Molecular Modelling in Chemistry




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Course Contents

Brief Review of the basic Principles of quantum mechanics of atoms and molecules.
Potential energy surfaces and intermolecular interactions: Quantum mechanical ab initio calculations within Born-Oppenheimer approximation and modelling of calculated energies by model potentials for simple atoms, molecules and ions. Energy calculations using molecular mechanics. (16)

Simple applications of molecular modelling: Study of an assembly of atoms or molecules (clusters and/or bulk phases). Approximation of the total potential energy as the sum of pair potentials. Concept of large number of microstates, averages and basic principles of simulations. Study of cluster and bulk properties through simulations. (10)

Modelling of water and small organic molecules: Nonpolarizable and polarizable rigid models. Flexible models and calculation of force constants. Structural, dielectric and dynamical properties of a polar medium: Continuum models versus molecular models. Calculation of free energy using molecular models. (10)

Modelling of macromolecules: Study of self-organized assemblies, biomolecules like peptides, proteins, membranes and ion channels. Concept of hydrophobic and hydrophilic interactions. Use of molecular modelling in drug design, QSAR (6)


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  • A.R. Leach, Molecular Modeling : Principles and Applications, Longman (1996).

  • J. H. Jensen, Molecular Modeling Basics, CRC Press (2010).

  • C. J. Cramer, Essentials of Computational Chemistry: Theories and Models, 2nd Ed., Wiley (2004).

  • J. Israelachvili, Intermolecular and surface Forces, Academic (1991)

  • M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press (1987)

  • D. Frenkel and B. Smit, Understanding Molecular Simulation : From algorithms to Applications, Academic Press (1996)

  • P.W. Atkins, Molecular Quantum Mechanics, Oxford (1997)

  • W. Koch & M. C. Holthausen, A Chemist’s Guide to Density Functional Theory, Wiley-VCH.

  • Szabo, Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory, Dover Publications (1996).



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