing Group).
2. Quinones in photosystem I
A quinone molecule is a perfect electron transfer cofactor due to its reversible
electrochemical redox properties and plays a key role in photosynthetic electron transfer
process. For example, both type I and type II reaction centers contain a quinone that
operates as an intermediate electron acceptor and as a one-electron carrier. However, the
local protein environment and chemical properties of the quinone in these two types of
reaction centers must be different. EPR measurements revealed that there are striking
difference in the binding and function of phylloquinone (A1) in PS I and ubiquione (QA) in
the bacterial center of R. sphaeroides (Kamlowski et al., 1998). As a type I center, PS I
contain a bound menaquinone, usually phylloquinone (A1, vitamin K1, 2-methyl-3-phytyl-

1,4-naphthoquinone). In contrast, PS II uses the plasoquinone (Ap). The chemical structures
of A1 and AP are shown in Figure 3.
To investigate the function of ubiquinone in bacterial photosynthesis, the native quinone can
be removed by organic solvent extraction and replaced with 22 other quinones. The rate of
electron transfer in these reconstituted reaction center, Gibbs free energy, enthalpy changes,
and apparent entropy changes were determined by EPR, transient time-resolved absorption
spectroscopy, theoretical calculation and modeling, and photoacoustic spectroscopy
(Gunner and Dutton, 1989; Edens et al., 2000). The molecular volume changes of charge
separation due to electrostriction correlates with the size of quinones as expected (Edens et
al., 2000). However, the methodology of replacement of quinone is not successful in PS I.
Figure 3. Chemical structures of quinones in photosynthesis. A1 is native quinone in photosystem I, and

AP is a plastoquinone in photosystem II.
A biological method to replace phylloquinone was devised by Chitnis and Golbeck (Johnson
et al., 2000; Semenov et al., 2000). The strategy to disallow A1 function is to inactivate genes
that code for enzymes involved in the biosynthetic pathway of phylloquinone. The synthesis
of the phylloquione in Synechocystis sp. PCC 6803 was shown in Figure 4, which is similar to
the biosynthesis of menoquinone in E. coli (Sharma et al., 1996). It is proposed that
menF/entC, menD, menE, and menB are responsible for 1,4-dihydroxy-2-naphthoate
synthesis. The menA catalyzes the addition of phytyl chain. The gerC2 gene codes for the 2-
thytyl-1,4-naphthoquinone methyl transferase enzyme, which catalyzed the methylation
step to produce phylloquinone.
To generate a recombinant DNA construction for inactivation of the menA gene, two DNA
fragment were amplified from Synechocystis sp. PCC 6803 genomic DNA by polymerase
chain reaction (PCR) (Figure 5). The PstI and ApaI restriction sites were incorporated in both
fragments. The first amplification product was digested with EegI and PstI, and the second
fragment was digested with PstI and ApaI restriction enzymes. The fragments was ligated
with the pBluescript vector, and the kanamycin resistance gene was cloned. The 442-bp part
of the menA gene was yielded. The transformation of the wild type strain of Synechocystis
6803 and isolation of segregated mutants was performed to obtain the menA null strain. The
recombinant DNA construct of inactivation of the menB gene was generated in the similar
way. Two 1.0 kb fragments from upstream and downstream of the menB gene were
amplified by PCR. The amplified fragments were cloned into pBluescript and a 2.0-kb EcoRI
fragment containing the streptomycine/spectinomycine resistance cassettes.
Figure 4. Biosynthetic pathway of phylloquinone in cyanobacterium Synechocystis sp. PCC 6803

(Johnson et al., 2000) (Reproduced with permission from the American Society for Biochemistry and
Molecular Biology).
In the left of the panel A in Figure 5 shows the restriction maps of the genomic regions
surrounding menA gene in the wild type and mutant strains. A 440-bp fragment in the menA
gene was deleted and replaced by a 1.3 kb kanamycine resistance cartridge. PCR
amplification of the menA locus of the wild type produced the expected 1.9 kb fragment
(panel A right, Figure 5). Southern blot hybridization analyses confirmed the interruption of
the menA gene as expected. Insertional inactivation of the menB gene was also confirmed by
both Southern blot hybridization and PCR amplification of menB locus from the mutant
strain. The part of the menB gene was deleted and replaced with a 2-kb spectinomycin
resistance cartridge (left, panel B in Figure 5). The PCR amplification of the menB locus of
the wild type produced the expected fragment of 920 bp (right, panel B in Figure 5),
confirming the inactivation of the menB gene.
Figure 5. Construct and confirmation of menA and menB null mutants by inactivation of menA and
menB genes in Synechocystis sp. PCC 6803 (Johnson et al., 2000) (Reproduced with permission from the
American Society for Biochemistry and Molecular Biology).
3. Physiological, structural, and kinetics of menA and menB null mutants

The menA and menB null mutants are able to grow photoheterotrophically and
photoautotrophically under low light conditions. The expression level of active PS I in the
menA and menB mutant are 50-60% of the wild type stain. HPLC analysis indicates that the
absence of phylloquinone in PS I and that the presence of high level of plastoquinone in PS I
(Johnson et al., 2000). EPR, electron nuclear double resonance, and electron spin echo
modulation data suggested that the orientation and distance of the foreign quinone AP are
almost identical to those of the phylloquinone A1 in the wild type PS I. In addition, EPR
measurements show that plastoquinone has been recruited into the A1 site and functions as
an efficient one electron carrier (Zybailov et al., 2000).
As shown in Figure 6, the rates of electron transfer from P700 to A0 and A1 in the mutants are
similar to the wild type PS I. However, the kinetic parameter from A1 anion to FX is quite
different in the menA and menB null mutants. The time-resolved optical studies revealed that
the forward electron transfer from A1 anion to FX is slowed 1000-fold, to 15 and 300 s,
compared to 20 and 200 ns in the wild type PS I (Semenov et al., 2000; Johnson et al., 2001).
Based the kinetic data of electron transfer in menA and menB mutant, the redox potential of
AP in menA and menB PS I is estimated to be more oxidizing than phylloquinone so that
electron transfer from AP anion to FX is thermodynamically unfavorable in the mutants
(right panel of Figure 6).
Figure 6. Kinetic data of electron transfer steps in native and menA/menB null mutants of Synechocystis
sp. PCC 6803
4. Thermodynamics of menA and menB Null Mutants

Pulsed photoacoustic spectroscopy can provide a direct measurement of thermodynamic
parameters such as volume change and enthalpy changes that accompany electron transfer
reactions (Braslavsky, 1985; Carpentier et al., 1990; Arnaut et al., 1992; Small et al., 1992; Losi
et al., 1995; Edens et al., 2000; Malkin, 2000; Herbert et al., 2001; Feitelson and Mauzerall,
2002; Delosme, 2003; Hou and Mauzerall, 2006; Hou and Sakmar, 2010; Hou, 2011; Hou and
Mauzerall, 2011). With prior knowledge of the change in Gibbs free energy of the
corresponding reactions, the apparent entropy change (TS) of the reaction can be
calculated. This is an important parameter, knowledge of which is required to fully
understand the mechanism of electron transfer, and it has been largely underreported in the
literature. The H, V, and TS of electron transfer in the photosynthetic reaction center
from Rb. sphaeroides have been measured using pulsed photoacoustics (Edens et al., 2000;
Nagy et al., 2001). In oxygenic photosynthetic systems, the same parameters of electron
transfer in PS I trimers and in Mn depleted PS II reaction center cores from Synechocystis sp.
PCC 6803 and higher plants have been investigated using similar techniques (Delosme et al.,
1994; Hou et al., 2001). These data were confirmed by photoacoustic measurements on
whole cells of Synechocystis sp. PCC 6803 (Boichenko et al., 2001). The thermodynamic
parameters of bacterial reaction centers were found to be similar to those of PS I and
dramatically different from those of PS II.
Using the fit by convolution of photoacoustic waves on the nanosecond and microsecond
time scales, the thermodynamic parameters of different kinetic steps in Synechocystis PS I
were resolved (Hou and Mauzerall, 2006). A large negative enthalpy (-0.8 eV) and large
volume change (-23 3) for the P700* to A1-FX step and a positive enthalpy (+0.4 eV) and a
small volume change (-3 3) for the A1-FX to FA/B-step were observed. For the fast reaction the
free energy change for the P700* A1-FX step is -0.63 eV, and the entropy change (TS, T=25 C)
is -0.2 eV. For the slow reaction, A1-FX to FA/B-, the free energy is -0.14 eV (43), and the
entropy change (TS) is positive, +0.54 eV. The positive entropy contribution is even larger
than the positive enthalpy, indicating that the A1-FX to FA/B - step in Synechocystis PS I is
entropy driven.
The photoacoustic waves produced by forming a charge-separated radical pair upon light
excitation of PS I trimers consist of at least two major components: (1) the heat output (QRC),
which includes the enthalpy change of the reaction and other rapidly released heat, and (2)
the volume change of the reaction (VRC). The thermal signal disappears at the temperature
of maximum density of the suspending medium, Tm, near or below 4 C, thus leaving only
the volume term (Hou, 2011). Wild-type PS I trimers produced large negative PA signals at
3.8 C (Figure 7, curve 2) which originate directly from the volume contraction via
electrostriction. The volume change in wild-type PS I is -25 3. In contrast, menA/B PS I
shows a smaller signal (Figure 7, curves 3 and 4). There is no major difference in the volume
contraction between menA PS I and menB PS I. This may be expected since plastoquinone-9
is present in the A1 sites in PS I in both mutants.
To confirm the values of the volume change and to estimate the quantum yield of charge
separation in menA/B PS I, two different approaches are utilized: (1) volume yield
measurements and (2) saturation measurements. The detailed description of these two
procedures has been given previously (Hou et al., 2001; Hou, 2011). The fits of the volume
yield curves for the mutants and wild-type PS I are shown in Figure 8. The apparent volume
contractions of menA PS I and menB PS I are -14 and -16 3, respectively, compared to -25 3
for wild-type PS I. In the second saturation method, every PS I complex is excited to obtain
the maximum PA signal. In this method, one must calculate the number of PS I centers in the
illuminated volume of the cell (0.34 mL), N, to obtain the real volume change Vs. In this
analytical method, the volume change does not contain the quantum yield. As shown in
Figure 8, the saturation value of volume change (Vs) in menA/B PS I was -17 3, which is
slightly higher than that using the volume yield method. These findings confirm the previous
results and argue that the quantum yield of photochemistry in the mutants is not low.
Figure 7. Photoacoustic waves of photosystem I complexes from the photoacoustic reference sample
(curve 1), menA (curve 3), menB (curve 4), and wild-type (curve 2) strains of Synechocystis sp. PCC 6803
on the 1-microsecond time scale (Hou et al., 2009) (Reproduced with permission from the American
Chemical Society).
The quantum yield of photochemistry can be estimated from measurements of the effective
cross section (). In Figure 8 (lower panel), the quantum yield of charge separation in
menA/B PS I was estimated to be 85%, a value slightly lower than the 96% quantum yield in
wild-type PS I. Taken together, they suggest that the volume contractions in menA/B PS I on
the microsecond time scale are -172 3, and the quantum yields of photochemistry are ca.
8510%. The observed reaction on the microsecond time scale is attributed to the formation
of P700+FA/B- from excited P700*for the wild-type PS I and of P700+AP- for menA/B PS I. The
enthalpy changes in menA and menB null mutants were determined to be 0.640.1 eV and
0.740.1 eV from the difference in slopes in Figure 9, respectively, according to the method
described previously (Hou et al., 2001; Hou et al., 2009).
Figure 10 is the typical photoacoustic wave on the fast nanosecond time scale reaction.
Curve 1 is the positive signal from a photoacoustic reference at 25 C, and curves 2, 3, and 4
show large negative signals from wild-type PS I, menA PS I, and menB PS I, respectively, at
3.8 C. They indicate that the volume contractions of the mutants are roughly two thirds of
the wild type and are similar to those on the microsecond time scale. Figure 11 shows the
analysis of photoacoustic data of the mutants and the wild type on the nanosecond time
scale. The volume changes during charge separation in menA/B PS I were smaller, -17 3,
than that of wild type PS I, -21 3. These values are identical to those of the mutants on the
microsecond time scale, which indicate that there are no kinetic volume components
between the 20 ns and 1 s time scales in the mutants. It also demonstrates that the
photoacoustic methodology on both time scales is reliable. The data in Figure 11 indicate
that the enthalpy changes in both mutants are similar, -0.7 eV, which is very close to that on
the microsecond time scale.
Figure 8. Molecular volume changes determined by volume yield method (left panel) and saturation
curve method (right panel) on the 1-microsecond time scale (Hou et al., 2009) (Reproduced with
permission from the American Chemical Society).
Figure 9. Enthalpy changes determined by analyzing the linear fit of the photoacoustic intensity vs.
temperature (water expansitivity) on the 1-microsecond time scale (Hou et al., 2009) (Reproduced with
Figure 10. Photoacoustic waves of the photoacoustic reference sample (curve 1), wild-type (curve 2),
menA (curve 3), and menB (curve 4) mutants of Synechocystis sp. PCC 6803 on the nanosecond time scale
(Hou et al., 2009) (Reproduced with permission from the American Chemical Society).
Figure 11. Enthalpy changes determined by plotting the linear fit of the photoacoustic intensity vs.
temperature (water expansitivity) on the nanosecond time scale (Hou et al., 2009) (Reproduced with
To summarize the thermodynamic data, the volume changes, free energies, and enthalpy
and entropy changes on menA/B PS I in comparison with those on the wild-type PS I are
listed in Figure 12. Opened arrows are the early step forming P700+A1- from P700* for the wild-
type PS I or P700+AP- from P700* for the mutants, and solid arrows are the number of the
following reaction: P700+AP- to P700+FA/B-. As shown in panel A, the volume contraction of the
early step of the photoreaction in the mutants (-17 3) is smaller than that in the wild type (-
21 3). Similarly, the enthalpy change (-0.7 eV) of the early step in the mutants is smaller
than that (-0.8 eV) in wild-type PS I (Figure 12B). Assuming a redox potential of -0.6 V for
plastoquinone-9 in the A1 site (21), the free energy (-0.7 eV) of this early reaction in the
mutants is larger than the value (-0.6 eV) in the wild type as indicated in Figure 12C. Taking
the difference of free energy and enthalpy change in the mutants, the apparent entropy
change of the early step in mutants is zero. In contrast, the apparent entropy change in the
wild type is calculated to be +0.2 eV. Since the apparent entropy change for the overall
reaction of the generation of P700+FA/B- from P700* is +0.35 eV (32), it implies that the latter
reaction in the mutants, i.e., the P700+AP-FA/B to P700+APFA/B- reaction, is almost completely
entropy driven (TS ) +0.4 eV and G ) -0.1 eV) (Figure 12D).
Figure 12. Thermodynamics of electron transfer reactions in photosystem I from the menA/menB null
mutants and wild-type strains of Synechocystis sp. PCC 6803 (Hou et al., 2009) (Reproduced with
In the case of menA/B PS I, photoacoustic measurements on the microsecond time scale

