CY 20202 Physical Chemistry II

Module 3:
Physical Chemistry of Soft matter:
Colloids, Surfaces and Macromolecules

LECTURE 16-18

Department of Chemistry
Indian Institute of Technology Kharagpur
Spring 2023-2024
1

Macromolecules – synthetic and biological

• The structures of macromolecules

• Properties of macromolecules
• Determination of size and shape

Macromolecular structure description

Atomistic:
• Use of atoms, small molecules or functional groups as building
blocks for macromolecular structures

Statistical/physical:
• Applicable for disordered or flexible macromolecules
• Emphasis on a statistical description of molecules that could have
multiple configurations

Swagata Dasgupta, Chemistry IIT Kharagpur 1

 Macromolecules – synthetic and biological

Naturally occurring macromolecules include

• polysaccharides e.g cellulose
• polypeptides e.g. proteins, enzymes
• polynucleotides e.g. deoxyribonucleic acid
(DNA)

Synthetic macromolecules include polymers

such as nylon and polystyrene -
manufactured by stringing together and/or
cross-linking smaller units known as
monomers

Macromolecules – synthetic and biological

Many proteins (specifically enzymes) are monodisperse - have a single molar mass
Small variations possible - one amino acid replacing another etc.

A synthetic polymer is polydisperse – the sample is a mixture of molecules with

various chain lengths and molar masses.

The number-average molar mass, 𝑀 is the value obtained by multiplying

each molar mass by the numerical fraction (𝑁 /𝑁) of molecules of that mass
present in the sample:

𝑁𝑀 𝑁𝑀 ⋯
𝑀
𝑁
⋯
Dividing by 𝑁 we get 𝑀

Swagata Dasgupta, Chemistry IIT Kharagpur 2

 Macromolecules – synthetic and biological

A synthetic polymer is polydisperse –

the sample is a mixture of molecules with various chain lengths and molar
masses.

Weight-average molar mass, 𝑀 is the average calculated by multiplying the

molar masses of the molecules by the mass fraction (𝑚 /𝑚) of each one present
in the sample

𝑚 𝑀 𝑚 𝑀 ⋯
𝑀
𝑚

mi is the total mass of molecules of molar mass Mi and m is the total mass of the
sample

Macromolecules – synthetic and biological

These two averages are different and the ratio 𝑀 /𝑀 is called the
heterogeneity index (or ‘polydispersity index’).

For protein molar masses we expect the various averages to be the same
because unless there has been degradation the sample is monodisperse.

A synthetic polymer normally spans a range of molar masses and the different
averages yield different values. Typical synthetic materials have 𝑀 /𝑀 ≈ 4.

The term ‘monodisperse’ is conventionally applied to synthetic polymers in

which this index is less than 1.1.

Commercial polyethylene samples might be much more heterogeneous, with

an index of close to 30.

Swagata Dasgupta, Chemistry IIT Kharagpur 3

 Statistical Models

• Structure described in terms of spatial probability distribution functions

• Constraints on geometry and/or energy functions that describe interactions

Models for a continuous chain in space that varies in stiffness, constraints on

conformation, and excluded volume.

• Segment models: random coils, feely jointed chain, freely rotating chain
• Lattice models: Flory–Huggins theory
• Continuum model: worm-like chain

Segment Models
• 𝑛 1 beads linked by 𝑛 segments or bonds of length 𝑙

• Each bead has a position 𝑟

• Each bond is assigned a vector 𝑙 𝑟 -𝑟

• The bending angle between adjacent segments 𝑖 and

𝑖 1 is 𝜃

• cos 𝜃 𝑙 .𝑙

• For each bending angle there is an associated dihedral

angle 𝜑 defined as the rotation between line segments

• There are 𝑛 1 separate bending and dihedral angles

Swagata Dasgupta, Chemistry IIT Kharagpur 4

 Random coil
The most likely conformation of a chain of identical units not capable of
forming hydrogen bonds or any other type of specific bond is a random coil.

Polyethene is a simple example

The simplest model of a random coil is a ‘freely jointed chain’, in which any
bond is free to make any angle with respect to the preceding one

Each bond is constrained to a cone of angles

around a direction defined by its neighbor

Real chains are self-avoiding in the sense that

distant parts of the same chain cannot fold
back and occupy the same space.

Measures of size

The size of a freely jointed chain is related to the probability that its ends are a
certain distance apart.

This probability can be calculated by considering a one-dimensional random coil.

How is

Probability distribution in a one-dimensional random coil

Calculate the probability, P, that the ends of a long one-dimensional freely jointed
chain composed of 𝑁 units of length 𝑙 (and therefore of total length 𝑁𝑙) are a
distance 𝑛𝑙 apart.

Swagata Dasgupta, Chemistry IIT Kharagpur 5

 Step 1

Write expressions for the numbers of bonds pointing to the left or right

Conformation of a one-dimensional freely jointed chain can be described by stating the

number of bonds pointing to the right (𝑁𝑅 ) and the number pointing to the left (𝑁𝐿)

The distance between the ends of the chain is (𝑁𝑅 − 𝑁𝐿)𝑙

it follows that n = 𝑁𝑅 − 𝑁𝐿. The total number of units is 𝑁 𝑁𝑅 + 𝑁𝐿

therefore, 𝑁𝑅 = 𝑁 𝑛 and 𝑁𝐿 = 𝑁 𝑛

Step 2 Write an expression for the probability that a polymer has a specified
end-to-end separation

The probability, P, that the end-to-end separation of a randomly selected

polymer is nl is

number of conformations with end−to−end distance nl

𝑃
total number of possible conformations

Each of the N monomer units of the polymer may in principle lie to the left or
the right, so the total number of possible conformations is 2N

The total number of ways, W, of forming a chain of N units with the end-to-
end distance nl is the number of ways of having 𝑁𝑅 right-pointing units, the
rest being left-pointing units.

Swagata Dasgupta, Chemistry IIT Kharagpur 6

 To calculate W, count the number of ways of achieving 𝑁𝑅 right-pointing units
given a total of N units.

This is the same problem as selecting 𝑁𝑅 objects from a collection of N objects

𝑁!
𝑊
𝑁 ! 𝑁 𝑁 !
𝑁!
𝑊
1 1
𝑁 𝑛 ! 𝑁 𝑛 !
2 2

number of conformations with end−to−end distance nl

𝑃
total number of possible conformations

number of conformations with end−to−end distance nl 𝑊

𝑃
total number of possible conformations 2

𝑁!
𝑃
1 1
𝑁 𝑛 ! 𝑁 𝑛 !2
2 2

Step 3 Consider the case of compact chains

/
When the chain is compact n << N 2 /
𝑃 𝑒
𝜋𝑁
it is more convenient to evaluate ln P

Swagata Dasgupta, Chemistry IIT Kharagpur 7

 Equation can be adapted to calculate the probability that the ends of a long
three-dimensional freely jointed chain lie in the range 𝑟 to 𝑟 𝑑𝑟. The
probability is written as 𝑓 𝑟 𝑑𝑟
𝑎
where 𝑓 𝑟 4𝜋 /
𝑟 𝑒
𝜋
/
3
𝑎
2𝑁𝑙

probability distribution [3D random coil]

Statistical Variables for Macromolecules

End-to-end distance
The contour length is the full length of the polymer along the contour of the chain:

𝑅 𝑁𝑙

The contour length is proportional to the number of monomers and the length
occupied by each monomer. Each chain will have the same contour length but
varying dimensions in space due to flexibility

Conformational variation is measured by the end-to-end vector between the first

and last bead, 𝑅 𝑟 𝑟 or 𝑅 ∑ 𝑙

Swagata Dasgupta, Chemistry IIT Kharagpur 8

 The dimensions of a polymer can be characterized by the statistics of the end-
to-end distance.

𝑅 𝑅·𝑅 𝑙 · 𝑙

Expanding these sums - two sets of terms:

(1) the self-terms with 𝑖 𝑗 and
(2) the interbond correlations 𝑖 𝑗
Angle between segments
𝑅 𝑛𝑙 𝑙 ·𝑙 𝑖 𝑎𝑛𝑑 𝑗

𝑛𝑙 𝑙 ∑ cos 𝜃

Random walks

• N “steps” each of length l

• Expected end-to-end distance is 𝑅 = l √𝑁
• Expected 𝑅 𝑙 √ 𝑁/6

Swagata Dasgupta, Chemistry IIT Kharagpur 9

 Lattice Models
• The “hydrophobic zipper” effect:

Ken Dill ~ 1997

Scoring Lattice Models

• H/P model scoring: count noncovalent hydrophobic interactions.

