Last revised February 23, 1998
This tutorial will give you some basic skills of computer modeling using the computer program Spartan 5.0 on Silicon Graphic Computers. Computer modeling provides two different kinds of tools for the chemist. The graphical display on the computer allows us to visualize and manipulate the molecule in three dimensions; unlike models which are physically constructed, the computer generated molecules can easily be shown in many different styles and formats, and bond angles, bond lengths, and distances between atoms are easily measured. However, computer modeling is more than a visualization tool. Modeling software also enables us to calculate the energy of a particular molecular conformation and to determine (for a given structure) the molecular geometry which is lowest in energy. This latter process is called geometry optimization (or energy minimization)
Molecular mechanics is an approach to calculating the energies of molecules by treating the atoms as "weights" and the bonds as "springs". With this assumption, we can use equations from "classical" physics (i.e., not quantum mechanics) to approximate the changing bond lengths and bond angles on the energy of the molecule. In the energy minimization process, the computer calculates the energy of a molecule by taking into account the contributions from all bond lengths, bond angles, dihedral angles, and van der Waals interactions. In an iterative process, the program alters the structure slightly and then recalculates the energy, until a minimal energy is reached (i.e., until the energy does not get lower upon making a change to the structure). Thus, although the calculations involved in molecular mechanics are quite simple, a geometry optimization procedure involves a large number of these calculations.