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Experimental techniques that determine atomic arrangements in single metal–molecule–metal junctions will enable a mechanistic understanding and control of electronic properties on the nanoscale. Here, we develop a method to determine average gold and silver nanogap widths with Angstrom resolution using single molecule junction conductance and distance measurements of N,N′-diamino alkanes in a scanning tunneling microscope break junction setup. Our experiments are supported by density functional theory (DFT) calculations, which suggest that the alkane-conducting trans-configurations can be outcompeted by the nonconducting cis conformers when the nanogap distance is shorter than the length of the molecule. As a result, the distribution of binding geometries during the conductance plateau is peaked when the gap width is comparable to the molecule length. We apply this conductance ruler to …