  The alignment of molecular levels with the Fermi energy in single molecule
junctions is a crucial factor in determining their conductance or the
observability of quantum interference effects. In the present study which is
based on density functional theory calculations, we explore the zero-bias
charge transfer and level alignment for nitro-bipyridyl-phenyl adsorbed between
two gold surfaces which we find to vary significantly with the molecular
conformation. The net charge transfer is the result of two opposing effects,
namely Pauli repulsion at the interface between the molecule and the leads, and
the electron accepting nature of the NO$_2$ group, where only the latter which
we analyze in terms of the electronegativity of the isolated molecules depends
on the two intra-molecular torsion angles. We provide evidence that the
conformation dependence of the alignment of molecular levels and peaks in the
transmission function can indeed be understood in terms of charge transfer for
this system, and that other properties such as molecular dipoles do not play a
significant role. Our study is relevant for device design in molecular
electronics where nitrobenzene appears as a component in proposals for
rectification, quantum interference or chemical gating.