• Sometimes:
– Penalize for buried polar or surface hydrophobic residues

Swagata Dasgupta, Chemistry IIT Kharagpur 10

 A Simple 2D Lattice

3.5Å

Lattice Folding

Swagata Dasgupta, Chemistry IIT Kharagpur 11

 Lattice Folding
• Build a “n x m” matrix (a 2D array)
• Choose an arbitrary point as your N terminal • Red = hydrophobic
residue (start residue) • Blue = hydrophilic
• Add or subtract “1” from the x or y position of
the start residue • If Red is near empty space E = E+1
• Check to see if the new point (residue) is off the • If Blue is near empty space E = E-1
lattice or is already occupied • If Red is near another Red E = E-1
• Evaluate the energy • If Blue is near another Blue E = E+0
• Go to step 3 and repeat until done • If Blue is near Red E = E+0

Radius of Gyration of a Polymer Coil

The radius of gyration Rg is defined as the RMS distance of the
collection of atoms from their common centre of gravity.

For a polymer coil with rms end-to-end distance R ;

1 2 1/ 2 l
RG  R  N 1/ 2
6 6

1 N N
R 2
G
2N 2
 r
i 1 j 1
2
ij

Distance between particles i and j

Swagata Dasgupta, Chemistry IIT Kharagpur 12

 Radius of Gyration
Radius of gyration

• structural variable closely related

to experimental observables

• polymer dimensions are expressed

as extensions relative to the center
of mass for the chain

• useful for branched polymers and

heteropolymers (such as proteins)

Position and mass of 𝒊𝒕𝒉 bead 𝒓𝒊 and 𝒎𝒊

Center of mass of the polymer defined as a mass-weighted mean position

of the beads in space:

∑ 𝑚𝑟
𝑅
∑ 𝑚

The denominator corresponds to the mass of the polymer M ∑ 𝑚

If all beads have the same mass then 𝑚𝑖 /𝑀 1/ 𝑛 1

𝑅0 is the geometrical mean of their positions 𝑅 ∑ 𝑟

Swagata Dasgupta, Chemistry IIT Kharagpur 13

 The radius of gyration RG for a configuration of the polymer describes the
mass-weighted distribution
1
𝑅 𝑆
𝑛 1

𝑆 is the gyration radius – the radial

distance of the 𝑖𝑡ℎ bead from the center

𝑆 𝑟 𝑅 (mass weighted)

𝑆 𝑟 𝑅 (equal mass beads)

Deriving an expression for the restoring force of a perfect elastomer

An elastomer is a flexible polymer that can expand or contract easily upon

application of an external force.

Elastomers are polymers with numerous crosslinks that pull them back into their

original shape when a stress is removed.

A freely jointed chain behaves as an elastomer for small extensions.

It is a model of a ‘perfect elastomer’, a polymer in which the internal energy is

independent of the extension, and can be used to deduce the restoring force

associated with stretching or compression of the chain.

Swagata Dasgupta, Chemistry IIT Kharagpur 14

 Deriving an expression for the restoring force of a perfect elastomer

The goal is to find an expression for the restoring force, F, of an elastomer,

modelled as a one-dimensional random coil composed of N units each of length l,

when the chain is stretched or compressed by a distance x, given as,

𝒙 𝒗𝒍 … … … … 1

Step 1:
Using thermodynamics to relate the restoring force to the entropy
The work done on an elastomer when it is extended reversibly through a distance dx is
Fdx.
The change in internal energy, from
𝒅𝑼 dwrev+dqr𝒆𝒗
With
dqrev TdS
is therefore given as,
dU Fdx TdS

Swagata Dasgupta, Chemistry IIT Kharagpur 15

 Step 1:
Using thermodynamics to relate the restoring force to the entropy
For an isothermal extension,

