Molecular Models by Dr. B.W. Tattershall

This website is available off-campus.

Much of it requires the viewing of models using the Chime plugin to a web browser. 

To do some of the practical work on this website, you will need also an id on the University's unix computer systems, which will be obtained for you  if you do not have one already.  Instructions for setting up your unix id, which you should do sooner rather than later, are given in Using Unix from a Cluster PC running Exceed


Book recommendations

Notes: What is a molecular model?
Chime rotatable model of P3(tBu)3(SiMe3)2
with geometry optimised at the RHF/PM3 semiempirical level
Notes: What we can see in this model

.xyz file for P3(tBu)3(SiMe3)2
Chime model of P3(tBu)3(SiMe3)2, using .xyz file directly instead of using script
Rasmol/Chime script .spt file for P3(tBu)3(SiMe3)2

Notes: What else could be in a molecular model, besides geometry?
Notes: An electronic model of methyl thiirane
Chime model of methyl thiirane
with geometry optimised at the RHF/3-21G* ab initio level
Chime total electron density for methyl thiirane
at 0.12 contour level.
Chime LUMO for methyl thiirane
at 0.2 contour level. All lobes have been made positive to enable the Chime contour routine to work.
Notes: Why do molecular modelling?
Notes: How do we get to a model of geometry?
Practical work: Using Molden to view a geometry optimisation
Notes: The process of energy minimisation, used to optimise geometry
Notes: Conformation searching

Drylab: Building Z matrices using Molden

Notes: Modelling methods overview
Notes: Force field methods
Notes: Semi-empirical methods
Notes: Ab initio methods
3-21G basis set for H, C and N

Drylab: Modelling using Arguslab
Numerical answers to the Arguslab modelling exercise ©

Drylab: Geometry optimisation using Gaussian

Notes: Electronic properties
NBO plots
Practical work: Using more in unix to view an NBO analysis

Drylab: Calculating Surfaces using Arguslab

Notes: Using Energies
Practical work: Using more and molden in unix to view a vibrational analysis

Drylab: Vibrational modes using Gaussian

Notes: Viewing an enzyme structure
Chime crystal structure of an enzyme