Systematic study of low energy geometries of copper nano-junctions exposed to water and to species that can result from dissociation of water.

A detailed computational analysis has been performed, considering copper atomic contacts that are exposed directly to water molecules, hydroxyl groups, and monatomic as well as molecular hydrogen and oxygen species. The optimized physical bonding structure, electrical conductance and inelastic tunneling spectra (IETS) have been determined theoretically for moderately large structures by performing appropriate ab initio and semi-empirical calculations. By considering the aforementioned properties, it has been possible to determine that some of the molecular bridging structures may be regarded as being highly-probable outcomes, resulting from the exposure of copper electrodes to the atomic/molecular contaminants. We specifically identify the conductance properties of a variety of configurations including examples with very high and very low conductance values. This is done in order to identify junction geometries that may be realized experimentally and their conductance and IETS signatures. By reporting geometries with very high and very low conductance values here, we intend to provide a wider perspective view than previous studies of copper-molecular junctions that have focused on high conductance structures. In addition, we explore the properties of metal junctions with multiple molecules, a class of systems for which little theoretical work has been available in the molecular electronics literature. We find that water molecules surrounding the junction can influence the bonding geometry of the molecules within the junction and consequently can affect strongly the calculated conductances of such junctions.

Controlling the thermoelectric effect by mechanical manipulation of the electron's quantum phase in atomic junctions.

The thermoelectric voltage developed across an atomic metal junction (i.e., a nanostructure in which one or a few atoms connect two metal electrodes) in response to a temperature difference between the electrodes, results from the quantum interference of electrons that pass through the junction multiple times after being scattered by the surrounding defects. Here we report successfully tuning this quantum interference and thus controlling the magnitude and sign of the thermoelectric voltage by applying a mechanical force that deforms the junction. The observed switching of the thermoelectric voltage is reversible and can be cycled many times. Our ab initio and semi-empirical calculations elucidate the detailed mechanism by which the quantum interference is tuned. We show that the applied strain alters the quantum phases of electrons passing through the narrowest part of the junction and hence modifies the electronic quantum interference in the device. Tuning the quantum interference causes the energies of electronic transport resonances to shift, which affects the thermoelectric voltage. These experimental and theoretical studies reveal that Au atomic junctions can be made to exhibit both positive and negative thermoelectric voltages on demand, and demonstrate the importance and tunability of the quantum interference effect in the atomic-scale metal nanostructures.

Electrical conductance 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 = 2e(2)/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 G0 prior to the junction rupture and abrupt conductance drop.

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

It is widely believed that when a molecule with thiol (S-H) end groups bridges a pair of gold electrodes, the S atoms bond to the gold and the thiol H atoms detach from the molecule. However, little is known regarding the details of this process, its time scale, and whether molecules with and without thiol hydrogen atoms can coexist in molecular junctions. Here, we explore theoretically how inelastic tunneling spectroscopy (IETS) can shed light on these issues. We present calculations of the geometries, low bias conductances, and IETS of propanedithiol and propanedithiolate molecular junctions with gold electrodes. We show that IETS can distinguish between junctions with molecules having no, one, or two thiol hydrogen atoms. We find that in most cases, the single-molecule junctions in the IETS experiment of Hihath et al. [Nano Lett. 8, 1673 (2008)] had no thiol H atoms, but that a molecule with a single thiol H atom may have bridged their junction occasionally. We also consider the evolution of the IETS spectrum as a gold STM tip approaches the intact S-H group at the end of a molecule bound at its other end to a second electrode. We predict the frequency of a vibrational mode of the thiol H atom to increase by a factor ~2 as the gap between the tip and molecule narrows. Therefore, IETS should be able to track the approach of the tip towards the thiol group of the molecule and detect the detachment of the thiol H atom from the molecule when it occurs.

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.

Communication: Identification of the molecule-metal bonding geometries of molecular nanowires.

