Identification of the atomic scale structures of the gold-thiol interfaces of molecular nanowires by inelastic tunneling spectroscopy

Abstract

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.

Inelastic tunneling spectroscopy of gold-thiol and gold-thiolate interfaces in molecular junctions: The role of hydrogen

“…We do this in the present article, considering as a specific exam-ple molecular junctions with gold electrodes bridged by molecules derived from 1,3-propanedithiol (PDT) that retain one or both thiol hydrogen atoms. We also compare our results for these systems with our previous findings [75,78] for 1,3-propanedithiolate molecules (with no thiol hydrogen atoms) bridging gold electrodes and with the experimental statistical STM break junction IETS data of Hihath et al [26]. We find IETS to be able to distinguish molecules bridging gold electrodes with no hydrogen atoms bound to the sulfur atoms of the molecule from molecules with a hydrogen atom bound to one of the sulfur atoms, and from molecules with hydrogen atoms bound to both sulfur atoms.…”

“…75 and 78. In the work reported in those papers [75,78] this approach was very successful in accounting for the relevant experimental IETS data [26] and identifying for the first time the experimentally realized gold-sulfur bonding geometries in gold-propanedithiolate-gold molecular junctions. An in depth discussion of the underlying theory and the relevant mathematical derivations have been presented in Ref.…”

“…An in depth discussion of the underlying theory and the relevant mathematical derivations have been presented in Ref. 78. We therefore present only a brief summary of the theoretical approach that we use here and refer the reader to Ref.…”

“…We therefore present only a brief summary of the theoretical approach that we use here and refer the reader to Ref. 78 for further details.…”

“…These IETS experiments together with the theoretical work demonstrated conclusively that particular molecular species are involved in electrical conduction through metal-molecule-metal junctions. It has also been shown that IETS can be sensitive to the molecular conformation [29,38,74,78], the orientation of molecules relative to the electrodes [56,77] and the gold-sulfur atomic bonding geometries at the molecule-metal interfaces [75,76,78].…”