reveal the volume contraction to be -17 3. Considering our time window of 0.1-10 s, this
value is assigned to the formation of P700+AP- from P700*AP. The intermediate step of electron
transfer from P700+AP-FA/B to P700+APFA/B- would be accompanied by a volume change of -9 3,
assuming the replacement of A1 with AP causes no change in the FA/B clusters. For menA/B PS
I, the size of the benzoquinone ring in plastoquinone-9 (AP) is smaller than the
naphthoquinone ring in phylloquinone. Electron spin-echo modulation experiments showed

that the distance between P700+ and AP- (25.3 ) in menA/B PS I is the same as the distance
between P700+ and A1- in wild-type PS I. The volume contraction of electron transfer from P700
to AP is estimated to be larger (-30 3) than the observed one (-17 3). Thus a positive
volume due to a protein conformational change may be possible. We offer a molecular
explanation of the difference in the volume change predicted via electrostriction and that of
the observed value (-17 3). A simple explanation would be that the quantum yield of
photochemistry is lower (for example, 0.7) in menA/B PS I. This, however, is unlikely
because our pulse saturation data revealed a quantum yield of 85% in PS I from both
mutants, which is only sufficiently lower than the quantum yield of 96% in wild type PS I to
explain less than half of the effect. Further support for a high quantum yield is that the light
saturation dependence of the flavodoxin reduction rate in menA/B PS I is similar to that of
wild-type PS I. These two arguments are consistent in showing that the smaller volume
change in the menA/B PS I is not caused by a low quantum yield.
The smaller volume contraction may be caused by the following two factors: compressibility
of protein and polarity of quinone pocket. The first factor is the effect of the foreign
plastoquinone on the compressibility of the local environment of the protein. The
orientation and distance of plastoquinone- 9 in the mutants are known to be similar to
phylloquinone in the wild-type PS I. However, since the pocket of A1 is adapted to
phylloquinone, the smaller plastoquinone with the longer tail may not fit well into the
protein. If the effect of the larger tail is to crowd the hydrophobic site, this could decrease
the compressibility of the local domain and so decrease Vel. Alternatively, the A1 binding
region in menA/B PS I may be more polar; i.e., it has a larger effective , compared to the
wild-type PS I. This could be due to the small size of plastoquinone-9, allowing a water
molecule to be present. This possibility also could explain the change in potential of the
quinone because of hydrogen bonding to the water.
By use of the electron transfer theory and kinetic data, the redox potential of plastoquinone
at the A1 site was estimated to be -0.61 V (Hou et al., 2009). However, the error to be at least
0.1 V. The G for producing P700+AP- from P700* is then -0.71 eV. Similarly, the free energy for
producing P700+FA/B- from P700*FA/B is -0.77 eV (35). Thus we infer that the free energy of
P700+AP-FA/B to P700+APFA/B- reaction is -0.060.10 eV in the mutants. Knowing the free energy
of the electron transfer step in wild-type PS I and menA/B PS I, the entropic contribution (T
S) can be determined by the Gibbs relation G = H - TS. The enthalpy change
occurring on the formation of P700+AP- from P700* in menA/B PS I is -0.7 0.07 eV. This is close
to the estimated free energy of this reaction (-0.70 eV), and thus the apparent entropy
change is close to zero (Figure 12). Considering the enthalpy change (-0.4 eV) of the overall
reaction for the formation of P700+FA/B- from P700* in the wild-type PS I, the electron transfer
reaction from AP- to FA/B would be associated with a positive enthalpy change of +0.3 eV and
thus is completely entropy driven as the free energy is zero in the mutants.
The entropy of electron transfer reactions is often assumed to be zero. However, the free
energy calculated from kinetic measurements of reverse electron transfer in bacterial
reaction centers shows that the free energy is time- and temperature dependent, particularly
on the less than nanosecond time scale. The kinetics of these decays can only be described as
distributed, and simple analysis in terms of a single component is not trustworthy.
Protein dynamics may play a key role in this electron transfer step. However, the question
of whether these relaxations are enthalpy and/or entropy driven remains to be answered.
The slow (microsecond) component observed in wild-type PS I could be such a relaxation,
but only the V was determined. The difference between observed enthalpies and
estimated free energies as entropies highlights the problem. In addition to reaction centers
of Rb. sphaeroides, similar positive entropic contribution in PS I preparations of
Synechocystis sp. PCC 6803 were observed, but not in PS II preparations. Charge movement,
but not charge separation due to proton transfer, may be the difference in PS II on the 1 s
time scale. Clear-cut and large negative entropic contribution is seen in the model system of
triplet porphyrin-to-ferricyanide electron transfer in aqueous solution, where relaxations
are too fast to be relevant.
5. Conclusion
In this chapter, thermodynamics of electron transfers in biological system can be assessed by
using a combination of molecular genetics and sophisticated biophysical techniques, in
particular, pulsed photoacoustic spectroscopy. Photosynthesis involves light-induced
charge separation and subsequently a series of electron transfer reactions and is an ideal
system for the detailed study on electron transfer mechanisms in chemistry and biology. In
contrast to the susceptible and vulnerable of photosystem II complex to environment,
photosystem I complex is much more stable and a perfect choice for such a study. As
quinones play a central role in electron transfer reactions in both anoxygenic and oxygenic
photosynthesis, the phylloquinone (A1) of photosystem I is chosen as a probe to explore the
effect and regulation of electron cofactors on kinetics and thermodynamics in vivo. The
usual approach of chemical modification or replacement of phylloquinone may alter the
bonding pocket of the cofactor and the interaction with its proteins.
Molecular genetic technique is utilized to block the biosynthesis of the cofactor,

phylloquinone, in the cynobacterium Synechocystis sp. PCC 6803 and replace the
phylloquinone in the A1 site with different foreign quinones. The effect of the foreign
quinones on the electron transfer is systematically studied by biophysical methodologies.
Specifically, the menA and menB genes, which code for phytyl transferase and 1.4-
dihydroxy-2-naphthoae synthase, respectively, are inactivated to prevent the synthesis of
phylloquinone. In spite of the demonstrated absence of phylloquinone, the menA and menB
null mutants grow photoheterotrophically. HPLC and EPR measurement show that
plastoquinone-9 (AP) has been recruited into the A1 site and functions as an efficient one-
electron transfer carrier. The orientation and distance between the plastoquinone and other
cofactors are the same as that of the wild type. Time-resolved optical studies indicate that
the forward electron transfer from A1 anion to the iron-sulfur cluster (FX) is slowed 1000-
fold, to 15 to 300 s, compared to 20 and 200 ns in the wild type. Using the electron transfer
theory and kinetic data, the redox potential of plastoquinone at the A1 site was estimated to
be -0.61 V, more oxidizing that phylloquinone. The electron transfer from AP anion to FX is
thermodynamically unfavorable in the menA and menB null mutants.
Photoacoustic measurements reveal that the quantum yield of charge separation in menA
and menB is slightly lower (85%) than that of the wild type. The thermodynamic parameters
of the two electron transfer steps, including molecular volume changes, reaction enthalpy
and apparent entropy, were obtained in menA and menB null mutants and are considerable
different from the wild type. The experimental data demonstrates that the not only the
kinetics but also the thermodynamics of electron transfer reaction in photosystem I are
affected by the recruitment of the foreign quinone into the A1 site. One of the most
intriguing conclusions is that although free energy for the electron transfer from AP anion to
FX in menA and menB mutant is close to zero, the apparent entropy (TS) for this reaction is
positive, +0.4 eV. This indicates that the entropy plays a key role in the electron transfer
from AP anion to FX. As shown in Figure 13, the electron transfer from P700 to A1 is enthalpy
driven; the electron transfer from A1 to FA/FB is entropy driven. The driving force of electron
transfer in photosynthetic systems is not only dependent on the bonding energy of the
cofactor and interaction energy with the protein (enthalpy) but also dependent on the
available states of interaction with the protein (entropy).
Figure 13. The enthalpy and entropy driven steps in Synechocystis 6803 photosystem I
Author details
Xuejing Hou
University of Massachusetts Dartmouth, USA
Harvey J.M. Hou*

University of Massachusetts Dartmouth, USA
Alabama State University, USA
Acknowledgement
This work was supported by the Alabama State University and University of Massachusetts
Dartmouth. The photoacoustic measurements were conducted in the laboratory of Professor
David Mauzerall at Rockefeller University. The author thanks Professor John Golbeck and
Dr. Gaozhong Shen for their collaboration and stimulating discussions on menA/menB
project. He is also grateful to his students, Fan Zhang and Lien-Yang Chou, for data analysis
and assistance.
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Chapter 20
Fuzzy Spheres Decays and Black Hole

Thermodynamics
C.A.S. Silva
1. Introduction
A black hole is, by denition, a region in spacetime in which the gravitational eld is so strong
that it precludes even light from escaping to innity. A black hole is formed when a body of
mass M contracts to a size less than the so called gravitational radius r g = 2GM/c2 . (G is the
Newtons gravitational constant, and c is the speed of light). The velocity required to leave the
boundary of the black hole and move away to innity (the escape velocity) equals the speed
of light. In this way, one easily concludes that neither signals nor particles can escape from
the region inside the black hole since the speed of light is the limiting propagation velocity for
physical signals. From the fact that no signals can escape from a black hole, while physical
objects and radiation can fall into it, the surface bounding the black hole in spacetime (called
the event horizon) is a lightlike surface.
The term black hole" was introduced by Wheeler in 1967 although the theoretical study of
these objects has quite a long history. The very possibility of the existence of such objects was
rst discussed by Michell and Laplace within the framework of the Newtonian theory at the
end of the 18th century [13]. In general relativity context, the problem arose within a year
after the theory had been developed, i.e., after Schwarzschild (1916) obtained the rst exact
(spherically symmetric) solution of Einsteins equations in vacuum.
In particular, black hole developments in the last forty years have shown that black holes
have thermodynamics properties like entropy and temperature, and as a consequence of the
instability of the vacuum in strong gravitational elds, they are sources of quantum radiation
[46]. String theory and loop quantum gravity, lately, showed that the origin of the black
hole thermodynamics must be related with the quantum structure of the spacetime, bringing
together the developments in black hole physics and the improvement of our understanding
on the nature of the spacetime in quantum gravity regime [7, 8]. In this way, it is believed
that black holes may play a major role in our attempts to shed some light on the quantum
nature of the spacetime such as the role played by atoms in the early development of quantum
mechanics.
However the understanding of black hole thermodynamics in the semiclassical and

furthermore in quantum regime has been a very difcult, and still unsolved problem. To
explain the situation, it is known that, in statistical physics, entropy counts the number
of accessible microstates that a system can occupy, where all states are presumed to occur
with equal externally observable classical parameters: mass, electric charge, and angular
momentum. All other information about the matter which formed a black hole disappears
behind its event horizon, and therefore the nature of these microstates is obscure. Thus,
the origin of the black hole entropy is not clear. Furthermore, in order to justify the name
entropy, one must to explain also why the sum of the entropy of a black hole and the entropy
of its vicinity is a non-decreasing function of time. In other words, why black holes obey the
so called Generalized Second Law of thermodynamics (GSL).
The situation becomes even worse if black hole evaporation is considered. Since black holes
evaporate, one could expect, from black hole radiation, any information about the state which
collapsed into the black hole. However, Hawking showed, through semiclassical arguments,
that black hole radiation is thermal, and therefore does not carry any information about its
initial state. In this situation, the matter that formed the black hole, which initially was in a
pure state has evolved into a mixed state. This fact bring us a contradiction with quantum
mechanics, where a pure state can only evolve into another pure state because of the unitarity
of the evolution operator [4, 5, 9, 10].
In this context, a new phenomenon arises as one way to solve the drawbacks between black
hole physics and quantum mechanics. This phenomenon is related with quantum gravity,
and consists in a topology change of the spacetime, where a new topologically disconnected
region arises inside the black hole, and information can be stored and preserved there. This
scenario can be produced by the gravitational collapse, which would lead to a region of
Planckian densities and curvature where quantum gravitational effects becomes important.
Topology change must occur deep inside the black hole horizon, in a way that, it is entirely
invisible to observers outside the black hole, which see the usual Hawking evaporation. In
this situation, a complete state specication of the (now topologically non-trivial) universe
requires a wavefunction which has a component on the new topologically disconnected region
too. In this way, observers without access to this new region, have incomplete information
about the universe as a whole.
In this chapter, the black hole thermodynamics will be addressed in the context of topology
change, as conceived for some classes of quantum spaces, called fuzzy spheres. It will be
argued that a model based on the topology change of these fuzzy manifolds can be used to
shed some light on the origin of the black hole entropy, including why black hole evaporation
process obeys the GSL. In this sense, the selection rules will be addressed for the black hole
area transitions in a black hole evaporation process driven by topology change. Moreover,
the information loss problem will be discussed, including the possibility of some information
about the black hole initial state could be recovered by an observer in our universe, where one
can perform measures.
This chapter is organized as follows. In the second section, the black hole thermodynamics
will be addressed, introducing the laws of black hole mechanics and the Hawking effect. In
the third section, the fuzzy sphere model and the topology change process for fuzzy spaces
will be addressed. In the forth section, the relation between fuzzy spaces topology change and
black hole thermodynamics will be addressed, where the selection rules for the black hole area
Fuzzy Spheres Decays and Black Hole Thermodynamics Fuzzy Spheres Decays and Black Hole Thermodynamics3 503
transitions in the evaporation process are obtained. In the fth section, it will be investigated
the obedience to GSL by the black hole evaporation in the fuzzy topology change approach.
The sixth section is devoted to conclusions.
2. Black hole thermodynamics

