Binding configurations and intramolecular strain in single-molecule devices

Methods for the analysis, interpretation, and prediction of single-molecule junction conductance behaviour

This article offers a broad overview of measurement methods in the field of molecular electronics, with a particular focus on the most common single-molecule junction fabrication techniques, the challenges in data analysis and interpretation of single-molecule junction current-distance traces, and a summary of simulations and predictive models aimed at establishing robust structure-property relationships of use in the further development of molecular electronics.

Evolution of Single-Molecule Electronic Interfaces

Single-molecule electronics can fabricate single-molecule devices via the construction of molecule-electrode interfaces and also provide a unique tool to investigate single-molecule scale physicochemical processes at these interfaces. To investigate single-molecule electronic devices with desired functionalities, an understanding of the interface evolution processes in single-molecule devices is essential. In this review, we focus on the evolution of molecule-electrode interface properties, including the background of interface evolution in single-molecule electronics, the construction of different types of single-molecule interfaces, and the regulation methods. Finally, we discuss the perspective of future characterization techniques and applications for single-molecule electronic interfaces.

Probing Energy-Level Alignment in Molecular Multilayers by Frequency-Modulation Electrostatic Force Microscopy under Tapping-Mode-Combined Fowler-Nordheim Tunneling Spectroscopy

The alignment of molecular electronic levels in a molecular multilayer is of crucial importance to realize desired functions for molecular devices. Amplitude-modulation-feedback frequency-modulation electrostatic force microscopy combined with Fowler-Nordheim tunneling spectroscopy is utilized as a probe for the energy-level alignment in an organic multilayer. Bias-dependent electrostatic force spectra were examined for bilayers including a Ru complex as a benchmark multilayer system. Electrostatic properties in the low-bias region were captured well by a single-capacitor model, which indicates weak coupling at the bilayer interface between the Ru complex and self-assembled monolayer. In contrast, in the high-bias region, significant disagreement with the expected electrostatic force was recognized for the bilayers and evaluated as the loss of electrostatic energy through the Fowler-Nordheim tunneling process. Alignment of the lowest unoccupied molecular orbital (LUMO) level of the Ru complex was determined by Fowler-Nordheim emission through resonant tunneling. These results indicate an effective method to probe level alignment at interfaces inside multilayers and to provide the partition factor β that depicts a divided electric field.

Controlling piezoresistance in single molecules through the isomerisation of bullvalenes

Nanoscale electro-mechanical systems (NEMS) displaying piezoresistance offer unique measurement opportunities at the sub-cellular level, in detectors and sensors, and in emerging generations of integrated electronic devices. Here, we show a single-molecule NEMS piezoresistor that operates utilising constitutional and conformational isomerisation of individual diaryl-bullvalene molecules and can be switched at 850 Hz. Observations are made using scanning tunnelling microscopy break junction (STMBJ) techniques to characterise piezoresistance, combined with blinking (current-time) experiments that follow single-molecule reactions in real time. A kinetic Monte Carlo methodology (KMC) is developed to simulate isomerisation on the experimental timescale, parameterised using density-functional theory (DFT) combined with non-equilibrium Green's function (NEGF) calculations. Results indicate that piezoresistance is controlled by both constitutional and conformational isomerisation, occurring at rates that are either fast (equilibrium) or slow (non-equilibrium) compared to the experimental timescale. Two different types of STMBJ traces are observed, one typical of traditional experiments that are interpreted in terms of intramolecular isomerisation occurring on stable tipped-shaped metal-contact junctions, and another attributed to arise from junction‒interface restructuring induced by bullvalene isomerisation.

Stretch Evolution of Electronic Coupling of the Thiophenyl Anchoring Group with Gold in Mechanically Controllable Break Junctions

The current-voltage characteristics of a single-molecule junction are determined by the electronic coupling Γ between the electronic states of the electrodes and the dominant transport channel(s) of the molecule. Γ is profoundly affected by the choice of the anchoring groups and their binding positions on the tip facets and the tip-tip separation. In this work, mechanically controllable break junction experiments on the N,N'-bis(5-ethynylbenzenethiol-salicylidene)ethylenediamine are presented, in particular, the stretch evolution of Γ with increasing tip-tip separation. The stretch evolution of Γ is characterized by recurring local maxima and can be related to the deformation of the molecule and sliding of the anchoring groups above the tip facets and along the tip edges. A dynamic simulation approach is implemented to model the stretch evolution of Γ, which captures the experimentally observed features remarkably well and establishes a link to the microscopic structure of the single-molecule junction.

Local cation-tuned reversible single-molecule switch in electric double layer

The nature of molecule-electrode interface is critical for the integration of atomically precise molecules as functional components into circuits. Herein, we demonstrate that the electric field localized metal cations in outer Helmholtz plane can modulate interfacial Au-carboxyl contacts, realizing a reversible single-molecule switch. STM break junction and I-V measurements show the electrochemical gating of aliphatic and aromatic carboxylic acids have a conductance ON/OFF behavior in electrolyte solution containing metal cations (i.e., Na⁺, K⁺, Mg²⁺ and Ca²⁺), compared to almost no change in conductance without metal cations. In situ Raman spectra reveal strong molecular carboxyl-metal cation coordination at the negatively charged electrode surface, hindering the formation of molecular junctions for electron tunnelling. This work validates the critical role of localized cations in the electric double layer to regulate electron transport at the single-molecule level.

