# BMC2050 - Computational Chemistry

## 6 points, SCA Band 2, 0.125 EFTSL

#### Offered

Parkville Second semester 2007 (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.