  We report on electronic transport calculations for self-assembled mono-layers
(SAM) of 1,4-phenylene diisocyanide on Au(111) contacts. Experimentally one
observes more structure (i.e peaks) within the measured conductance curve for
this molecule with two cyanide end-groups, compared to measurements with
molecules having thiol end-groups. The calculations are performed on the
semi-empiric extended H\"{u}ckel level using elastic scattering quantum
chemistry (ESQC) and we investigate three possible explanations for the
experimental findings. Comparing the experimental and theoretical data, we are
able to rule out all but one of the scenarios. The observed additional peaks
are found to be only reproduced by a mono-layer with additional molecules
perturbing the periodicity. It is conjectured that the weaker coupling to Au of
cyanide end-groups compared to thiol end-groups might be responsible for such
perturbations.

Mesoscale and Nanoscale Physics