Advances in single-molecule junctions as tools for chemical and biochemical analysis

The development of miniaturized electronics has led to the design and construction of powerful experimental platforms capable of measuring electronic properties to the level of single molecules, along with new theoretical concepts to aid in the interpretation of the data. A new area of activity is now emerging concerned with repurposing the tools of molecular electronics for applications in chemical and biological analysis. Single-molecule junction techniques, such as the scanning tunnelling microscope break junction and related single-molecule circuit approaches have a remarkable capacity to transduce chemical information from individual molecules, sampled in real time, to electrical signals. In this Review, we discuss single-molecule junction approaches as emerging analytical tools for the chemical and biological sciences. We demonstrate how these analytical techniques are being extended to systems capable of probing chemical reaction mechanisms. We also examine how molecular junctions enable the detection of RNA, DNA, and traces of proteins in solution with limits of detection at the zeptomole level.

Characterization and Application of Supramolecular Junctions

The convergence of supramolecular chemistry and single-molecule electronics offers a new perspective on supramolecular electronics, and provides a new avenue toward understanding and application of intermolecular charge transport at the molecular level. In this review, we will provide an overview of the advances in the characterization technique for the investigation of intermolecular charge transport, and summarize the experimental investigation of several non-covalent interactions, including π-π stacking interactions, hydrogen bonding, host-guest interactions and σ-σ interactions at the single-molecule level. We will also provide a perspective on supramolecular electronics and discuss the potential applications and future challenges.

Voltage-Modulated van der Waals Interaction in Single-Molecule Junctions

Understanding how molecular geometry affects the electronic properties of single-molecule junctions experimentally has been challenging. Typically, metal-molecule-metal junctions are measured using a break-junction method where electrode separation is mechanically evolving during measurement. Here, to probe the impact of the junction geometry on conductance, we apply a sinusoidal modulation to the molecular junction electrode position. Simultaneously, we probe the nonlinearity of the current-voltage characteristics of each junction through a modulation in the applied bias at a different frequency. In turn, we show that junctions formed with molecules that have different molecule-electrode interfaces exhibit statistically distinguishable Fourier-transformed conductances. In particular, we find a marked bias dependence for the modulation of junctions where transmission is mediated thorough the van der Waals (vdW) interaction. We attribute our findings to voltage-modulated vdW interactions at the single-molecule level.

Scaling of quantum interference from single molecules to molecular cages and their monolayers

The discovery of quantum interference (QI) is widely considered as an important advance in molecular electronics since it provides unique opportunities for achieving single-molecule devices with unprecedented performance. Although some pioneering studies suggested the presence of spin qubit coherence and QI in collective systems such as thin films, it remains unclear whether the QI can be transferred step-by-step from single molecules to different length scales, which hinders the application of QI in fabricating active molecular devices. Here, we found that QI can be transferred from a single molecule to their assemblies. We synthesized and investigated the charge transport through the molecular cages using 1,3-dipyridylbenzene (DPB) as a ligand block with a destructive quantum interference (DQI) effect and 2,5-dipyridylfuran (DPF) as a control building block with a constructive quantum interference (CQI) effect using both single-molecule break junction and large area junction techniques. Combined experiments and calculations revealed that both DQI and CQI had been transferred from the ligand blocks to the molecular cages and the monolayer thin film of the cages. Our work introduced QI effects from a ligand to the molecular cage comprising 732 atoms and even their monolayers, suggesting that the quantum interference could be scaled up within the phase-coherent distance.

Conductance Growth of Single-Cluster Junctions with Increasing Sizes

Quantum-tunneling-based nanoelectronics has the potential for the miniaturization of electronics toward the sub-5 nm scale. However, the nature of phase-coherent quantum tunneling leads to the rapid decays of the electrical conductance with tunneling transport distance, especially in organic molecule-based nanodevices. In this work, we investigated the conductance of the single-cluster junctions of a series of atomically well-defined silver nanoclusters, with varying sizes from 0.9 to 3.0 nm, using the mechanically controllable break junction (MCBJ) technique combined with quantum transport theory. Our charge transport investigations of these single-cluster junctions revealed that the conductance grows with increasing cluster size. The conductance decay constant was determined to be ∼-0.4 nm^-1, which is of opposite sign to that of organic molecules. Comparison between experiment and theory reveals that although charge transport through the silver single-cluster junctions occurs via phase-coherent tunneling, this is compensated by a rapid decrease in the energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital (HOMO-LUMO gap) with size and the increase in the electrode-cluster coupling, which results in their conductance increase up to lengths of ∼3.0 nm. These results demonstrate that such families of nanoclusters provide unique bottom-up building blocks for the fabrication of nanodevices in the sub-5 nm size range.

