- To understand the role and purpose of computational chemistry in general and in molecular modelling
- to understand the fundamental mathematical expression that need to be solved in the various forms of molecular modelling
- Introduction and scope of computational chemistry, potential energy surface, conformational search, global minimum, local minima, saddle
- Ab initio methods: A review of Hartee-Fock method, self consistent field (SCF) Roothan concept basis functions. Basis sets and its classification :Slater type and Gaussian type basis sets, minimal basis set, Pople style basis sets .Hartree- Fock limit. Post Hartree-Fock methods – introduction to Møller Plesset perturbation theory, configuration interaction, coupled cluster and semi empirical methods.
- Introduction to Density Functional Theory (DFT) methods: Hohenberg-Kohn theorems, Kohn-Sham orbitals, exchange correlation functional, local density approximation, generalized gradient approximation, hybrid functionals (only the basic principles and terms need to be introduced).
- Comparison of ab initio, semi empirical and DFT
- Molecular geometry input: Cartesian coordinates and internal coordinates, Z matrix, Z-matrix of single atom, diatomic molecule, non-linear triatomic molecule, linear triatomic molecule, polyatomic molecules like ammonia, methane and General format of GAMESS / Firefly input file , single point energy calculation, geometry optimization, constrained optimization and frequency calculation. Koopmans’ theorem.
- Features of molecular mechanics force field-bond stretching, angle bending, torsional terms, non-bonded interactions and electrostatic interactions. Commonly used force fields- AMBER and CHARMM.
The session serves as an introduction to the field of molecular modeling and focuses on the four major methods in use: Molecular Mechanics, Ab Initio, Semi empirical, Density Functional Theory, Some of the advantages and disadvantages of these four approaches will also be discussed. The Laboratory is an introduction to the interfaces used to construct molecules and perform simple calculations.
Density Function Theory
Comparison of three methods
Construction of Z matrix
General format of Gamess/Firefly input file