Determination of the conductance through a metal-molecule-metal structure presents a difficult computational problem. One normally divides the problem into two parts: computation of the band structure and then computation of the transport through the device. The choice of a basis set for the band structure calculation presents an interesting challenge, in that the results can significantly affect the resulting energy structure throughout the device. An important consequence of the band structure calculation is the surface dipole, which generates the work function, and is therefore an important aspect of the surface barrier between the "contact" and the molecule. If this is not determined accurately, which is quite often the case, one cannot expect to achieve good results for the transport calculation. Nevertheless, we can use the results to compare differences between different molecules without having good quantitative results for the conductance, and this is demonstrated here. (c) 2006 American Vacuum Society.