Amine-terminated molecules show well-behaved conductance in the scanning tunneling microscope break-junction experimental measurements. We performed density functional theory based electron transport calculations to explain the nature of this phenomenon. We find that amines can be adsorbed only on the apex Au atom, while the thiolate group can be attached equally well to undercoordinated and clean Au surfaces. Our calculations show that only one adsorption geometry is sterically and energetically possible for the amine-anchored junction whereas three different adsorption geometries with very distinct transport properties are almost equally probable for the thiolate-anchored junction. We calculated the conductance as a function of the junction stretching when the molecules are pulled by the scanning tunneling microscope tip from the Au electrode. Our calculations show that the stretching of the thiolate-anchored junction during its formation is accompanied by significant electrode geometry distortion. The amine-anchored junctions exhibit very different behavior—the electrode remains intact when the scanning tunneling microscope tip stretches the junction.

• Received 21 February 2007

DOI:https://doi.org/10.1103/PhysRevB.76.035415