Biomolecules in Solution

§ Most biomolecules are present in solution and are subject to Brownian

motions. In other words, there is no straight path from one position to another
for transport of molecules.

§ Because of Brownian motions, it is hard (impossible) to predict the path and

destination of each individual molecule. But one can predict the group
behavior of a large ensemble of particles. This works in most cases because
biological system (e.g. cells) often produce a large number of the same type of
molecules (e.g. proteins, RNAs, enzyme, carbohydrate, lipid, etc.).

§ However, there are situations that biological molecules have to follow a more
definite path, so “active transport” is necessary (e.g. DNAs or chromosomes).
Such active transport has to consume energy.

§ Active transport will consume ATP (“cash” of the energy for biological systems).

§ Active or “directional” transport may not directly consume ATPs. For example,
one part of the system may consume ATPs to create a potential difference
between two positions, and then charged particles (e.g. protons, ions) may
then move following the potential gradient.
ATP Molecules and “Phosphates”

Adenosine diphosphate (ADP)

Adenine
Adenosine monophosphate (AMP)
Nicotinamide adenine dinucleotide (NAD) Nicotinamide adenine dinucleotide
phosphate (NADP)
 We will discuss
Ø Thermal molecular motion

Ø Molecular and ionic Interactions

Ø Water structure and effects of hydration

Ø Ions in aqueous solutions, the Dybye-Huckel radius

Ø Intermolecular interactions
 Thermal Molecular Movement:
Random Flight Model
The random flight model produces a simple description of the behavior of a “long
molecule” (e.g. protein and nucleic acid).

The random flight chain is characterized by the length “l” and the number “n” of its
segments.

The mean value of distance between the end points of the chain:

𝑑=𝑙 𝑛
1
2
3
d
7 4
6
5
Derivation of Molecular End Points Distance
l $ $ $
𝜃 𝑦!"# = 𝑦! + 𝑙 𝑐𝑜𝑠𝜃 + 𝑙 𝑠𝑖𝑛𝜃
𝑦!"# $
𝑦!"# = 𝑦!$ + 𝑙$ + 2𝑙𝑐𝑜𝑠𝜃

𝑦! 𝑙$ + 2𝑙𝑐𝑜𝑠𝜃
𝑦!"# − 𝑦! = Since 𝑐𝑜𝑠𝜃 =0
𝑦!"# + 𝑦!
𝑙$
𝑊ℎ𝑒𝑛 𝑛 ≫ 1 𝑦!"# − 𝑦! =
2 𝑦!

𝑦!"# − 𝑦!
2 𝑦! =𝑙
𝑛+1 −𝑛 𝑙
𝑑𝑦
Define: 𝑥! = 𝑛𝑙 𝑑𝑥 = 𝑙 Then 2𝑦 =𝑙
𝑑𝑥

Solving the above differential equation: 𝑑𝑦 $ = 𝑙𝑑 𝑥

$ = 𝑙𝑥 = 𝑙$ 𝑛
𝑦 𝑦 =𝑙 𝑛
 Radius of Gyration
The geometric dimension of a molecule can be approximately described by the mean
of the square distance of all atoms of the molecule from the common center of gravity
of the molecule. This is called “radius of gyration: RG.

Based on the “random flight chain model with 𝑛 → ∞,

∑ &!"
𝑟$=
!
$
𝑟 : mean square distance between each atom and the center of gravity.

&" !
Radius of gyration of a molecule: 𝑅' = =𝑙
( (

§ The “radius of gyration” is proportional to 𝑛.

§ For compact molecules, 𝑅' ~𝑛#/* .
§ For rod-shaped molecules, 𝑅' ~𝑛.
 Stock’s Radius (𝑅! )
§ Stock’s radius predicts how a molecule moves in water-like medium as a sphere
with a hydrophilic surface.

§ Stock’s radius can be experimentally measured.

§ Stock’s law: 𝐷𝑟𝑎𝑔 𝑓𝑜𝑟𝑐𝑒: 𝑭 = 6𝜋η𝑅+ 𝒗

 Relations Between 𝑅! 𝑎𝑛𝑑 𝑅"
The relationship between the experimentally determined RG and RS gives important
hints about the configuration of a given macromolecule.

If the molecule resembles a random flight chain, one gets: 𝑅' /𝑅+ = 1.51

,#
If the macromolecule has a spherical but compact structure, = 0.8
,$

Real molecular chains, composed of covalently bound atoms, are usually not as
flexible as predicted by the random flight chain model.

The stiffer the molecules are, the larger the characteristic length of the
segment “𝑙“ should be chosen.

e.g. poly-L-glycine: 𝑙 = 1.38 𝑛𝑚 (𝑎𝑏𝑜𝑢𝑡 4 𝑎𝑚𝑖𝑛𝑜 𝑎𝑐𝑖𝑑𝑠);

a stiffer molecule poly-L-alanine: 𝑙 = 4.10 𝑛𝑚 𝑎𝑏𝑜𝑢𝑡 12 𝑎𝑚𝑖𝑛𝑜 𝑎𝑐𝑖𝑑𝑠 ;
a double strain DNA dsDNA : 𝑙 = 90 𝑛𝑚.
 Brownian Motions
𝑥: a random variable corresponding to the displacement (in 3D space) of a particle
over a time interval 𝛿𝑡. By making the measurements n times in a time sequence,
we obtain values: 𝑥# , 𝑥$ , … … 𝑥! .

