Basic concepts in molecular modeling, coordinate systems, potential energy surfaces, molecular graphics, units of length and energy and basic mathematical concepts.
Quantum mechanical models: Polyelectron atoms and molecules, the concept of interatomic and intermolecular interactions, modeling of calculated interaction energies by model potentials for simple atoms, ions and molecules.
Empirical force field models: Molecular Mechanics. General features of molecular mechanics force fields, bond stretching, angle bending and torsion, electrostatic interactions, effective pair potentials. Force field models of water and other simple molecular systems.
Computer simulation methods: Concept of microstates of macroscopic systems, averages and basic ideas of simulations. The Monte Carlo and molecular dynamics methods. Applications to various molecular and macromolecular systems. Calculation of free energy through molecular modeling and simulations.
The use of molecular modeling to discover and design new molecules: Molecular modeling in drug discovery, deriving and using three dimensional pharmacophores, molecular docking, quantitative structure-activity relationships etc.