Course

Unit 1

Introduction (8 hours)

Introduction to computational chemistry: Overview of Classical and Quantum Mechanical Methods. Ab initio methods, Introduction to Density Functional Theory, Semi-empirical methods, Molecular Mechanics, Molecular Dynamics and Monte Carlo Simulations.

Unit 2

Potential Energy Surfaces (7 hours)

Intrinsic Reaction Coordinates, Stationary points, Equilibrium points – Local and Global minima, Geometry optimization and energy minimization – gradient-based algorithms, steepest descent and conjugate gradient methods, concept of transition state with examples, Hessian matrix – frequency calculation, normal modes.

Unit 3

Molecular Mechanics & Molecular Dynamics (10 hours)

Molecular Mechanics, Classical Force Fields – Introduction to terms appearing in the potential energy, basic idea of MM1, MM2, MM3, MM4, MM+, AMBER, BIO+, OPLS.

Molecular Dynamics Simulations – Concept of the periodic box, periodic boundary conditions, Introduction to thermodynamic ensembles (microcanonical, canonical, isothermal – isobaric), Choice of ensembles and effect of ensembles on simulations, barostats and thermostats, steps to set up and run a typical Molecular Dynamics simulation.

Unit 4

Huckel Molecular Orbital Theory (8 hours)

Introduction to Huckel MO theory with examples: ethene and propenyl systems, Calculation of properties using Huckel theory- energy, charges, bond order, electronic energies, resonance energies.

Unit 5

Computational Methods (12 hours)

Ab-initio methods: Antisymmetry principle and Slater determinants, Self-Consistent Field (SCF) method, Hartree-Fock method.

Basis sets, Basis functions, Slater Type Orbitals (STOs) and Gaussian Type Orbitals (GTOs), diffuse and polarization functions. Minimal basis sets, Basis set superposition error (BSSE) – Effective core potentials (ECP) and its applications.

Advantages of ab initio calculations – Accuracy and prediction of properties of molecules with examples for cases where experimental study is difficult or impossible.   

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, Concepts of atomic charges, electrostatic potential maps, computation of thermodynamic, properties and spectroscopic observables.

Lab Component: (15 lab sessions)

1. Construction of Z-Matrix of a given set of molecules.
2. Calculation of energy of the following chemical species and determination of their relative stability. 1-hexene, 2-methyl-2-pentene, (E)-3-methyl-2-pentene, (Z)-3-methyl-2-pentene, and 2,3- dimethyl-2-butene.
3. Geometry optimization of the following molecules and comparison of their shapes and dipole moments. Compare the results with experimental values. 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.
4. Determination of heat of hydrogenation of Propylene through electronic structure calculations.
5. Geometry optimization & energy calculations of following species and obtain Frontier Molecular Orbitals. Visualize the Molecular Orbitals of these species and interpret the results for bonding in Benzene, Naphthalene, and Anthracene.
6. Determination of enthalpy of isomerization of cis and trans 2-butene based on results of geometry optimization and energy calculations.
7. Perform a conformational analysis of butane. Plot the graph between the angle of rotation and the energy of the conformers.
8. Computation of resonance energy of benzene by comparison of its enthalpy of hydrogenation with that of cyclohexene.
9. Calculation of the electronic UV/Visible absorption spectrum of Benzene.
10. Molecular docking of Sulfonamide-type D-Glucose inhibitor into MurrD active site.
11. Molecular Dynamics Simulation of a (a) protein (b) organic liquid (c) interface between organic and aqueous phases.

Text Books / References

Textbooks:

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, 2 nd Edition, Elsevier.
6. McQuarrie, D.A. (2016), Quantum Chemistry, Viva Books.
7. Levine, I. N.; Physical Chemistry, 5 th Edition, McGraw –Hill.

Course Outcome:

• CO1: Describe the fundamental principles of computational chemistry, including classical and quantum mechanical methods.
• CO2: Analyze potential energy surfaces, identify stationary points, transition states, local and global minima.
• CO3: Describe the principles of Molecular Dynamics simulations using force fields and steps involved in a simulation.
• CO4: Describe computation of electronic properties using Huckel MO theory, ab initio methods, DFT, and semi-empirical approaches.
• CO5: Apply ab initio, semi empirical quantum mechanical methods and classical molecular dynamics to explain and predict properties of organic compounds.

CO-PO Mapping: