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 distances, 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. Due to the close proximity of the highest occupied molecular orbital (HOMO) of the isolated PDT molecule to the gold Fermi level, this leads to the counterintuitive increase of conductance with increasing top-metal-molecule distance that decreases only after the energy level line up saturates to that of the molecule chemisorbed on the substrate. We find that the effect on molecular transport from adding an apex atom onto the surface of a semi-infinite electrode is similar to that from increasing the metal-molecule distance. The similarity is reflected in both the charge and potential response of the molecular junction and consequently also in the nonlinear transport characteristics. Changing the molecular adsorption geometry from a threefold to a top configuration leads to slightly favorable energy level lineup for the molecular junction at equilibrium and consequently larger conductance, but the overall transport characteristics remain qualitatively the same. The presence of an additional hydrogen end atom at the top-metal-molecule contact substantially affects the electronic processes in the molecular junction due to the different nature of the molecular orbitals involved and the asymmetric device structure, which leads to reduced conductance and current. 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.