Adsorption of benzene-1,4-dithiol on the Au(111) surface and its possible role in molecular conductance

It is a consensus in the field of molecular electronics that the transport of charge across a single molecule depends sensitively on the details of the interaction between the molecule and the metallic leads, such as the molecular orientation. To advance the design of complex molecular devices, it is crucial to have a detailed understanding of these many aspects that influence the electron transport. A simple system that has been used as a paradigm of the class of conjugated aryl molecules is the benzene-1,4-dithiol (BDT). However, we still do not have a full understanding of the BDT transport experiments. Usually the geometries considered in transport calculations assumed that the BDT was connected to the two Au leads via the S atoms, and that the molecule was either perpendicular or close to a perpendicular configuration relative to the Au surfaces. Using ab initio calculations, we show that, for an isolated molecule, the configuration with largest adsorption energy has the BDT phenyl ring closer to being parallel to the surface, and we then argue, based on nonequilibrium Green's function-density functional theory calculations, that, depending on the experimental procedure, this may be the relevant configuration to be used in the transport calculations.