Fermi level alignment in single molecule junctions and its dependence on interface structure

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