Microscopic study of electrical transport through individual molecules with metallic contacts: II. Effect of the interface structure

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.