Recent Advances in Single-Molecule Sensors Based on STM Break Junction Measurements

Single-molecule recognition and detection with the highest resolution measurement has been one of the ultimate goals in science and engineering. Break junction techniques, originally developed to measure single-molecule conductance, recently have also been proven to have the capacity for the label-free exploration of single-molecule physics and chemistry, which paves a new way for single-molecule detection with high temporal resolution. In this review, we outline the primary advances and potential of the STM break junction technique for qualitative identification and quantitative detection at a single-molecule level. The principles of operation of these single-molecule electrical sensing mainly in three regimes, ion, environmental pH and genetic material detection, are summarized. It clearly proves that the single-molecule electrical measurements with break junction techniques show a promising perspective for designing a simple, label-free and nondestructive electrical sensor with ultrahigh sensitivity and excellent selectivity.

Tuning the binding configurations of single-molecule junctions by molecular co-assembly

Significant variability issues in metal-molecule contacts, such as adsorption geometry, lead to characteristic variability in the electrical responses of individual molecules. Herein, co-assembling 1-ethylimidazole (EIM) on Au(111) has been shown to be a feasible and effective strategy for tuning the binding configurations of pyridine-linked molecular junctions in the most common aqueous environments and atmospheric environments. The single-molecule conductance measurements clearly show a transition from multiple conductance peaks to a single conductance peak with increasing EIM concentration. Raman spectroscopy and DFT calculations suggest that the thermodynamically favorable EIM adsorbate results in the vertical orientation of the bipyridine.

Single-molecule conductance of double-stranded RNA oligonucleotides

RNA oligonucleotides are crucial for a range of biological functions and in many biotechnological applications. Herein, we measured, for the first time, the conductance of individual double-stranded (ds)RNA molecules and compared it with the conductance of single DNA : RNA hybrids. The average conductance values are similar for both biomolecules, but the distribution of conductance values shows an order of magnitude higher variability for dsRNA, indicating higher molecular flexibility of dsRNA. Microsecond Molecular Dynamics simulations explain this difference and provide structural insights into the higher stability of DNA : RNA duplex with atomic level of detail. The rotations of 2'-OH groups of the ribose rings and the bases in RNA strands destabilize the duplex structure by weakening base stacking interactions, affecting charge transport, and making single-molecule conductance of dsRNA more variable (dynamic disorder). The results demonstrate that a powerful combination of state-of-the-art biomolecular electronics techniques and computational approaches can provide valuable insights into biomolecules' biophysics with unprecedented spatial resolution.

Mechanically Induced Switching between Two Discrete Conductance States: A Potential Single-Molecule Variable Resistor

The fabrication of solid-state single-molecule switches with high on-off conductance ratios has been proposed to advance conventional technology in areas such as molecular electronics. Herein, we employed the scanning tunneling microscope break junction (STM-BJ) technique to modulate conductance in single-molecule junctions using mechanically induced stretching. Compound 1a possesses two dihydrobenzothiophene (DHBT) anchoring groups at the opposite ends linked with rigid alkyne side arms to form a gold-molecule-gold junction, while 1b contains 4-pyridine-anchoring groups. The incorporation of ferrocene into the backbone of each compound allows rotational freedom to the cyclopentadienyl (Cp) rings to give two distinct conductance states (high and low) for each. Various control experiments and suspended junction compression/retraction measurements indicate that these high- and low-conductance plateaus are the results of conformational changes within the junctions (extended and folded states) brought about by mechanically induced stretching. A high-low switching factor of 42 was achieved for 1a, whereas an exceptional conductance ratio in excess of 2 orders of magnitude (205) was observed for 1b. To the best of our knowledge, this is the highest experimental on-off conductance switching ratio for a single-molecule junction exploiting the mechanically induced STM-BJ method. Computational studies indicated that the two disparate conductance states observed for 1a and 1b result from mechanically induced conformational changes due to an interplay between conductance and the dihedral angles associated with the electrode-molecule interfaces. Our study reveals the structure-function relationship that determines conductance in such flexible and dynamic systems and promotes the development of a single-molecule variable resistor with high on-off switching factors.

Simultaneous Electrical and Mechanical Characterization of Single-Molecule Junctions Using AFM-BJ Technique

The fabrication and characterization of single-molecule junctions provide a unique platform to study the physical phenomena of a single molecule, and the electrical characterization enables us to understand the electrical transport properties of a single molecule and guide the fabrication of molecular electronic devices. However, the electrical characterization of single-molecule junctions is sometimes insufficient to extract the structural information on single-molecule junctions, and an alternate method to address this problem is to characterize the mechanical properties of single-molecule junctions. Simultaneous measurement of mechanical and electrical properties can provide complementary information on single molecules to analyze the correlations of their electrical and mechanical properties in the evolution of single-molecule junctions. In this mini-review, we summarize the progress on the simultaneous characterizations of mechanical and electrical properties for single-molecule junctions, and discuss the challenges and perspectives of this research area.

