  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 apex Au
atom, while thiolate group can be attached equally well to undercoordinated and
clean Au surfaces. Our calculations show that only one adsorption geo metry is
sterically and energetically possible for amine anchored junction whereas three
different adsorption geometries with very distinct transport pro perties are
almost equally probable for 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 distortio n. The
amine anchored junctions exhibit very different behavior -- the electrode
remains intact when the scan ning tunneling microscope tip stretches the
junction.
