Exercise on modelling, using Arguslab

This exercise is intended primarily to be used in a three-hour drylab session, with active teaching by demonstrators.  After that, it should be very useful for private study as a revision aid.  Arguslab is available directly on Campus cluster PCs.  It may be run by Start, Programs, Departmental Software, Chemistry, ArgusLab3, ArgusLab

Arguslab offers quite good on-screen molecule-building facilities, with a moderate library of useful molecules.  The viewer is mouse-controlled quite similarly to Rasmol/Chime.  Arguslab can do geometry optimisations using the UFF force field.  This covers all elements of the Periodic Table because it is not restricted to known atom types in its parameterisation, though it does use some common ones.  The resulting energies are distinctly different from those obtained using some of the more conventional force fields, and wherever possible one needs to reoptimise at a higher level.  For this, Arguslab offers geometry optimisation using the MNDO, AM1 or PM3 semiempirical levels, as well as single point calculations using these, though the range of elements covered is much less.  There are also single point semiempirical calculations using Extended Huckel (for a bigger element coverage) or ZINDO (for excited states for UV/visible absorption prediction).  Version 3.1 of Arguslab has good facilities for calculating electron density or orbital surfaces at the semiempirical levels, and displaying them.  It can also map another property, e.g. electrostatic potential, onto a surface, similarly to the display facilities of Chime (see Notes: An electronic model of methyl thiirane).  This will be the subject of a further document:  Drylab: Calculating Surfaces using Arguslab

File storage

Arguslab writes its own format of molecule file, .xml, but it can also write .xyz files for input to other programs, e.g. molden.  It creates (and leaves behind) a lot of temporary files, which need to be managed.

Starting and Stopping in Arguslab

Conformations of cyclohexane and methylcyclohexane

Chair cyclohexane

Twist boat cyclohexane

Energy comparison of the cyclohexane conformers

Symmetry of twist-boat cyclohexane

The five conformers of methylcyclohexane

In this part of the exercise, you use the models of the two conformers of cyclohexane, which you have saved, to create models of the five conformers of methylcyclohexane.  For each, do a preliminary UFF optimisation, then a PM3 geometry optimisation, then a PM3 single point calculation to get relative energies.  Write these down, and calculate energies relative to that of the most stable of the five conformers.


It is intended to post numerical answers for this drylab on the course website, late in the course.