Hard-Soft Chemistry Design Principles for Predictive Assembly of Single Molecule-Metal Junctions

The achievement of atomic control over the organic-inorganic interface is key to engineering electronic and spintronic properties of molecular devices. We leverage insights from inorganic chemistry to create hard-soft acid-base (HSAB) theory-derived design principles for incorporation of single molecules onto metal electrodes. A single molecule circuit is assembled via a bond between an organic backbone and an under-coordinated metal atom of the electrode surface, typically Au. Here, we study molecular composition factors affecting the junction assembly of coordination complexes containing transition metals atoms on Au electrodes. We employ hetero- and homobimetallic lantern complexes and systematically change the coordination environment to vary the character of the intramolecular bonds relative to the electrode-molecule interaction. We observe that trends in the robustness and chemical selectivity of single molecule junctions formed with a range of linkers correlate with HSAB principles, which have traditionally been used to guide atomic arrangements in the synthesis of coordination complexes. We find that this similarity between the intermolecular electrode-molecule bonding in a molecular circuit and the intramolecular bonds within a coordination complex has implications for the design of metal-containing complexes compatible with electrical measurements on metal electrodes. Our results here show that HSAB principles determine which intramolecular interactions can be compromised by inter molecule-electrode coordination; in particular on Au electrodes, soft-soft metal-ligand bonding is vulnerable to competition from soft-soft Au-linker bonding in the junction. Neutral donor-acceptor intramolecular bonds can be tuned by the Lewis acidity of the transition metal ion, suggesting future synthetic routes toward incorporation of transition metal atoms into molecular junctions for increased functionality of single molecule devices.

RNA BioMolecular Electronics: towards new tools for biophysics and biomedicine

The last half-century has witnessed the birth and development of a new multidisciplinary field at the edge between materials science, nanoscience, engineering, and chemistry known as Molecular Electronics. This field deals with the electronic properties of individual molecules and their integration as active components in electronic circuits and has also been applied to biomolecules, leading to BioMolecular Electronics and opening new perspectives for single-molecule biophysics and biomedicine. Herein, we provide a brief introduction and overview of the BioMolecular electronics field, focusing on nucleic acids and potential applications for these measurements. In particular, we review the recent demonstration of the first single-molecule electrical detection of a biologically-relevant nucleic acid. We also show how this could be used to study biomolecular interactions and applications in liquid biopsy for early cancer detection, among others. Finally, we discuss future perspectives and challenges in the applications of this fascinating research field.

Probing Interfacial Electronic Effects on Single-Molecule Adsorption Geometry and Electron Transport at Atomically Flat Surfaces

Clarifying interfacial electronic effects on molecular adsorption is significant in many chemical and biochemical processes. Here, we used STM breaking junction and shell-isolated nanoparticle-enhanced Raman spectroscopy to probe electron transport and adsorption geometries of 4,4'-bipyridine (4,4'-BPY) at Au(111). Modifying the surface with 1-butyl-3-methylimidazolium cation-containing ionic liquids (ILs) decreases surface electron density and stabilizes a vertical orientation of pyridine through nitrogen atom σ-bond interactions, resulting in uniform adsorption configurations for forming molecular junctions. Modulation from vertical, tilted, to flat, is achieved on adding water to ILs, leading to a new peak ascribed to CC stretching of adsorbed pyridyl ring and 316 % modulation of single-molecule conductance. The dihedral angle between adsorbed pyridyl ring and surface decreases with increasing surface electronic density, enhancing electron donation from surface to pyridyl ring.

Fine-tuning the DNA conductance by intercalation of drug molecules

In this work we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modeling approach where extensive ab initio calculations are performed on numerous MD-simulated configurations of dsDNA and dsDNA intercalated with two different intercalators, ethidium and daunomycin. DNA conductance is found to increase by one order of magnitude upon drug intercalation due to the local unwinding of the DNA base pairs adjacent to the intercalated sites, which leads to modifications of the density of states in the near-Fermi-energy region of the ligand-DNA complex. Our study suggests that the intercalators can be used to enhance or tune the DNA conductance, which opens new possibilities for their potential applications in nanoelectronics.

The Characterization of Electronic Noise in the Charge Transport through Single-Molecule Junctions

With the goal of creating single-molecule devices and integrating them into circuits, the emergence of single-molecule electronics provides various techniques for the fabrication of single-molecule junctions and the investigation of charge transport through such junctions. Among the techniques for characterization of charge transport through molecular junctions, electronic noise characterization is an effective strategy with which issues from molecule-electrode interfaces, mechanisms of charge transport, and changes in junction configurations are studied. Electronic noise analysis in single-molecule junctions can be used to identify molecular conformations and even monitor reaction kinetics. This review summarizes the various types of electronic noise that have been characterized during single-molecule electrical detection, including the functions of random telegraph signal (RTS) noise, flicker noise, shot noise, and their corresponding applications, which provide some guidelines for the future application of these techniques to problems of charge transport through single-molecule junctions.

