Note: Examination scheme and mode shall be as prescribed by the Examination Branch,

University of Delhi, from time to time.

DISCIPLINE SPECIFIC ELECTIVE COURSE -12 (DSE-12): Computational

Methods & Molecular Modelling

CREDIT DISTRIBUTION, ELIGIBILITY AND PRE-REQUISITES OF THE COURSE

Course title & Credits Credit distribution of the Eligibility Pre-

Code course criteria requisite
Lecture Tutorial Practical/ of the
Practice course
(if any)
Computational 04 03 -- 01 Class 12th --
Methods & with
Molecular Physics,
Modelling Chemistry
(DSE-12) and
Mathematics

Learning Objectives

The Objectives of this course are as follows:

To make students learn the theoretical background of computational techniques in

molecular modelling.
To give the different flavours of computational chemistry by the end of this course.
To provide hands-on experience in molecular modelling on various software

Learning outcomes

By studying this course, the students will be able to:

Explain the theoretical background of computational techniques and selective
application to various molecular systems.
Compare computational and experimental results and explain deviations.
Perform Optimization of geometry parameters of a molecule (such as shape, bond
length and bond angle) through the use of software like Chem Sketch and Argus Lab in
interesting hands-on exercises.
Perform analysis of molecular properties using various software.

46
SYLLABUS OF DSE-12

UNIT-1 : Introduction (Lectures: 6)

Introduction to computational chemistry: Overview of Classical and Quantum Mechanical

Methods (Ab initio, DFT, Semi-empirical, Molecular Mechanics, Molecular Dynamics, and
Monte Carlo)

UNIT – 2: Potential Energy Surfaces (Lectures: 6)

Intrinsic Reaction Coordinates, Stationary points, Equilibrium points – Local and Global
minima, Geometry optimization and energy minimization, the concept of transition state with
examples, Hessian matrix

UNIT – 3 : Molecular Mechanics & Molecular Dynamics (Lectures: 9)

Molecular Mechanics

Force Fields (A brief explanation of all the terms of a basic force field), the basic idea of MM1,
MM2, MM3, MM4, MM+, AMBER, BIO+, OPLS.

Molecular Dynamics

The concept of the periodic box, ensembles (microcanonical, canonical, isothermal – isobaric),
steps in a typical MD simulation.

UNIT-4: Huckel Molecular Orbital Theory (Lectures: 6)

Huckel MO with examples: ethene and propenyl systems, Properties calculated – energy,
charges, bond order, electronic energies, resonance energies.

UNIT- 5: Computational Methods (Lectures: 18)

Ab-initio methods
Antisymmetry principle, Slater determinants, SCF method, Hartree-Fock method.
Basis sets, Basis functions, STOs and GTOs, diffuse and polarization functions. Minimal basis
sets, Basis set superposition error (BSSE) - Effective core potentials (ECP)
Advantages of ab initio calculations.

Density Functional Theory

A brief description of Density Functional Theory (DFT). Calculation of Electronic Properties
in ground and Excited states

Semi-empirical methods
Basic idea about Zero differential overlap (ZDO) approximation

47
Some important concepts
Concepts of atomic charges, electrostatic potential maps, computation of thermodynamic
properties and spectroscopic observables

Practical component
Practical: Credits: 01
(Laboratory periods:15 classes of 2 hours each)

1) Write the Z-Matrix of a given set of molecules.

2) Carry out geometry optimisation on H2O, H2S, H2Se molecules compare the optimized
bond angles and dipole moments from the results obtained. Obtain the ESP-mapped
density surfaces and interpret the results obtained with reference to bonding in these
molecules.

Suggestive: A comparative analysis of results of the above exercise may be carried out
using different quantum mechanical methods.

3) Calculate the energy of the following chemical species and arrange them in order of
increasing stability.

1-hexene, 2-methyl-2-pentene, (E)-3-methyl-2-pentene, (Z)-3-methyl-2-pentene, and

2,3- dimethyl-2-butene in order of increasing stability.

4) Carry out geometry optimisation on the following chemical species and compare the
shapes and dipole moments of the molecules.

1-pentanol, 2-pentanol, 3-pentanol, 2-methylbutan-1-ol, 3-methylbutan-1-ol, 2-

methylbutan-2-ol, 2-methylbutan-3-ol and 2,2-dimethylpropanol.

Correlate the computationally obtained values of the dipole moments with the
experimental values of the boiling points: (118 ºC, 100 ºC, 108 ºC, 82 ºC, of 1-butanol,
2-butanol, 2-methyl-1-propanol, and 2-methyl-2- propanol respectively).

