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