A Review of Molecular Mechanics in the Curriculum

Before closing this section it should be mentioned that most of the methods discussed above can be solved using commercially available programs such as symbolic computation (Mathematica, Maple, or Mathcad 3.0), equation solvers (TK Solver Plus or Mathcad 3.0), spreadsheets (e.g., Lotus 123, Quattro Pro, Microsoft Excel, or Wingz), simulators (Extend or Stella), or Microsoft FORTRAN 5.0. For example, one can introduce the idea of molecular mechanics on model systems using a spreadsheet. Actual applications of molecular mechanics are much better carried out on a software package designed for that purpose, however. 

As described above, the molecular mechanics method is based on an empirical (classical) force field. As such, it is very intuitive and relatively easy for a student to comprehend, compared to solving and interpreting Schrddinger s equation. Hence, for routine insight into the (predicted) molecular structure of ground-state molecules, with no unusual valence, molecular mechanics is preferred over quantum mechanics. This is aside from the issue of computational requirements. Of course, molecular mechanics does not provide insight into electron distribution or the nature of excited states of molecules. 

In 1968 Bartell published an article on the use of molecular models in the curriculum. In this paper the qualitative valence shell electron pair repulsion (VSEPR) model and the relative role of bonded and nonbonded interaaion in directed valence is discussed. The author correctly predicted the increasing importance of model force fields for geometry prediction. An early discussion of the use of molecular mechanics in teaching can be found in a paper by Cox. 07 A cursory description of the methodology of force field calculations is presented, along with computational results on the relative energy of the rotamers of butane and the conformers of cyclohexane. 

Another approach to the introduction of molecular mechanics into the curriculum is described in a paper by Biali. The stereochemical exercise discussed here involves the calculation of relative energies of the six possible isomers/conformers of [3.3]metacyclophanes. Even in this case, however, the input coordinates are calculated laboriously from framework molecular models and the calculations performed on a VAX 11/750 computer. An important development, however, described in this paper, is the transfer of coordinate data files to a visualization program (Ball and Stick) on the Macintosh microcomputer for simple visualization. This is one of the first descriptions of the use of file transfer on simple microcomputer programs to produce visually attractive structural representations. 

In the following sections we show how various computational methods have been introduced into the curriculum at University of South Alabama, Calvin College, St. John s University, and California State University, Los Angeles. 

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