𝑥 $ = [𝑥#$ +𝑥$$ + ⋯ + 𝑥!$ ]/𝑛; then the standard deviation or the mean travel
distance for a particle over a time interval 𝛿𝑡 is:

𝑥̅ = 𝑥$
𝑥$
𝑘𝑇 = 𝐹+ 𝑥 $ = 6𝜋𝜂𝑅+ 𝑣$ 𝑥$ = 6𝜋𝜂𝑅+
𝛿𝑡
𝑘: 𝐵𝑜𝑙𝑡𝑧𝑚𝑎𝑛 𝑐𝑜𝑛𝑠𝑡. = 1.38𝑥10-$* 𝐽𝑜𝑢𝑙𝑒/𝐾

𝑘𝑇𝛿𝑡
𝑥$ =
6𝜋𝜂𝑅+
./01
Note: Textbook (2.3.37) has the expression: 𝑥 $ = *23& . 𝑇ℎ𝑒 "r" should be
"diameter" instead of "radius".
For 1um “diameter” particle in water at room temperature, in 1 sec the particle
would create a displacement by Brownian motion of 𝑥̅ = 𝑥 $ ~0.7𝑢𝑚
 Diffusion Coefficient
Einstein relation: the ratio of diffusivity and mobility of a particle is constant,
depending only on the absolute temperature. Strictly speaking, Einstein relation is
true for particles following Boltzman distribution.

𝐷
= 𝑘𝑇
𝜇
Note that the definition of “mobility” may vary depending on specific situations.

In some cases, “mobility” is defined as the ratio between the velocity and force. In
other cases (e.g. electrons in semiconductor or charged molecules under electric
field such as electrophoresis), mobility is defined as the ratio of velocity and applied
electric field. Therefore, the Einstein relation may be written in different ways:
4 4 ./
= 𝑘𝑇 for the former and = for the latter where “Ze” is the charge of the particle.
5 5 67

./
We obtain the diffusivity: 𝐷 = (23,
$
 Water Structure, Effects of Hydration
Crystal water: ice

The tetrahedral ice structure is not destroyed fully when the ice melts. “Structural water
clusters exist and these clusters consist of interconnected water molecules similar to that of
ice.

Near the melting point, about 90-650 water molecules are clustered together. Near the
boiling temperature, 25-75 molecules are connected in a cluster. This gives temperature
dependent viscosity.
 “Ions” in water
Radius of hydration: 𝑅!
Salts in aqueous solution

hydration

Note that the “radius of hydration” does not follow the trend of “ionic radius” in ionic crystal.
 Hydration
The radius of hydration of the alkali ions decreases with increasing atomic mass.

Two types of molecular surfaces to consider: proton donor surface and proton
acceptor surface.

Hydrophobic molecules behave in relation to surrounding water like an “air bubble” n

a layer of 0.1 to 0.2nm, the “effective dielectric constant of water (typically 78)”
decreases to the value of 10.
 Debye-Huckel Radius (Debye Length)
Purposes:

• To calculate the potential profile for charged particles in the buffer solution with
cations (+) and anions (-).

• Understand the concept of Debye length, ionic strength, and introduction of colloidal
physics.

Assume all ions in the buffer solution follows Boltzman distribution. The concentration of
the ion i can be written as
-:7;
𝑐8 𝜑 = 𝐶89 𝑒 ./
𝐶89 : equilibrium concentration of ion “i”, far away from the influence of the central ion.
In other words, 𝑐8 𝜑 = 0 = 𝐶89 .
−1 −1 ! −1 !
From the Poisson equation: =𝛻$𝜑 𝜌= • 𝑐8 𝑧8 𝑁𝑒 = • 𝑐8 𝑧8 𝐹
𝜖9 𝜀 𝜖9 𝜀 8<# 𝜖 9 𝜀 8<#
𝑁: 𝐴𝑣𝑜𝑔𝑎𝑑𝑟𝑜 = 𝑠 𝑛𝑢𝑚𝑏𝑒𝑟 6.02𝑥10$* , 𝐹 𝐹𝑎𝑟𝑎𝑑𝑦 = 𝑁𝑒
 Debye-Huckel Radius (Debye Length)
$
−1 −1 ! -:! 7;
𝛻 𝜑= 𝜌= • 𝑐89 𝑧8 𝐹 𝑒 ./
𝜖9 𝜀 𝜖9 𝜀 8<#

The above equation is a non-linear partial differential equation . To find the analytical
solution, assume 𝑧8 𝑒𝜑 ≪ 𝑘𝑇,
−1 ! 𝑧8 𝑒𝜑
$
𝛻 𝜑~ • 𝑐89 𝑧8 𝐹 (1 − )
𝜖9 𝜀 8<# 𝑘𝑇

