  The alignment of the Fermi level of a metal electrode within the gap of the
highest occupied and lowest unoccupied orbital of a molecule is a key quantity
in molecular electronics. Depending on the type of molecule and the interface
structure of the junction, it can vary the electron transparency of a
gold/molecule/gold junction by at least one order of magnitude. In this article
we will discuss how Fermi level alignment is related to surface structure and
bonding configuration on the basis of density functional theory calculations
for bipyridine and biphenyl dithiolate between gold leads. We will also relate
our findings to quantum-chemical concepts such as electronegativity.