𝝏𝑼 𝝏𝑺
𝑭 𝑻
𝝏𝒙 𝑻
𝝏𝒙 𝑻
In a perfect elastomer, as in a perfect gas, the internal energy is independent of the
𝝏𝑼
dimensions (at constant T), so 𝟎
𝝏𝒙 𝑻

The restoring force is therefore,

𝝏𝑺
𝑭 𝑻
𝝏𝒙 𝑻

Step 2
To evaluate the force from the change in conformational entropy

𝒙
𝝀
𝑵𝒍
For small displacements (λ ≪ 1, corresponding to x ≪ Nl and therefore x ≪ Rc)
𝝀𝒌𝑻 𝒌𝑻
𝑭 𝒙
𝒍 𝑵𝒍𝟐

For small displacements the sample obeys Hooke’s law: the restoring force is
proportional to the displacement and the force constant kf (the constant of
proportionality between the force and the displacement) is

𝒌𝑻
𝒌𝒇
𝑵𝒍𝟐

Swagata Dasgupta, Chemistry IIT Kharagpur 16

 Thermal properties

 The crystallinity of synthetic polymers can be destroyed by thermal motion at sufficiently high
temperatures
 This change in crystallinity may be thought of as a kind of intramolecular melting from a crystalline
solid to a more fluid random coil
 Polymer melting also occurs at a specific melting temperature, Tm, which increases with the
strength and number of intermolecular interactions in the material
 Polyethene, which has chains that interact only weakly in the solid, has Tm = 414 K
 Whereas, nylon-66 fibers, where there are strong hydrogen bonds between chains, have Tm =
530 K
 High melting temperatures are desirable in most practical applications involving fibers and plastics

 All synthetic polymers undergo a transition from a state of high to low chain mobility at the glass
transition temperature, Tg
 To visualize the glass transition, we can consider what happens to an elastomer as its temperature is
lowered
 There is sufficient energy available at normal temperatures for limited bond rotation to occur and the
flexible chains writhe
 At lower temperatures, the amplitudes of the writhing motion decrease until a specific temperature, Tg, is
reached at which motion is frozen completely and the sample forms a glass
 Glass transition temperatures well below 300 K are desirable in elastomers that are to be used at normal
temperatures
 Both the glass transition temperature and the melting temperature of a polymer may be measured by
calorimetric methods
 As the motion of the segments of a polymer chain increase at the glass transition temperature, Tg may also
be determined from a plot of the specific volume of a polymer (the reciprocal of its mass density) against
temperature

Swagata Dasgupta, Chemistry IIT Kharagpur 17

 The variation of specific volume with temperature of a synthetic polymer. The glass transition
temperature, Tg, is at the point of intersection of extrapolations of the two linear parts of the curve.

Hydrodynamic radius, Rh

• Rh is the radius of a hypothetical hard sphere that diffuses with the same
speed as the particle under examination

• The radius calculated from the diffusional properties of the particle is

indicative of the apparent size of the dynamic hydrated/solvated particle
+ _
_ H2O
+
H2O
+ H2O
_ H2O
H2O

Swagata Dasgupta, Chemistry IIT Kharagpur 18

 Hydrodynamic radius from diffusion coefficient
k bT
D 
f
kbT
Einstein equation D
and 6Rh
f  6Rh Stokes-Einstein equation
Stokes equation
k bT
R 
6  D
h
T

translational diffusion coefficient, DT

Rh and shape of particles

• For the center-of-mass motion, an ellipsoid with a
hydrodynamic radius Rh receives the same friction as sphere of
radius Rh does
• A linear chain with a hydrodynamic radius Rh diffused with the
same diffusion coefficient as the sphere of radius Rh

Rh
Rh
Rs=Rh

sphere ellipsoid linear chain

Swagata Dasgupta, Chemistry IIT Kharagpur 19

 Protein structure

 Proteins are single polypeptide chains where multiple amino acids

form a sequence & interact with each other following a three-
dimensional arrangement.

 Four levels of Protein structure are commonly defined.

• Primary Structure
• Secondary structure
• Tertiary structure
• Quaternary structure

Proteins can be of different types with varying their

functions such as an enzyme, a hormone, a structural
protein, or an antibody.

