BMC2050

Computational Chemistry ( 6 points, SCA Band 2, 0.125 EFTSL)

Leader: Dr David Chalmers

Offered:
Parkville Second semester 2006 (Day)

Synopsis: An introduction to the techniques and applications of molecular modelling with particular emphasis on methods used in drug design: Concepts in computational chemistry. Introduction to quantum mechanics. Molecular mechanics. Optimization. Molecular simulation. Molecular modelling of water. Molecular structure. Drug design.

Objectives: At the completion of this unit the student will have: - A broad understanding of computational chemistry and its application to drug biomolecular problems. - An understanding of common molecular modelling terminology. - An appreciation of the factors involved in performing quantum mechanical (QM) calculations and the information that these calculations can provide. - An appreciation of molecular mechanisms energy calculations and the information that these calculations can provide. - An understanding of the components making up molecular mechanic force fields including bond stretching, angle bending and dihedral angle terms and nonbonded interactions (van der Waals and electrostatic). - An understanding of molecular potential energy surfaces and the concepts of global and local minima. - An appreciation of energy optimisation methods including steepest descents and conjugate gradient methods. - An appreciation of approaches to finding global energy minima. - An understanding of the Boltzmann distribution and the relationship between temperature and teh population of energetic states. - An appreciation of Monte Carlo methods. - An appreciation of Molecular Dynamics methods including molecular vibrations. - An appreciation of the physical properties of temperature and pressure; the principles of conservation of momentum and energy; how molecules behave when they collide. - An understanding of the importance of conformational flexibility in biomolecules including Ramachandran plots for proteins. - An understanding of the concept of a pharmacophore. - An appreciation of the applications of databases in drug development. - The ability to use a specific molecular modelling package to study molecular conformation and analyse drug-receptor interactions.

Assessment: Practical work / tests 30%; Examination 70%

Contact Hours: 12 weeks of 3 Lectures, 1 week of 1 Tutorial / 1 Lecture, and 9 x 4 hour Practicals.

Prerequisites: CHM1011, CHM1022, BMC1021.