PHYSICAL CHEMISTRY LABORATORY

Basic Computational Chemistry

The Goal of the Class

 Computational Chemistry emerges to be an excellent

field of research

 The goal is to show how computers help us in answering

and solving scientific problems in Chemistry
What is Computational Chemistry ?

Why do we need to know about Computational Chemistry ?

• Computational Chemistry is already an established field of

research

• Computational Chemistry is a valuable tool for experimental

chemists to bypass tedious, time consuming, expensive and
some times dangerous experiments

• Predict to design too unstable molecules to be studied

experimentally

• Properties which are not experimentally observable

 Experiment and Computer Modelling

Nature Theoretical and Computational Model

Experiment Computer Simulation Theory

Numerical Techniques Analytical
Solutions

Experimental Simulated Theoretical

Measurements Predictions Predictions

Comparisons
 Why do we need computational modelling?

➢ Experimental methods have intrinsic and practical

limitations like spatial and temporal resolution

➢ Theoretical analytical solutions to given certain problems

may be too difficult or impractical

➢ Computer modelling or simulation can predict

complementary information on the problems and form the
bridge between Experiment and Theory.
 Electron Atoms Domains Grid

TIME (s)

100

Atomistic Mesoscale methods

(ms) 10-3 Simulation
Methods Finite elements methods

(s) 10-6

Semi-empirical
(ns) 10-9 methods
Monte Carlo
Molecular dynamics
(ps) 10-12 Ab initio
methods
Tight-binding
(fs) 10-15

10-10 10-9 10-8 10-7 10-6 10-5 10-4

(nm) (m)
LENGTH (m)
Scientific problems it address (Length Scale Few Å)

➢ Structure and properties of a molecule

➢ Formation of new compounds in a chemical reaction

➢ Possibility of formation of a certain transition state in a

chemical reaction

➢ Molecular response towards electric, magnetic field

➢ Molecular spectroscopy etc.

Extends from molecules to materials(Length Scale nm ~ cm)
• The structure and properties of nanomaterials,
biomaterials, solid state

• The structure of proteins, how protein binds with ligands,

conformation dynamics of proteins

• Formation of nanostructures with time

• Motion of solute molecules as a function of time in a

solvent etc.
Computational Chemistry is based on solving Mathematical
Equations framed with the knowledge of theoretical
understanding about the System in use.

• Choice of Mathematical Equations depends on System

Size or Temperature

• Numerical Techniques are required to solve the

mathematical equations

• Computer programming language required to implement

the Numerical Techniques

• Finally Numerical solutions help us to compute the

desired properties of system.
Length scale or size and the temperature of the system are
very important

Classical Mechanics and Statistical Quantum Mechanics

Mechanics Low Temperature
Temperature comparatively or
high or Length Scale nm ~ m
Length Scale ~ Few Å

Single molecules and small molecular cluster

Biological molecules and nanomaterials
MD simulation starts with a concept of a simulation box

As if doing the experiment in a box

Motions of atoms or molecules with time

Evolution in Time

Time step of evolution t ~ 10−15 s

Concentration of the molecules or the mixture of molecules

determine the # of molecules and size of simulation box

Introduction of periodic boundary condition

to give the simulation more realistic feature
 Systems with large number of molecules
• Classical Mechanics governed by the laws of Newtonian
Mechanics solving F = mx = ma = − dV
dr
• Classical Molecular Dynamics Simulation (MD Simulation),
best tools to predict the structure, dynamics and
thermodynamics of biological or nanomaterials
 ( t = 0)
Start with initial positions r , choose short t

Get forces F = −V (r i ) and a = F / m

i 2 i
i +1 dr 1d r
Move atoms r (t + t ) = r (t ) + t +  + ...
i 2
2
t
dt 2 dt
1
r (t ) + v t + f t 2 + .........
i (i )

2
Move time forward t new = t old + t

Repeat as long as needed

MD trajectories for Oil and water mixture
 MD simulation on protein folding

CHARMS, GROMACS, DLPOLY some of the classical software

Packages which deal with Classical Simulation
 Electron Atoms Domains Grid

TIME (s)

100

Atomistic Mesoscale methods

(ms) 10-3 Simulation
Methods Finite elements methods

(s) 10-6

Semi-empirical
(ns) 10-9 methods
Monte Carlo
Molecular dynamics
(ps) 10-12 Ab initio
methods
Tight-binding
(fs) 10-15

10-10 10-9 10-8 10-7 10-6 10-5 10-4

(nm) (m)
LENGTH (m)
Behaviour of classical particles (nm ~ cm ) discussed till now

These classical particles are dealt with laws of Classical

Physics or Newtonian / Classical Mechanics
Particles with length scale <= nm are termed as Quantum
Particles [electrons, protons, atoms , or any subatomic
particles (Indistinguishable Particles)]

But as the system size keeps decreasing (from cm to nm) laws

of classical mechanics fail to explain the properties of those
particles

Failure of Classical Mechanics leads to the Invention of

Quantum Mechanics at the beginning of the 20th century.

