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
Aims
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