Structural variations

Insulin

Immunoglobulin
Trypsin

Swagata Dasgupta, Chemistry IIT Kharagpur 20

 Classes of Proteins

Based on structure and solubility,

proteins can be grouped into three large classes:

Fibrous Globular Membrane

Backbone Torsion Angles

Swagata Dasgupta, Chemistry IIT Kharagpur 21

 Backbone Torsion Angles
• ω angle tends to be planar (0º - cis, or 180 º -
trans) due to delocalization of carbonyl pi
electrons and nitrogen lone pair
• φ and ψ are flexible, therefore rotation occurs here
• However, φ and ψ of a given amino acid residue
are limited due to steric hindrance

Alpha helices
phi(deg) psi(deg) H-bond pattern
------------------------------------------------------------------
right-handed alpha-helix -57.8 -47.0 i+4
pi-helix -57.1 -69.7 i+5
3-10 helix -74.0 -4.0 i+3

(omega is 180 deg in all cases)

-----------------------------------------------------------------
From http://www.imb-
jena.de

April 8, 2003 Claus Lundegaard

Swagata Dasgupta, Chemistry IIT Kharagpur 22

 Beta Strands
phi(deg) psi(deg) omega (deg)
------------------------------------------------------------------
beta strand -120 120 180
-----------------------------------------------------------------

Hydrogen bond patterns in beta sheets. Here a four-stranded

beta sheet is drawn schematically which contains three
antiparallel and one parallel strand. Hydrogen bonds are
indicated with red lines (antiparallel strands) and green lines
(parallel strands) connecting the hydrogen and receptor oxygen.

From http://broccoli.mfn.ki.se/pps_course_96/

April 8, 2003 Claus Lundegaard

Structure Stabilizing Interactions

• Noncovalent
– van der Waals forces (transient, weak electrical
attraction of one atom for another)
– Hydrophobic (clustering of nonpolar groups)
– Hydrogen bonding
δ- δ+ δ-
D–H A
• Covalent
– Disulfide bonds

Swagata Dasgupta, Chemistry IIT Kharagpur 23

 The hydrophobic effect
H H
H
H H
H H
H H H
H H H H
H
H H H -
H + H H
H H H H
H H H H
+
H
- H
H
H
H H H H H
H
H

Non-polar solute Polar solute

The dissolution of a non-polar solute in water is unfavourable –

for polar solutes there is favourable hydrogen bonding

Forces driving protein folding

• It is believed that hydrophobic collapse is a key driving force

for protein folding
– Hydrophobic core
– Polar surface interacting with solvent
• Minimum volume (no cavities)
• Disulfide bond formation stabilizes
• Hydrogen bonds
• Polar and electrostatic interactions

Native state is typically only 5 to 10 kcal/mole

more stable than the unfolded form

Swagata Dasgupta, Chemistry IIT Kharagpur 24

 Aggregation of individual protein.

1. Hydrophobic attraction: the close association

attraction of hydrocarbon side-chains.
2. Ionic bond: between positively charged groups and
negatively charged groups.
3. Hydrogen bonds
4. Disulfide bonds

A protein has size and shape as well as unique arrangement

through hydrogen, ionic, hydrophobic and disulfide bonds.

End-to-end distance
The contour length is the full length of the polymer along
the contour of the chain:

𝑅 𝑁𝑙

The contour length is proportional to the number of monomers and the length
occupied by each monomer. Each chain will have the same contour length but
varying dimensions in space due to flexibility

Conformational variation is measured by the end-to-end vector between the first

and last bead, 𝑅 𝑟 𝑟 or 𝑅 ∑ 𝑙

Swagata Dasgupta, Chemistry IIT Kharagpur 25

 Random coil
l
Radius of the random coil formed is proportional to

the square root of N because steps – bonds – that can

double back as the chain grows

Root mean square separation 𝑅 𝑅 / is a measure

of the average separation of the two ends of a random coil.