> >
In spherical coordinate, assuming center symmetric (i.e. = 0, = 0)
>? >∅
1 𝜕 $ 𝜕𝜑 −1 ! 𝑧8 𝑒𝜑
𝛻$𝜑 = $ 𝑟 = • 𝑐89 𝑧8 𝐹 (1 − )
𝑟 𝜕𝑟 𝜕𝑟 𝜖9 𝜀 8<# 𝑘𝑇
-&

The solution of 𝜑: 𝑧8 𝑒 𝑒 A%
𝜑 𝑟 =
4𝜋𝜖9 𝜀 𝑟
!
𝜖9 𝜀𝑅𝑇 1
Debye length: 𝐿4 = 𝐼𝑜𝑛𝑖𝑐 𝑠𝑡𝑟𝑒𝑛𝑔𝑡ℎ: 𝐼 = • 𝐶89 𝑧8$
2𝐹 $ 𝐼 2
8<#

𝑅 = 𝑘𝑁; 𝐹 = 𝑁𝑒
Debye-Huckel Radius (Debye Length)
!
1
𝐼𝑜𝑛𝑖𝑐 𝑠𝑡𝑟𝑒𝑛𝑔𝑡ℎ: 𝐼 = • 𝐶89 𝑧8$
2
8<#

Debye length: A measure of the penetration of the electric field produced by a

charged particle in the buffer with ionic components.

B&C,/ F.*FH
𝐿4 = $D "E
= E
(𝑛𝑚) Note that the Debye length depends only on the ionic
strength of the buffer. It is independent of the detailed structure of the particle.

Ion concentration distribution

(assuming the center charge
particle is negatively charged)
Debye-Huckel Radius (Debye Length)
Physiological Ringer’s solution: LD=0.7 nm
105 mM NaCl, 5mM KCl, 25 mM Na2HPO4, 2mM CaCl2

Phosphate-buffered saline (PBS):

The most common composition of PBS (1X)

Concentration
Salt Concentration (g/L)
(mmol/L)
NaCl 137 8.0
KCl 2.7 0.2
Na2HPO4 10 1.42
KH2PO4 1.8 0.24
 Electrical Double Layers Model: Stern Model
When a surface is in contact with liquid, there will be a “local charge transfer” between
the two phases. Depending on the chemical potential of the two phases, charge may
either move from the solid surface to the liquid or vice versa. However, it is important
to keep in mind that the whole system including the solid and liquid is “charge neutral”.

One can envision that due to the local charge transfer, there is a fixed layer of charge
developed on the solid surface (e.g. SiO2 surface, or Au surface, etc.). Immediately
next to this surface charge layer, there is another layer of counter charged ions in the
liquid phase. The attractive force between the two layers of charge is so strong that
the charged layer in the liquid can hardly move. We call this layer of charge Helmholtz
layer.

Next to the Helmholtz layer, ions can move around due to diffusion or electric field. As
a result, the ionic distribution will follow the Debye-Huckel model, and the electric
potential decays almost exponentially as characterized by the Debye length.

Note that ions in the Helmholtz layer are considered fixed even though they are in the
liquid. On the other hand all ions outside the Helmholtz layer can move with the liquid.
 Stern Model
A simplified model A more complete model
 Stern Model
!
$
−𝜌 𝐹 : 7;
- !
𝛻 𝜑= =− • 𝑐89 𝑧8 𝑒 ./
𝜀9 𝜖 𝜀9 𝜖
8<#

Assuming we have one-one valent electrolytes (NaCl, KCl), it reduces to

' () () ()
D ! - ! DI& - $DI& 7; $DI& 7;
𝛻$𝜑 = − ∑ 𝑐 𝑧 𝑒 *+ =− 𝑒 *+ −𝑒 *+ = sinh( ) ~
C&B 8<# 89 8 C& B C& B ./ C&B ./

Boundary conditions: 𝜑 ∞ = 0 𝜑 0 = 𝜑J (𝑜𝑟 ζ) Helmholtz potential or zeta potential

Solution of the above equation:

𝜑 𝑥 = ζ 𝑒 -K/A%
 Stern Model
7.0
0
+ +
-7;
-K/A% 𝐻 = [𝐻 ]o𝑒 ./
𝜑 𝑥 =ζ𝑒
pH 𝑒𝜑
ζ= -10 mV 𝑝𝐻 = 𝑝𝐻9 − 0.434
6.2 𝑘𝑇
-50 mV

Helmholtz layer
(Stern layer)

100mM
" "
-7; 𝑒ζ -K/A
𝑁𝑎 = 𝑁𝑎 9 𝑒 ./ ~ 𝑁𝑎" 9 1− 𝑒 %
Na+ 𝑘𝑇
10mM
Cl- "7; 𝑒ζ -K/A
- - -
𝐶𝑙 = 𝐶𝑙 9 𝑒 ./ ~ 𝐶𝑙 9 1+ 𝑒 %
𝑘𝑇
1mM