Module Details
The information contained in this module specification was correct at the time of publication but may be subject to change, either during the session because of unforeseen circumstances, or following review of the module at the end of the session. Queries about the module should be directed to the member of staff with responsibility for the module.
Title MOLECULAR MODELLING
Code CHEM473
Coordinator Dr N Berry
Chemistry
Year CATS Level Semester CATS Value
Session 2008-09 M Level First Semester 7.5

Aims

To introduce students to molecular modelling techniques in chemistry.


Learning Outcomes

By the end of this module students will have:

  • Be able to predict the ground state energy and structure of isolated molecules (for relatively simple systems).
  • Be able to estimate equilibrium constants, rate constants and calculate transition states for simple reactions.
  • Be able to rationalise some aspects of reactivity (charge density, frontier orbitals).
  • Have some understanding of intermolecular forces and complexes (pharmacological example)

Syllabus
0 

Students will be introduced to many of the skills necessary to perform basic molecular modelling calculations.

Computational Chemistry (Ab initio, semi-empirical, molecular mechincs), Molecular Simulation, Molecular Graphics - Definitions, Applications

Ab initio - Born-Oppenheimer approximation, Orbital approximation, Linear combination of atomic orbitals, Self consistent field, Variational principle and Hartree-Fock, Basis sets, Solving approximate Schrodinger equation, Limitations of Hartree-Fock calculations, Accuracy and utility (e.g. isodesmic reactions) of calculations

Semi-emipirical - Assumptions, Formulation, Inclusion of experimental data in model, Advantages and disadvantages of the method, Application using frontier molecular orbitals (orbital control versus charge control)

Solvation models - Importance in chemistry, Difficulty in modelling, Explicit and implicit models

Geometry optimisation - Pote ntial energy surface, Energy minima (local and global), Transition state

Electron correlation - DFT theory includes some electron correlation, Assumptions, Advantages and disadvantages of DFT

Molecular mechanics - Assumptions, Formulation, Inclusion of experimental data in model, Advantages and disadvantages of the method

Conformational searching - Systematic and Monte-Carlo methods, Boltzmann distribution

Non-covalent forces - Electrostatic, Hydrogen bonding, pi-pi stacking, Dispersion, Hydrophobic, Cooperativity, Hunter-Sanders model of pi-pi stacking, Biological example


Teaching and Learning Strategies

Molecular modelling is taught through lectures and assignments. The assignments are started under supervision and completed in the students' own time.


Teaching Schedule
  Lectures Seminars Tutorials Lab Practicals Fieldwork Placement Other TOTAL
Study Hours 6

     6

     12
Timetable (if known) Mon 2-3 (1-6)
  		    Mon 3-4 (1-6)
  		     
Private Study 63
TOTAL HOURS 75

Assessment
EXAM Duration Timing
(Semester)		 % of
final
mark		 Resit/resubmission
opportunity		 Penalty for late
submission		 Notes
             
CONTINUOUS Duration Timing
(Semester)		 % of
final
mark		 Resit/resubmission
opportunity		 Penalty for late
submission		 Notes
Six Computer modelling Exercises    Semester 1  100  According to University policy  Standard University Policy applies - see Department/School handbook for details.  This work is not marked anonymously.  

Recommended Texts

Essential

i) A guide to Molecular Mechanics and Quantum Chemical Calculations, W. J. Hehre

Background (basic)

i) Computational Chemistry, G. H. Grant, W. G. Richards

ii) Chemical Applications of Molecular Modelling, J. Goodman

Background (advanced)

iii) Molecular Modelling, Principles and Applications, A. R. Leach

iv) Essentials of Computational Chemistry, C. J. Cramer

v) Introduction to Computational Chemistry, F. Jensen