LAB

MANUAL
CHY1005: Introduction to Computational Chemistry
Index
 School of Advanced
Sciences and Languages, Chemistry
Introduction to Computational
Chemistry
Name: Branch:
Registration Number: Duration: 90 min.
Practical 1: Molecular
Visualization
Aim
To build and visualize molecules using Avogadro.
Theory:
There are many tools to visualize the molecule. In this session, we will
be using Avogadro, an open-source software. Generally, computational
chemistry allows chemists to analyze properties of molecules using a
computer. The computer can predict quantities such as: molecular
geometry (bond length, bond angle), molecular orbitals, bonding,
spectroscopy, and energy. It can also simulate the motion of molecules
(molecular dynamics). The first step for these calculations is building
the molecule. Building a molecule in computer involves describe the
molecule to the computer and tell it what you want it to calculate. If you
wanted to calculate the bond length in carbon dioxide you would specify
an initial guess for the (x,y,z) coordinates of the three atoms. Then you
would add some keywords to tell the computer to find the optimum
geometry. This can be accomplished using one of the dedicated
software. The generated structures can be saved in either of the
following two formats:
1. Cartesian format
2. Z-matrix

Cartesian Geometry of Water:

Z-matrix of Geometry of Benzene:

Procedure:
Molecules can be built using the Draw Tool of Avogadro GUI window.
Open Avogadro, select the Draw Tool.
Select the Draw tool (at the left end of the toolbar; looks like a pencil) to
start building a molecule. In the left pane, make sure that the Adjust
Hydrogens checkbox is checked.
Select carbon from the dropdown menu. Click once in the drawing
window (the black field). To create a bond to a second carbon, click the
first carbon and drag away from it.
If you want to delete an atom, you can right-click it while in drawing
mode. If you want to add another type of atom, you can select it from
the dropdown menu (select “Other…” and choose any element from
the periodic table)
Single click puts an isolated atom, eventually with its hydrogen atoms. If
you want to create a bond, drag until the bond is long enough and
release the mouse button.
Bond order can be changed through the Bond Order drop down menu, or
by typing the numbers "1", "2", or "3". Bonds can also be added to a
molecule by left clicking on a bond that has already been created (this
process cycles through single, double, and triple bonds). Right clicking
on a bond will delete the bond, and the atom it's bonded to.
Click "File" --> "Save" to save the molecule for later use.
Results:
Draw these molecules and paste here the output as a snapshot of the molecule
and XYZ file.
1. Ethylene
2. Acetaldehyde
3. Glucose
4. Alanine
5. 2-heptene
 School of Advanced
Sciences and Languages, Chemistry
Introduction to Computational
Chemistry
Name: Branch:
Registration Number: Duration: 90 min.
Practical 2: Single Point Energy Calculation of
Molecules
Aim
To calculate single point energy of molecules using a quantum mechanical method.
Theory:
Single point energy is the potential energy of a molecule for a given
arrangement of the atoms in the molecule. Single point energies are the
lowest energy solution for the Schrödinger equation and are the
simplest properties one might aim to obtain. It consists in the
calculation of the wave function and energy for a given system with a
well-specified geometric structure, i.e. at a single, fixed point on the
potential energy surface. The computed energy is the total energy, sum
of the electronic energy and nuclear repulsion energy. To perform a
single point energy calculation a well-defined level of calculation must
be specified. A level of calculation is uniquely defined by the
combination of a theoretical method with a basis set.
Many aspects of the system’s behaviour can be understood when the
total energy of the system is known, or more often, when the energy
difference between two or more electronic or nuclear configurations is
known as a function of some parameters.
Procedure:
Build a water molecule using ChemCompute server or any other molecular
builder.
Prepare the input for single point energy calculation. Choose an
appropriate method and basis set.
Submit the job by clicking on submit button.
Note down the electronic energy of the water molecule.
Results:
-74.9658051821
-5.6145715450 Draw the following molecules and
report their single point energy.
-55.454649196
4

