Molecular Modeling and Simulation

PEN-521

Module 2: Polymer Chain Models

Lpp ~ 0.56 N Å

3N 0.5 Å

R ~ 0.8N 0.5 Å

Course Instructor
Dr. Gaurav Manik
Department of Polymer and Process Engineering
06/23/2025 Indian Institute of Technology Roorkee 1
 Polymer Chain Conformations and
models
• End-to-end distance & Radius of Gyration
• Concept of Characteristic Ratio
• Spatial Distributions and Moments of Distributions
• The Unperturbed State and Excluded Volume
• Chain Models
• The Random Walk Chain
• The Freely Jointed Chain
• The Freely Rotating Chain
• The Freely Orienting Chain

2
 End-to-end distance, r
• Chain pictured as made of N steps of each step length, Ii
joining atoms, A0 to AN
A3

A2

A1

A0
AN
r
𝑛
𝑟 =∑ I 𝑖
𝑖=1
2

• Direction of r dependent on direction taken for A1

 End-to-end distance, r
• Chain pictured as made of N steps of each step length, Ii
joining atoms, A0 to AN
A3
𝑟 =𝑟 ∙𝑟 =∑ I i ∙I j
2
A2
𝑖, 𝑗

𝑟 =∑ 𝑙 +2 ∑
2 2
A1
𝑖 I i ∙I j
𝑖 0<𝑖< 𝑗 ≤𝑛
A0
AN
r

• In general, for distance b/w two atoms

𝑗
𝑟 2𝑖𝑗 = ∑ 𝑙 2𝑖 +2 ′ ∑ I i 2∙ I j
′ ′

𝑖 ′ =𝑖+1 𝑖<𝑖 ′ < 𝑗 ′ ≤ 𝑗

 End-to-end distance, r

A3 ⟨ 𝑟 ⟩ =∑ ⟨𝑙 ⟩ +2 ∑ ⟨ I i ∙I j ⟩
2 2
𝑖
𝑖 𝑖< 𝑗
A2

∑ ⟨ 𝑖 ⟩= ⟨ ⟩
∑𝑖 ⟨ ⟩
2 2 2
𝑙 𝑙 =𝑛 𝑙
𝑖 𝑖
A1
Average bond or step length
A0
AN
r
Hence, ⟨ 𝑟 2 ⟩ =𝑛 ⟨ 𝑙2 ⟩ +2 ∑ ⟨ I i ∙I j ⟩
𝑖< 𝑗

2
 Radius of Gyration
Root mean squared distance of collection of atoms, or
groups, from their center of gravity 𝑛
𝑠2 =( 𝑛+1 ) ∑ 𝑠2𝑖
−1
A3
0
A2
si  distance of atom i from
center of gravity of chain in
A1
specific configuration
𝑥
A0
AN 𝑠2 =𝑥 −1 ∑ 𝑠2𝑘
r 1

x  number of repeating units in

chain
 Radius of Gyration
Root mean squared distance of collection of atoms, or
groups, from their center of gravity
A3
According to Langrange,

∑
A2 2 −2 2
𝑠 =( 𝑛+1 ) 𝑟 𝑖𝑗
0 ≤ 𝑖< 𝑗≤𝑛

A1

A0
AN
r
• For N+1 particles, mean squared distance from center of gravity
directly related to sum of squares of distances between every pair
of particles
• Interatomic distances dictate the spatial domain of a polymer
configuration
 Characteristic Radio, Cn or C

A3 ⟨ 𝑟 2 ⟩ =𝑛𝑙2 +2 ∑ ⟨ I i ∙I j ⟩
A2 𝑖< 𝑗

Defined as:
A1
𝐶 𝑛 =⟨ 𝑟 2 ⟩0 /𝑛 𝑙 2
A0
AN
r

If freely jointed, then ??

2
 Spatial Distributions
• Function that models random
processes  Gaussian Function
• Wij(rij) denotes distribution of vector
r
distance rij
• Wij(rij)drij  probability that atom j
rij
situated within element of volume drij
r drij
located at rij relative to atom i.
• Likewise, W(r)  distribution of end-to-
end distance

• For chain unperturbed by self-
interactions & external constraints,
W(r)  Gaussian3in nature  [ ( ⟨ ⟩ )r ] 3
𝑟
2 2

( )
3/ 2 − 2
2 𝑟
W ( r ¿= 𝑒
2𝜋 ⟨ 𝑟2⟩
 Spatial Distributions
[ ( 3
) 𝑟
2

]
( )
3/ 2 −
3 2 ⟨ 𝑟2 ⟩
W ( r ¿= 𝑒
2𝜋 ⟨𝑟 ⟩
2

• Probability that chain end-to-end length lies between r & r+dr


• Normalizing we get, ∞

AND ∫ 𝑊 ( 𝑟 ) 4 𝜋 𝑟
4
𝑑𝑟 = ⟨ 𝑟
2
⟩
0

2
Gaussian Distribution Function of the end-to-end vector plotted
against r for a polymer chain with  =30nm
 Polymer Chain Models