Over the last forty years, black holes have been shown to have a number of surprising
properties. These discoveries have revealed unforeseen relations between the otherwise
distinct areas of general relativity, quantum physics and statistical mechanics. This interplay,
in turn, led to a number of deep puzzles at the very foundations of physics. Some have
been resolved while others remain open. The starting point of these fascinating developments
remounts to the early 1970s, where a set of relations among neighboring black hole solutions
were found, culminating in Bardeen, Carter, and Hawkings Four Laws of Black Hole
Mechanics [11]. These laws dictate the behavior of black holes in equilibrium, under small
perturbations away from equilibrium, and in fully dynamical situations. While they are
consequences of classical general relativity alone, they have a close similarity with the laws of
thermodynamics. The origin of this seemingly strange coincidence lies in quantum physics.
2.1. The laws of black hole mechanics

1 - (Zeroth law) If the energy-momentum tensor T obeys the dominant energy condition,
then the surface gravity is constant on the future event horizon H + .
Although the surface gravity is dened locally on the horizon, it turns out that it is always
constant over the horizon of a stationary black hole. This constancy is reminiscent of the
Zeroth Law of Thermodynamics which states that the temperature is uniform everywhere
in a system in thermal equilibrium. The zeroth law of black hole mechanics can be proved
without eld equations or energy conditions [1215] assuming that the horizon is a Killing
horizon (i.e. there is a Killing eld tangent to the null generators of the horizon) and that the
black hole is either (i) static (i.e. stationary and time reection symmetric) or (ii) axisymmetric
and t reection symmetric. Alternatively it can be proved (Hawking) assuming only
stationarity together with Einsteins eld equations with the dominant energy condition for
matter [16, 17]. 1
2 - (First law) If a stationary black hole of mass M, charge Q and angular momentum J, with
future event horizon of surface gravity , electric potential H and angular velocity H , is
perturbed such that it settles down to another black hole with mass M + dM, charge Q + dQ
and angular momentum J + dJ, then,

dM = dA + H dJ + H dQ . (1)
8
The rst law relates nearby stationary black hole solutions of the Einsteins equation, and
has been derived in many ways. If stationary matter (other than the electromagnetic eld) is
present outside the black hole, then there are additional matter terms on the right hand side
of the equation (1). The surface gravity evidently plays the hole of temperature. Although
the quantities , H , and H are all dened locally on the horizon, they are always constant
1
Assuming also hyperbolic eld equations for matter, and analyticity of the spacetime, Hawking also shows that the
event horizon must be a Killing horizon, and that the spacetime must be either static or axisymmetric.
over the horizon of a stationary black hole (modulo some assumptions; see for example the
assumptions above for ).
3 - (Second law) If T satises the weak energy condition, and assuming that the cosmic
censorship hypothesis is true then the area of the future event horizon of an asymptotically
at spacetime is a non-decreasing function of time:
A 0 . (2)
4 - (Third law) It is impossible by any procedure to reduce the surface gravity to zero in a
nite number of steps. 2
Bardeen, Carter, and Hawking noted that these laws closely parallel the ordinary laws of
thermodynamics, with the horizon area playing the role of entropy and the surface gravity
playing the role of temperature. But can one truly considers that this analogy is something
more than a mere formal coincidence?
The physical temperature of a black hole in classical general relativity is absolute zero. The
existence of the event horizon prevents the black hole to emit anything, and it can be regarded
as a perfect absorber, with absolute zero temperature. In this way, the identication of the
surface gravity of a black hole with a temperature, in the context of the classical theory, is
completely non-physical, and so the identication of the event horizon area with an entropy.
This was the general view of most physicists before the discovery of the Hawking effect.
The most notable exception was Bekenstein, who put forward the idea of a real physical
connection between entropy and area of the event horizon, even before the work of Hawking.
He also suggested a generalized second law for black holes:
Generalized Second Law (GSL) :
The sum of the black holes entropy and the entropy of matter outside black holes would
never decrease"
1
Sout + A 0. (3)
8
The existence of black holes is not compatible with the ordinary second law of
thermodynamics. If matter can fall into a black hole and disappear, the entropy of matter for
the external observer decreases. However, the area of the event horizon increases. Bekenstein
suggested that the generalized entropy S = Sout + A/8 does not decrease.
A more detailed inspection of this suggestion shows that it is not consistent. One can considers
a black hole immersed in a thermal bath at a temperature lower that c2 /G. Since the black
hole will absorb part of the radiation without emitting anything, one has a heat ow from
a cold thermal radiation to a hotter" black hole. This would disagree with the generalized
second law because the loss of entropy from the thermal radiation would be greater than the
increase in black hole entropy. An additional physical input is required to pass from a formal
to a physical analogy.
Some insights can be gained analyzing the dimension of the constant . A simple look
unravels that, since S has the dimension of Boltzmanns constant k B . In this way, k B must
2
As in ordinary thermodynamics, there are a number of formulations of the third law, which are not strictly equivalent.
The version given here is analogous to the Nernst form of the third law of thermodynamics.
have dimensions of length squared. With the physical constants that one has in classical
general relativity (i.e., Newtons constant G and the velocity of light c) it is not possible to
form a constant (to be identied with k B ) with dimensions of length squared. The Plancks
constant is necessary for that.
From G, c and , one can form the Planck length

G
lP = . (4)
c3
With this fundamental length available (k B l P2 ), one can go further in the analogy and write
k B c3
T , S A. (5)
kB c G
The lesson of this brief discussion is that the input required to properly establish a physical
analogy between black holes and thermodynamics involves considering quantum effects. This
will be the topic of the next section.
2.2. The Hawking effect

In 1974, Hawking demonstrated that all black holes emit blackbody radiation [4]. The
original derivation of the Hawking effect made direct use of the formalism for calculating
particle creation in a curved spacetime. Hawking considered a classical spacetime describing
gravitational collapse to a Schwarzschild black hole. A free (i.e., linear) quantum eld
propagating in this background spacetime was considered, which is initially in its vacuum
state prior to the collapse, and the particle content of the eld at innity at late times
was computed. This calculation involves taking the positive frequency mode function
corresponding to a particle state at late times, propagating it backwards in time, and
determining its positive and negative frequency parts in the asymptotic past. Hawkings
calculation revealed that at late times, the expected number of particles at innity corresponds
to emission from a perfect black body (of nite size)
( + )
N = (6)
e2/ 1
at the Hawking temperature

, T= (7)
2k B
where is a scattering coefcient sometimes called the gray-body factor since it indicates
the emissivity of the black hole which is not that of a perfect blackbody.
It should be noted that this result relies only on the analysis of quantum elds in the region
exterior to the black hole, and it does not make use of any gravitational eld equations. In this
way, Hawkings calculation has two main ingredients: the rst is that the quantum mechanical
vacuum is lled with virtual particle-antiparticle pairs that uctuate briey into and out of
existence. Energy is conserved, so one member of each pair must have negative energy. 3
Normally, negative energy is forbidden - in a stable quantum eld theory, the vacuum must
3
To avoid a common confusion, note that either the particle or the antiparticle can be the negative-energy partner.
be the lowest energy state - but energy has a quantum mechanical uncertainty of order /t,
so a virtual pair of energy E can exist for a time of order /E. The second ingredient is the
observation that, in general relativity, energy - and, in particular, the sign of energy - can be
frame dependent. The easiest way to see this is to note that the Hamiltonian is the generator
of time translations, and thus depends on ones choice of a time coordinate. 4
In this way, one can conclude that a black hole may radiate its energy at a temperature given
by equation (7). This result makes the relation between the laws of black hole mechanics and
the laws of thermodynamics to be more than a mere analogy.
From the results above, one can attribute an entropy to black hole which is given by:
A
S BH = . (8)
4l P2
Another interesting result is a consequence of the Stephan law. For a black hole with a horizon
area A:
dE
ATH 4
, (9)
dt
where = 2 k4B /603 c2 .

Moreover, from the fact that
c3
E = Mc2 , k B TH , (10)
GM
and, for a Schwarzchild black hole:
MG 2
A = 4 , (11)
c2
another result is that
dE c4
2 2 . (12)
dt G M
In this way, a Schwarzchild black hole possess a nite lifetime which is given by:
G2
M3 . (13)
c4
4
One must therefore be careful about what one means by positive and negative energy for a virtual pair. In particular,
consider the Schwarzschild scenario. Outside the event horizon, t is the usual time coordinate, measuring the proper
time of an observer at innity. Inside the horizon, though, components of the metric change sign, and r becomes a time
coordinate, while t becomes a spatial coordinate: an observer moving forward in time is one moving in the direction of
decreasing r, and not necessarily increasing t. Hence an ingoing virtual particle that has negative energy relative to an
external observer may have positive energy relative to an observer inside the horizon. The uncertainty principle can
thus be circumvented: if the negative-energy member of a virtual pair crosses the horizon, it need no longer vanish in
a time /E, and its positive-energy partner may escape to innity [18].
3. Open questions
The results described in the previous sections provide a remarkably compelling case that
stationary black holes are localized thermal equilibrium states of the quantum gravitational
eld, and that the laws of black hole mechanics are simply the ordinary laws of
thermodynamics applied to a system containing a black hole. Although no results on black
hole thermodynamics have been subject to any experimental or observational tests, the
theoretical foundation of black hole thermodynamics appears to be sufciently rm to provide
a solid basis for further research and speculation on the nature of quantum gravitational
phenomena. In this section, it will be briey discussed two key unresolved issues in black
hole thermodynamics which may shed considerable further light upon quantum gravitational
physics.
3.1. The origin of black hole entropy

From the results above, it is clear that black holes are really thermodynamical systems with
an actual temperature and entropy. What remains to be understood is the meaning of this
entropy in terms of statistical mechanics.
It is known that in statistical physics, entropy counts the number of accessible microstates
that a system can occupy, where all states are presumed to occur with equal probability. In the
thermodynamical description, entropy S is related to the number of all consistent microscopic
states N as
S = k B lnN . (14)
In analogy, it is expected that there might be a microscopic description of the black hole
thermodynamics, too. However, it is also known that black holes can be completely
characterized by only three externally observable classical parameters: mass, electric charge,
and angular momentum. All other information about the matter which formed a black hole
disappears behind its event horizon, and therefore the nature of these microstates is obscure.
Then, what is the origin of the black hole entropy?
It is widely believed that the black hole entropy might be related to a number of microscopic
states. Since the microscopic description seems to require a quantum theory of gravity,
detailed investigations of the black hole entropy should contribute a lot toward construction
of the theory of quantum gravity. This is one among the several reasons why the origin of
the black hole entropy needs to be understood at the fundamental level. Another question
is related with GSL. In order to justify the name entropy, one must to explain also why
S = Sbh + Sout is a non-decreasing function of time, in other words, why black holes obey a
GSL.
A strong motivation to investigate the black hole entropy is the so-called information loss
problem, which will be addressed in the next section.
3.2. The information loss problem