• N “steps” each of length l

• Expected end-to-end distance is 𝑅 = l √𝑁
• Expected 𝑅 𝑙 √ 𝑁/6

Random coil

Least structures conformation of a polymer

Random coil model does not consider the role of the solvent
Poor solvent :
Causes coil to tighten to minimize solute-solvent interactions
- Compact structure
Good solvent
- More flexible because of favorable solute-solvent interactions

Swagata Dasgupta, Chemistry IIT Kharagpur 26

 The protein sequence contains all information needed to
create a correctly folded protein.

• Many proteins fold spontaneously to their native structure

• Protein folding is relatively fast
• Chaperones speed up folding, but do not alter the structure

Energy Terms
Covalent q 
r

Bending Torsional
Stretching
K(i -  j) 2 K(cos(nj))2
Kr(ri - rj)2

Noncovalent
r r
r

van der Waals Coulomb H-bond

Aij/r6 - Bij/r12 qiqj/4rij Cij/r10 - Dij/r12

Swagata Dasgupta, Chemistry IIT Kharagpur 27

 Approx. bond strength in
Interaction
kJ/mole
Covalent bonds > 200 (ranging up to 900)
Ionic 20-40
Hydrogen bond ~5-10
Hydrophobic ~8
van der Waals ~4

AMBER (Assisted Model Building with Energy Refinement ) force field

3 Vn
E total   Kr (r  req ) 2   K (   eq ) 2    2
[1  cos(n )]
bonds angles dihedrals 1

atoms  aij bij  atoms qi q j

   12  6  
r 
i j  ij rij  i  j  rij

Representations of myoglobin

Swagata Dasgupta, Chemistry IIT Kharagpur 28

 Methods to determine molar mass

Mass spectrometry

Laser light scattering

Ultracentrifugation

Electrophoresis

Viscosity

Mass Spectrometer

Mass spectrometer consists of

• An ionization Source: The ionization of molecules produces gas
phase ions that can be moved by external electric and magnetic
fields
• Mass Analyzer: According to the mass-to-charge (m/z) ratio ions
are sorted and separated
• Ion detection system: The separated ions are then detected by a
detector

Swagata Dasgupta, Chemistry IIT Kharagpur 29

 Types of Ionization techniques

doi: 10.1038/nature01511

Matrix-Assisted Laser Desorption Ionization (MALDI)

• Soft ionization technique
• Strikes large molecule with a laser into minimal ion fragments and
produces very few multi-charged ions
• Applicable in the analysis of biomolecules

https://www.creative-proteomics.com/technology/maldi-tof-mass-spectrometry.htm

Swagata Dasgupta, Chemistry IIT Kharagpur 30

 MALDI-Time of Flight (ToF)
The m/z ratio of an ion is calculated by analyzing the time needed for it
to travel the length of the flight tube

https://www.shimadzu.com/an/products/maldi/ms-applications/principle-of-malditofms/index.html

MALDI-Time of Flight (ToF)

Multiple peaks in a spectrum arise from polymers of different lengths

Intensity of each peak is proportional to the abundance of each

polymer in the sample

Values of 𝑀 and 𝑀 and the heterogeneity index can be calculated

from the data

Swagata Dasgupta, Chemistry IIT Kharagpur 31

 Scattering by macromolecules

E
Scattered Light

B
Incident light

particle

• Oscillating E field from light makes electronic cloud oscillate

surrounding the particle
• Accelerating charges means EM radiation is produced which radiates
into different directions
 Scatter

Measurement of scattered light

The intensity, polarization and angular distribution of the light

scattered from a colloidal system depend on

• size and shape of the scattering particles,

• the interactions between them, and

• the difference between the refractive indices of the

particles and the dispersion medium.

64

Swagata Dasgupta, Chemistry IIT Kharagpur 32

 Light scattering

Scattering from particles moving or placed randomly

Scattering from particles placed orderly – reflection,

refraction, diffraction

Light beam attenuated – loss in intensity

If the attenuation is due to absorption

then 𝐼 𝐼 10 ; 𝛼 absorption coefficient

And if it is due to scattering then 𝐼 𝐼 𝑒 ; 𝜏 turbidity

Bases 10 and e are by convention

Setup to measure light scattering

Rayleigh scattering, dispersion of electromagnetic radiation by particles that

have a radius less than ~ 1/10 the wavelength of the radiation

The intensity or the power of the

scattered light is measured as a
function of the scattering angle, 

Swagata Dasgupta, Chemistry IIT Kharagpur 33

 Sample is irradiated with monochromatic light from a laser

Intensity of scattered light measured as a function of the angle,  that

the direction of the laser beam makes with respect to the detector from
the sample at a distance, r