Knowledge of Quantum Mechanics is required

Scientists fail to explain the behaviour of experimental curve
of black-body radiation emission spectra with the laws of
Classical Mechanics in ~ 1900

8 k BT
E ( ) d  = d
 4

Rayleigh-Jeans Radiation law

 Hypothesis of Plank
Atomic vibration in solid is Simple Harmonic Vibration

Classical Harmonic Oscillator

Classical Harmonic Oscillator

1
E = m(2 ) a
2 2

2 1
1 2  = Frequency
F = − Kx V ( x) = Kx T
2
 Hypothesis of Plank

➢ The atoms in a blackbody follow S.H.M, but they are

Quantum Harmonic Oscillator
➢ But the energy of absorption and emission is not continuous,
it is quantized h = 6.626 10−34 joule − sec
E = nh n = 0,1, 2,3, 4,5,.......
➢ Plank could derive a mathematical function for energy
density of radiation within a frequency range  and
 + d 8 h 2 1
E ( )d = h
d c
c3 as =
e k BT
−1 
Within a wavelength range  and  + d
8 hc 2
1
E ( ) d  = d
 5 hc
 k BT
e −1
 8 hc 2 1
E ( ) d  = d
 5 hc
 k BT
e −1
Plank’s radiation law derived from energy quantization
hypothesis reproduces the experimental curve
When  High , it reduces to Rayleigh Jeans Law

hc hc hc hc 2
is, exp( ) = 1+ +( ) + .....
 k BT  kBT  k BT  k BT

8 hc 2 1
E ( ) d  = d
 1 + hc − 1
5

 k BT
8 hc 2 1 8 k BT
E ( ) d  = d = d
 5
hc
1  4

 k BT Rayleigh Jeans Law

Energy Quantization was a hypothesis of Plank later explained
by Einstein while explaining Photoelectric Effect in 1905
Light behaves both as wave and particle
The particle form, known as photon, has energy h
and momentum h and it is massless
c
Light
E = nh
LIGH

n = 0,1, 2,3, 4,5,.......

Intensity of light depends on n
Emission of photoelectrons depends on 
1 2
h h − W = mvmax
W = h 0 2
Work Function of the metal
0 Threshold Frequency
 Photocurrent  Intensity of Light Classical Idea
Wrong
Photocurrent  Photoelectrons  Number of photons
Correct
Photoelectron Emission only depends on the frequency
of the light , on its intensity

  0 Photoelectron emits
Particle or material behaviour of light is established through
Photoelectric Effect
1 2
h − W = mvmax
2
1 2
h − h 0 = mvmax
2
 Compton Effect 1923 Electromagnetic
Radiation behaves
both as wave and
particle
X Ray

Scattered radiation
So electromagnetic radiation also sometime behave as
particles

Refraction, Reflection, Diffraction

Wave like behaviour

Photoelectric effect, Compton effect

Particle like behaviour

• Photons are the particles form of Light wave with E = h
• Photons are massless particles with momentum h
c
Concept of material wave first introduced by De Broglie
A quantum particle in motion having a momentum p
will be associated with a material wave of wavelength 

h
= h = 6.626 10−34 joule − sec
p
h For typical case of an electron
= −31
−10
 is in 10 m or Å
mv m = 9.110 kg
v = 6 106 m / sec
For typical Classical m = 10kg  is in −41
10 m
Particle v = 6 103 m / sec
 The concept of material wave is the central part in
h Quantum Mechanics
=
p
The wavelength of the wave associated with
particle is motion is inversely proportional to its
corresponding momentum.
The quantum particle’s position and corresponding
momentum can not be measured simultaneously at
the same time

h Error in finding the position of the particle

x x
px
px Error in finding the momentum of the particle

x px  Heisenberg uncertainty principle

2
Energy and time related to quantum particle also obey uncertainty principle
 For classical particle , the wavelength ~0
Motion of atoms, electrons or any subatomic particles can
h
be associated with a wave having a wavelength  = p and
can be written down as a mathematical wavefunction of
position and time.

f ( x, y , z , t ) =  ( x, y , z , t )
The wavefunction is a mathematical function , examples
− x2 −x
sin x , e , e etc. depending on the quantum
system and boundary in which the system is enclosed

As dimensions of the quantum particles are too tiny, the

presence of these subatomic particles in space can be
predicted only with a probabilistic approach. This is a major
difference between classical and quantum particles.
 dV = dxdydz Elementary volume of box
The probability of finding a quantum
particle within a box of dimension dx, dy and
dz is |  ( x, y, z , t ) | dV =  * dV
dy 2
dx
Total Probability of finding a particle in a box of
dimension L . The probability 0  P  1
L L L

  2
| ( x , y , z , t ) | dxdydz
0 0 0
Linear operators are used to operate on this wavefunction to
obtain the measurement Eigen value equation

