| We present a series of studies that apply various computational tools to explain experimental data obtained using the techniques of Scanning Tunneling Microscopy and Temperature Programmed Desorption. The systems studied included n-alkanes, haloalkanes and carboxylic acids on graphite. The computer simulations that were performed included minimizations, molecular dynamics, Monte Carlo studies, and electronic structure calculations. We attempt to describe the motivation for the theoretical work, and the reasons for the use of each type of calculation for the specific application, in addition to the actual results. For the simulation of monolayers on graphite, the simulation data has provided structural and energetic information that breaks down the minute interplay of relevant interactions into intermolecular and surface-molecule competitively driven forces. The prediction of the barriers of n-alkanes to desorption from graphite as described in the potential of mean force calculation is very much a work in progress but looks promising as a general method for obtaining information regarding the desorption process. The same is true for calculations of the orbitals of the conjugated systems, which are beginning to provide results that are interesting in comparison to the STM data. |
