  Based on the matrix Green's function method combined with hybrid
tight-binding / density functional theory, we calculate the conductances of a
series of gold-dithiol molecule-gold junctions including benzenedithiol (BDT),
benzenedimethanethiol (BDMT), hexanedithiol (HDT), octanedithiol (ODT) and
decanedithiol (DDT). 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. [{\it Science} 301, 1221 (2003);
{\it J. Am. Chem. Soc.} 125, 16164 (2003); {\it Nano. Lett.} 4, 267 (2004).]
