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We investigate electron transport through single conjugated molecules -including benzenedithiol, oligo-phenylene-ethynylenes of different lengths, anda ferrocene-containing molecule sandwiched between two gold electrodes withdifferent contact structures - by using a single-particle Green function methodcombined with density functional theory calculation. We focus on the effect ofthe basis set in the ab initio calculation. It is shown that the position ofthe Fermi energy in the transport gap is sensitive to the molecule-lead chargetransfer which is affected by the size of basis set. This can dramaticallychange, by orders of magnitude, the conductance for long molecules, though theeffect is only minor for short ones. A resonance around the Fermi energy tendsto pin the position of the Fermi energy and suppress this effect. The result isdiscussed in comparison with experimental data.

Electron transport through single conjugated organic molecules: Basis set effects in ab initio calculations