Black holes can be completely characterized by only three externally observable classical
parameters: mass, electric charge, and angular momentum. All other information about the
matter which formed a black hole disappears behind the black hole event horizon, and
therefore the nature of these microstates is obscure. Since black holes evaporate, one could
expect, from the Hawking radiation, any information about the state which collapsed into
the black hole. However, Hawking showed that this radiation is thermal, and therefore does
not carry any information about the black hole initial state. That is to say, no information can
escape from inside of the black hole horizon. In this situation, the matter that formed the black
hole, which initially was in a pure state has evolved into a mixed state. But, it contradict our
basic knowledge about quantum mechanics. There, a pure state can only evolve into another
pure state because of the unitarity of the evolution operator U (U U = 1). This problem is
known as the black hole information loss paradox.
Some possibilities to solve this paradox have already been proposed. Among these
possibilities, one has
i - The evolution is indeed non-unitary and the basics concepts of quantum mechanics must
be revised [5, 19]. However, these proposal has difculties related with violation of energy
conservation and the absence of an empty vacuum as the ground state [2023].
ii - The black hole radiation is not thermal and carries information. The problem is that a new
physics is necessary, which is radically different from the one is known: concepts as locality
and causality must be left, since matter behind the horizon has to inuence matter outside the
horizon [2426].
iii - The information is stored in a stable black hole remnant [27]. The main problem with
remnants is that, since the initial black hole could have been arbitrarily massive, the remnant
must be capable of carrying an arbitrarily large amount of information (about M2 /M2Planck
bits, if the initial mass was M). This means that there must be an innite number of species
of stable remnants, all with mass comparable to M Planck . Black hole remnants have appeared
in several noncommutative approaches of black holes, including one where the fuzzy sphere
model is used [2830].
iv - Information could be stored in a topological disconnected region which arises inside of the
black hole [31]. Gravitational collapse leads to a region of Planckian densities and curvature
where quantum gravitational effects can lead to a topology change process where a new
topologically disconnected region (a baby universe) appears. Information about the black
hole initial state can be stored there. It is possible, but not necessary, that information returns
via quantum gravity tunneling after some long timescale. In this point, the baby universe
ceases to exist, and the black hole evolution as seen by an observer outside the black hole
is unitary. Topology change had been claim to be non-unitary and therefore to suffer from
the same problems of the rst proposal. The other objection against topology change is the
violation of cluster decomposition(locality) [31, 32].
In this chapter, the topology change approach will be addressed. The main idea present
here is to see the black hole event horizon as a fuzzy sphere, and using its known quantum
symmetries properties, nd out a topology change process to black holes, which is free of the
problems related with unitarity and locality. If this is possible, a solution to the information
loss paradox will be gotten. Moreover, this model, based on the topology change of a quantum
manifold, is used to explain the origin of the black hole thermodynamics. It will be argued
that this model can explain the origin of the black hole entropy, and why black holes obey
a generalized second law of thermodynamics. In the following sections, all fundamental
constants will be considered equals to one
4. Fuzzy spaces topology change and black hole thermodynamics

4.1. The fuzzy sphere model
Fuzzy spheres consist in one of the most simplest example of noncommutative spaces and
appear as vacuum solutions in Euclidean gravity [3335]. It is obtained when one quantizes
the usual sphere S2 replacing the commutative algebra of functions on this manifold by the
noncommutative algebra of matrices.
It is known that any function dened on the usual sphere can be expanded in terms of the
spherical harmonics Ylm as
l
f ( x ) | S2 = clm Ylm ( x ) , (15)
l =0 m = l
where clm are complex coefcients, and the product of these functions is commutative.
The introduction of the noncommutative geometry is performed as one quantizes the
coordinates x ( = 1, 2, 3) on S2 , through the transformation
x x = J , (16)
with
x x = r2 1 , (17)
where J
form the n-dimensional irreducible representation of the SU (2) algebra, whereas r
is the fuzzy sphere radius, and
r
= . (18)
N2 1
In this way, the coordinates on the fuzzy sphere S2F satisfy the following commutation relations
[ x , x ] = i/r 1 x , (19)
where / has a dimension of (length)2 ,

and plays here a role analogous to that played by
Plancks constant in quantum mechanics. The fact that the coordinates x do not commute
anymore implies that the points on the sphere are smeared out, and one has to substitute
the idea of points for the idea of elementary (Planck) cells.
A consequence of the process above is the introduction of a cutoff N on the expansion (15), in
a way that it becomes
N l
f ( x ) | S2 =
F
clm Ylm ( x ) , (20)
l =0 m = l
where now Ylm ( x ) are matrices. In this way the function f ( x ) is replaced by a matrix ( N +
1) ( N + 1) in a way that its product becomes noncommutative. The commutative limit is
given by / 0 or N .
In the context of black hole physics, the use of fuzzy spheres is mostly motivated by the
Bekensteins limit [6], which says that the black hole entropy is nite and proportional to the
event horizon area. Since fuzzy spheres, are obtained from quantization of a compact space,
they are described by nite dimensional matrices, in a way that the number of independent
states dened on the fuzzy sphere is limited, and the entropy associated with these states is
nite, in agreement with the Bekensteins limit [28, 34, 3639].
510 10
4.2. Fuzzy spheres and Hopf algebras

Another important feature of fuzzy spheres is its close relationship with Hopf algebras, which
allow us to dene a linear operation (the coproduct of a Hopf algebra) on S2F and compose
two fuzzy spheres preserving algebraic properties intact. This operation produces a topology
change process where a fuzzy sphere splits into two others [40], and can be used as a good
mathematical model to black hole topology change [36, 37].
In order to dene a Hopf algebra, one has that a bi-algebra is a vector space A over a eld of
scalars F which is both an algebra and a coalgebra in a compatible way. The algebra structure
is given by F-linear maps m : A A A (the product) and : F A (the unit map),
where xy : = m( x, y) and (1) = 1A. The coalgebra structure is likewise given by linear maps
: A A A (the coproduct) and : A F (the counit map). One writes : A A, or
sometimes A , to denote the identity map on A. The required properties are
Associativity: m(m ) = m( m) : A A A A;
Unity: m( ) = m( ) = : A A;
Coassociativity: ( ) = ( ) : A A A A;
Counity: ( ) = ( ) = : A A;
A Hopf algebra is dened as a bi-algebra H together with a (necessarily unique) convolution

inverse S for the identity map = H ; the map S is called the antipode of H.
Fuzzy spaces possess quantum groups properties related with a Hopf algebra [40].5 To
describe the fuzzy sphere topology change, one has that under the quantization procedure
(16), functions dened on S2 are replaced by matrices on S2F [33]. In this way, let a matrix M
describing a wave function on S2F , the Hopf coproduct : S2F ( j) S2F (K ) S2F ( L ) acts on M
as
( K,L) ( M ) = CK,L,J;1,2 CK,L,J;m1,m2 (21)

1 ,2 ,m1 ,m2
M1 +2 ,m1 +m2 e1 m1 (K ) e2 m2 ( L ) ,
where Cs are the Clebsh-Gordan coefcients and ei m j s are basis for a matrix space dened
on the fuzzy sphere [40].
The coproduct has the following properties:
( K,L) ( M ) = ( K,L) ( M ) ,
(22)
( K,L) ( MN ) = ( K,L) ( M ) ( K,L) ( N ) ,
(23)
Tr ( K,L) ( M ) = Tr ( M ) ,
5
Actually, fuzzy spaces possess algebraic properties more general than a Hopf algebra. It is due to the fact that a
coproduct of two different algebras is possible, whereas in an ordinary Hopf algebra only the coproduct of an algebra
by itself is possible.
Fuzzy Spheres Decays and Black Hole Thermodynamics Fuzzy Spheres Decays and Black Hole Thermodynamics
11 511
and
( K,L) ( M ), ( K,L)( N ) = M, N (24)
In this way, the coproduct preserves the Hermitian conjugation, the matrix product, the
matrix trace, and the matrix inner product. These properties of the coproduct assure that
(21) is a unitary process, and preserves the algebraic properties of the operators dened on
the fuzzy sphere [36, 37, 40].
4.3. Fuzzy spaces topology change and black hole thermodynamics

The basic assumptions in this chapter stay in the meaning of the eq. (21). This equation says
that a wavefunction M S2F ( J ) splits into a superposition of wavefunctions on S2F (K ) S2F ( L ).
In this way, the information in M is divided between two regions of the spacetime, i.e, the two
fuzzy spheres with spins K and L respectively. The following consequences are imminent:
(i) If one use the fuzzy sphere Hilbert space as the ones of the black hole, the maximum of
information about the black hole that an outside observer can obtain would be encoded in
wave functions dened on the fuzzy sphere Hilbert space.
(ii) One will nd out, through the Hopf coproduct , a topology change process for the black
hole. In this process the information about the black hole initial state, will be divided into two
spacetime regions. One of them is a fuzzy sphere with spin K, which will be considered as
the original world and name it the main world. The other one is a fuzzy sphere with spin L
which will be named the baby world.
(iii) The process is unitary, in this way there is no information loss. However, since the baby
world arises in the black hole interior, an observer in the main world can not access the
degrees of freedom there. In this way, from his standpoint, the black hole will appear to
evolve from a pure to a mixed state described by a density matrix . It enable us to dene an
entropy, measured by the observer in the main world, associated to the black hole horizon.
Now, in order to analyze how the topology change process drives the black hole evaporation,
it will be necessary to investigate how the fuzzy topology change drives the black hole area
transitions. It will be admitted that the selection rules for the black hole area transitions are
the ones for the topology change. These rules are obtained from the eq. (21), when one traces
over the degrees of freedom in the baby universe.

The splitting process (21) for a matrix M = | J, m J, m | with L = 1/2, and K = J 1/2 is
given by:

(| J, m J, m |) =

( K + mK +1)( K + mK +1)
2K +1 | K, m 1/2K, m 1/2 |

( K mK +1)( K mK +1)
+ 2K +1 | K, m + 1/2K, m + 1/2 | . (25)
In that point, it still necessary to ensure that the splitting process above can be performed
repeatedly, under identical circumstances, with statistically independent results to outside
observers in different regions of spacetime. That is to say, it is necessary to ensure that locality
512 12
is preserved in this process. In ordinary quantum eld theory these requirements are insured
by the Cluster Decomposition Theorem.
Cluster decomposition theorem
The vacuum expectation value of a product of many operators - each of them being either
in different regions A and B, where A and B are very separated - asymptotically equals to
the expectation value of the product of the operators in A, times a similar factor from the
region B. Consequently, sufciently separated regions behave independently. If A1 , ..., An are
n operators each localized in a bounded region and one picks some subset of the n operators
to translate xi into x i = xi + a,
lim M0 , A1 ( x1 ) A2 ( x2 ), ..., A j1 ( x j1 ) A j ( x j ), ...An ( xn ), M0 (26)

= M0 , A1 ( x1 ) A2 ( x2 ), ..., A j1 ( x j1 ), M0
M0 , A j ( x j ), ...An ( xn ), M0 ,
where M0 represents the vacuum state.

If one admits that (26) is valid for an outside observer is easy to see, from Eq. (24) that
lim ( M0 ), ( A1 ( x1 )) ( A2 ( x2 )), ..., ( A j1 ( x j1 )) ( A j ( x j )), ..., ( An ( xn )), ( M0 )

= ( M0 ), ( A1 ( x1 )) ( A2 ( x2 )), ..., ( A j1 ( x j1 )), ( M0 )
( M0 ), ( A j ( x j )), ..., ( An ( xn )), ( M0 ) , (27)
where ( A j ( x j )) and ( A j ( x j )) represent the splitting process in different points of spacetime.

The splitting process, then, occurs in a way that cluster decomposition is preserved and
locality is not violated.
From the equation (25), and from the fact that the splitting process (21) obeys cluster
decomposition, in a way that different steps J J 1/2, in the black hole evaporation, are
independent events, the probability amplitude for a n-steps transition is given by
2J + 1
a Jn = . (28)
2J n + 1
Now, in order to analyze the black hole area transitions, it will be introduced a canonical
ensemble in which our system (the BH) can occupy different area microstates. The idea of
using these types of ensembles goes back to Krasnov [4143] and is, somehow, a necessity in
the Loop Quantum Gravity formalism as the count of states is naturally done by using the
horizon area instead of BH mass [44, 45]. In this framework, the probability amplitude for the
BH evaporate is given by
a Jn = e A Jn , (29)
where is a temperature-like parameter dual to the black hole area [4648].
The probability amplitude (28) will be identied with (29), in a way that the value of the black
hole area in the J-state will be written as
A J = 1 ln(2J + 1) . (30)
13 513
Moreover, the density matrix describing the black hole quantum states can be written as
Dim ( S2F )
= (1/Z ) e A J | J J |= (1/Z )e A , (31)
J =0
where Z = Tre A is the partition function.

