Figures show the optimized geometry and HOMO, respectively, of the benzene-1,4-dithiol (BDT) molecule. Similar to the HOMO of BDA, the HOMO of BDT has π-antibonding character on the benzene ring and lone-pair characters on the terminal sulphur atoms. The transport orbital of the gold-BDT-gold junction containing atop-site electrodes is formed from the σ * overlap of the HOMO of BDT with the d x 2 -y 2 orbitals of the two atop gold atoms, and creates a π-type conductance channel across the benzene ring (Figs. ). However, the nature of the thiol-gold bond is qualitatively different between atop and FCC electrodes. Whereas at the atop site, the sulphur uses its doublyoccupied 3p orbital to form a coordinate-covalent bond similar to the nitrogen-gold bond, at the FCC site, the hydrogen atoms dissociate from the thiol groups during geometry optimizations and each sulphur atom to binds to the hollow site using a singlyoccupied 3p orbital. Consequently, the transport properties of the BDT junction change significantly between atop-site and FCC-site electrodes, as shown in Section 3.2. The transport orbitals of BDA and BDT junctions containing silver or copper electrodes possess the same characteristics as the corresponding junctions with gold electrodes, and their conductance properties are discussed in Section 3.3.