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Long-chain alkane thiols use in metal to organic self-assembled monolayer to metal junctions may be limited by orientational disorder, and photoemission studies suggest that several molecular layers may be needed for the dielectric layer to be effective. Several alkane thiols were investigated in a range of junctions areas 10–102 μm2. Top layer contact deposition, activated with Pd clusters resulted in a high yield of junctions that were not electrically shorted and are stable over a wide temperature range. Zerobias anomalies, observed at low temperatures, are attributed to a Coulomb blockade associated with the Pd clusters.