Molecular Modelling for Organic Chemistry

Podcasts: iTunes or an RSS Reader/Web browser
iPhone/iPad/Kindle eBook version: Follow instructions here

A course of seven lectures and lecture-demonstrations given by
Henry Rzepa,
at the Department of Chemistry, Imperial College London.

Importance of Molecular Modelling

The 1998 Nobel Chemistry Prize was awarded to Pople and Kohn for their work in Computational Chemistry and Molecular Modelling.

The 1999 Nobel Chemistry Prize was awarded to Ahmed Zewail for his work in developing spectroscopic methods for studying reactions and in particular transition states, an essential aspect of molecular modelling.

Modelling is an essential component of the Grand challenge of Dial-a-Molecule.

Course Aims and synopsis

Molecular modelling is a collection of (computer based) techniques for deriving, representing and manipulating the structures and reactions of molecules, and those properties that are dependent on these three dimensional structures. This lecture course aims to introduce in a simple way the hierarchy of computational modelling methods used nowadays as standard tools by organic chemists for searching for, rationalising and predicting structure and reactivity of organic, bio-organic and organometallic molecules. The emphasis will be on helping to develop a feel for the correct "tool" to use in the context of a typical problem in structure, activity or reactivity, by describing the limitations and strengths of each method. The techniques described include:
  1. Molecular visualisation
  2. Methods for Equilibrium and transition state geometry location
  3. Introduction to Molecular mechanics methods
  4. Applications of Semi-empirical, ab initio and density functional molecular orbital methods
  5. Methods for topological analysis of wavefunctions

The course does NOT deal with: excited states and photochemistry, hybrid (layer) models and inorganics.

The use of these tools is illustrated via the following case studies:

2011 Exam Paper and outline answer

Background texts and workbooks:

  1. Wikipedia entry
  2. Computational Organic Chemistry, Steven Bachrach, Wiley, 2007, ISBN 978-0-471-71342-5.
  3. Computational Chemistry Workbook: Learning Through Examples Thomas Heine, Jan-Ole Joswig, Achim Gelessus ISBN: 978-3-527-32442-2, 2009.
  4. Essentials of Computational Chemistry, Chris Cramer, Wiley, 2002.
  5. Chemical Applications of Molecular Modelling, Jonathan Goodman, RSC, 1999. (ISBN 0-85404-579-1)
  6. Molecular Modelling Workbook for Organic Chemistry, W. J. Hehre, A. J. Shusterman and J. E. Nelson, 1998.
  7. Brief Guide to Molecular Mechanics and Quantum Chemical Calculations, W. J. Hehre, J. Yu, P. E. Klunzinger and L. Lou, 1998.
  8. Laboratory Book of Computational Organic Chemistry, W. J. Hehre, A. J. Shusterman, W. Wayne Huang, 1996.
  9. Laboratory Exercises using HyperChem from Hypercube Educational Publications, M. L. Caffery, Caffery, Dobosh and Richardson. (ISBN 1-896164-30-7)
  10. Molecular Mechanics across Chemistry. Anthony Rappe and Carla Casewit (ISBN: 0-935702-77-6).
  11. Molecular Modelling. Principles and Applications, A. R. Leach, Longman, 1996. ISBN 0-582-23933-8
  12. Introduction to Computational Chemistry, by Frank Jensen, Wiley, 1999 (ISBN 0-471-98425-6).
  13. Introduction to Theoretical Organic Chemistry and Molecular Modelling by William B. Smith. ISBN: 978-0-471-18643-4
  14. Encyclopaedia of Computational Chemistry, the definitive reference work for Computational Chemistry.
  15. WATOC Congress, 1999, 2002, 2005, 2008, 2011.

Return to overview| Forward to scales|Forward to visualisation|Forward to Mechanics| Forward to MO Reactant|Forward to MO TS| Forward to MO Advanced|
(c) H. S. Rzepa 1998-2012. No reproduction rights granted to this material without permission.