Identification of the Atomic Scale Structures of the Gold-Thiol Interfaces of Molecular Nanowires by Inelastic Tunneling Spectroscopy

We examine theoretically the effects of the bonding geometries at the gold-thiol interfaces on the inelastic tunneling spectra of propanedithiolate (PDT) molecules bridging gold electrodes and show that inelastic tunneling spectroscopy combined with theory can be used to determine these bonding geometries experimentally. With the help of density functional theory, we calculate the relaxed geometries and vibrational modes of extended molecules each consisting of one or two PDT molecules connecting two gold nanoclusters. We formulate a perturbative theory of inelastic tunneling through molecules bridging metal contacts in terms of elastic transmission amplitudes, and use this theory to calculate the inelastic tunneling spectra of the gold-PDT-gold extended molecules. We consider PDT molecules with both trans and gauche conformations bound to the gold clusters at top, bridge and hollow bonding sites. Comparing our results with the experimental data of Hihath et al. [Nano Lett. 8, 1673 (2008)], we identify the most frequently realized conformation in the experiment as that of trans molecules top-site bonded to both electrodes. We find the switching from the 42 meV vibrational mode to the 46 meV mode observed in the experiment to be due to the transition of trans molecules from mixed top-bridge to pure top-site bonding geometries. Our results also indicate that gauche molecular conformations and hollow site bonding did not contribute significantly to the experimental inelastic tunneling spectra. For pairs of PDT molecules connecting the gold electrodes in parallel we find total elastic conductances close to twice those of single molecules bridging the contacts with similar bonding conformations and small splittings of the vibrational mode energies for the modes that are the most sensitive to the molecule-electrode bonding geometries.Comment: 14 pages, 8 figures, 1 table. arXiv admin note: significant text overlap with arXiv:1103.2378; http://jcp.aip.org/resource/1/jcpsa6/v136/i1/p014703_s

Electrical Conduction and Structure of Copper Atomic Junctions in the Presence of Water Molecules

We have investigated Cu atomic contacts in the presence of H2O both experimentally and theoretically. The conductance measurements showed the formation of H2O/Cu junctions with a fixed conductance value of around 0.1 G0 (G0 = 2e2/h). These structures were found to be stable and could be stretched over 0.5 nm, indicating the formation of an atomic or molecular chain. In agreement with the experimental findings, theoretical calculations revealed that the conductance of H2O/Cu junctions decreases in stages as the junction is stretched, with the formation of a H2O/Cu atomic chain with a conductance of ca. 0.1 G0 prior to junction rupture. Conversely, in the absence of H2O, the conductance of the Cu junction remains close to 1 G0prior to the junction rupture and abrupt conductance drop