Electron-phonon interactions in single octanedithiol molecular junctions

Binding structure, breaking forces and conductance of Au-Octanedithiol-Au molecular junction under stretching processes: a DFT-NEGF study

Au-n-octanedithiol-Au molecular junction (Au-SC8S-Au) has been investigated using density functional theory combined with the nonequilibrium Green's function approach. Theoretically calculated results are used to build the relationship between the interface binding structures and single-molecule quantum conductance of n-octanedithiol (SC8S) embodied in a gold nanogap with or without stretching forces. To understand the electron transport mechanism in the single molecular nanojunction, we designed three types of Au-SC8S-Au nanogaps, including flat electrode through an Au atom connecting (Model I), top-pyramidal or flat electrodes with the molecule adsorbing directly (Model II), and top-pyramidal Au electrodes with Au atomic chains (Model III). We first determined the optimized structures of different Au-SC8S-Au nanogaps, and then predicted the distance-dependent stretching force and conductance in each case. Our calculated results show that in the Model I with an Au atom bridging the flat Au (111) gold electrodes and the SC8S molecule, the conductance decreases exponentially before the fracture of Au-Au bond, in a good agreement with the experimental conductance in the literature. For the top-pyramidal electrode Models II and III, the magnitudes of molecular conductance are larger than that in Model I. Our theoretical calculations also show that the Au-Au bond fracture takes place in Models I and III, while the Au-S bond fracture appears in Model II. This is explained due to the total strength of three synergetic Au-Au bonds stronger than an Au-S bond in Model II. This is supported from the broken force about 2 nN for the Au-Au bond and 3 nN for the Au-S bond.

Inelastic Electron Tunneling Spectroscopic Analysis of Bias-Induced Structural Changes in a Solid-State Protein Junction

A central issue in protein electronics is how far the structural stability of the protein is preserved under the very high electrical field that it will experience once a bias voltage is applied. This question is studied on the redox protein Azurin in the solid-state Au/protein/Au junction by monitoring protein vibrations during current transport under applied bias, up to ≈1 GV m^-1 , by electrical detection of inelastic electron transport effects. Characteristic vibrational modes, such as CH stretching, amide (NH) bending, and AuS (of the bonds that connect the protein to an Au electrode), are not found to change noticeably up to 1.0 V. At >1.0 V, the NH bending and CH stretching inelastic features have disappeared, while the AuS features persist till ≈2 V, i.e., the proteins remain Au bound. Three possible causes for the disappearance of the NH and CH inelastic features at high bias, namely, i) resonance transport, ii) metallic filament formation, and iii) bond rupture leading to structural changes in the protein are proposed and tested. The results support the last option and indicate that spectrally resolved inelastic features can serve to monitor in operando structural stability of biological macromolecules while they serve as electronic current conduit.

Moving Electrons Purposefully through Single Molecules and Nanostructures: A Tribute to the Science of Professor Nongjian Tao (1963-2020)

Electrochemistry intersected nanoscience 25 years ago when it became possible to control the flow of electrons through single molecules and nanostructures. Many surprises and a wealth of understanding were generated by these experiments. Professor Nongjian Tao was among the pioneering scientists who created the methods and technologies for advancing this new frontier. Achieving a deeper understanding of charge transport in molecules and low-dimensional materials was the first priority of his experiments, but he also succeeded in discovering applications in chemical sensing and biosensing for these novel nanoscopic systems. In parallel with this work, the investigation of a range of phenomena using novel optical microscopic methods was a passion of his and his students. This article is a review and an appreciation of some of his many contributions with a view to the future.

Automatic classification of single-molecule charge transport data with an unsupervised machine-learning algorithm

Single-molecule electrical characterization reveals the events occurring at the nanoscale, which provides guidelines for molecular materials and devices. However, data analysis to extract valuable information from the nanoscale measurement data remained as a major challenge. Herein, an unsupervised deep leaning method, a deep auto-encoder K-means (DAK) algorithm, is developed to distinguish different events from single-molecule charge transport measurements. As validated by three single-molecule junction systems, the method applies to the recognition for multiple compounds with various events and offers an effective data analysis method to track reaction kinetics at the single-molecule scale. This work opens the possibility of using deep unsupervised approaches to studying the physical and chemical processes at the single-molecule level.

Can Molecular Quantum Interference Effect Transistors Survive Vibration?

