We have investigated electrical transport through the molecular model systems benzenedithiol, benzenediamine, hexanedithiol and hexanediamine. Conductance histograms under different experimental conditions indicate that measurements using mechanically controllable break junctions in vacuum are limited by the surface density of molecules at the contact. Hexanedithiol histograms typically exhibit a broad peak around 7 * 10^{-4} G_0. In contrast to recent results on STM-based break junctions in solution we find that the spread in single-molecule conductance is not reduced by amino anchoring groups. Histograms of hexanediamine exhibit a very wide peak around 4 * 10^{-4} G_0. For both benzenedithiol and benzenediamine we observe a large variability in low-bias conductance. We attribute these features to the slow breaking of the lithographic mechanically controllable break junctions and the absence of a solvent that may enable molecular readsorption after bond breaking. Nevertheless, we have been able to acquire reproducible current-voltage characteristics of benzenediamine and benzenedithiol using a statistical measurement approach. Benzenedithiol measurements yield a conductance gap of about 0.9 V at room temperature and 0.6 V at 77 K. In contrast, the current-voltage characteristics of benzenediamine-junctions typically display conductance gaps of about 0.9 V at both temperatures.
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