Theoretical description of the STM images of alkanes and substituted alkanes adsorbed on graphite

A theoretical model based on perturbation theory has been developed to predict the scanning tunneling microscopy (STM) images of molecules adsorbed on graphite. The model is applicable to a variety of different molecules with reasonable computational effort and provides images that are in qualitative agreement with experimental results. The model predicts that topographic effects will dominate the STM images of alkanes on graphite surfaces. The computations correlate well with the STM data of functionalized alkanes and allow assessment of the structure and orientation of most of the functionalized alkanes that have been studied experimentally. In addition, the computations suggest that the highly diffuse virtual orbitals of the adsorbed molecules, despite being much farther in energy from the Fermi level of the graphite than the occupied orbitals, may play an important role in determining the STM image contrast of such systems.