-39.7264988882

-111.2245335962
 School of Advanced
Sciences and Languages, Chemistry
Introduction to Computational
Chemistry
Name: Branch:
Registration Number: Duration: 90 min.
Practical 3: Energy Minimization of Diatomic
Molecules
Aim
To perform energy minimization of diatomic molecules using a quantum
mechanical method.
Theory:
The energy minimization is a way to get the stable structure of
molecule which is the main aim of computational chemistry. The
resultant molecular structure is refereed as “Optimized geometry”.
Here, we mainly do the minimization of energy as the function of
nuclear coordinate.
Let us take the Energy (E) is a function of cartesian coordinate (‘x,y,z’)
of a given molecular structure i.e;, E (xyz), and represented as E(Q). As
the geometry changes its energy also varies. We change the geometry
of the molecule is such a way that energy gets minimum. This will be
the most stable structure, and known as “Optimized geometry”.
Mathematically,
We do the following operations:
And, 𝜕𝐸(𝑄)
=
𝜕𝑄
Procedure:
𝜕2𝐸(𝑄) >0
𝜕𝑄

i d th
e oxygen molecule using ChemCompute server or any other molecular builder.
Bu
Prepare the input for energy minimization calculation. Choose an appropriate
method and basis set.
Submit the job by clicking on submit button.
Note dow
n the optimized energy of the molecule.

Report the cartesian optimized geometry of oxygen molecule.

Results:
Draw these molecules and optimize it. Report the optimized energy.


hool o
 f Advanced Sciences and
Languages, Chemistry Introduction
to Computational Chemistry

Name: Branch:
Registration Number: Duration: 90 min.
Practical 4: Geometry Optimization of Polyatomic Molecules
Aim
To perform energy minimization of diatomic molecules using a
quantum mechanical method.
Theory:
The energy minimization is a way to get the stable structure of molecule which
is the main aim of computational chemistry. The resultant molecular structure is
refereed as “Optimized geometry”. Here, we mainly do the minimization of energy
as the function of nuclear coordinate.
Let us take the Energy (E) is a function of cartesian coordinate (‘x,y,z’)
of a given molecular structure i.e;, E (xyz), and represented as E(Q). As
the geometry changes its energy also varies. We change the geometry
of the molecule is such a way that energy gets minimum. This will be
the most stable structure, and known as “Optimized geometry”.
Mathematically,
We do the following operations:
And,
𝜕𝐸(𝑄)
= 0
𝜕𝑄
Pr
cedur
e:
𝜕2𝐸(𝑄) >0
 𝑄
𝜕

Build a H
w 2O
ter
molecule using ChemCompute server or any other molecular builder.
Prepare the input for energy minimization calculation. Choose an appropriate
method and basis set.
Submit the job by clicking on submit button.
Note down the optimized energy of the molecule.
Report the cartesi
an optimized geometry of molecule.
•
Results:

Draw these molecules and optimize it. Report the optimized energy.

School of Advance
Sciences
and Languages, Chemistry Introduction to
Computational Chemistry
Name: Branch:

Registration Number:
Duration: 90 min.

Practical 5: Generation And Visualization of Molecular Orbitals

Aim
To generate and visualize the molecular orbitals using
computational chemistry tools.
Theory:
The molecular orbital is a fundamental concept in Quantum chemistry. In the
Schrodinger picture, the MO’s represents the wavefunction of molecules which
stores all information pertaining to the molecule. It is important to visualize the
MO’s to get the bonding feature of the molecule. Generally, these MO’s are linear
combination of the Hydrogenic wavefinction “s, p, d, f” orbitals, known as atomic
orbitals. In this session, we will generate the atomic orbitals of Ne atom.
In Quantum Chemistry,
Ψ = ∑ 𝐶𝑖Φi
Where Φ is molecular orbitals. In case of atoms these are atomic orbitals.
In this lab, we will yenerate and visualize the Mos of the Neon atom. The electronic
s w
configuration of Ne atom is 1s2, 2s2, 2px2, 2p 2, 2p z2. All the e orbitals ill be
visualized here.
Procedure:
Build a “Carbon” atom in Chemcompute or any other molecular
builder.

Prepare the input for single point energy calculation. Choose an appropriate
method and basis set.
Visualize and report the energy of its different orbitals.Results:
Draw the fol
lowing molecules and generate their atomic/molecular orbitals.
C

Figures: 1s, 2s, 2px, 2py, 2pz orbitals

O2
Figures: Highest Occupied Molecular Orbital (HOMO), Lowest Unoccupied Molecular
Orbital (LUMO)
Ethylene
Figures: Highest Occupied Molecular Orbital (HOMO), Lowest Unoccupied
Molecular Orbital (LUMO)
School of Advanced
ciences and Languages, Chemistry Introduction to
Computational Chemistry

Name: Branch:

Registration Number:
Duration: 90 min.

