MOLECULAR MODELLING IN CHEMISTRY
COURSE SYLLABUS
( CHM 695) |

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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 energy by model potentials for simple atoms, ions and molecules. Concept of short range and long range interactions. Modelling of interactions involving macrobodies like planar surfaces, macrospheres etc. Molecular Mechanics calculations.

Simple applications of molecular modelling :

Study of an assembly of atoms or molecules (cluster
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 Monte carlo and Molecular Dynamics simulations.

Water and small organic molecules :

Non-polarizable and polarizable rigid models.
Flexible models and calculation of force constants.
Structural and dielectric
properties of a polar medium : Continuum models versus molecular models.
Calculation of structure, energy and free energy through simulations
using molecular models.

Macromolecules :

Study of self organized assemblies, bio-molecules
like peptides, proteins, membranes and ion channels through simulations.
Concept of hydrophobic and hydrophilic interactions.
Use of molecular modelling in drug design.

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