LAB MANUAL

CHY1005: Introduction to Computational Chemistry

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: 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
opensource 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:

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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

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2. Acetaldehyde

3. Glucose

4. Alanine

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5. 2-heptene

School of Advanced Sciences and Languages, Chemistry

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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.
• 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.

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S. No. Molecule Single Point Energy (Hartree)

1 H2O -76.3718260301

2 He2 -5.7928248173

3 NH3 -56.5113915199

4 CH4 -40.4823859608

5 CO -115.6471328188

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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:
𝜕𝐸(𝑄)
=0
𝜕𝑄
And,
𝜕 𝐸(𝑄)
2

>0
𝜕𝑄

Procedure:
• Build the oxygen 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 cartesian optimized geometry of oxygen molecule.
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Results:
Draw these molecules and optimize it. Report the optimized energy.

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

(Hartree) Initial Optimized
1 O2
2 He2
3 Cl2
4 Br2
5 I2

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Name:
School of Advanced Sciences and Languages, Chemistry Introduction to
Computational Chemistry
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:
𝜕𝐸(𝑄)
=0
𝜕𝑄
And,
𝜕 𝐸(𝑄)
2

>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.
• Submit the job by clicking on submit button.
• Note down the optimized energy of the molecule.

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• Report the cartesian optimized geometry of molecule.

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

S. No. Molecule Optimized Energy (Hartree)

1 H2O

2 Ethyelene

3 Glucose

4 Methane

5 NH3

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Name:
School of Advanced Sciences and Languages, Chemistry
Introduction to Computational Chemistry
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 generate and visualize the Mos of the Neon atom. The electronic configuration of
Ne atom is 1s2, 2s2, 2px2, 2py2, 2pz2. All these orbitals will 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:

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Draw the following molecules and generate their atomic/molecular orbitals.

• C2

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)

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

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• 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.

S. No. Bond Distance (Å) Electronic Energy (Hartree) Relative Energy (Hartree)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

Figure: Relative energy vs bond distance

School of Advanced Sciences and Languages, Chemistry

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- Date:
Name:
Introduction to Computational Chemistry
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
eigenvector 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 spectra of the water
molecule.

Procedure:
• 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.

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• 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

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Name:
School of Advanced Sciences and Languages, Chemistry Introduction to
Computational Chemistry
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: • Build the N2 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:

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• N2 + 3 H2 ⇌ 2 NH3
N2 = -109.3426403817 = -109.3426403817

H2 = 3 (-1.1673385838)= - 3.5020157514

NH3 = 2x(-56.5113596852)= -113.0227193704

ΔH= ΔHp -ΔHr

ΔHrxn = (-113.0227193704) – [(-109.3426403817)+ (- 3.5020157514)

= (-113.0227193704)- (-112.8446561331)

• CH4 + H2O ⇌ CO + 3 H2

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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
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.

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

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Figure: Steps to create high quality rendering.

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

School of Advanced Sciences and Languages, Chemistry

Introduction to Computational Chemistry
Name: Branch:
Registration Number: Duration: 90 min.

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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
highperformance 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.

• 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.

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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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