Practical 6: Potential Energy Scan of Molecules

Aim
To scan the potential energy scan of a
molecule using a quantum mechanical method.
Theory:
The potential energy curve (PEC) or surface is the plot of electronic energy as a
variation of nuclear geometry. The origin of PEC is due to heavy mass of nuclei, the
electron move much faster than nuclei, as a result we may separate the electronic
and nuclei motion – Born- Oppenheimer Approximation. This is the fundamental
theory in the area of molecular dynamics. The PEC is also considered as a tool for
visualization of chemical reaction. It is assumed that molecule undergoes to
chemical reaction by moving over the PEC.


Figure: General Pote tial

energy surface and Potential energy curve

In this session, we will generate the PEC of O2 molecule by

varying its bond distance.
Procedure:
Build O2
the atom in ChemCompute or any other tool.
Prepare the input for single point energy calculation. Choose an appropriate
method and basis set.
Change the bond distance of O2 molecule at intervals of 0.1 Å and repeat
the calculation.

Repeat the procedure for 15 steps by changing the distance by 0.2 Å in each
step.
Record the Electronic Energy (above the molecule box) and the bond distance
Results:
Draw O2 molecule and generate its PECs.


Figure: Relative

nergy vs bond distance

School of Advanced
Sciences
and Languages, Chemistry Introduction to
Computational Chemistry
Name: Branch:

Registration Number:
Duration: 90 min.

Practical 7: Frequency calculation of Molecules

Aim
To perform frequency calculation of a molecule
by computational chemistry tools.
Theory:
Frequency calculation is a crucial step in molecular modeling, which helps in
predicting the vibrational spectrum of a molecule. This involves calculating the
frequencies of various modes of vibrations of a molecule and their corresponding
energies. The vibrations of a molecule can be divided into three types: stretching,
bending, and torsional. The stretching mode is associated with the stretching of
bonds between atoms in the molecule, the bending mode with the bending of
bonds, and the torsional mode with the rotation of atoms around a bond.
To get the vibrational structure of the molecule, Hessian calculation is
performed. Hessian is the second order energy derivative with respect
to the nuclear coordinate. It represents the curvature of the energy
surfaces. The eigen value of Hessian matrix leads to the vibrational
frequencies and eigen-vector leads to the vibrational mode of the
molecules. The Hessian gives important information of the molecules
whether it is minimum or not? If the all eigen- values is positive, then
the molecule is present at one of the minima. Therefore, to confirm the
minima structure of molecule, Hessian calculation is important.
Additionally, after getting the vibrations of the molecule, Infrared
spectra can also be simulated.
In this session, we generate the vibrational frequencies, vibrational
mode and IR spectraProcedure:
Build the
water molecule in Chemcompute or any other software.

Perform energy optimization of the water molecule at B3LYP/6-31G level of

theory.
Set up the calculation for the Frequency calculation using the optimized
geometry.
Submit the job.
Under the Vibrationals visualizations, choose the vibrational frequencies to
animate the three vibrational mode.
Results:

Draw the following molecules and generate its Vibrational

frequencies. Report the four vibrational frequencies.

CO2

CH4

School of Advanced
 Sciences and Languages,
Chemistry Introduction to
Computational Chemistry

Name: Branch:

Registration Number:
Duration: 90 min.

Practical 8: Computational Thermochemistry

Aim
To calculate reaction enthalpy for a reaction
computational chemistry tools.
Theory:
Chemical reactions involve changes in energy as well as matter. Enthalpy
change of a reaction is one of the most useful thermodynamic quantities. The
experimental determination of the reaction using a standard bomb calorimeter
requires great attention to detail to achieve the desired precision and accuracy. The
tools of quantum chemistry can also be used to calculate thermodynamic
properties, such as enthalpy (ΔH), entropy (ΔS), and Gibbs free energy (ΔG) of
reactions.
In this laboratory, you will determine the ΔH associated with the Haber-
Bosch process:
N2 + 3 H2 ⇌ 2 NH3
Procedure:
the N2
Build

molecule in Chemcompute or any

other software.

Perform energy optimization of the water molecule at B3LYP/6-31G level of

theory.
Set up the calculation for the Frequency and thermochemistry calculation using
the optimized geometry.
Repeat the optimization for the molecules involved in the Haber-Bosch
process at the same level of theory.
Calculate the reaction enthalpy (ΔH).
Results:
Calculate
(ΔH) for the following reactions:
N2 + 3 H2 ⇌ 2 NH3

CH4 + H2O ⇌ CO + 3 H2

School of Advanced
Sciences
and Languages, Chemistry Introduction to
Computational Chemistry
Name: Branch:

Registration Number:
Duration: 90 min.

