  We investigate the effect on molecular transport due to the different
structural aspects of metal-molecule interfaces. The example system chosen is
the prototypical molecular device formed by sandwiching the phenyl dithiolate
molecule (PDT) between two gold electrodes with different metal-molecule
distance, atomic structure at the metallic surface, molecular adsorption
geometry and with an additional hydrogen end atom. We find the dependence of
the conductance on the metal-molecule interface structure is determined by the
competition between the modified metal-molecule coupling and the corresponding
modified energy level lineup at the molecular junction. The results of the
detailed microscopic calculation can all be understood qualitatively from the
equilibrium energy level lineup and the knowledge of the voltage drop across
the molecular junction at finite bias voltages.