Correlated Energy-Level Alignment Effects Determine Substituent-Tuned Single-Molecule Conductance

The rational design of single-molecule electrical components requires a deep and predictive understanding of structure-function relationships. Here, we explore the relationship between chemical substituents and the conductance of metal-single-molecule-metal junctions, using functionalized oligophenylenevinylenes as a model system. Using a combination of mechanically controlled break-junction experiments and various levels of theory including non-equilibrium Green's functions, we demonstrate that the connection between gas-phase molecular electronic structure and in-junction molecular conductance is complicated by the involvement of multiple mutually correlated and opposing effects that contribute to energy-level alignment in the junction. We propose that these opposing correlations represent powerful new "design principles" because their physical origins make them broadly applicable, and they are capable of predicting the direction and relative magnitude of observed conductance trends. In particular, we show that they are consistent with the observed conductance variability not just within our own experimental results but also within disparate molecular series reported in the literature and, crucially, with the trend in variability across these molecular series, which previous simple models fail to explain. The design principles introduced here can therefore aid in both screening and suggesting novel design strategies for maximizing conductance tunability in single-molecule systems.

Simulated mechanical properties of finite-size graphene nanoribbons

There are many simulation studies of mechanical properties of graphene nanoribbons (GNR), but there is a lack of agreement regarding elastic and plastic behavior. In this paper we aim to analyze mechanical properties of finite-size GNR, including elastic modulus and fracture, as a function of ribbon size. We present classical molecular dynamics simulations for three different empirical potentials which are often used for graphene simulations: AIREBO, REBO-scr and REAXFF. Ribbons with and without H-passivation at the borders are considered, and the effects of strain rate and different boundaries are also explored. We focus on zig-zag GNR, but also include some armchair GNR examples. Results are strongly dependent on the empirical potential employed. Elastic modulus under uniaxial tension can depend on ribbon size, unlike predictions from continuum-scale models and from some atomistic simulations, and fracture strain and progress vary significantly amongst the simulated potentials. Because of that, we have also carried out quasi-static ab-initio simulations for a selected size, and find that the fracture process is not sudden, instead the wave function changes from Blöch states to a strong interaction between localized waves, which decreases continuously with distance. All potentials show good agreement with DFT in the linear elastic regime, but only the REBO-scr potential shows reasonable agreement with DFT both in the nonlinear elastic and fracture regimes. This would allow more reliable simulations of GNRs and GNR-based nanostructures, to help interpreting experimental results and for future technological applications.

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.

Cross-plane transport in a single-molecule two-dimensional van der Waals heterojunction

Two-dimensional van der Waals heterojunctions (2D-vdWHs) stacked from atomically thick 2D materials are predicted to be a diverse class of electronic materials with unique electronic properties. These properties can be further tuned by sandwiching monolayers of planar organic molecules between 2D materials to form molecular 2D-vdWHs (M-2D-vdWHs), in which electricity flows in a cross-plane way from one 2D layer to the other via a single molecular layer. Using a newly developed cross-plane break junction technique, combined with density functional theory calculations, we show that M-2D-vdWHs can be created and that cross-plane charge transport can be tuned by incorporating guest molecules. The M-2D-vdWHs exhibit distinct cross-plane charge transport signatures, which differ from those of molecules undergoing in-plane charge transport.

Chemically and Mechanically Controlled Single-Molecule Switches Using Spiropyrans

Developing molecular circuits that can function as the active components in electrical devices is an ongoing challenge in molecular electronics. It demands mechanical stability of the single-molecule circuit while simultaneously being responsive to external stimuli mimicking the operation of conventional electronic components. Here, we report single-molecule circuits based on spiropyran derivatives that respond electrically to chemical and mechanical stimuli. The merocyanine that results from the protonation/ring-opening of the spiropyran form showed single-molecule diode characteristics, with an average current rectification ratio of 5 at ±1 V, favoring the orientation where the positively charged end of the molecule is attached to the negative terminal of the circuit. Mechanical pulling of a single spiropyran molecule drives a switch to a more conducting merocyanine state. The mechanical switching is enabled by the strong Au-C covalent bonding between the molecule and the electrodes, which allows the tensile force delivered by the STM piezo to break the molecule at its spiropyran C-O bond.

Single-Molecule Measurement of Adsorption Free Energy at the Solid-Liquid Interface

Adsorption plays a critical role in surface and interface processes. Fractional surface coverage and adsorption free energy are two essential parameters of molecular adsorption. However, although adsorption at the solid-gas interface has been well-studied, and some adsorption models were proposed more than a century ago, challenges remain for the experimental investigation of molecular adsorption at the solid-liquid interface. Herein, we report the statistical and quantitative single-molecule measurement of adsorption at the solid-liquid interface by using the single-molecule break junction technique. The fractional surface coverage was extracted from the analysis of junction formation probability so that the adsorption free energy could be calculated by referring to the Langmuir isotherm. In the case of three prototypical molecules with terminal methylthio, pyridyl, and amino groups, the adsorption free energies were found to be 32.5, 33.9, and 28.3 kJ mol^-1 , respectively, which are consistent with DFT calculations.