The matrix in the eq. (31) satisfy the Bloch equation
A
i = , (32)
8
where has been replaced by i/8.
The equation (32) will govern the transitions between black hole area states. It must be
used when working in the Euclidean continuation of the black hole, supplementing the
Wheeler-DeWitt equation, where plays the role of a sort of dimensionless internal time
associated with the horizon [4648]. Moreover, = i E , where E is the Euclidian angle.
Regularity of the Euclidean manifold at the horizon imposes a xed Euclidean angle given by
E = 2. In this way, at the horizon = 1/4.
From the equation (30), and the results above, the entropy S = Tr (ln ) = ln (2J + 1),
associated for an outside observer to black hole is given by
A
S= , (33)
4
which corresponds to the Bekenstein-Hawking formula.
The logarithmic dependence of the black hole area spectrum on J, in the expression (30), tell
us that the decrease in the horizon area is continuous at large values of J, and discrete to small
values of J, when the black hole approaches the Planck scale. The black hole area spectrum is
showed in the gure (1).
BH Area
15
10
Figure 1. The black hole area spectrum for topology change approach
In this way, if one models a black hole horizon by a fuzzy sphere and consider its quantum
symmetry properties, a topological change process which can be used to solve the black hole
514 14
information loss paradox is obtained. In this process a black hole event horizon, modeled
by a fuzzy sphere with spin J , splits into two others. The fuzzy sphere splitting can be
used to describe a black hole evaporation process in which information about the black hole
initial state is divided between two topologically disconnected regions: the main and the baby
world. Nor unitarity or locality is broken in the evolution of the whole system. On the other
hand, an observer in the main world sees the topology change process occurs in a non-unitary
way, due to the impossibility of access the degrees of freedom in the baby world.
It is possible, but not necessary, that information returns via quantum gravity tunneling at
the nal stages of black hole evaporation. In this point, the baby universe ceases to exist,
and the black hole evolution as seen by an observer outside the black hole is unitary. In
the next section it will seen how the selection rules, inherited from the topology change
process, will bring essential consequences to the way how entropy is emitted by black holes.
One has that Hawkings radiation is known semi-classically to be continuous. However, the
Hawking quanta of energy are not able to hover at a xed distance from the horizon since the
geometry of the horizon has to uctuate, once quantum gravitational effects are included.
Thus, one suspects a modication of the black hole radiation when quantum geometrical
effects are taken into account. As will be seen in the next section, a possible modication
on the description of the black hole emission process occurs at the nal stages of black hole
evaporation, where its area spectrum becomes discrete.
4.4. Entropy emitted during the evaporation process

It is known that the entropy of a system measures ones lack of information about its actual
internal conguration. Suppose that everything one knows about the internal conguration
of the system is that it may be found in any of a number of states, with probability pn for
the nth state. Then the entropy associated with the system is given by Shannons well-known
relation S = pn lnpn [4952].
The probability for a black hole to emit a specic quantum should be given by the expression
(28), in which one must yet include a gray-body factor (representing a scattering of the
quantum off the spacetime curvature surround the black hole). Thus, the probability pn to the
A Jn
black hole goes n steps down in the area ladder is proportional to (n ) e 4 . Moreover, the
discrete area spectrum (30) implies a discrete line emission from a quantum black hole.
To gain some insight into the physical problem, it will be considered a simple toy model
suggested by Hod [53, 54]. To begin with, it is well known that, for massless elds, ( M )
approaches 0 in the low-frequency limit, and has a high-frequency limit of 1. A rough
approximation of this effect can be archived by introducing a low frequency cutoff at some
= c [55]. That is, ( ) = 0 for < c , and ( ) = 1 otherwise, where = M [5658].
The ratio R =| Srad /S BH | of entropy emission rate from the quantum black hole to the rate of
black hole entropy decrease is given by:

A Jn
Ns 2J A Jn
i=1 n=1 C (n )e 4 ln C (n )e 4

R= A Jn , (34)
Ns 2J A Jn
i=1 n=1 C (n )e 4 4
15 515
where C is a normalization factor, dened by the normalization condition:

Ns 2J A Jn
C(n)e 4 =1 . (35)
i =1 n =1
For the effective number of particle species emitted ( Ns ), it will be taken into account the
various massless modes emitted. Here, Ns will be considered as

2J + 1 for 2J + 1 < 112 ,
Ns =
112 for 2J + 1 112 .
In this way Ns is upper limited by the number of modes of massless particles in nature
which make the dominant contribution to the black-hole spectrum (the 1/2, 3/2, 5/2 neutrino
modes, the 1 and 2 photon modes, and the 2 and 3 graviton modes [53, 54, 5658]), and by the
size of the fuzzy sphere Hilbert space.
In the gure (2), R has been plotted down taking c 0.2 (the location of the peak in the
total power spectrum [5658]). With this frequency cutoff, the minimal non-null value to the
quantum number J, in order to have = 0, is J = 6.0. In this point, the black hole must
evaporate completely.
From the graphic for R, one has that the non-unitary evolution of the black hole geometry in
the main world, due to the topology change process, imposes obedience to a second law of
thermodynamics on the black hole evolution process, since R is ever larger than (or equal) to
unity. The value of R approaches the value of 1.3 at the large J limit in agreement with known
Zureks semiclassical results [55]
R
1.2
1.0
0.8
0.6
0.4
0.2
J
500 1000 1500
Figure 2. The ratio of entropy emission rate from the quantum black hole to the rate of black hole
entropy decrease.
It is important to notice that the entropy emitted from the black hole decreases as the area
spacing increases. The entropy of the radiation should be maximal in the semiclassical limit
where the black hole can be in any area state, and the various transitions have almost the
same probabilities. On the other hand, in the quantum limit, only special values are allowed
to the black hole area, and then only special transitions are allowed. In this way, the entropy
of the radiation emitted by the black hole becomes smaller. The striking consequence of this
516 16
is the possibility that, since the black hole radiation becomes less and less entropic as the
evaporation process takes place, some information about the black hole initial state could leak
out from its interior and be accessible to an observer in our universe, where measures can
be performed. The possibility of information leakage from a black hole with a discrete area
spectrum is already pointed out by Hod [53, 54]
5. Remarks and conclusions

It has been argued that a model based on the topology change of a quantum manifold can be
used to shed some light on the problems of the origin of black hole entropy and information
loss. In this approach, black hole entropy is generated because of the non-unitary evolutions of
the main world geometry due to the topology change process in black hole interior. To do this,
the process of emission of quanta of radiation by black holes has been putted in connection
with topology changes in the quantum manifold which is assumed to describe the horizon
(the fuzzy sphere).
Nor unitarity or locality is broken in the evolution of the whole system in topology change
approach in a way that no information is lost. Moreover, from the topology change model,
the selection rules for the black hole area transitions have been obtained. In this way,
an expression for the probability amplitudes of black hole transitions has been derived.
From them, an understanding of the Bekenstein-Hawking formula for black hole entropy is
provided. The topology change approach gives us a relation of states to points that brings
together the black hole entropy and our standard concept of entropy as the logarithm of the
number of microstates.
Through the study of the black hole evaporation process, an area spectrum, which is
continuous in the semiclassical limit, and becomes discrete as the black hole approaches the
Planck scale has been obtained. In order to investigate the inuences of the area spectrum
shape to the black hole emission, the ratio R between the rates of entropy emission and black
hole entropy decrease has been calculated. At rst, R is found to be larger than 1, showing
that the considered mechanism is able to produce a generalized second law. Then, R approach
1 as the black hole shrinks to the Planck scale, and the area spectrum becomes discrete. These
results point to a possible information leak out from black hole, since its radiation becomes less
and less entropic as the black hole evaporates, and could alleviate the information problem for
an observer outside the black hole. Since the possible information leakage would occurs more
strongly in the quantum gravity limit, it would not require radical modications in the laws
of physics above the Planck scale. The task of found an appropriate quantum mechanism for
information leakage remains.
Acknowledgements
The author thanks to Instituto Federal de Educao, Cincia e Tecnologia da Paraba - Campus
Campina Grande, for the nancial support.
Author details
C.A.S.Silva
Instituto Federal de Educao Cincia e, Tecnologia da Paraba, Campus Campina Grande, Rua
Tranquilino Coelho Lemos, 671, Jardim Dinamrica I, Campina Grande, Paraba, Brazil
17 517
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Chapter 21
Bibliometric Analysis
of Thermodynamic Research:
A Science Citation Index
Expanded-Based Analysis
Hui-Zhen Fu and Yuh-Shan Ho
1. Introduction
Thermodynamics is the study of energy and its transformation (Holman, 1985). This subject
has evolved since the beginning of the eighteenth century (Look & Saucer, 1982). Most
studies of thermodynamics are primarily concerned with two forms of energy: heat and
work (Holman, 1985; Keizer, 1985; Rosakis et al., 2000). Thermodynamics advanced
dramatically in the 1960s and 1970s, primarily in the area of critical phenomena (Callen,
1985). In recent years, thermodynamic research has been conducted in more systems, such
as corn-ethanol biofuel cycle (Patzek, 2004), lipid-peptide interactions (Seelig, 2004), DNA
structural motifs (SantaLucia & Hicks, 2004), and glass-forming substances (Ngai, 2000).
Bibliometrics, as a measure of scientific performance, has been widely applied to research

evaluation for a long period (Saracevi & Perk, 1973; Luukkonen, 1990; Friedberg, 2000). It
has been employed to evaluate various researches, for example biology (Sainte-Marie 2010),
desalination research (Tanaka & Ho, 2011), solid waste research (Fu et al., 2010),
acupuncture research (Han & Ho, 2011), and global climate change (Li et al., 2011). In exited
bibliometric analyses, the analyzed aspects usually covering languages (Alfaraz & Calvino,
2004; Chiu & Ho, 2007; Ferrara, 2011), annual publication outputs (Chiu & Ho, 2007; Tsay,
2008), journals (Schubert et al., 1989; Tsay, 2008), categories (Moed et al., 1995; Yamazaki,
1994), and contributing countries and institutions (Schubert et al., 1989; Chiu & Ho, 2007;
Tanaka & Ho, 2011; Li et al., 2011). In recent years, author keywords which could provide a
reasonably detailed picture of the articles subject (Garfield, 1990), have been quantitatively
analyzed to figure out the research emphases and trends (Chiu & Ho, 2007; Fu et al., 2010; Li
et al., 2011). To analyze these aspects, the common evaluation indicators number of
publications and their publication share were utilized (Schubert et al., 1989; Rehn et al.,
2007). Impact factor was introduced by Garfield and Sher (1963) to help select additional
source journals using the recent citations received from other journals, and has been also
widely used to rank and evaluate journals (Garfield, 1996; Moed, 2002). In particular, the
five indicators including total, independent, collaborative, first author, and corresponding
author articles have been recently used to compare the publication performance of countries
and institutions in the researched of Japanese lung cancer (Ho et al., 2010), solid waste
research (Fu et al., 2010), desalination research (Tanaka & Ho, 2011), acupuncture research
(Han & Ho, 2011), global climate change (Li et al., 2011), and estuary pollution (Sun et al.,
2012). In addition, rankings are useful indicators, especially in terms of institutions and
researchers in urgent demand by politics (Weingart, 2003). These indicators including
number of publication, publication share, impact factor, rankings, and five newly indicators
were utilized for the evaluation of thermodynamics research.
The aim of this study was to systematically evaluate not only the publication characteristics
of languages, annual publication outputs, journals and Web of Science categories, and
national and inter-institutional contributors, but also the research emphases and trends by
author keywords to obtain an overview of thermodynamic research during the period from
1991 to 2010.
2. Methodology
2.1. Data collection
Documents used in this study were derived from the Science Citation Index Expanded (SCI-
Expanded) database of the Web of Science, the Thomson Reuters. According to Journal
Citation Reports (JCR), it indexes 8,073 journals with citation references across 174 scientific
disciplines in 2010. The data was collected on November 20 in 2011, and the detail data
collection process is illustrated in Fig. 1. Firstly, thermodynamics related keywords
including thermodynamic, thermodynamics, free energy change, enthalpy change,
and entropy change were searched in terms of topic (including four parts: title, abstract,
author keywords, and KeyWords Plus) within the publication year limitation from 1991 to
2010 based on SCI-Expanded. Total 157,140 documents were therefore found out. However,
these 157,140 documents contained the documents not closely relating to thermodynamics
which was searched only in terms of KeyWords Plus which providing search terms
extracted from the titles of papers cited in each new article listed in Current Contents
(Garfield, 1990). To efficiently obtain the characteristics of thermodynamics, this study only
focused on the documents (50,865) with searching keywords in front page which including
three parts: title, abstract, and author keywords, while the documents where searching
keywords only appeared in KeyWords Plus were excluded. These documents consists of 19
document types, where articles (41,245) dominants with a percentage of 81%, followed by
proceedings paper (4,860; 10%), meeting abstract (1,787; 3.5%), and review (1,407; 2.8%).
Bibliometric Analysis of Thermodynamic Research: A Science Citation Index Expanded-Based Analysis 521
Finally, the journal articles (41,245) were extracted from the 50,865 documents for
subsequent analyses.
Topic = thermodynamic or thermodynamics

or free energy change or enthalpy change or
Web of Science
entropy change
SCI-Expanded
Lemmatization = off
Year published = 1991-2010
thermodynamic, thermodynamics, free

energy change, enthalpy change, and entropy
157140 documents
change in front page (title, abstract, and author
keywords)
50865 documents Document type = article
41245 articles
Figure 1. Data collection process for searching thermodynamic related research
2.2. Analyzing structure

The analyzing aspects were divided into five sections from different angles. To be specific,
the analytic structure of analytic structure of bibliometric analysis of thermodynamic
research is presented in Fig. 2. The first section dealt with the basic information covering the
distribution of languages and annual production. The second section revealed the
performance of productive journals and Web of Science categories. Then national
contributors countries and institutional contributors institutions were analyzed in the
following third and fourth sections. Finally, recent research emphases and trends were
examined by the frequency of author keywords.
Figure 2. Analytic structure of bibliometric analysis of thermodynamic research

2.3. Indicators and acronyms

The indicators displayed in Fig. 2 for detail analysis are explained in Table 1. As for the
section of national and institutional contributors, some newly indicators (CP, SP, FP, and RP)
were employed to evaluate the performance of countries/territories and institutions. The
institutions and countries/territories contributions were identified by the appearance of at
least one author in the publications. Collaboration type was determined by the addresses of
the authors. The articles were classified by four types for country/territory and institution. (1)
The term single country article was assigned if the researchers addresses were from the
same country. The term single institution article was assigned if the researchers addresses
were from the same institution. (2) The term internationally collaborative article was
designated to those articles that were coauthored by researchers from multiple countries. The
term inter-institutionally collaborative article was assigned if authors were from different
institution. (3) The term first author article was assigned if the first author was from the
country/territory or institution for analysis. (4) The term corresponding author article was
assigned if the corresponding author was from the country/territory or institution for
analysis. In addition, the acronyms used in the following analysis were listed in Table 2.
Abbreviation Indicators
TP Number of scientific publications by the analyzed unit (document type,
language, year, journal, Web of Science category, country/territory,
institution, or author keyword)
% Number of papers of an actor (document type, language, journal,
country/territory, institution, or author keyword) as a share of the total
number of articles
%C Number of articles of internationally collaborative articles or inter-
institutionally collaborative articles as a share of the number of articles of
an actor (country/territory or institution)
IF Impact factor reported in Journal Citation Reports 2010
SP Number of single country articles or single institution articles
CP Number of internationally collaborative articles or inter-institutionally
collaborative articles
FP Number of first author articles
RP Number of corresponding author articles
R Rankings of number of articles (TP, SP, CP, RP, or FP) by countries or
institutions
Table 1. Explanation of the abbreviations used in subsequent analysis
3. Results and discussion

