Syllabus
Unit I
IntroductionIntroduction to computational chemistry (molecular modelling), questions commonly investigated computationally, principle and application of methods (tools) of computational chemistry – molecular mechanics, ab initio method, semiempirical methods, density functional theory and molecular dynamics, STOs, GTOs, basis sets, specification of molecular geometry using Cartesian coordinates and internal coordinates, Z- matrix, Z-matrix of simple molecules (water, ethanol), potential energy surface (PES), potential energy surface of diatomic molecules and triatomic molecules (H2O and HOF) – hypersurface and process of slicing, stationary points on potential energy surface – potential energy surface of the isomerization reaction of ozone to isoozone, stationary points (ozone, isoozone and transition state), intrinsic reaction coordinate, minimum, relative minimum, saddle-shaped surface, saddle point, higher-order saddle point and mathematical treatment of stationary points, Born-Oppenheimer approximation and its significance and frozen-nuclei energy.
Unit II
Molecular MechanicsIntroduction to molecular mechanics, forcefield, developing a force field – expression for potential energy of a molecule, bond stretching term, angle bending term, torsional term and nonbonded interaction term, parameterizing a forcefield – parameterizing bond stretching term, angle bending term, torsional term and nonbonded interaction term, calculation using forcefield – compare the energies of two 2, 2, 3, 3- tetramethylbutane geometries, illustration of application (use) of molecular mechanics – calculation of geometries and energies of small-sized and medium-sized molecules, polymers and transition states (transition state for the Diels-Alder reaction of butadiene with ethene to form cyclohexene), in organic synthesis for predicting the more suitable path for carrying out the synthesis and calculation of normal-mode vibrational frequencies for characterizing a species as a minimum or a transition state or higher-order saddle point, for obtaining zero-point energies to correct frozen-nuclei energies and for interpreting or predicting IR spectra, strength (merit) and weakness (demerit) of molecular mechanics.
Unit III
Semiempirical Methods Part 1Introduction to semiempirical (SE) methods, Simple Huckel Method (SHM) – theory – expression for calculating energy of a molecular species, expression for molecular wave function based on LCAO approximation, secular equations and the single matrix equation, H, C, S and ? matrices and their interpretation, the values of Hij as zero, coulomb integral ? and bond integral ? and their physical significance, the H matrix in terms of ?, ? and zero for ethene system(ethene neutral molecule, ethene radical cation and ethene radical anion), propenyl system (propenyl cation, propenyl neutral radical and propenyl anion) and cyclobutadiene system (square cyclobutadiene dication, square cyclobutadiene neutral molecule and square cyclobutadienedianion), the H matrix in terms of zero, ? = 0 and ? =? 1for ethene systems (ethene neutral molecule, ethene radical cation and ethene radical anion), propenyl system (propenyl cation, propenyl neutral radical and propenyl anion) and cyclobutadiene system (square cyclobutadiene dication, square cyclobutadiene neutral molecule and square cyclobutadiene dianion), result of diagonalization of the H matrices written for ethene system, propenyl system and cyclobutadiene system, molecular orbital energy level diagrams and expressions for energy and molecular wave functions for ethene system, propenyl system and cyclobutadiene system based on the result of diagonalization of the H matrices, and molecular orbital energy level diagrams for ethene system, propenyl system and cyclobutadiene system showing ground state and excited state electronic configurations.
Unit IV
Semiempirical methods Part 2Application of SHM – nodal properties of molecular orbitals and Woodward-Hoffmann orbital symmetry rule, stability towards oxidation and reduction of various species in ethene system, propenyl system and cyclobutadiene system, geometry of cyclobutadiene molecule as predicted by SHM and its Jahn-Teller distortion, aromaticity and Huckels (4n + 2) ? electron rule, and calculation of resonance (stabilizing) energy, bond order and atomic charges of various species in ethene system, propenyl system and cyclobutadiene system, strength of SHM, weakness of SHM (detailed explanation) – basis set is limited to p orbitals (pz orbitals), it treats only ? electrons, and the overlap integrals, Fock matrix elements, electron spin and electron-electron repulsion are not calculated/accounted properly, extended Huckel method (EHM) – minimal valence basis set, calculation of Fock matrix elements, and calculation of overlap integrals by Lowdin orthogonalization, EHM procedure, EHM calculation on protonated helium molecule, application of EHM – an overall idea, strength and weakness of EHM, SCF SE methods – Pariser-Parr-Pople (PPP) method and complete neglect of differential overlap (CNDO) method – basic principle (an exhaustive treatment is not expected).
Unit V
Density Functional Theory and ab initio Method(An exhaustive treatment is not expected)Introduction to Density Functional theory and calculations, Kohn-Sham approach – the first and the second Hohenberg-Kohn theorems, introduction to ab initio method and calculation, basis sets for H, He and first, second and third row elements used in ab initio calculations – STO-3G, 3-21G, 3-21G(*) and 6-31G*, these basis sets for a few molecular species (water, methane and carbene), basic principles of ab initio method (an idea only).
Text Books / References
1. Computational Chemistry-Introduction to the Theory and Applications of Molecular and Quantum Mechanics – Errol Lewars