Metal-Single-Molecule-Semiconductor Junctions Formed by a Radical Reaction Bridging Gold and Silicon Electrodes

Here we report molecular films terminated with diazonium salts moieties at both ends which enables single-molecule contacts between gold and silicon electrodes at open circuit via a radical reaction. We show that the kinetics of film grafting is crystal-facet dependent, being more favorable on ⟨111⟩ than on ⟨100⟩, a finding that adds control over surface chemistry during the device fabrication. The impact of this spontaneous chemistry in single-molecule electronics is demonstrated using STM-break junction approaches by forming metal-single-molecule-semiconductor junctions between silicon and gold source and drain, electrodes. Au-C and Si-C molecule-electrode contacts result in single-molecule wires that are mechanically stable, with an average lifetime at room temperature of 1.1 s, which is 30-400% higher than that reported for conventional molecular junctions formed between gold electrodes using thiol and amine contact groups. The high stability enabled measuring current-voltage properties during the lifetime of the molecular junction. We show that current rectification, which is intrinsic to metal-semiconductor junctions, can be controlled when a single-molecule bridges the gap in the junction. The system changes from being a current rectifier in the absence of a molecular bridge to an ohmic contact when a single molecule is covalently bonded to both silicon and gold electrodes. This study paves the way for the merging of the fields of single-molecule and silicon electronics.

Endohedral Fullerene Fe@C28 Adsorbed on Au(111) Surface as a High-Efficiency Spin Filter: A Theoretical Study

We present a theoretical study on the adsorption and spin transport properties of magnetic Fe@C₂₈ using Ab initio calculations based on spin density functional theory and non-equilibrium Green’s function techniques. Fe@C₂₈ tends to adsorb on the bridge sites in the manner of C–C bonds, and the spin-resolved transmission spectra of Fe@C₂₈ molecular junctions exhibit robust transport spin polarization (TSP). Under small bias voltage, the transport properties of Fe@C₂₈ are mainly determined by the spin-down channel and exhibit a large spin polarization. When compressing the right electrode, the TSP is decreased, but high spin filter efficiency (SFE) is still maintained. These theoretical results indicate that Fe@C₂₈ with a large magnetic moment has potential applications in molecular spintronics.

Paving the way to single-molecule chemistry through molecular electronics

Since our understanding of single-molecule junctions, in which single molecules are connected between nanoelectrodes, has deepened, we have paved the way to single-molecule chemistry. Herein, we review fundamental properties, including the number of molecules connected to the electrode, their structure and type, the bonding force between the single molecule and electrode and the thermopower and quantum interference in single-molecule junctions. Additionally, we review the application of single-molecule junctions to biomolecules. Finally, we explore single-molecule chemical reaction analysis, which is one direction of single-molecule junction research.

Force-conductance spectroscopy of a single-molecule reaction

We demonstrate how simultaneous measurements of conductance and force can be used to monitor the step-by-step progress of a mechanically-activated cis-to-trans isomerization single-molecule reaction, including events that cannot be distinguished using force or conductance alone. To do so, we simulated the force-conductance profile of cyclopropane oligomers connected to graphene nanoribbon electrodes that undergo a cis-to-trans isomerization during mechanical elongation. This was done using a combination of classical molecular dynamics simulation of the pulling using a reactive force field, and Landauer transport computations of the conductance with nonequilibrium Green's function methods. The isomerization events can be distinguished in both force and conductance profiles. However, the conductance profile during the mechanical elongation distinguishes between reaction intermediates that cannot be resolved using force. In turn, the force signals non-reactive deformations in the molecular backbone which are not visible in the conductance profile. These observations are shown to be robust to the choice of electrode and Hamiltonian model. The computations exemplify the potential of the integration of covalent mechanochemistry with molecular conductance to investigate chemical reactivity at the single-entity limit.

Non-chemisorbed gold-sulfur binding prevails in self-assembled monolayers

Gold-thiol contacts are ubiquitous across the physical and biological sciences in connecting organic molecules to surfaces. When thiols bind to gold in self-assembled monolayers (SAMs) the fate of the hydrogen remains a subject of profound debate-with implications for our understanding of their physical properties, spectroscopic features and formation mechanism(s). Exploiting measurements of the transmission through a molecular junction, which is highly sensitive to the nature of the molecule-electrode contact, we demonstrate here that the nature of the gold-sulfur bond in SAMs can be probed via single-molecule conductance measurements. Critically, we find that SAM measurements of dithiol-terminated molecular junctions yield a significantly lower conductance than solution measurements of the same molecule. Through numerous control experiments, conductance noise analysis and transport calculations based on density functional theory, we show that the gold-sulfur bond in SAMs prepared from the solution deposition of dithiols does not have chemisorbed character, which strongly suggests that under these widely used preparation conditions the hydrogen is retained.