3.1. Language and publication outputs
There are 41,245 articles with 17 languages used. English which had 38,976 articles (94%) is
the most frequently used language in thermodynamic research. The other languages used in
more than 100 articles were Russian (863), Chinese (156), French (151), Japanese (147), and
Full Name Acronyms

Canada, France, Germany, Italy, Japan, Russia, the UK, and the USA G8
Canada, France, Germany, Italy, Japan, the UK, and the USA G7
Chinese Academy of Sciences CAS
Russian Academy of Sciences RAS
Central South University CSU
Naval University of Engineering NUE
calculation of phase diagram CALPHAD
Table 2. Introduction of the acronyms used in subsequent analysis
German (146). Some other languages that were less used were as follows: Spanish,
Portuguese, Polish, Czech, Korean, Ukrainian, Croatian, Hungarian, Slovak, Serbo-Croatian,
and Romanian. The high proportion of English also appears in other research areas, such as
94% of desalination research (Tanaka & Ho, 2011), and 93% in acupuncture research (Han &
Ho, 2011). Non-English language publications considerably dilute the the measured impact
of published articles (van Raan, 2005).
Figure 3. The growth trend of articles in thermodynamic research

Journal TP (%) IF Web of Science category (rankings by IF)

Russian Journal of 827 (2.0) 0.503 physical chemistry (114/127)
Physical Chemistry A
Journal of Alloys and 768 (1.9) 2.134 physical chemistry (63/127);
Compounds multidisciplinary materials science
(50/225); metallurgy & metallurgical
engineering (5/76)
Physical Review B 741 (1.8) 3.774 condensed matter physics (13/68)
Journal of Chemical 716 (1.7) 2.920 atomic, molecular & chemical physics
Physics (7/33)
Journal of Chemical 697 (1.7) 2.794 thermodynamics (3/51); physical
Thermodynamics chemistry (46/127)
Thermochimica Acta 652 (1.6) 1.899 analytical chemistry (33/73); physical
chemistry (71/127)
Biochemistry 601 (1.5) 3.226 biochemistry & molecular biology
(120/286)
Journal of Physical 584 (1.4) 3.603 physical chemistry (32/127)
Chemistry B
Fluid Phase Equilibria 483 (1.2) 2.253 thermodynamics (5/51); physical
chemistry (61/127); chemical engineering
(24/135)
CALPHAD-Computer 450 (1.1) 1.429 thermodynamics (16/51); physical
Coupling of Phase chemistry (81/127)
Diagrams and
Thermochemistry
Physical Review E 444 (1.1) 2.352 fluids & plasmas physics (8/31);
mathematical physics (4/54)
Journal of Colloid and 411 (1.0) 3.066 physical chemistry (40/127)
Interface Science
Journal of Chemical and 400 (1.0) 2.089 multidisciplinary chemistry (44/147);
Engineering Data chemical engineering (28/135)
Surface Science 382 (0.93) 2.010 physical chemistry (69/127); condensed
matter physics (19/68)
Journal of Solution 360 (0.87) 1.335 physical chemistry (85/127)
Chemistry
Journal of Molecular 339 (0.82) 4.008 biochemistry & molecular biology (86/286)
Biology
Journal of the American 317 (0.77) 9.019 multidisciplinary chemistry (11/147)
Chemical Society
Physical Review D 278 (0.67) 4.964 astronomy & astrophysics (8/55); particles
& fields physics (5/27)
Physical Review Letters 262 (0.64) 7.621 multidisciplinary physics (5/80)
Journal TP (%) IF Web of Science category (rankings by IF)

Langmuir 242 (0.59) 4.268 multidisciplinary chemistry (24/147);
physical chemistry (29/127);
multidisciplinary materials science
(26/225)
Table 3. Characteristics of top 20 journals with the most articles in thermodynamics
The thermodynamic research revealed a growth trend through the study period, especially
in recent years. The number of articles has been climbing up from 1991 to 2010 in Fig. 3.
According to the annual growth rate, it can be divided into two stages: 1991-2003 and 2004-
2010. In the first stage, the growth rate was 48 articles per year from 1,412 in 1991 to 1,988 in
2003, while in the second stage the growth rate has risen four-fold to 203 articles per year
from 2,169 in 2004 to 3,410 in 2010.
3.2. Journals and Web of Science categories

3.2.1. Journals
The total articles (41,245) were published in 2,434 sources among 150 Web of Science
categories. Table 3 lists the top 20 journals with the greatest number of articles. The impact
factors of these journals were also exhibited as reputation of a journal attached much attention
by the authors and editors (van Raan, 2001). Approximately 24% of the articles resided in
these 20 journals. Russian Journal of Physical Chemistry A (IF = 0.523) which was founded
in 1930, published the most articles (827; 2.0%). Its former was Zhurnal fizicheskoi khimii
(1930-1999) and Russian Journal of Physical Chemistry (1999-2006). Articles published in this
journal concern chemical thermodynamics and thermochemistry (http://www.maik.ru/cgi-
perl/journal.pl?name=physcha&page=main) which is closely related to the topic of this study.
Among the total institutions (1,004) contributing to Russian Journal of Physical Chemistry A,
831 institutions (83%) belonged to Russia while only 173 institutions (17%) belonged to other
countries. Following three journals: Journal of Alloys and Compounds (IF = 2.134), Physical
Review B (IF = 3.774), and Journal of Chemical Physics (IF = 2.920), all had the more than 700
articles. However, the journal which had the highest IF (9.019) was Journal of the American
Chemical Society in the category of multidisciplinary chemistry which was ranked 17th.
Physical Review Letters in multidisciplinary physics category was ranked 19th in the list and
ranked 2nd in terms of IF (7.621). Furthermore, of these 2,434 sources, 1,828 (75%) sources
only contained less than 10 articles; 519 (21%) sources contained 11-100 articles, 60 (2.5%)
sources contained 101-200 articles; 20 (0.82%) sources contained 201-600 articles; and seven
sources (0.28%) contained more than 600 articles, accounting for 11 percent of the total
articles. The trends of the annual publication outputs of the top core seven journals are
displayed in Fig. 4. The curves of these seven journals (Russian Journal of Physical Chemistry
A, Journal of Alloys and Compounds, Physical Review B, Journal of Chemical Physics, Journal of
Chemical Thermodynamics, and Thermochimica Acta Biochemistry) had been interlacing in the
study period. However, after 2008, Journal of Alloys and Compounds which published 108
articles in 2009 and 70 articles in 2010 showed its domination in the thermodynamic field.
Figure 4. The trends of top seven journals with more than 600 articles
3.2.2. Web of Science categories

As for category analysis, excluding the 84 articles without subject category information, the
remained 41,161 articles were analyzed. The most common category was physical
chemistry (10,295; 25%), followed distantly by other categories. A half of the above top 20
journals are assigned to the category of physical chemistry. Within the total 150 Web of
Science categories, 92 categories (61%) published articles less than 100 articles; 40 categories
(27%) published 101-1000 articles; 12 categories (8.0%) published 1,001-3,000 articles; only
six categories (4.0%) published more than 3,000 articles. The six core categories including
physical chemistry, multidisciplinary materials science, multidisciplinary chemistry,
metallurgy & metallurgical engineering, chemical engineering, and biochemistry &
molecular biology, took the majority of the total articles with a great percentage of 55%. As
illustrated in Fig. 5, these categories showed greater growth rates in recent years than those
in 1990s. These trends were similar to the above trends of annual total publication outputs.
The articles of position 1st category of physical chemistry which contained 127 journals
increased from 390 in 1991 to 777 in 2010. The 2nd position category of multidisciplinary
materials science which included 225 journals increased six-fold from 70 in 1991 to 423 in
2010.
Figure 5. The trends of top seven Web of Science categories with more than 3000 articles
3.3. National contributors

3.3.1. Global geographical distribution
Excluding 263 articles without any author address information on the Web of Science, the
40,982 articles originated from 128 countries. Articles originating from England, Scotland,
Northern Ireland, and Wales were reclassified as being from the United Kingdom (UK)
(Chiu & Ho, 2005). Articles from Hong Kong were included in the ones from China. The
geographical global distribution of thermodynamic research is shown in Fig. 6. According to
their production, the 128 countries were divided into five parts. Particularly, 81 countries
(63%) belonged to the first part of 1-100 articles; 36 countries (28%) belonged to the second
part of 101-1,000 articles; seven countries (Japan, France, India, Italy, UK, Spain, and
Canada) belonged to the third part of 1,001-3,000 articles; three countries (China, Russia, and
Germany) belonged to the fourth part of 3,001-5,000 articles; and only one country (USA)
which totally published 9,161 articles, belonged to the fifth part of 5,001-10,000 articles.
Although there were only 11 countries which published more than 1,000 articles, these 11
countries produced 77% articles. The majority of articles originated from a small number of
particular countries. Furthermore, five continents contributed to the thermodynamics
research differently. Europe with 42 countries published the most articles 22,969 (56%); Asia
with 42 countries published the second most articles 13,163 (32%); and America with sixteen
countries published the third most articles 12,333 (30%). Africa, and Oceania two continents
made much less contributions, and the quantity of them were 933 (2.3%), and 667 (1.6%),
respectively. It is noticeable that Europe is taking the leading position of thermodynamic
research. Asia was seeing a striking increase to catch up with Europe in terms of scientific
output (Friedberg, 2000; von Bubnoff, 2005).
Figure 6. Global geographical distribution of thermodynamics research outputs
3.3.2. Characteristics of top 20 countries/territories

With respect to international collaboration, 33,234 (81%) were independent publications and
7,748 (19%) were internationally collaborative publications. The collaboration rate was a little
greater than that of other areas, such as 14% biosorption technology for water treatment (Ho,
2008), 16% of desalination research (Tanaka & Ho, 2011), 16% of solid waste research (Fu et
al., 2010), and 14% of acupuncture research (Han & Ho, 2011). Table 4 shows the
characteristics of the top 20 productive countries. The eight major industrialized countries G8,
ranked in the top 11 in Table 4, had 59% over the investigation period. Similarly, the seven
major industrialized countries G7 the USA, Germany, the UK, Japan, France, Canada, and
Italy accounted for a significant proportion exited in many researches (Li et al., 2009; He,
2009; Fu et al., 2010; Wang et al., 2010). The USA dominated, ranking 1st in independent and
collaborative articles, as well as first author and corresponding author articles. Total 1,421
contributing institutions (13%) were affiliated with USA, followed by China (824 institutions,
7.7%), and Russia (792 institutions, 6.5%). The 2nd position China, the 7th position India, and
the 19th position Iran had low percentages of collaboration less than 20%. It was not
coincident that China emerged as a leading nation in science production (Zhou &
Leydesdorff, 2006; Zhou & Leydesdorff, 2008). In most fields, the USA had the quantity
(number of papers) lead, although the China has made dramatic strides to overtake the USA,
except the biomedical field and some aspects of environmental science (Kostoff, 2008).
Country IN TP TP R (%) SP R (%) CP R (%) FP R (%) RP R (%) %C

USA 1,421 9,162 1 (22) 1 (20) 1 (33) 1 (19) 1 (18) 28
China 824 4,652 2 (11) 2 (12) 5 (10) 2 (11) 2 (11) 17
Russia 792 3,792 3 (9.3) 3 (9.1) 6 (10) 3 (8.2) 3 (8.6) 20
Germany 724 3,421 4 (8.3) 6 (5.5) 2 (21) 4 (6.3) 4 (6.2) 47
Japan 580 2,804 5 (6.8) 4 (6.3) 7 (9.0) 5 (5.8) 5 (5.8) 25
France 792 2,515 6 (6.1) 7 (4.1) 3 (15) 7 (4.6) 7 (4.5) 46
India 652 2,201 7 (5.4) 5 (5.7) 15 (3.8) 6 (5.1) 6 (5.0) 13
Italy 390 1,858 8 (4.5) 8 (3.6) 8 (8.6) 8 (3.8) 8 (3.8) 36
UK 315 1,797 9 (4.4) 9 (2.5) 4 (12) 9 (3.0) 9 (2.9) 53
Spain 210 1,487 10 (3.6) 11 (2.5) 9 (8.4) 10 (2.9) 10 (2.8) 44
Canada 192 1,446 11 (3.5) 10 (2.5) 10 (7.8) 11 (2.7) 11 (2.6) 42
Poland 171 934 12 (2.3) 12 (1.6) 11 (5.1) 12 (1.7) 12 (1.7) 42
Netherlands 145 741 13 (1.8) 18 (1.1) 13 (4.7) 17 (1.3) 19 (1.2) 50
Brazil 196 733 14 (1.8) 14 (1.5) 19 (3.1) 13 (1.5) 13 (1.5) 33
Ukraine 229 720 15 (1.8) 15 (1.4) 18 (3.1) 14 (1.4) 14 (1.4) 34
Switzerland 111 690 16 (1.7) 21 (0.93) 12 (4.9) 19 (1.2) 18 (1.2) 55
Sweden 106 645 17 (1.6) 19 (1.1) 16 (3.5) 20 (1.2) 20 (1.1) 42
South Korea 176 632 18 (1.5) 17 (1.3) 22 (2.5) 16 (1.3) 16 (1.4) 31
Iran 173 587 19 (1.4) 13 (1.5) 32 (1.0) 15 (1.4) 15 (1.4) 14
Australia 106 566 20 (1.4) 23 (0.79) 14 (3.9) 21 (1.0) 21 (1.0) 54
IN: Number of institutions.
Table 4. Characteristics of the top 20 productive countries/territories
Besides, the 9th position UK, the 13th position Netherlands, the 16th position Switzerland, and
the 20th position Australia had high cooperation rates no less than 50%. It was also reported
that international collaboration in both within and outside the European Communities
played an increasing role for European scientific literature (Narin et al., 1991; Glnzel, 1999).
South Korea and Iran had higher rankings in terms of FP and RP than that of TP, while
Netherlands and Sweden had lower rankings in terms of FP and RP. Moreover, from the
above languages analysis, except English, the popular languages (Russian, Chinese, French,
Japanese, and German) were just the mother tongue of the top five countries China, Russia,
Germany, Japan, and France except the USA. The excellent performance of these countries
was consistent with the results of language analysis.
3.3.3. Comparison of top six countries

