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Summary form only given. Molecular electronics has traditionally concentrated on metal substrates, motivated by thiol-gold chemistry and easier self-assembly. Description of transport through nanoscale devices, by self-consistently combining a suitable bandstructure calculation for metal contacts with a non-equilibrium Green's function (NEGF) formulation of transport is worked out in this paper. This method can be used to reproduce the conductance quantization of gold quantum point contacts. The performance limitation of a generic molecular transistor gated either electrostatically or conformationally has also been outlined.