An Electromechanical Approach to Understanding Binding Configurations in Single-Molecule Devices

The configuration of the molecule-electrode contact region plays an important role in determining the conductance of a single-molecule junction, and the variety of possible contact configurations have yielded multiple conductance values for a number of molecular families. In this report, we perform simultaneous conductance and electromechanical coupling parameter measurements on a series of oligophenylene-dithiol single-molecule junctions. These molecules show two distinct conductance values, and by examining the conductance changes, the electromechanical coupling, and the changes in the I- V characteristics coupled with a combination of analytical mechanical models and density functional theory (DFT) structure calculations, we are able to determine the most-probable binding configuration in each of the conductance states. We find that the lower-conductance state is likely due to the thiols binding to each electrode at a gold top site, and in the higher-conductance state, the phenylene π orbitals interact with electrodes, drastically modifying the transport behavior. This approach provides an expanded methodology for exploring the relationship between the molecule-electrode contact configuration and molecular conductance.

How Structural Defects Affect the Mechanical and Electrical Properties of Single Molecular Wires

We report how individual defects affect single graphene nanoribbons by scanning tunneling and atomic force microscopy pulling experiments simultaneously accessing their electrical and mechanical properties. The on-surface polymerization of the graphene nanoribbons is controlled by cooperative effects as theoretically suggested. Further, we find, with the help of atomistic simulations, that defects substantially vary the molecule-substrate coupling and drastically increase the flexibility of the graphene nanoribbons while keeping their desirable electronic properties intact.

Towards Controlled Single-Molecule Manipulation Using "Real-Time" Molecular Dynamics Simulation: A GPU Implementation

Molecular electronics saw its birth with the idea to build electronic circuitry with single molecules as individual components. Even though commercial applications are still modest, it has served an important part in the study of fundamental physics at the scale of single atoms and molecules. It is now a routine procedure in many research groups around the world to connect a single molecule between two metallic leads. What is unknown is the nature of this coupling between the molecule and the leads. We have demonstrated recently (Tewari, 2018, Ph.D. Thesis) our new setup based on a scanning tunneling microscope, which can be used to controllably manipulate single molecules and atomic chains. In this article, we will present the extension of our molecular dynamic simulator attached to this system for the manipulation of single molecules in real time using a graphics processing unit (GPU). This will not only aid in controlled lift-off of single molecules, but will also provide details about changes in the molecular conformations during the manipulation. This information could serve as important input for theoretical models and for bridging the gap between the theory and experiments.

Effect of molecular conformations on the electronic transport in oxygen-substituted alkanethiol molecular junctions

The relationship between the molecular structure and the electronic transport properties of molecular junctions based on thiol-terminated oligoethers, which are obtained by replacing every third methylene unit in the corresponding alkanethiols with an oxygen atom, is investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. Our calculations show that the low-bias conductance depends strongly on the conformation of the oligoethers in the junction. Specifically, in the cases of trans-extended conformation, the oxygen-dominated transmission peaks are very sharp and well below the Fermi energy, E_F, thus hardly affect the transmission around E_F; the Au-S interface hybrid states couple with σ-bonds in the molecular backbone forming the conduction channel at E_F, resulting in a conductance decay against the molecular length close to that for alkanethiols. By contrast, for junctions with oligoethers in helical conformations, some π-type oxygen orbitals coupling with the Au-S interface hybrid states contribute to the transmission around E_F. The molecule-electrode electronic coupling is also enhanced at the non-thiol side due to the specific spatial orientation introduced by the twist of the molecular backbone. This leads to a much smaller conductance decay constant. Our findings highlight the important role of the molecular conformation of oligoethers in their electronic transport properties and are also helpful for the design of molecular wires with heteroatom-substituted alkanethiols.

Specific single-molecule detection of glucose in a supramolecularly designed tunnel junction

Scanning tunneling microscopy tips were functionalized with a boronic acid derivative. In combination with a similarly modified substrate, the molecular tip forms a supramolecular complex selectively with a glucose molecule. The conductance of the resulting single complex allows one to achieve the specific single-molecule detection of glucose.

Signatures of Conformational Dynamics and Electrode-Molecule Interactions in the Conductance Profile During Pulling of Single-Molecule Junctions

We demonstrate that conductance can act as a sensitive probe of conformational dynamics and electrode-molecule interactions during the equilibrium and nonequilibrium pulling of molecular junctions. To do so, we use a combination of classical molecular dynamics simulations and Landauer electron transport computations to investigate the conductance of a family of Au-alkanedithiol-Au junctions as they are mechanically elongated. The simulations show an overall decay of the conductance during pulling that is due to a decrease in the through-space electrode-molecule interactions, and that sensitivity depends on the electrode geometry. In addition, characteristic kinks induced by level alignment shifts (and to a lesser extent by quantum destructive interference) were also observed superimposed to the overall decay during pulling simulations. The latter effect depends on the variation of the molecular dihedral angles during pulling and therefore offers an efficient solution to experimentally monitor conformational dynamics at the single-molecule limit.

DNA-Based Single-Molecule Electronics: From Concept to Function

Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I–V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed.