The comparison of top six countries with the most articles in 2010 is illustrated in Fig. 7. The
USA hold the trump card based on the total number of articles in the study period, but did
not have the highest growth rate. China which was ranked 1st according to the 2010
production had the highest growth rate of 32 articles per year, and surpassed the USA in
2009, following distantly by other countries. USA, India, and Russia had the lower growth
rate of 10 - 13 articles per year. The following Germany and France had the growth rate of
6.3 and 5.9 articles per year. Particularly, Russia experienced a sharply increase in the first
three year from 6 articles in 1991 to 174 articles in 1993, may due to its large fund for
recovery of the politic reason (Goodman, 1993; Webb, 1994). The Russian annual output
grew from 1980 to 1990, but fell after the dissolution of the USSR in late 1991; from 1994
there has been an inconsistent partial recovery, and by 2000 the annual output had
approximately regained its 1980 value (Wilson & Markusova, 2004). It seems that the
recovery time of Russian thermodynamic research was shorter.
Figure 7. Trends of top six countries with most articles in 2010
3.3.4. Comparison of China and USA

In order to compare the most productive country in 1991-2010, the USA and the most active
country in 2010, China, annual number of articles and citations per publication (CPP) of
both were presented in Fig. 8. Total citations were collected on November 20 in 2011 from
web of Science. From the above analysis, China experienced a high grow rate and got ahead
of the USA in 2009 and kept on top in 2010. However, in terms of CPP, the mean number of
China was 7.1 which was much less than that of the USA (23). The annual CPP of the USA
showed a declined trend in 1991-2010, ranging from 53 in 1991 to 2.8 in 2010. Except the year
of 1993, the annual CPP of China fluctuated ranging 6.2-11 in 1991-2006, and decreased after
2007 down to 1.9 in 2010. Both countries indicated declines as for annual CPPs, which can be
attributed to that it needs time to accumulate their citations (Picknett & Davis, 1999). The
outstanding performance of Chinas CPP in 1993 might be owned to the two highly cited
articles of a series by the same authors. They were thermodynamics of molecular recognition
by cyclodextrins. 1. calorimetric titration of inclusion complexation of naphthalenesulfonates
with -, -, and -cyclodextrin: enthalpy entropy compensation (Inoue et al., 1993a) with 344
citations and thermodynamics of molecular recognition by cyclodextrins. calorimetric
titration of inclusion complexation with modified -cyclodextrins. enthalpy-entropy
compensation in host-guest complexation: from ionophore to cyclodextrin and
cyclophane(Inoue et al., 1993b) with 198 citations, respectively. Furthermore, the most
frequently cited article was a modified UNIFAC model. 2. present parameter matrix and
results for different thermodynamic properties (Gmehling et al., 1993) with 727 citations.
Although this article was published by authors from Germany only, it was also assigned to
China according to its address record from Web of Science, because one of the authors had
permanent address of China. It is a bias of address information for articles from Web of
Science. Chinas CPP in 1993 were still high (CPP = 20) without these highest citations articles.
Likewise, the well performance of the USAs CPP in 1991 can be ascribed to the top cited
article protein folding and association: insights from the interfacial and thermodynamic
Figure 8. Comparison of USA and China by number of articles and citations per publication
properties of hydrocarbons which was published in 1991 (Nicholls et al., 1991) and
received 4,999 citations. Most scientific publications from China have a lower citation impact
than the world average and have a lower citation rate than expected (Glnzel et al., 2002). It
is suggested that Chinas science needs to move from the quantitative expansion phase in
nowadays to a rising quality phase (Jin & Rousseau, 2005). In general, China showed a
high growth rate in recent years and dominant now in annual production, but still needs to
make efforts on increasing their citations in thermodynamics.
3.4. Institutional contributors

3.4.1. Characteristics of top 20 institutions
After examining the national contributors, the characteristics of institutional contributors
institutions were identified. Of 40,982 articles from 10,696 institutions in 128 countries,
16,628 (41%) were inter-institutionally collaborative publications, and 24,354 (59%) were
independent publications. The percentage of collaboration among institutions was much
higher than that among countries (19%). The inter-institutional collaboration rate was
usually greater than international collaboration rates (Fu et al., 2010; Han & Ho, 2011; Li et
al., 2011; Tanaka &Ho, 2011). The number of articles of institutions was smaller than the
country, and it was reported that the collaboration was more likely to happen when the size
of actors was small (Narin et al., 1991). Nevertheless, the inter-institutional collaboration
rate (41%) of thermodynamic research was observed to be lower than that of many other
fields, such as 62% of global climate change (Li et al., 2011), 53% in atmospheric simulation
(Li et al., 2009), 44% in solid waste research (Fu et al., 2010), and 53% of acupuncture
research (Han &Ho, 2011). Four institutions in the USA and Japan, three in China, two each
in Russia, and one each in Sweden, Ukraine, UK, India, France, and Italy were ranked in the
top 20 productive institutions (16%) as shown in Table 5. It is worth noting that the Russian
Academy of Sciences ranked 1st and Chinese Academy of Sciences ranked 2nd are both
integrated research centers and made up of many relatively independent institutions
distributed throughout their country. At present, the publications of these institutions were
pooled as one heading, and publications divided into branches would result in different
rankings. A bias appeared because national research institutions might have many branches
in different cities, for example the CAS (Li et al., 2009), the RAS (Li et al., 2009), and Indian
Institute of Technology (Tanaka & Ho, 2011). RAS founded the most productive
thermodynamic journal of Russian Journal of Physical Chemistry A. In particular, 228 articles
(28%) were contributed by RAS, and 117 articles (14%) were contributed by Moscow
Lomonosov State University in Russia based on the total articles (817 articles with author
information) of Russian Journal of Physical Chemistry A during 1991-2010. With the exception
of these two institutions, the most productive institution is Moscow Lomonosov State
University in Russia (425; 1.0%), followed by Tohoku University in Japan (335; 0.82%), and
Centre National de la Recherche Scientifique in France (313; 0.76%). However, a bias would
appear in the analysis of institutions which was used by different names in their
publications. It is strongly recommended that an international identity number for all
institutions when authors published their paper with an institution as affiliation in a Web of
Science-listed journal (Chiu &Ho, 2007).
Institution TP TP R SP R CP R FP R RP R %
(%) (%) (%) (%) (%) C
Russian Academy of Sciences, Russia 1,604 1 (3.9) 1 (3.7) 1 (4.2) 1 (3.0) 1 (3.1) 43
Chinese Academy of Sciences, China 720 2 (1.8) 3 (0.92) 2 (3.0) 2 (1.1) 2 (1.1) 69
Moscow Lomonosov State University, 425 3 (1.0) 2 (0.93) 5 (1.2) 3 (0.75) 3 (0.80) 47
Russia
Tohoku University, Japan 335 4 (0.82) 10 (0.52) 4 (1.3) 8 (0.46) 7 (0.45) 62
Centre National de la Recherche 313 5 (0.76) 23 (0.34) 3 (1.4) 11 (0.41) 13 (0.39) 73
Scientifique, France
University of Tokyo, Japan 280 6 (0.68) 6 (0.57) 11 (0.84) 6 (0.46) 6 (0.45) 50
University of Science and Technology 265 7 (0.65) 9 (0.53) 14 (0.82) 5 (0.47) 5 (0.48) 52
Beijing, China
Royal Institute of Technology, Sweden 261 8 (0.64) 14 (0.45) 7 (0.91) 12 (0.41) 11 (0.40) 58
Pennsylvania State University, USA 256 9 (0.62) 5 (0.58) 19 (0.69) 9 (0.45) 10 (0.43) 45
Central South University, China 247 10 (0.60) 11 (0.51) 18 (0.74) 4 (0.50) 4 (0.52) 50
University of Wisconsin-Madison, USA 245 11 (0.60) 14 (0.45) 15 (0.81) 14 (0.41) 18 (0.37) 55
Indian Institute of Technology, India 242 12 (0.59) 4 (0.67) 42 (0.48) 6 (0.46) 8 (0.44) 33
University of California, USA 241 13 (0.59) 18 (0.39) 8 (0.88) 16 (0.39) 22 (0.33) 61
Osaka University, Japan 240 14 (0.59) 16 (0.41) 11 (0.84) 17 (0.37) 15 (0.38) 58
Massachusetts Institute of Technology, 222 15 (0.54) 8 (0.55) 35 (0.53) 10 (0.42) 11 (0.40) 40
USA
University of Cambridge, UK 220 16 (0.54) 29 (0.30) 8 (0.88) 22 (0.34) 24 (0.33) 66
Polish Academy of Sciences, Poland 219 17 (0.53) 24 (0.33) 13 (0.83) 22 (0.34) 21 (0.35) 63
National Research Council, Italy 208 18 (0.51) 166 6 (1.1) 52 (0.20) 58 (0.19) 87
(0.11)
National Academy of Sciences of 201 19 (0.49) 7 (0.57) 80 (0.37) 12 (0.41) 9 (0.43) 31
Ukraine, Ukraine
Kyoto University, Japan 200 20 (0.49) 18 (0.39) 27 (0.63) 18 (0.36) 17 (0.37) 53
Table 5. Characteristics of the top 20 productive institutions.
More independent institutions might lead to more first author articles and corresponding
author articles or vice versa. Some institutions which had low collaboration rates no more
than 40% usually had a higher rank in FP and RP. For example, the 12th place Indian
Institute of Technology in India with the low collaboration rate of 33% ranked 6th in FP and
8th in RP; the 15th position Massachusetts Institute of Technology in USA with the low
collaboration rate of 40% ranked 10th in FP and 11th in RP; the 19th position National
Academy of Sciences of Ukraine in Ukraine with the low collaboration rate of 31% ranked
12th in FP and 9th in RP. On the other hand, some institutions which had high collaboration
rates more than 70% were ranked lower in the rankings of FP and RP. For example, the 5th
position Centre National de la Recherche Scientifique in France with the high collaboration
rate of 73% ranked 11th in FP and 13th in RP; the 18th position National Research Council in
Italy with the high collaboration rate of 87% ranked 52th in FP and 58th in RP.
3.4.2. Comparison of top seven institutions

To identify the growth trends of active institutions in recent years, the trends of top seven
productive institutions with most articles in 2010 are shown in Fig. 9. The most productive
institution - RAS had an overwhelming majority in the total articles, and CAS was just down
by three articles in 2010, following distantly by the other institutions. CAS as the Chinas
highest academic institution in natural sciences played an active role in terms of scientific
outputs in recent years as the exponentially growth scientific production in China (Li et al.,
2009; Fu et al., 2010; Tanaka &Ho, 2011; Fu et al., 2011; Li et al., 2011).
Figure 9. Trends of top seven institutions with most articles in 2010
Although three universities in China including Central South University, Naval University
of Engineering, and SiChuan University just ranked 10th, 39th, and 43rd of total articles from
1991 to 2010, but they had high rankings (3rd, 4th, and 7th) with respect to the number of
articles in 2010. The growth rates of the top institutions differed from each other.
Particularly, based on the last decade (2001-2010), CAS showed the highest growth rate of
7.2 articles per year; CSU and NUE showed the growth rate of 4 5 articles per year. The
other four institutions, RAS, Moscow Lomonosov State University, University of Science
and Technology Beijing, and SiChuan University showed the growth rate of 1 2 articles
per year. About 14% percent articles in RAS were published in Russian Journal of Physical
Chemistry A which was founded by RAS. It was interesting that the top three institutions
(CAS, CSU, and NUE) with the greatest growth rates were all in China. CSU was
established in 2000 by merging three separate universities: Hunan Medical University,
Changsha Railway University, and Central South University of technology, and was
involved in 985 Project and 211 Project which were supported by Chinese government
to promote the development and reputation of the Chinese higher education system
(http://iecd.csu.edu.cn/en-US/ColumnS.aspx?cid=12). Moreover, CSU hold one SCI journal
named Transactions of Nonferrous Metals Society of China which published 11% thermodynamic
related articles of CSU in the study period. Another institution, NUE ranks as a military
university of higher learning subjected to the leadership of the Central Military Commission
and the Party Committee of the PLA Navy, and is listed as one of the five comprehensive
universities in the armed forces and the army 2110 project that enjoys the priority in
development. It falls into the category of key national university specializing in engineering
(http://english.chinamil.com.cn/site2/special-reports/2007-06/21/content_853791.htm).
3.5. Research emphases and trends

