LAB MANUAL

CHY1005: Introduction to Computational Chemistry

Submitted By: Vedic Gautam (23BAI10756)

Submitted To: Prof. Satyam Ravi

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Index

S. Title of the Experiment Page

No. No.
1. Molecular Visualization 2
2. Single Point Energy Calculation of Molecules 4
3. Energy Minimization of Diatomic Molecules 6
4. Geometry Optimization of Polyatomic Molecules 8
5. Generation and Visualization of Molecular Orbitals 10
6. Potential Energy Scan of Molecules 12
7. Frequency Calculation of Molecules 14
8. Computational Thermochemistry 16
9. Visualization of Molecules In VMD 18
10. Molecular Modeling of Ar Gas using NAMD 21

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School of Advanced Sciences and Languages, Chemistry

Introduction to Computational Chemistry
Name: Vedic Gautam Branch: BAI
Registration Number: 23BAI10756 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:

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Z-matrix of Geometry of Benzene:

Procedure:

● Molecules can be built using the Draw Tool of WxMacmolPLT GUI window.

● The WxMacMolPlt has three mode, Edit, View, and Select. To build the molecule you
need to choose Edit mode.

● Open WxMacMolplt, Go to the Builder tool, select build tool. This will open in another
window

● Select the atom from periodic table, and choose its proper coordination number.

● Bring the cursor at the main window, and press the center button of the mouse.You can
see the atom with its coordination number. The coordination number will be
represented by the sticks.

● Go to Builder tool, select add Hydrogen. The Hydrogens will be added.

● If you want to delete an atom, you can right-click it while in edit mode. If you want to
add another type of atom, you can select atom from build tools. Bring cursor at the
respective atom, and right click. You will get option to replace atom.

● You may bring two atoms to make a single, double or triple bond.

● 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.

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● Click "File" --> "export" to save the molecule in XMOL (*.xyz) format.

Results:
Draw these molecules and paste here the output as a snapshot of the molecule and XYZ file.
1. Ethylene
2. CH4
3. Benzene
4. NH3
5. C2F6

1. Ethylene

2. Methane CH4

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3. Benzene

4. Ammonia [NH3]

5. Hexafluoroethane[C2F6]

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School of Advanced Sciences and Languages, Chemistry

Introduction to Computational Chemistry
Name: Vedic Gautam Branch: BAI

Registration Number: 23BAI10756 Duration: 90 min.

Practical 2: Single Point Energy Calculation of Molecules

Aim
To calculate Ionization Potential and Electron Affinity by 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.

Ionization potential EIP = E(Neutral) – E (Cation)

Electron Affinity EA = E(Neutral) – E (Anion)

Convert this energy difference into electron volt. I Hartree = 27.2107 eV

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Procedure:

● Build a water molecule using WxMacMolPlt.

● Prepare the input for single point energy calculation. Choose an appropriate method and

basis set. For Multiplicity, choose spin = 2S+1, where S = Total spin Q. No. For
example, In H2O, Neutral Number of electron is 10, so S =1 and for Cation , S = 1/2

● Submit the job on ChemCompute server.

● Note down the electronic energy of the water molecule.

● To perform calculations on a new molecule click the Submit Tab at the top.

Results:
Draw the following molecules and report their single point energy.

S. No. Molecule Single Point Energy (Hartree)

1 H2O -76.34672 a.u.

2 NH3 -56.51139 a.u.

Calculate Ionization Potential and Electron Affinity in eV.

Click on Input Builder to generate

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Results

S. No. Molecule Ionization Potential (eV) Electron Affinity (eV)

1 H2O 75 ± 3 eV 1.3 eV

2 NH3 9.74 ± 0.73 eV 0.16 ± 0.22 eV

Control Block
Basis block (Choose basis
set)
Control block (Type of
calc. and Method)
Data block (Geometry

Select appropriate options and write the file as *.inp

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School of Advanced Sciences and Languages, Chemistry

Introduction to Computational Chemistry
Name: Vedic Gautam Branch: BAI
Registration Number: 23BAI10756 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:
∂ E(Q)
=0
∂Q
And,
2
∂ E (Q )
>0
∂Q
Procedure:

● Build the oxygen molecule using the WxMacMolPltmolecular builder.

● Prepare the input for energy minimization calculation. Choose an appropriate method

and basis set.

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● Submit the job by clicking on the submit button.

● Note down the optimized energy of the molecule.

● Report the cartesian optimized geometry of oxygen molecules.

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

S. No. Molecule Optimized Energy Bond Distance (Å)

(Hartree) Initial Optimized
1 O2 -150.181414 1.440 1.227
2 He2 -5.79282 1.700 2.594
3 Cl2 -920.218 2.020 2.041
4 Br2 -5147.475 2.300 2.326
5 I2 -25.539 2.660 2.538

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School of Advanced Sciences and Languages, Chemistry

Introduction to Computational Chemistry
Name: Vedic Gautam Branch: BAI
Registration Number: 23BAI10756 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 referred to as
“Optimized geometry”. Here, we mainly do the minimization of energy as the function of
nuclear coordinate.
Let us take the Energy (E) as a function of the 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 in 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:
∂ E(Q)
=0
∂Q
And,
2
∂ E (Q )
>0
∂Q
Procedure:

● Build a H2O water molecule using ChemCompute server or any other molecular

builder.

● Prepare the input for energy minimization calculation. Choose an appropriate method

and basis set.

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● Submit the job by clicking on the submit button.

● Note down the optimized energy of the molecule.

● Report the cartesian optimized geometry of the molecule.