Practical 9: Visualization of Molecules in VMD

Aim
The aim of this lab is to learn how to use VMD
(Visual Molecular Dynamics) software to visualize molecules and
analyze their properties.
Theory:

VMD is a powerful visualization tool for studying and analyzing molecules,

biomolecules, and materials. It provides a wide range of capabilities for
visualizing structures, trajectories, and data from molecular simulations. VMD
is designed to be highly extensible and customizable, with support for a wide
range of molecular file formats and data types.

In this lab, you wi l learn how to

use VMD to visualize and analyze molecules. You should now be able to
load, manipulate, and analyze various types of molecules and generate
visualizations and plots of their properties.

Procedure:

Installing VMD

Download and install

 o VMD from the official website:
https://www.ks.uiuc.edu/Research/vmd/
o Follow the installation instructions for your
operating system.
o Loading a molecule
o Open VMD and select "New Molecule" from the File menu.
o Choose the appropriate file format for your molecule (e.g. PDB, XYZ,
etc.) and select the corresponding file.
o VMD will automatically load the molecule and display it in the
graphics window.
o Manipulating the molecule
o Use the mouse to rotate, translate, and zoom in/out of the molecule in
the graphics window.
o Use the "Display" menu to change the representation of the
molecule (e.g. ball- and-stick, space-filling, etc.).
o Use the "Color" menu to change the color of the molecule based
on various properties (e.g. atom type, charge, etc.).
o Use the "Graphics" menu to adjust various display settings (e.g.
lighting, shadows, etc.).
o 
o Analyzing the molec

le

Use the "Measure" menu to calculate various properties of the molecule (e.g.
bond length, angle, dihedral, etc.).
o Use the "Graph" menu to generate plots of various properties
(e.g. RMSD, energy, etc.) over time.
o Use the "Extensions" menu to access additional plugins and
tools for analyzing and visualizing molecular data.
o Saving the molecule
o Select "Save Molecule" from the File menu to save the current state of
the molecule (including all display and analysis settings) to a VMD file.
o Select "Write PDB" from the File menu to save the current state
of the molecule in PDB format (with optional additional data
fields).
o 
o 
o Results:
Figur :

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tein (PDB ID: 1UBQ) in VMD. Submit rendered geometry of the molecule.

School of Advanced S
ciences
and Languages, Chemistry Introduction to
Computational Chemistry
Name: Branch:

Registration Number:
Duration: 90 min.

Practical 10: Molecular modeling of Ar gas using NAMD

Aim
The aim of this lab is to perform molecular modeling of
Ar gas using simulation software, and to analyze the properties of the Ar
gas molecules.
Theory:

Molecular modeling is a technique that uses computer simulations to

study the behavior of molecules and their interactions in different
conditions. NAMD is a software package designed for high-performance
molecular dynamics simulations. In this lab, we will use NAMD to
simulate the behavior of Ar gas molecules in a box, where the
molecules will interact with each other according to the Lennard-Jones
potential.

The Lennard-Jones potential is a mathematical model that describes

the interaction between two neutral atoms or molecules. It consists of
two terms: a short-range repulsive term and a long-range attractive
term. The repulsive term prevents the atoms or molecules from getting
too close to each other, while the attractive term allows them to
interact at larger distances.
Using NAMD, we will perform a series of simulations with different
parameters to study the properties of Ar gas molecules such as
diffusion coefficient, density, and pressure.
Procedure:
Installing VMD

Download and install VMD from the official website:

https://www.ks.uiuc.edu/Research/namd/
o Follow the installation instructions for your
operating system.
o Molecular Dynamics Simulation:
Open the NAMD graphical interface and create a new project.
o Choose the
input file for the simulation, which should contain the
parameters for the Ar gas molecules, the size of the box, and the initial positions of
the molecules.
o Set up the simulation parameters such as the time step, the
temperature, the pressure, and the number of steps to be run.
o Run the simulation and monitor the progress of the simulation
using the NAMD graphical interface.
o Once the simulation is complete, analyze the results by
calculating the temperature, potential energy, kinetic energy
and pressure of the Ar gas molecules.
o 
o Repeat the simulati

nwith different
parameters to study the effect of external factors on the
properties of the Ar gas molecules.
o Compile the results and create a report summarizing the
findings.
o 
o Results:
Run 10 ns D simulation of the Argon gas. Plot
time evolution of temperature, potential energy, kinetic energy, total energy and
pressure.