• Random Walk (or Random Flight) Model

• Freely jointed (or hinged chain) model
• Freely Rotating Model
• Freely Orienting Model
 Polymer Chain Models

Random Walk (or Random Flight) Model

• Random walk from origin of coordinate system; Each
successive step can take all orientations in space with
equal probability, independent of its predecessors

Drinking is injurious to health

 Polymer Chain Models

Random Walk (or Random Flight) Model A3

• Angles may assume any values randomly A2

⟨ 𝑟 2 ⟩ =𝑛 ⟨ 𝑙2 ⟩ +2 ∑ ⟨ I i ∙I j ⟩
𝑖< 𝑗 A1

• No correlations b/w successive bonds A 0

AN
• Hence, ⟨ I i ∙ I j ⟩ =0 ,𝑖 ≠ 𝑗 r

⟨ 𝑟 2 ⟩ =𝑛 ⟨ 𝑙2 ⟩
 Polymer Chain Models

Random Walk (or Random Flight) Model

• Step length, l, varies according to prob. Distribution,
P(l), of any form.
• Unperturbed (excluded vol compensated & no external
forces present) or  state, mean squared end-to-end
distance given by- 2
⟨ 𝑟 ⟩0 =𝑛 𝑙
2

• Mean squared radius of

gyration given by-− 2
2
𝑠 =( 𝑛+1 ) ∑ 𝑟
2
𝑖𝑗
0 ≤ 𝑖< 𝑗≤𝑛
2
¿ 𝑠 ≥( 𝑛+1 )
−2
∑ 2
¿𝑟 >¿¿
𝑖𝑗
0 ≤ 𝑖< 𝑗≤ 𝑛
 Polymer Chain Models

Random Walk (or Random Flight) Model

• Dimensionless ratios of higher even powers of r & s
important for several properties.
 Polymer Chain Models

Freely jointed (or hinged chain) model

• First developed by Kuhn and Grun
3
• Considers a chain to consist of ‘n’
2
independent, freely jointed segments n
(bonds) of fixed length ‘a’ or ‘l’. 1
n-2
n-1 a or L

• ETE distance given by –

⟨ 𝑟 2 ⟩0 =𝑛 𝑙2
• RG given by -
⟨ 𝑠2 ⟩0 / 𝑛 𝑙 2= 1 (𝑛 +2 ) /( 𝑛+1)
6
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 Polymer Chain Models
Freely Jointed Chain Model 2
𝑠 =( 𝑛+1 ) ∑ 𝑟
−2 2
𝑖𝑗
Radius of Gyration 0 ≤ 𝑖< 𝑗≤𝑛

A3
⟨ 𝑠 ⟩0 =𝑙 (𝑛+1) ∑ ( 𝑗− 𝑖 )
2 2 −2

0 ≤𝑖< 𝑗≤ 𝑛
A2 𝑛 𝑗
¿ 𝑙 2 (𝑛+1)−2 ∑ ∑ 𝑘
𝑗 =1 𝑘=1

A1 𝑛
¿ 𝑙 2 (𝑛+1)−2 ∑ 𝑗 ( 𝑗+1)/2
𝑗=1
A0
AN ⟨ 𝑠2 ⟩0 / 𝑛 𝑙 2= 1 (𝑛 +2 ) /( 𝑛+1)
r 6

Freely jointed, and large chain, n 

( ⟨ 𝑠 2 ⟩ 0 / 𝑛 𝑙2 ) ∞ = 61 Debye Relation 2
 Polymer Chain Models

Freely jointed (or hinged chain) model

• FJ chain equivalent to real chain of n skeletal
bonds of equal length, l 3
2
• Condition  <r >0 and length of fully
2
n
1
extended chain  same n-2
a or L
n-1
′ ′
𝑛 𝑙 =𝑟 𝑚𝑎𝑥

𝑛 𝑙 =⟨ 𝑟 ⟩0
′ 2
(
′
) 2

• Fully extended length ?? PE ??

• nl sin (/2) = 0.83nl, l =1.54Å,  (C-C-C)=112o
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 Polymer Chain Models

Freely Rotating Chain model

• Considers n bonds of fixed length joined
at fixed bond angles () 3
2
=cos n
1
⟨ I i ∙ I i+ k ⟩ =𝑙 2 𝛼 𝑘 n-2
a or L
n-1

⟨ 𝑟 2 ⟩0 =𝑛𝑙2 +2 𝑙 2 ∑ 𝛼 𝑗− 𝑖
𝑖< 𝑗
𝑛−1
𝐶 𝑛 ≡ ⟨ 𝑟 2 ⟩ 0 /𝑛𝑙2=1+ ( 2/𝑛 ) ∑ ( 𝑛−𝑘 ) 𝛼𝑘
𝑘=1
𝑛− 1 𝑛−1
¿ 1+2 ∑ 𝛼 − ( 2/𝑛 ) ∑ 𝑘𝛼
𝑘 𝑘

