The alignment of the Fermi level of a metal electrode within the gap of the hi ghest occupied (HOMO) and lowest unoccupied orbital (LUMO) of a molecule is a key quantity in molecular electronics, which can vary the electron transparency of a single molecule junction by orders of magnitude. We present a quantitative analysis of the relation between this level alignment (which can be estimated from charging free molecules) and charge transfer for bipyridine and biphenyl dithiolate (BPDT) molecules attached to gold leads based on density functional theory calculations. For both systems the charge distribution is defined by a balance between Pauli repulsion with subsequent electrostatic screening and the filling of the LUMO, where bipyridine loses electrons to the leads and BPDT gains electrons. As a direct consequence the Fermi level of the metal is found close to the LUMO for bipyridine and close to the HOMO for BPDT.
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