Intensity of light scattered is given by the Rayleigh ratio

𝐼 𝜃
𝑅 𝜃 𝑟
𝐼

Where 𝐼 is the intensity of the incident laser radiation

Factor 𝑟 occurs in the definition because the light wave spreads out
over a sphere of radius 𝑟 and surface area 4𝜋𝑟

Intensity 𝐼 𝜃 decreased by a factor proportional to 𝑟

When the size of the particle is negligible compared to the wavelength

of the incident radiation

In general,

𝑅 𝜃 𝐾𝑃 𝜃 𝑐 𝑀 where 𝑃 𝜃 is the structure factor related to the size of

the molecule

Swagata Dasgupta, Chemistry IIT Kharagpur 34

 For larger particles, we define a function P(), sometimes called the particle form
factor, which is the ratio of scattering from the finite-sized particle to that from an
infinitely small particle of the same mass.

P() = scattering by real particle at θ / scattering by hypothetical particle at θ

P() is sensitive to the shape of the particle. Typically, calculations are carried out for a
variety of shapes and compared to the experimental data.

q 2 RG2
P( )  1  where RG2 is the
3
radius of gyration and q  (4 /  ) sin( / 2)

ln(1  x)   x
q 2 RG2
Thus, ln P( )  
3

Atomic Force Microscopy

http://www.micromemanalytical.com/AFM/AFM-WEB.htm

Swagata Dasgupta, Chemistry IIT Kharagpur 35

 Atomic Force Microscopy Piezo-crystal converts
pressure to voltage

Probe Has potential for very

high resolution
Cantilever arm attached to
piezo-electric crystal
Path

Image
in 3D
An image of double-stranded
DNA molecules, taken using
tapping mode in air

Molecule in an Electric Field

f*u Q+ QE

http://web.ncf.ca/ch865/englishdescr/EFld2Plates.html

Swagata Dasgupta, Chemistry IIT Kharagpur 36

 Used to model electrostatic mobility.
𝑍𝑒
𝜇
𝑓
Assume that the particle is a sphere,
then Stokes equation applies.
𝑍𝑒
𝜇
6𝜋𝜂𝑅

Electrophoresis (SDSPAGE)

Swagata Dasgupta, Chemistry IIT Kharagpur 37

 Viscosity
Viscosity average molecular mass can be determined from measurements of the
viscosity of macromolecules

Ostwald viscometer – viscosity measured by measuring the time required

for the liquid to drain through a capillary between two specific marks on the viscometer

At low concentrations the viscosity, 𝜂 of the solution is related to the

viscosity of the pure solvent, 𝜂 by

𝜂 𝜂 1 𝜂𝑐 𝜂 𝑐 ⋯

/
The intrinsic viscosity 𝜂 is given by 𝜂 lim =lim
→ →

For measuring viscosity in the Ostwald viscometer

Most work based on empirical observations

Determination of molar mass based on comparisons with standard

primarily monodisperse systems.

Solutions that behave ideally fit the empirical

Mark-Kuhn-Houwink-Sakurada equation: 𝜂 𝐾𝑀

K and a are constants that depend on the solvent and the type pf
macromolecule

Viscosity values for a series of concentrations measured

𝜂/𝜂 1
𝜂 lim
→ 𝑐

Swagata Dasgupta, Chemistry IIT Kharagpur 38

 Viscosity

MODULE 3
1. Colloidal state of matter; Properties of lyophilic and lyophobic colloids
2. Stability of colloidal solutions, Molecular self-assembly
3. Introduction to thermodynamics of electrified interfaces
4. Introduction to thermodynamics of surfaces: surface energy; adsorption
isotherms
5. Macromolecules – synthetic and biological; The structures of macromolecules;
Properties of macromolecules; Determination of size and shape

Swagata Dasgupta, Chemistry IIT Kharagpur 39