The two molecular mechanics modules, Merck (MMFF) and Sybyl in SPARTAN are intended chiefly for "cleaning up" input structures, prior to submitting them to various kinds of molecular orbital calculations. They also can be used to search for stable conformers of very flexible molecules. Consequently they have limited functionality and atom types, especially the Sybyl force field; both were originally devised for working with polypeptides.
However, they still can serve to familiarize us with SPARTAN input, and with the variability of molecular mechanics force fields. Projects 1 and 2 require you to remember your sophomore organic chemistry.
- Create axial and equatorial methylcyclohexanes with the SPARTAN Builder module. Minimize them with both available force fields. Send me an e-mail comparing the strain energies, and the difference in strain energies for axial and equatorial, with those that you calculated earlier using PCModel.
- Chose another pair of isomeric compounds, such as cis- and trans-9-methyldecalin (1-methylbicyclo[4.4.0]decane), and make the same comparison. Use only first-row elements. E-mail me the results of your comparison.
- Use the amino acid module to build a simple tripeptide, such as Arg-Gly-Phe (arginine, glycine, phenylalanine). Then set up a Monte Carlo (random) conformation search on the single bonds in the backbone, using the Merck force field. How many stable minima do you find? E-mail me the Cartesians of the most stable one.
This set of exercises should take you no more than 1 - 2 hours. It is intended to familiarize you with the molecular mechanics capabilities (and deficiencies) of SPARTAN.