Electronic Structure Calculations, Molecular Simulation and Macromolecular Modelling


Unit code: CHEM30242
Credit Rating: 10
Unit level: Level 3
Teaching period(s): Semester 2
Offered by School of Chemistry
Available as a free choice unit?: N

Requisites

None

Aims

 

  • Equip students with a more detailed knowledge of the principles and some applications of electronic structure calculations.
  • Understand the main techniques in computer simulation and learn how simulation is used to investigate molecular behaviour.
  • Be familiar with models for molecular and macromolecular interactions in aqueous solution, and their application.

Overview

Electronic Structure Calculations (Prof Popelier, 7.5 lectures + 0.5 workshop)

The focus of this section is on a deeper understanding of the physics and mathematical approximations behind modern quantum mechanical calculations. After establishing a few prerequisites, we will cover Hamiltonians for multi-electron systems, the Hartree-Fock methods, Slater determinants, basis sets, electron correlation and density functional theory.

Molecular Simulation (Dr Henchman, 6 lectures + 2 workshops)

Computer simulation predicts the properties of large and complex molecular systems. It provides detailed molecular insight beyond what experiment can generate. This course covers:

  • How molecules are modelled and their parameters derived.
  • Simulation techniques: setting up, minimization, molecular dynamics, Monte Carlo, conformational searching and docking.
  • Analysis and calculation of structural, thermodynamic and dynamic properties.

Macromolecular Modelling (Dr Warwicker, 6 lectures + 2 workshops)

Classical electrostatics methods enable the calculation of the properties of macromolecules in aqueous solution, starting from the Debye-Hückel law, and proceeding to more complex solutions of the Poisson-Boltzmann equation. Such modelling is extensively used in biological chemistry, and applications discussed will include enzyme catalysis, interactions between macromolecules, and molecular stability. These areas will be discussed in the contexts of both the underlying chemistry and the biological processes they underpin.

Learning outcomes

 Students successfully completing this unit should have developed the ability to:

  • Understand the basic underlying principles of modern electronic structure calculations.
  • Understand how one develops molecular models, how the main simulation techniques work, how one connects with data from different sources and what information can be produced by simulation.
  • Understand how models for calculating the properties of macromolecules are developed and applied.

Transferable skills and personal qualities

Analytical skills, problem-solving skills, investigative, numeracy and mathematical skills, computing and IT skills.

Assessment methods

  • Written exam - 100%

Recommended reading

  • Leach, A. R. Molecular Modelling: Principles and Applications, Prentice Hall, 2001, 2nd Edition.
  • Goodman, J. Chemical Applications of Molecular Modelling, 1998.
  • Grant, G. H. and Richards. W. G. Computational Chemistry, 1995.
  • Hinchliffe, A. Molecular Modelling for Beginners, Oxford: Wiley-Blackwell, 2008, 2nd Edition.
  • Cramer, C. J. Essentials of Computational Chemistry, Wiley, 2004, 2nd Edition.
  • Lewars, E. Computational Chemistry, Kluwer Academic Publishers, 2003.
  • Lowe, J. P. Quantum Chemistry, Academic Press, 2005, 3rd Edition.
  • Atkins, P. W., Friedman, R. S, Molecular Quantum Mechanics, Oxford University Press, 2010, 5th edition.
  • Haken, H. and Wolf, H. C., Molecular Physics and Elements of Quantum Chemistry: Introduction to Experiments and Theory, Springer, 2004.
  • Demtroder, W., Laser Spectroscopy: Vol. 1: Basic Principles, Springer, 2008, 4th edition.
  • Hobza, P. Muller-Dethlefs, K. Non-covalent Interactions, Theory and Experiment, Royal Society of Chemistry, 2009.

Feedback methods

 Blackboard quizzes, workshops, practice questions and past exam papers.

Study hours

  • Assessment written exam - 2 hours
  • Lectures - 19.5 hours
  • Practical classes & workshops - 4.5 hours
  • Independent study hours - 74 hours

Teaching staff

Richard Henchman - Unit coordinator

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