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

S. No. Molecule Optimized Energy (Hartree)

1 H2O -76.37183

2 Ethylene -78.52905

3 Glucose -686.77393

4 Methane -40.48239

5 NH3 -46.51139

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School of Advanced Sciences and Languages, Chemistry

Introduction to Computational Chemistry
Name: Vedic Gautam Branch: BAI
Registration Number: 23BAI10756 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 combinations of the Hydrogenic wave
function “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 the case of atoms these are atomic orbitals.

In this lab, we will generate and visualize the Mos of the Neon atom. The electronic
configuration of the Ne atom is 1s2, 2s2, 2px2, 2py2, 2pz2. All these orbitals will be
visualized here.

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Procedure:

● Build a “Carbon” atom in the WxMacMolPlt 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 following molecules and generate their atomic/molecular orbitals.

● C

Figures: Highest Occupied Molecular Orbital (HOMO), Lowest Unoccupied Molecular Orbital
(LUMO)

● Ethylene

Figures: Highest Occupied Molecular Orbital (HOMO), Lowest Unoccupied Molecular Orbital
(LUMO)
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Export the orbital
picture from File Tool bar
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C Figures: 1s, 2s, 2px , 2py , 2pz orbitals

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Ethylene Figures: Highest Occupied Molecular Orbital (HOMO), Lowest Unoccupied Molecular Orbital (LU

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School of Advanced Sciences and Languages, Chemistry

Introduction to Computational Chemistry
Name: Vedic Gautam Branch: BAI
Registration Number: 23BAI10756 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 the heavy mass of nuclei, the electron
moves much faster than nuclei, as a result we may separate the electron 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 a molecule undergoes a chemical reaction by moving over the
PEC.

Figure: General Potential energy surface and Potential energy curve

In this session, we will generate the PEC of the O2 molecule by varying its bond distance.

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Procedure:

● Build O2 the atom in WxMacMolPlt.

● Prepare the input for single point energy calculation. Choose an appropriate method and

basis set.

● Change the bond distance of the 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.

S. No. Bond Distance (Å) Electronic Energy (Hartree) Relative Energy (Hartree)
1 1.3800000 -149.2256877102 -0.2079788945
2 1.8400000 -149.0177088157 -0.272700123
3 1.2000000 -149.2897000123 -0.998744619
4 1.0000000 -149.1914981578 -0.2101023489
5 0.9000000 -148.9813526031 -0.4521245670
6 0.8000000 -148.5232690519 -0.987612230
7 0.6000000 -145.8114683008 -0.235467239
8 0.7000000 -147.6021891690 -0.2144532787
9 0.7400000 -148.0462291677 -0.123248978
10 0.4000000 -135.2393287442 -0.012455672
11 0.5000000 -142.3126856648 -0.891233200
12 0.5800000 -145.2878951162 -0.2231157800
13 1.2000000 -149.2868071968 -0.2334155677
14 1.3000000 -149.2568440368 -0.621000843
15 0.2000000 -86.1265265664 -0.000234778

Figure: Relative energy vs bond distance

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School of Advanced Sciences and Languages, Chemistry

Introduction to Computational Chemistry
Name:Vedic Gautam Branch: BAI
Registration Number: 23BAI10756 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 eigenvalue of the Hessian matrix leads to the
vibrational frequencies and the 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 all eigen-values are positive, then the molecule is present at one of the
minima. Therefore, to confirm the minimum structure of a molecule, Hessian calculation

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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 spectra of
the water molecule.

Procedure:

● Build the water molecule in WxMacMolPlt 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 vibrational
frequencies.

● CO2

a. 668.94
b. 1320.74
c. 2338.6

● CH4

a. 1368.44
b. 1591.61
c. 3183.24

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School of Advanced Sciences and Languages, Chemistry

Introduction to Computational Chemistry
Name:Vedic Gautam Branch: BAI
Registration Number: 23BAI10756 Duration: 90 min.

Practical 8: Computational Thermochemistry

Aim
To calculate reaction enthalpy for 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:
CO2 + CH4 ⇌ 2 H2CO

Procedure:

● Build the CO2 molecule in WxMacMolPlt.

● Perform energy optimization of the water molecule.

● Set up the calculation for the Frequency and thermochemistry calculation using the

optimized geometry.

● Repeat the optimization for the other molecules involved in the Haber-Bosch process at

the same level of theory.

● Calculate the reaction enthalpy (ΔH).

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Results:
Calculate (ΔH) for the following reactions:

● CH4 + H2O ⇌ CO + 3 H2

-(126.192 KJ/mol + 62.98 KJ/mol) + (23.263 + 109.470) = -56.446 KJ/mol

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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 will 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

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o Download and install VMD from the official website:

https://www.ks.uiuc.edu/Research/vmd/
o Follow the installation instructions for your operating system.
● 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.).

● Analyzing the molecule

o 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.

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o Select "Write PDB" from the File menu to save the current state of the molecule
in PDB format (with optional additional data fields).

Figure: Steps to create high quality rendering.

Results:
Load “Ubiquitin” protein (PDB ID: 1UBQ) in VMD. Submit rendered geometry of the
molecule.

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School of Advanced Sciences 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
o Download and install VMD from the official website:
https://www.ks.uiuc.edu/Research/namd/
o Follow the installation instructions for your operating system.

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● Molecular Dynamics Simulation:

o 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 Repeat the simulation with 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.

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Results:
Run 10 ns MD simulation of the Argon gas. Plot time evolution of temperature, potential
energy, kinetic energy, total energy and pressure.

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