Bibliometric analysis of author keywords has been only observed in recent years (Chiu
&Ho, 2007; Wang et al., 2010; Li et al., 2011). It tried to find the research emphases and
trends by quantitatively analyzing the frequency of author keywords. Excluding some
articles without author keywords information, 23,458 articles (57%) with records of author
keywords in the SCI-Expanded database were analyzed. There were 45,182 author
keywords listed by authors, 43,930 (97%) keywords were used no more than ten times,
which indicated that thermodynamic research involved diverse scientific literature and a
wide disparity in research focuses (Chuang et al., 2007). Only 74 (0.16%) author keywords
were used no less than 100 times, suggesting that the mainstream research in
thermodynamics was considered to focus on a small field. Four five-year intervals (1991-
1995, 1996-2000, 2001-2005, and 2006-2010) were employed to obtain the trends of these
author keywords as well as minimize the year-to-year fluctuations. The top 30 author
keywords (accounting for 37% of the total articles) in the latest interval 2006-2010 are listed
in Table 6.
Except the author keywords thermodynamics, thermodynamic properties,

thermodynamic parameters, and thermodynamic related to searching keywords, the
three most frequently used author keywords were kinetics (883; 3.8%), adsorption (736;
3.1%), and phase diagram (545; 2.3%). Thermodynamics and kinetics were related to
one another in ways, and were both commonly used to describe process (Kocks et al., 1975;
Astumian, 1997; Ho & Ofomaja, 2005). Adsorption was a widely applied process, for
example in environmental science (Wang et al., 2010; Wang et al., 2011; Chuang et al., 2011).
The term phase diagram is a type of chart used to obtaining thermodynamic data at
equilibrium (Kleppa, 1952; Svirbely, 1954).
Author keywords TP 1991-2010 1991-1995 1996-2000 2001-2005 2006-2010

R (%) R (%) R (%) R (%) R (%)
thermodynamics 5,943 1 (25) 1 (31) 1 (25) 1 (23) 1 (25)
thermodynamic 1,577 2 (6.7) 2 (5.5) 2 (8.4) 2 (5.9) 2 (6.7)
properties
kinetics 883 3 (3.8) 6 (2.5) 8 (2.2) 3 (3.6) 3 (4.8)
adsorption 736 5 (3.1) 11 (1.5) 10 (1.9) 6 (2.5) 4 (4.4)
thermodynamic 778 4 (3.3) 3 (2.6) 3 (3.5) 4 (3.2) 5 (3.5)
parameters
thermodynamic 503 9 (2.1) 26 (1.0) 15 (1.3) 10 (2.1) 6 (2.7)
phase diagram 545 7 (2.3) 21 (1.2) 6 (2.3) 9 (2.1) 7 (2.7)
entropy 548 6 (2.3) 8 (2.0) 7 (2.2) 7 (2.5) 8 (2.4)
thermodynamic 338 13 (1.4) 165 (0.27) 56 (0.50) 16 (1.3) 9 (2.2)
modeling
thermodynamic 385 11 (1.6) 12 (1.5) 14 (1.7) 12 (1.3) 10 (1.8)
analysis
heat capacity 533 8 (2.3) 3 (2.6) 5 (2.7) 5 (2.8) 11 (1.7)
calorimetry 503 9 (2.1) 5 (2.5) 4 (3.0) 8 (2.2) 12 (1.7)
phase diagrams 260 17 (1.1) 26 (1.0) 31 (0.68) 25 (0.83) 13 (1.5)
CALPHAD 186 25 (0.79) N/A 782 (0.068) 35 (0.66) 14 (1.3)
solubility 325 14 (1.4) 10 (2.0) 16 (1.3) 13 (1.3) 14 (1.3)
enthalpy 373 12 (1.6) 8 (2.0) 9 (1.9) 11 (1.7) 16 (1.3)
thermodynamic 212 20 (0.90) 59 (0.59) 64 (0.45) 25 (0.83) 17 (1.2)
property
density functional 158 36 (0.67) 1288 (0.045) 415 (0.11) 56 (0.53) 18 (1.1)
theory
isothermal titration 177 28 (0.75) 1288 (0.045) 108 (0.34) 31 (0.70) 19 (1.1)
calorimetry
thermodynamic 265 16 (1.1) 38 (0.77) 16 (1.3) 13 (1.3) 20 (1.0)
stability
isotherm 120 60 (0.51) 1288 (0.045) 565 (0.09) 231 (0.18) 21 (1.0)
equation of state 316 15 (1.3) 7 (2.4) 13 (1.7) 13 (1.3) 21 (1.0)
density 178 27 (0.76) 29 (1.0) 41 (0.59) 60 (0.51) 23 (0.94)
molecular dynamics 172 29 (0.73) 165 (0.27) 31 (0.68) 47 (0.61) 24 (0.93)
free energy 163 33 (0.69) 165 (0.27) 52 (0.52) 51 (0.59) 25 (0.92)
phase equilibria 228 19 (1.0) 32 (0.86) 25 (0.83) 18 (1.2) 26 (0.91)
biosorption 101 72 (0.43) N/A N/A 431 (0.11) 27 (0.89)
AB initio 121 59 (0.52) N/A 170 (0.25) 147 (0.26) 27 (0.89)
calculations
phase transition 158 36 (0.67) 52 (0.64) 58 (0.47) 60 (0.51) 29 (0.86)
nonequilibrium 190 24 (0.81) 23 (1.1) 27 (0.81) 39 (0.64) 30 (0.85)
thermodynamics
N/A: Not Available
Table 6. The most frequently used 30 author keywords in 2006-2010

In particular, there were also some emerging hotspots in thermodynamics recently. Some
author keywords including the 3rd adsorption, the 9th thermodynamic modeling, the 14th
CALPHAD, the 17th thermodynamic property, the 18th density functional theory, the
19th isothermal titration calorimetry, the 20th thermodynamic stability, the 21st
isotherm, the 25th free energy, the 27th biosorption, and the 28th AB initio
calculations in the list showed the increasing trends during the study period. It is
noticeable that CALPHAD, biosorption, and AB initio calculations increased rapidly
from zero articles in 1991-1995 into the top 30 rankings in 2006-2010. CALPHAD was
firstly used as the author keyword of the article entitled compilation of CALPHAD
formation enthalpy data - Binary intermetallic compounds in the COST507 Gibbsian
database in 1998 (Fries & Jantzen, 1998). However, CALPHAD method had been used as
the author keyword of the article titled thermodynamic study on the Ag-Sb-Sn system in
1996 (Oh et al., 1996). The first article which employed biosorption as author keyword was
titled determination of the equilibrium, kinetic and thermodynamic parameters of the
batch biosorption of nickel(II) ions onto Chlorella vulgaris in Process Biochemistry in 2002
(Aksu, 2002). Biosorption as a process for water treatment received increasing attention in
recent years (Ho, 2008). As for AB initio calculations, it was originally utilized as author
keywords of the article an AB initio study of structures and energetics of copper sulfide
clusters in 1996 (Dehnen et al., 1996). Similarly, density functional theory, isothermal
titration calorimetry, and isotherm grew fast from the 1288th (only one article) in 1991-
1995 to 18th, 19th, and 21st in 2006-2010. The article targeting at density functional theory
could be found in 1994 and it was entitled density-functional theory as thermodynamics
(Nagy & Parr, 1994). Thermodynamical interpretation of the density functional theory for an
electronic ground state was developed (Nagy & Parr, 1994). The following article which
utilized density functional theory as author keyword was published in 1999. For the
phrase isothermal titration calorimetry, the article which used it as author keyword
appeared in 1995, and it was titled comparative thermodynamic analyses of the Fv, Fab*
and Fab fragments of anti-dansyl mouse monoclonal-antibody (Shimba, 1995). However, it
should be noticed that there was a bias that all these analysis were based on the data (57%)
with author keywords information from SCI-Expanded.
4. Conclusion
Except the dominant language English, Russian, Chinese, French, Japanese and German were
the most common languages. Above all, the growth process of annual thermodynamic
scientific outputs can be divided into two stages, and the annual growth rate of the second
stage 2004-2010 was four times of that in the first stage 1991-2003. Secondly, Russian Journal of
Physical Chemistry was the most productive journal, and then Journal of Alloys and Compounds
and Journal of Chemical Physics. The most common category was found to be physical
chemistry. Thirdly, the global geographic distribution discovered that Europe took the
leading position, following by Asia, America, Africa and Oceania. In particular, the eight
major industrialized countries (G8: Canada, France, Germany, Italy, Japan, Russia, the UK,
and USA) played a prominent role with more than a half contribution, especially the USA.
However, China experienced the greatest growth rate, and surpassed the USA in 2009 in
terms of annual production, but needs to enhance its quality of publications. China and India
had low collaboration rates while the UK, Netherlands, and Switzerland in Europe with a
smaller size had high collaboration rates. In general, the thermodynamic research presented a
higher international collaboration rate but a lower inter-institutional collaboration rate in
comparison with other fields. Russian Academy of Sciences and Chinese Academy of
Sciences took the leading position of institutions, following distantly by Tohoku University in
Japan, and Centre National de la Recherche Scientifique in France. It was also revealed that
the institutions with lower collaboration rates usually published greater proportion of first
author articles and corresponding author articles, and vice versa. Finally, by analyzing the
latest most frequently used author keywords, it was concluded that the items
thermodynamic properties, kinetics, adsorption, thermodynamic parameters,
phase diagram, and entropy are the traditional research hotspots and will continue being
the emphases in the foreseeable future. CALPHAD, density functional theory,
isothermal titration calorimetry, isotherm, biosorption, and AB initio calculations, as
the quickly increasing concernings, are the newly thermodynamic research hotspots.
Author details
Hui-Zhen Fu1, Yuh-Shan Ho1,2,*
1Department of Environmental Sciences, Peking University, Peoples Republic of China
2Trend Research Centre, Asia University, Taiwan
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THERMODYNAMICS

Copyright 2012 InTech

Publishing Process Manager Marina Jozipovic

First published September, 2012

A free online edition of this book is available at www.intechopen.com

Thermodynamics Fundamentals and Its Application in Science,

Section 1 Classical Thermodynamics 1

Chapter 1 A View from the Conservation of

Chapter 2 Useful Work and Gibbs Energy 29

Section 2 Statistical Thermodynamics 45

Chapter 3 Gibbs Free Energy Formula for Protein Folding 47

Chapter 4 Information Capacity of Quantum Transfer

Chapter 5 Thermodynamics Microscopic Connotations 119

Section 3 Property Prediction and Thermodynamics 133

Chapter 6 Group Contribution Methods for Estimation of Selected

Chapter 7 Thermodynamic Properties and Applications

Chapter 8 Thermodynamics Simulations Applied to

Section 4 Material and Products 215

Chapter 9 Application of Thermodynamics

Chapter 10 Thermodynamics of Wool Dyeing 247

Chapter 11 Mesomechanics and Thermodynamics of

Chapter 12 Thermodynamics of Resulting Complexes

Chapter 13 Thermodynamics of Hydration in Minerals:

Chapter 14 Thermodynamics and Kinetics in

Chapter 15 Statistical Thermodynamics of Lattice Gas

Section 5 Non-Equilibrium Thermodynamics 417

Chapter 16 Influence of Simulation Parameters on the Excitable

Chapter 17 ECOP Criterion for Irreversible

Section 6 Thermodynamics in Diverse Areas 461

Chapter 18 Thermodynamics of Microarray Hybridization 463

Chapter 19 Probing the Thermodynamics of Photosystem I by

Chapter 20 Fuzzy Spheres Decays and Black Hole Thermodynamics 501

Chapter 21 Bibliometric Analysis of Thermodynamic Research:

This book is a result of a careful selection of scientific contributions involved in the

The property prediction in thermodynamics is presented in the following section. A

results on the designing of advances material. A wool dyeing phenomenon described

A View from the Conservation of

Ahmet Grses and Mehtap Ejder-Korucu

Additional information is available at the end of the chapter

Figure 2. A concept map for the conservation of energy law

If two thermodynamic systems, A and B, each of which is in thermal equilibrium

This observation has also been schematically shown in Fig.4

Figure 4. A schematic presentation of the zeroth law of thermodynamics.

Based on preceding observations, some of the physical properties of the system B

oR oF 459.67 oF 1.8 oC 32 oR 1.8 K (3)

2. The first law of thermodynamic (the conservation of energy)

Um T Um 0 RT monatomic gas; translation only (5)

Um T Um 0 5 / 2 RT linear molecule ; translation and rotation only (6)

Um T Um 0 3RT nonlinear molecule; translation and rotation only (7)

approximation; the contribution of molecular vibrations to the internal energy is negligible

It is usually sensible in thermodynamics to inspect the output of a manipulation like this to

constant pressure additionally includes changing of potential energy of particles due to

3. From conservation of energy to heat and work

The internal energy of an isolated system is constant.

The fundamental physical property in thermodynamics is work is done when an object is

Work is the transferred energy by virtue of a difference in mechanical properties from a

The workenergy theorem

Wtotal Wex Win (14)

Wex Wex,c Wnonex Ep,ex Wnonex (15)

Win Win,c Wnonin Ep,in Wnonin (16)