Quantum interference in cross-conjugated molecules can be utilized to construct molecular quantum interference effect transistors. However, whether its application can be achieved depends on the survivability of the quantum interference under real conditions such as nuclear vibration. We use two simulation methods to investigate the effects of nuclear vibration on quantum interference in a meta-linked benzene system. The simulation results suggest that the quantum interference is robust against nuclear vibration not only in the steady state but also in its transient dynamics, and thus the molecular quantum interference effect transistors can be realized.

Adsorption of single 1,8-octanedithiol molecules on Cu(100)

STM experiments and calculations have allowed identifying the most favorable conformation of a single octanedithiol molecule on a copper surface.

Insights into Solid-State Electron Transport through Proteins from Inelastic Tunneling Spectroscopy: The Case of Azurin

Surprisingly efficient solid-state electron transport has recently been demonstrated through "dry" proteins (with only structural, tightly bound H2O left), suggesting proteins as promising candidates for molecular (bio)electronics. Using inelastic electron tunneling spectroscopy (IETS), we explored electron-phonon interaction in metal/protein/metal junctions, to help understand solid-state electronic transport across the redox protein azurin. To that end an oriented azurin monolayer on Au is contacted by soft Au electrodes. Characteristic vibrational modes of amide and amino acid side groups as well as of the azurin-electrode contact were observed, revealing the azurin native conformation in the junction and the critical role of side groups in the charge transport. The lack of abrupt changes in the conductance and the line shape of IETS point to far off-resonance tunneling as the dominant transport mechanism across azurin, in line with previously reported (and herein confirmed) azurin junctions. The inelastic current and hence electron-phonon interaction appear to be rather weak and comparable in magnitude with the inelastic fraction of tunneling current via alkyl chains, which may reflect the known structural rigidity of azurin.

Strong overtones modes in inelastic electron tunneling spectroscopy with cross-conjugated molecules: a prediction from theory

Cross-conjugated molecules are known to exhibit destructive quantum interference, a property that has recently received considerable attention in single-molecule electronics. Destructive quantum interference can be understood as an antiresonance in the elastic transmission near the Fermi energy and leading to suppressed levels of elastic current. In most theoretical studies, only the elastic contributions to the current are taken into account. In this paper, we study the inelastic contributions to the current in cross-conjugated molecules and find that while the inelastic contribution to the current is larger than for molecules without interference, the overall behavior of the molecule is still dominated by the quantum interference feature. Second, an ongoing challenge for single molecule electronics is understanding and controlling the local geometry at the molecule-surface interface. With this in mind, we investigate a spectroscopic method capable of providing insight into these junctions for cross-conjugated molecules: inelastic electron tunneling spectroscopy (IETS). IETS has the advantage that the molecule interface is probed directly by the tunneling current. Previously, it has been thought that overtones are not observable in IETS. Here, overtones are predicted to be strong and, in some cases, the dominant spectroscopic features. We study the origin of the overtones and find that the interference features in these molecules are the key ingredient. The interference feature is a property of the transmission channels of the π system only, and consequently, in the vicinity of the interference feature, the transmission channels of the σ system and the π system become equally transmissive. This allows for scattering between the different transmission channels, which serves as a pathway to bypass the interference feature. A simple model calculation is able to reproduce the results obtained from atomistic calculations, and we use this to interpret these findings.

Single molecule conductance, thermopower, and transition voltage

We have measured the thermopower as well as other important charge transport quantities, including conductance, current-voltage characteristics, and transition voltage of single molecules. The thermopower has little correlation with the conductance, but it decreases with the transition voltage, which is consistent with a theory based on Landauer's formula. Since the transition voltage reflects the molecular energy level alignment, our finding also shows that the thermopower provides valuable information about the relative alignment between the molecular energy levels and the electrodes' Fermi energy level.

