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We present periodic Density Functional Theory calculations of the electronicproperties of molecular junctions formed by amine-, and thiol-terminated alkanechains attached to two metal (Au, Ag) electrodes. Based on extensive analysisthat includes molecular monolayers of varying densities, we establish arelationship between the alignment of the molecular energy levels and theinterface dipoles, which shows that the band alignment (BA) in the limit oflong, isolated chains is independent of the link group and can be computed froma reference system of non interacting molecule + metal electrodes. The maindifference between the amine and thiol linkers is the effective dipole momentat the contact. This is very large, about 4.5 D, for amine linkers, leading toa strong dependence of the BA on the monolayer density and a slow convergenceto the isolated molecule limit. Instead, this convergence is fast for S anchorsdue to the very small, ~ 0.2 D, effective dipoles at the contacts.

Band Alignment in Molecular Devices: Influence of Anchoring Group and Metal Work Function