𝑘=1 𝑘=1
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 Polymer Chain Models

Freely Rotating Chain model

• Considers n bonds of fixed length joined
at fixed bond angles 3
2
n
1
n-2
n-1 a or L

• In the limit of large n,

𝐶∞ =(1+𝛼)/(1−𝛼¿)=(1+cos𝜃)/ ( 1−cos𝜃 ) ¿

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 Polymer Chain Models
Geometrical correlations of Bond Vectors

• Ti  orthogonal matrix which by pre-multiplications

transforms a vector v with components vx, vy and vz
expressed in reference frame i+1 (of i+1th bond) to its
expression v’ in reference frame i (of ith bond)
′
v =T 𝑖 v

[ ]
cos 𝜃𝑖 sin 𝜃𝑖 0
T 𝑖= sin 𝜃𝑖 cos∅ 𝑖 −cos 𝜃 𝑖 cos∅ 𝑖 sin ∅ 𝑖
sin 𝜃𝑖 sin ∅ 𝑖 − cos𝜃 𝑖 sin ∅ 𝑖 − cos∅ 𝑖

06/23/2025 Indian Institute of Technology Roorkee 21

 Polymer Chain Models

Geometrical correlations of Bond Vectors

′
v =T 𝑖 v

[ ]
cos 𝜃𝑖 sin 𝜃𝑖 0
T 𝑖= sin 𝜃𝑖 cos∅ 𝑖 −cos 𝜃 𝑖 cos∅ 𝑖 sin ∅ 𝑖
sin 𝜃𝑖 sin ∅ 𝑖 − cos𝜃 𝑖 sin ∅ 𝑖 − cos∅ 𝑖
T 𝑖 ⋯T 𝑗 −2 T 𝑗 −1 I 𝑗

[] []
𝑙𝑗 1
I 𝑗= 0 = 𝑙 𝑗 0
0 0
𝑇
I 𝑖 ∙ I 𝑗 =I ( T 𝑖 ⋯ T 𝑗− 1 ) I 𝑗
𝑖

[]
1
¿ 𝑙𝑖 𝑙 𝑗 [ 1 0 0 ] ( T 𝑖 ⋯ T 𝑗 −1 ) 0 ⟨ I 𝑖 ∙ I 𝑗 ⟩ =𝑙 𝑖 𝑙 𝑗 ⟨ T 𝑖 ⋯ T 𝑗 −1 ⟩ 11
0
¿ 𝑙 𝑖 𝑙 𝑗 ( T 𝑖 ⋯ T 𝑗 −1 ) 11
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 Polymer Chain Models
Hindered rotation or Freely Orientating model
• Considers fixed bond angles &
steric hindrance effects on
torsion angles, 
• Bonds considered to exist only
in favorable bond
conformations (torsion angles).
H Me
2
1 C C 3
4
C C
H2 H2 n

Poly-isoprene

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 Polymer Chain Models
Hindered rotation model
• Considers fixed bond angles &
steric hindrance effects on torsion
angles  favorable bond
conformations (torsion angles).

[ ]
cos 𝜃𝑖 sin 𝜃𝑖 0
T 𝑖= sin 𝜃𝑖 cos ∅ 𝑖 −cos 𝜃 𝑖 cos ∅ 𝑖 sin ∅ 𝑖
sin 𝜃𝑖 sin ∅ 𝑖 − cos 𝜃 𝑖 sin ∅ 𝑖 − cos ∅ 𝑖

H
2
1 C C

[ ]
cos 𝜃𝑖 sin 𝜃𝑖 0 C
⟨ T 𝑖⟩= 0 0 0 H2
0 0 0
Poly-isoprene

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 Polymer Chain Models
Hindered rotation model
• Considers fixed bond angles &
steric hindrance effects on torsion
angles  favorable bond
conformations (torsion angles).

[ ]
cos 𝜃𝑖 sin 𝜃𝑖 0
⟨ T 𝑖⟩= 0 0 0
0 0 0

(
1+cos 𝜃
)( 1+ ⟨ cos ∅ ⟩
)
2
𝐶∞ = 1 C C
1− cos 𝜃 1 − ⟨ cos ∅ ⟩ C
H2
¿ ( 1+𝛼
1− 𝛼 )( ) 1+𝜂
1 −𝜂 Poly-isoprene

06/23/2025
( )( )( 1− 𝜂 )
𝛼
( ⟨ 𝑠 2 ⟩ 0 / 𝑛 𝑙2 )∞ = 16 11+−𝛼
1+𝜂
Indian Institute of Technology Roorkee 25
 Polymer Chain Models
Hindered rotation model

i+1

i
Conformational statistics of isotactic PP in all trans form#
• Rotational Isomeric States (RIS) Model: theory considers bond
torsions restricted to specific values corresponding to local minima
on energy-torsion surfaces.
• Monte-Carlo (MC) simulation coupled with RIS  employed to
generate realistic chains  RIS-MC
#
Suter & Flory, Macromolecules, pp 765, Vol 8, 1975.
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