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We consider the electronic transport through gold-dithiol-molecule-gold junctions. We used an atomicallycontacted extended molecule model for the description of such systems. The calculations are based on the matrix Green function method combined with the hybrid tight-binding density functional theory. In order to determine the position of Fermi level, we referenced the experimental results from ultraviolet photoelectron spectroscopy.Our calculation of molecular conductance near the Fermi level qualitatively reproduces the experimental values measured previously [Science 301 (2003) 1221; J. Am. Chem. Soc. 125 (2003) 16164; Nano Lett. 4 (2004) 267].In addition, we discuss the relationship between different molecular electronic structures and transport properties.