High resolution SPM imaging of organic molecules with functionalized tips

One of the most remarkable and exciting achievements in the field of scanning probe microscopy (SPM) in the last years is the unprecedented sub-molecular resolution of both atomic and electronic structures of single molecules deposited on solid state surfaces. Despite its youth, the technique has already brought many new possibilities to perform different kinds of measurements, which cannot be accomplished by other techniques. This opens new perspectives in advanced characterization of physical and chemical processes and properties of molecular structures on surfaces. Here, we discuss the history and recent progress of the high resolution imaging with a functionalized probe by means of atomic force microscopy (AFM), scanning tunnelling microscopy (STM) and inelastic electron tunneling spectroscopy (IETS). We describe the mechanisms responsible for the high-resolution AFM, STM and IETS-STM contrast. The complexity of this technique requires new theoretical approaches, where a relaxation of the functionalized probe is considered. We emphasise the similarities of the mechanism driving high-resolution SPM with other imaging methods. We also summarise briefly significant achievements and progress in different branches. Finally we provide brief perspectives and remaining challenges of the further refinement of these high-resolution methods.

Stretching-Induced Conductance Variations as Fingerprints of Contact Configurations in Single-Molecule Junctions

Molecule-electrode contact atomic structures are a critical factor that characterizes molecular devices, but their precise understanding and control still remain elusive. Based on combined first-principles calculations and single-molecule break junction experiments, we herein establish that the conductance of alkanedithiolate junctions can both increase and decrease with mechanical stretching, and the specific trend is determined by the S-Au linkage coordination number (CN) or the molecule-electrode contact atomic structure. Specifically, we find that the mechanical pulling results in the conductance increase for the junctions based on S-Au CN two and CN three contacts, while the conductance is minimally affected by stretching for junctions with the CN one contact and decreases upon the formation of Au monatomic chains. Detailed analysis unravels the mechanisms involving the competition between the stretching-induced upshift of the highest occupied molecular orbital-related states toward the Fermi level of electrodes and the deterioration of molecule-electrode electronic couplings in different contact CN cases. Moreover, we experimentally find a higher chance to observe the conductance enhancement mode under a faster elongation speed, which is explained by ab initio molecular dynamics simulations that reveal an important role of thermal fluctuations in aiding deformations of contacts into low-coordination configurations that include monatomic Au chains. Pointing out the insufficiency in previous notions of associating peak values in conductance histograms with specific contact atomic structures, this work resolves the controversy on the origins of ubiquitous multiple conductance peaks in S-Au-based single-molecule junctions.

Switching Effects in Molecular Electronic Devices

The creation of molecular electronic switches by using smart molecules is of great importance to the field of molecular electronics. This requires a fundamental understanding of the intrinsic electron transport mechanisms, which depend on several factors including the charge transport pathway, the molecule-electrode coupling strength, the energy of the molecular frontier orbitals, and the electron spin state. On the basis of significant progresses achieved in both experiments and theory over the past decade, in this review article we focus on new insights into the design and fabrication of different molecular switches and the corresponding switching effects, which is crucial to the development of molecular electronics. We summarize the strategies developed for single-molecule device fabrication and the mechanism of these switching effects. These analyses should be valuable for deeply understanding the switching effects in molecular electronic devices.

Single-molecule electrical contacts on silicon electrodes under ambient conditions

The ultimate goal in molecular electronics is to use individual molecules as the active electronic component of a real-world sturdy device. For this concept to become reality, it will require the field of single-molecule electronics to shift towards the semiconducting platform of the current microelectronics industry. Here, we report silicon-based single-molecule contacts that are mechanically and electrically stable under ambient conditions. The single-molecule contacts are prepared on silicon electrodes using the scanning tunnelling microscopy break-junction approach using a top metallic probe. The molecular wires show remarkable current–voltage reproducibility, as compared to an open silicon/nano-gap/metal junction, with current rectification ratios exceeding 4,000 when a low-doped silicon is used. The extension of the single-molecule junction approach to a silicon substrate contributes to the next level of miniaturization of electronic components and it is anticipated it will pave the way to a new class of robust single-molecule circuits.

The next level of miniaturization of electronic circuits calls for a connection between current single-molecule and traditional semiconductor processing technologies. Here, the authors show a method to prepare metal/molecule/silicon diodes that present high current rectification ratios exceeding 4,000.

Detecting Electron Transport of Amino Acids by Using Conductance Measurement

The single molecular conductance of amino acids was measured by a scanning tunneling microscope (STM) break junction. Conductance measurement of alanine gives out two conductance values at 10^−1.85 G₀ (1095 nS) and 10^−3.7 G₀ (15.5 nS), while similar conductance values are also observed for aspartic acid and glutamic acid, which have one more carboxylic acid group compared with alanine. This may show that the backbone of NH₂–C–COOH is the primary means of electron transport in the molecular junction of aspartic acid and glutamic acid. However, NH₂–C–COOH is not the primary means of electron transport in the methionine junction, which may be caused by the strong interaction of the Au–SMe (methyl sulfide) bond for the methionine junction. The current work reveals the important role of the anchoring group in the electron transport in different amino acids junctions.