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Molecular Modelling (CH926)

Module proposal information

Aim: To introduce students to molecular modelling techniques as applied to biological systems with particular emphasis on the methods used and their underlying theory. The student should gain a basic understanding of the available computational methods and their theoretical foundations; what time scales and length scales are accessible; what properties can be computed and to what level of accuracy; and what methods are most appropriate for different molecular systems and properties.
Syllabus: Coordinate systems: how to describe 3-D molecular structure. Potential energy surfaces: quantum & empirical; conformations, vibrations and transition states. Quantum Methods: review of basic quantum mechanics; introduction to MO theory and basis sets; awareness of HF-based, DFT and semi-empirical methods; illustrative applications. Intermolecular potentials. Classical Methods: Molecular Mechanics, Molecular Dynamics & Metropolis Monte Carlo; thermodynamic and transport properties; free energies; illustrative applications. Statistical & Comparative Methods: QSAR; homology modelling. Computer Aided Design: case studies from developing materials and pharmaceuticals. Applications to examples such as: simulation of conformational changes, chemical reactions, rare events; simulations incorporating experimental (structural, NMR) data; restrained dynamics; application of computer modelling to molecular aggregates such as membranes.
Illustrative Bibliography:
  1. G.H. Grant & W.G. Richards, Computational Chemistry
  2. A. R. Leach, Molecular Modelling, Principles and Applications
  3. D. Frenkel and B. Smit, Understanding Molecular Simulation