Mechanically controlled molecular orbital alignment in single molecule junctions

Research in molecular electronics often involves the demonstration of devices that are analogous to conventional semiconductor devices, such as transistors and diodes, but it is also possible to perform experiments that have no parallels in conventional electronics. For example, by applying a mechanical force to a molecule bridged between two electrodes, a device known as a molecular junction, it is possible to exploit the interplay between the electrical and mechanical properties of the molecule to control charge transport through the junction. 1,4'-Benzenedithiol is the most widely studied molecule in molecular electronics, and it was shown recently that the molecular orbitals can be gated by an applied electric field. Here, we report how the electromechanical properties of a 1,4'-benzenedithiol molecular junction change as the junction is stretched and compressed. Counterintuitively, the conductance increases by more than an order of magnitude during stretching, and then decreases again as the junction is compressed. Based on simultaneously recorded current-voltage and conductance-voltage characteristics, and inelastic electron tunnelling spectroscopy, we attribute this finding to a strain-induced shift of the highest occupied molecular orbital towards the Fermi level of the electrodes, leading to a resonant enhancement of the conductance. These results, which are in agreement with the predictions of theoretical models, also clarify the origins of the long-standing discrepancy between the calculated and measured conductance values of 1,4'-benzenedithiol, which often differ by orders of magnitude.

Inelastic transport and low-bias rectification in a single-molecule diode

Designing, controlling, and understanding rectification behavior in molecular-scale devices has been a goal of the molecular electronics community for many years. Here we study the transport behavior of a single molecule diode, and its nonrectifying, symmetric counterpart at low temperatures, and at both low and high biases to help elucidate the electron-phonon interactions and transport mechanisms in the rectifying system. We find that the onset of current rectification occurs at low biases, indicating a significant change in the elastic transport pathway. However, the peaks in the inelastic electron tunneling (IET) spectrum are antisymmetric about zero bias and show no significant changes in energy or intensity in the forward or reverse bias directions, indicating that despite the change in the elastic transmission probability there is little impact on the inelastic pathway. These results agree with first principles calculations performed to evaluate the IETS, which also allow us to identify which modes are active in the single molecule junction.

Laserlike vibrational instability in rectifying molecular conductors

We study the damping of molecular vibrations due to electron-hole pair excitations in donor-acceptor (D-A) type molecular rectifiers. At finite voltage additional nonequilibrium electron-hole pair excitations involving both electrodes become possible, and contribute to the stimulated emission and absorption of phonons. We point out a generic mechanism for D-A molecules, where the stimulated emission can dominate beyond a certain voltage due to the inverted position of the D and A quantum resonances. This leads to current-driven amplification (negative damping) of the phonons similar to laser action. We investigate the effect in realistic molecular rectifier structures using first-principles calculations.

Tunneling spectroscopy of organic monolayers and single molecules

Basic concepts in tunneling spectroscopy applied to molecular systems are presented. Junctions of the form M-A-M, M-I-A-M, and M-I-A-I'-M, where A is an active molecular layer, are considered. Inelastic electron tunneling spectroscopy (IETS) is found to be readily applied to all the above device types. It can provide both vibrational and electron spectroscopic data about the molecules comprising the A layer. In IETS there are no strong selection rules (although there are preferences) so that transitions that are normally IR, Raman, or even photon-forbidden can be observed. In the electronic transition domain, spin and Laporte forbidden transitions may be observed. Both vibrational and electronic IETS can be acquired from single molecules. The negative aspect of this seemingly ideal spectroscopic method is the thermal line width of about 5 k(B)T. This limits the useful measurement of vibrational IETS to temperatures below about 10 K. In the case of most electronic transitions where the intrinsic linewidth is much broader, useful experiments above 100 K are possible. One further limitation of electronic IETS is that it is generally limited to transitions with energy less than about 20,000 cm(-1). IETS can be identified by peaks in d(2) I/dV (2) vs bias voltage plots that occur at the same position (but not necessarily same intensity) in either bias polarity.Elastic tunneling spectroscopy is discussed in the context of processes involving molecular ionization and electron affinity states, a technique we call orbital mediated tunneling spectroscopy, or OMTS. OMTS can be applied readily to M-I-A-M and M-I-A-I'-M systems, but application to M-A-M junctions is problematic. Spectra can be obtained from single molecules. Ionization state results correlate well with UPS spectra obtained from the same systems in the same environment. Both ionization and affinity levels measured by OMTS can usually be correlated with one electron oxidation and reduction potentials for the molecular species in solution. OMTS can be identified by peaks in dI/dV vs bias voltage plots that do not occur at the same position in either bias polarity. Because of the intrinsic width of the ionization and affinity transitions, OMTS can be applied at temperatures above 500 K.This is not a comprehensive review of more than 20 years of research and there are many excellent papers that are not cited here. An absence of a citation is not a reflection on the quality of the work.