Molecular nanowires in which a single molecule bonds chemically to two metal electrodes and forms a stable electrically conducting bridge between them have been studied intensively for more than a decade. However, the experimental determination of the bonding geometry between the molecule and electrodes has remained elusive. Here we demonstrate by means of ab initio calculations that inelastic tunneling spectroscopy (IETS) can determine these geometries. We identify the bonding geometries at the gold-sulfur interfaces of propanedithiolate molecules bridging gold electrodes that give rise to the specific IETS signatures that were observed in recent experiments.

Electrochemically gated oligopeptide nanowires bridging gold electrodes: novel bio-nanoelectronic switches operating in aqueous electrolytic environments.

We present electronic structure and transport calculations that reveal that oligopeptide based molecular nanowires support unoccupied extended electronic states that span the length of the nanowire and are resistant to disorder. Electrochemical gating in aqueous electrolytes is shown to bring these extended states into resonance with the Fermi level of gold electrodes, transforming these nanowires from insulators into conductors. Thus oligopeptide nanowires are promising candidates for bionanoelectronic switches operating in the aqueous electrolytic environments native to biological systems.

Nonlocal conductance modulation by molecules: scanning tunneling microscopy of substituted styrene heterostructures on H-terminated Si(100).

One-dimensional organic heterostructures consisting of contiguous lines of CF3- and OCH3-substituted styrene molecules on silicon are studied by scanning tunneling microscopy and ab initio simulation. Dipole fields of OCH3-styrene molecules are found to enhance conduction through molecules near CF3-styrene/OCH_{3}-styrene heterojunctions. Those of CF3-styrene depress transport through the nearby silicon. Thus the choice of substituents and their attachment site on host molecules provide a means of differentially tuning molecule and substrate transport at the molecular scale.

A new approach to the realization and control of negative differential resistance in single-molecule nanoelectronic devices: designer transition metal-thiol interface States.

On the basis of ab initio and semiempirical calculations, we predict single alkane dithiolate molecules bridging transition metal nanoelectrodes (including Pd/Rh, Pt/Rh, and Pt/Pt) to exhibit negative differential resistance (NDR). The mechanism is resonant conduction via interface states arising from hybridization between molecular thiol groups and transition metal d orbitals. We show how the NDR realized in this new way can be controlled by tailoring interface state properties through appropriate choice of nanoelectrode transition metals and surface structures.

Controlling the charge of a specific surface atom by the addition of a non-site-specific single impurity in a Si nanocrystal.

We show, by use of self-consistent calculations, that the charge on a radical surface site (RSS) on a hydrogen-terminated silicon nanocrystal can be controlled by the addition of a non-site-specific dopant atom. An RSS is a surface defect where the H-termination is missing. This new effect has important implications for future hybrid semiconductor/molecular nanoelectronics. We also calculate the energy and wave function of the RSS state and its nanoscale interactions with the dopant atom.

The smallest molecular switch.

Ab initio total energy calculations reveal benzene-dithiolate molecules on a gold surface, contacted by a monatomic gold STM tip to have two classes of low-energy conformations with differing symmetries. Lateral motion of the tip or excitation of the molecule cause it to change from one conformation class to the other and to switch between a strongly and a weakly conducting state. Thus, surprisingly, despite their apparent simplicity, these Au/BDT/Au nanowires are shown to be electrically bistable switches, the smallest two-terminal molecular switches to date.

Charging effects, forces, and conduction in molecular wire systems.

Recently, experiments have shown that effects arising from charging and conformational changes in a molecular wire due to an applied voltage bias can have a significant influence on the transport characteristics of the system. We introduce a tractable theoretical approach based on Landauer theory and total energy methods that treats transport nonlinearities, conformational changes, and charging effects in molecular wires in a unified way. We apply this approach to molecular wires consisting of short chain molecules with different electronic and structural properties bonded to metal contacts. We find that the nonlinear conductance characteristics of these systems are remarkably similar and can be understood in terms of a single physical mechanism. We predict that negative differential resistance should occur at high bias in such molecular wires due to the combined effects of charging and conformational changes on their electronic structure.