PSC2142 - Computational chemistry - 2018

This unit provides an introduction to the techniques and applications of molecular modelling with particular emphasis on methods used in drug design.

The unit contains two streams:

1. modelling methods; which introduces quantum mechanics, molecular mechanics, energy optimisation and molecular simulation and
2. modelling applications; which covers quantitative structure-activity relationships (QSAR), pharmacophores, structure-based drug design and homology modelling.

   This will involve:

   • modelling methods in computational chemistry
   • applications of molecular modelling

At the end of this unit students will have:

1. A broad understanding of computational chemistry and its application to drug bimolecular problems;
2. 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;
3. An appreciation of molecular mechanisms energy calculations and the information that these calculations can provide;
4. 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);
5. An understanding of molecular potential energy surfaces and the concepts of global and local minima;
6. An appreciation of energy optimisation methods including steepest descents and conjugate gradient methods;
7. An appreciation of approaches to finding global energy minima;
8. An understanding of the Boltzmann distribution and the relationship between temperature and the population of energetic states;
9. An appreciation of molecular simulation methods;
10. An understanding of drug physicochemical properties including electronic, steric and hydrophobic characteristics;
11. An understanding of the statistical methods used to develop QSAR equations;
12. An appreciation of the application of QSAR in drug discovery;
13. An appreciation of impact of drug physicochemical parameters on biopharmaceutical properties;
14. An understanding of the pharmacophore concept and its use in drug discovery;
15. An appreciation of structure and ligand-based drug design;
16. An appreciation of homology modelling methods;
17. The ability to use a specific molecular modelling package to study molecular conformation and analyse drug-receptor interactions;
18. Describe the molecular interactions which govern molecular structure including bonded, non-bonded and electrostatic interactions.

    After completing this unit the student will have the following practical skills:

19. Perform simple molecular modeling studies using the molecular modeling package;
20. Describe the processes involved in molecular mechanics energy calculations;
21. Explain the processes involved in running quantum mechanics calculations;
22. Interpret and critique a QSAR equation;
23. Generate statistically acceptable QSAR equations from physicochemical parameters and biological activity data;
24. Derive simple pharmacophore models;
25. Describe protein-ligand interactions and how an understanding of these can be applied to drug design;
26. Investigate a research topic using literature sources and write a simple report.

Final exam (2 hour): 60%; mid-semester exam: 20%; practical assessment: 20%.

Contact hours for on-campus students:

• Thirty six hours of lectures
• Nine 4-hour practical classes

See also Unit timetable information

http://www.monash.edu/pharm/current/