Band Alignment in Molecular Devices: Influence of Anchoring Group and   Metal Work Function
  We present periodic Density Functional Theory calculations of the electronic properties of molecular junctions formed by amine-, and thiol-terminated alkane chains attached to two metal (Au, Ag) electrodes. Based on extensive analysis that includes molecular monolayers of varying densities, we establish a relationship between the alignment of the molecular energy levels and the interface dipoles, which shows that the band alignment (BA) in the limit of long, isolated chains is independent of the link group and can be computed from a reference system of non interacting molecule + metal electrodes. The main difference between the amine and thiol linkers is the effective dipole moment at the contact. This is very large, about 4.5 D, for amine linkers, leading to a strong dependence of the BA on the monolayer density and a slow convergence to the isolated molecule limit. Instead, this convergence is fast for S anchors due to the very small, ~ 0.2 D, effective dipoles at the contacts. 
Jian-guo Wang, Emil Prodan, Roberto Car, Annabella Selloni