Models of Electrodes and Contacts in Molecular Electronics
  Bridging the difference in atomic structure between experiments and theoretical calculations and exploring quantum confinement effects in thin electrodes (leads) are both important issues in molecular electronics. To address these issues, we report here, by using Au-benzenedithiol-Au as a model system, systematic investigations of different models for the leads and the lead-molecule contacts: leads with different cross-sections, leads consisting of infinite surfaces, and surface leads with a local nanowire or atomic chain of different lengths. The method adopted is a non-equilibrium Green function approach combined with density functional theory calculations for the electronic structure and transport, in which the leads and molecule are treated on the same footing. It is shown that leads with a small cross-section will lead to large oscillations in the transmission function, T(E), which depend significantly on the lead structure (orientation) because of quantum waveguide effects. This oscillation slowly decays as the lead width increases, with the average approaching the limit given by infinite surface leads. Local nanowire structures around the contacts induce moderate fluctuations in T(E), while a Au atomic chain (including a single Au apex atom) at each contact leads to a significant conductance resonance. 
San-Huang Ke, Harold U. Baranger, and Weitao Yang