5) Based on the implicit electronic structure calculations, determine the heat of

hydrogenation of Propylene.

6) Based on the calculations of enthanlies of the participating chemical species on

optimized geometry of the molecules, calculate the reaction enthalpy at 298 K for the
following, industrially important reactions:

+ +3 (steam reforming of methane)

(Haber-Bosch process)

48
7) Carry out geometry optimisation and determine the energy of the participating chemical
species in the following reactions Using these results calculate the resonance energy of
thiophene.

H2 H2

S S S

8) Carry out geometry optimisation & Energy calculations on the following species and
obtain Frontier Molecular Orbitals. Visualize the Molecular Orbitals of these species
and interpret the results for bonding in these molecules.
Benzene, Naphthalene, and Anthracene.

9) Compare the gas phase basicities of the methylamines by comparing the enthalpies of
the following reactions:

BH+ + NH3 B + NH4+

Where B = CH3NH2, (CH3)2NH, (CH3)3N

10) On the basis of results of geometry optimization and energy calculations, determine the
enthalpy of isomerization of cis and trans 2-butene.

11) Perform a conformational analysis of butane. Plot the graph between the angle of
rotation and the energy of the conformers using spreadsheet software.

12) Compute the resonance energy of benzene by comparison of its enthalpy of

hydrogenation with that of cyclohexene.

13) Calculate the electronic UV/Visible absorption spectrum of Benzene.

14) Calculate the electronic absorption spectra of formaldehyde.

15) Plot the electrostatic potential mapped on electron density for benzene and use it to
predict the type of stacking in the crystal structure of benzene dimer.

16) On a given set of molecules methylamine (CH3NH2) carry out geometry optimization,
single point energy and NBO calculations and interpret the output results treated at the
ab initio RHF/3-21G level.

17) Study the mechanism of SN2 reaction between Cl- and CH3Br involving a Walden
inversion computationally.

49
 18) Perform a geometry optimization followed by a frequency assessment (opt+freq
keyword) using the B3LYP method and 6-31-G(d) basis set on a given set of small
molecules i.e. BH3, CH4.
Suggestive: A greater number of molecules may be studied as per instructions received
from the concerned teacher.

19) Based on the fundamentals of conceptual DFT calculate the ionization potential (IP),
electron affinity (EA), electronegativity and electron chemical potential of a given set
of molecules.

20) Perform molecular docking of Sulfonamide-type D-Glucose inhibitor into MurrD

active site using Argus Lab.

21) Perform molecular dynamics (MD) simulation of a given alkali metal ion in aqueous
function (RDF)

Essential/recommended readings

Theory:
1. Lewars, E. (2003), Computational Chemistry, Kluwer academic Publisher.
2. Cramer, C.J. (2004), Essentials of Computational Chemistry, John Wiley & Sons.
3. Hinchcliffe, A. (1996), Modelling Molecular Structures, John Wiley & Sons.
4. Leach, A.R. (2001), Molecular Modelling, Prentice-Hall.
5. House, J.E. (2004), Fundamentals of Quantum Chemistry, 2nd Edition, Elsevier.
6. McQuarrie, D.A. (2016), Quantum Chemistry, Viva Books.
7. Levine, I. N.; Physical Chemistry, 5th Edition, McGraw –Hill.

Practical:
1. https://www.afs.enea.it/software/orca/orca_manual_4_2_1.pdf
2. https://dasher.wustl.edu/chem430/software/avogadro/learning-avogadro.pdf
3. http://www.arguslab.com/arguslab.com/ArgusLab.html
4. https://barrett-group.mcgill.ca/tutorials/Gaussian%20tutorial.pdf
5. https://gaussian.com/techsupport/
6. https://gaussian.com/man/
7. https://gaussian.com/wp-content/uploads/dl/gv6.pdf
8. https://dasher.wustl.edu/chem478/software/spartan-manual.pdf
9. http://www.mdtutorials.com/gmx/
10. https://vina.scripps.edu/manual/

Important Instruction Note on working approach:

50
 A student is required to perform/investigate a minimum of 10 exercises from the
given set of exercises.
The students may use open source softwares; ArgusLab, Avogadro and ORCA. In
case a licenced version softwares is available, if procured by the college, other
licenced softwares may also be used.

Note: Examination scheme and mode shall be as prescribed by the Examination Branch,
University of Delhi, from time to time.

51