Oˆ ( x, y, z, t ) = a ( x, y, z, t )
Ô can be any linear operators for which the measurement
is real 2
a
d d
Oˆ = , 2
dx dx
 Oˆ ( x, y, z, t ) = a ( x, y, z, t )
2
ˆ d d
O= , 2
dx dx 2
If  ( x ) = e
−b x ˆ d
0
O= 2
dx
2 − b0 x
d e 2 − b0 x Eigen value equation
2
= b0 e
dx 2
b0 = eigenvalue of the the operator O =
2
ˆ d
2
dx
A quantum system described by  ( x, y, z , t ) is very
important in quantum mechanics
 ( x, y , z , t )
• the wavefunction  ( x, y, z, t )should be well behaved
• it has all the information about quantum particle’s
position and momentum

• but the positions and momentum of the quantum

particles cannot be measured simultaneously accurately
like classical particles according to Uncertainty Principle
Master equation needed to solve in Quantum Mechanics
Hˆ  ( x, y, z , t ) = E ( x, y, z , t ) Schrodinger Equation
Eigen value equation
Ĥ Total energy operator of the system Hamiltonian
Operator
E Total energy eigenvalue
 Why do we need to have knowledge of Quantum
Mechanics in Chemistry ?
• Chemistry is all about atoms and molecules

The subject deals with Quantum Mechanics in Chemistry is

Quantum Chemistry

Structure and properties of molecules are governed by

Quantum Chemistry

Course on Quantum Chemistry will be taken by Prof. S. Pal

and Dr. Sangita Sen in the coming semester where fundamental
of Quantum Mechanics will be taught and its application to
Chemistry will be discussed.
 Hydrogen Atom
Can we get the minimum or ground state energy of hydrogen
atom using the Knowledge of Quantum Mechanics ?
Yes but How?
Solving the master equation

Hˆ  ( x, y, z , t ) = E ( x, y, z , t )
pˆ 2 2
Hˆ = + Vˆ (r ) = −  2 + V (r )
2m 2 2m
-e ˆ e
V (r ) = −
r
One can solve and calculate exactly ground
state and higher excited state energies using
+e Quantum Chemistry knowledge
E0  E1  E2 .....
E0 = ground state energy eigenvalue

0 = ground state energy eigenfunction

 E0
En = 2 eV
n

13.6
En = − 2 eV
n
n = 1, 2,3, 4,.....
Experimental excited state energies are reproduced by calculations
Schrodinger equation can be solved for hydrogen like
atom
+ 2+ 3+
He Li Be
2
z 13.6
En = − 2
eV
n
 1 1 
En − En +1 = − z 213.6  2 − 2
 n ( n + 1) 
1 1 
h = − z 13.6  2 −
2
2
 n ( n + 1) 
The ground and excited state energies can be exactly solvable for
Hydrogen like atom Course: Quantum Chemistry-1
Z=
-e ˆ
p 2
Hˆ = + Vˆ (r )
r1 2m
 2

+2e Hˆ = − + Vˆ (r )
2m
r2 ˆ
2
2e 2e 2
e 2

-e V (r ) = − − +
| r1 | | r2 | | r1 − r2 |

Depends on two electron

coordinates r and r
1 2

Hˆ  ( x, y, z , t ) = E ( x, y, z , t )
This makes the Schrodinger
equation not solvable exactly
In quantum chemistry , the energies are calculated considering
various approximations as they cannot be exactly solvable

2 2 2
ˆ 2e 2e e
V (r ) = − − +
| r1 | | r2 | | r1 − r2 |

• Treat the two-electron term as a perturbation

• Take the electron-electron interaction term as an average potential

or mean field approximation

Course : Quantum Chemistry 2

So we need to incorporate approximate methods to solve the many

electronic system

Mean field approximation is known as Hartree Fock method

 How to calculate the molecular energy?

r12 2
rA 1 rB

A B
R
2 2 2 2
2 2 2
e2 e2 e2 e e e
H = [− − ]− − +[ ]− − − − +
2mA 2mB 2m1 2m2 R r1 A r1B r2 A r2 B r12

Neuclear motion is assumed to be fixed as compared to electronic

Motion Born Oppenheimer Approximation
➢ Incorporating Born-Oppenheimer approximation

➢ Geometry optimization is the first step to perform

➢ Obtain the most stable structure or having minimum energy

by solving the Schrodinger equation with mean field approximation
or Hartree Fock method

➢ The minimum energy is called the ground state energy

➢ Calculated corresponding wavefunction is ground state wavefunction

➢ After calculation one can see the Molecular Orbitals

Highest Occupied Molecular Orbital (HOMO)

Lowest Unoccupied Molecular Orbital (LUMO)
 Quantum Mechanical Software: Gaussian and Gaussview
Gaussian (www.gaussian.com)

It is one of the robust computational chemistry softwares available.

Performs mostly calculations related to quantum chemistry
Performs geometry optimization and frequency calculation of molecules

Calculation of molecular properties, like energies, dipole moments

etc.
Gaussview (www.gaussian.com)
Graphical user interface (GUI) for Gaussian
Building molecules, visualizing results and submit calculations

List of softwares

http://www.ccl.net/chemistry/links/software/index.shtml
 How to first prepare an input file for Gaussian Software

The extension of the file in .com or .gjf

Use the Graphical User Interface (GUI) gview to prepare the input file
With a copy to ch1202spring2021@gmail.com

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