First-principles calculation of the transport properties of molecular wires between Au clusters under equilibrium

Based on the matrix Green's function method combined with hybrid tight-binding\char21{}density-functional theory, we calculate the conductances of a series of gold-dithiol molecule-gold junctions including benzenedithiol, benzenedimethanethiol, hexanedithiol, octanedithiol, and decanedithiol. An atomically contacted extended molecule model is used in our calculation. As an important procedure, we determine the position of the Fermi level by the energy reference according to the results from ultraviolet photoelectron spectroscopy (UPS) experiments. After considering the experimental uncertainty in UPS measurement, the calculated results of molecular conductances near the Fermi level qualitatively agree with the experimental values measured by Tao et al. [Science 301, 1221 (2003); J. Am. Chem. Soc. 125, 16164 (2003); Nano. Lett. 4, 267 (2004)].