Single-Molecule Junction Formation in Break-Junction Measurements

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.

Nuclear Magnetic Resonance Chemical Shift as a Probe for Single-Molecule Charge Transport

Existing modelling tools, developed to aid the design of efficient molecular wires and to better understand their charge-transport behaviour and mechanism, have limitations in accuracy and computational cost. Further research is required to develop faster and more precise methods that can yield information on how charge transport properties are impacted by changes in the chemical structure of a molecular wire. In this study, we report a clear semilogarithmic correlation between charge transport efficiency and nuclear magnetic resonance chemical shifts in multiple series of molecular wires, also accounting for the presence of chemical substituents. The NMR data was used to inform a simple tight-binding model that accurately captures the experimental single-molecule conductance values, especially useful in this case as more sophisticated density functional theory calculations fail due to inherent limitations. Our study demonstrates the potential of NMR spectroscopy as a valuable tool for characterising, rationalising, and gaining additional insights on the charge transport properties of single-molecule junctions.

Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions

Metal-metal contacts, though not yet widely realized, may provide exciting opportunities to serve as tunable and functional interfaces in single-molecule devices. One of the simplest components which might facilitate such binding interactions is the ferrocene group. Notably, direct bonds between the ferrocene iron center and metals such as Pd or Co have been demonstrated in molecular complexes comprising coordinating ligands attached to the cyclopentadienyl rings. Here, we demonstrate that ferrocene-based single-molecule devices with Fe-Au interfacial contact geometries form at room temperature in the absence of supporting coordinating ligands. Applying a photoredox reaction, we propose that ferrocene only functions effectively as a contact group when oxidized, binding to gold through a formal Fe3+ center. This observation is further supported by a series of control measurements and density functional theory calculations. Our findings extend the scope of junction contact chemistries beyond those involving main group elements, lay the foundation for light switchable ferrocene-based single-molecule devices, and highlight new potential mechanistic function(s) of unsubstituted ferrocenium groups in synthetic processes.

Manipulating Quantum Interference between σ and π Orbitals in Single-Molecule Junctions via Chemical Substitution and Environmental Control

Understanding and manipulating quantum interference (QI) effects in single molecule junction conductance can enable the design of molecular-scale devices. Here we demonstrate QI between σ and π molecular orbitals in an ∼4 Å molecule, pyrazine, bridging source and drain electrodes. Using single molecule conductance measurements, first-principles analysis, and electronic transport calculations, we show that this phenomenon leads to distinct patterns of electron transport in nanoscale junctions, such as destructive interference through the para position of a six-membered ring. These QI effects can be tuned to allow conductance switching using environmental pH control. Our work lays out a conceptual framework for engineering QI features in short molecular systems through synthetic and external manipulation that tunes the energies and symmetries of the σ and π channels.

Silver electrodes provide higher conductance than gold for thiol-terminated oligosilane molecular junctions: the interfacial effect

The understanding of the interfacial effect on charge transport is essential in single-molecule electronics. In this study, we elucidated the transport properties of molecular junctions comprising thiol-terminated oligosilane with three to eight Si atoms and two types of Ag/Au electrode materials employing different interfacial configurations. First-principles quantum transport calculations demonstrated that the interfacial configuration determines the relative magnitude of the current between the Ag and Au electrodes, wherein the Ag monoatomic contact configuration presented a larger current than did the Au double-atom configuration. Further, the mechanism of electron tunneling from the interfacial states through the central σ channel was revealed. In contrast to Au double-atom electrodes, Ag monoatomic electrodes exhibit a higher current due to the presence of Ag-S interfacial states closer to the Fermi level. Our findings show that the interfacial configuration is a plausible way to generate the relative magnitude of current of thiol-terminated oligosilane molecular junctions with Au/Ag electrodes and provide further insight into the interfacial effect on the transport properties.

Plasmon-Assisted Trapping of Single Molecules in Nanogap

The manipulation of single molecules has attracted extensive attention because of their promising applications in chemical, biological, medical, and materials sciences. Optical trapping of single molecules at room temperature, a critical approach to manipulating the single molecule, still faces great challenges due to the Brownian motions of molecules, weak optical gradient forces of laser, and limited characterization approaches. Here, we put forward localized surface plasmon (LSP)-assisted trapping of single molecules by utilizing scanning tunneling microscope break junction (STM-BJ) techniques, which could provide adjustable plasmonic nanogap and characterize the formation of molecular junction due to plasmonic trapping. We find that the plasmon-assisted trapping of single molecules in the nanogap, revealed by the conductance measurement, strongly depends on the molecular length and the experimental environments, i.e., plasmon could obviously promote the trapping of longer alkane-based molecules but is almost incapable of acting on shorter molecules in solutions. In contrast, the plasmon-assisted trapping of molecules can be ignored when the molecules are self-assembled (SAM) on a substrate independent of the molecular length.

Exploring relationships between chemical structure and molecular conductance: from α,ω-functionalised oligoynes to molecular circuits

The quantum circuit rule (QCR) allows estimation of the conductance of molecular junctions, electrode|X-bridge-Y|electrode, by considering the molecule as a series of independent scattering regions associated with the anchor groups (X, Y) and bridge, provided the numerical parameters that characterise the anchor groups (a_X, a_Y) and molecular backbones (b_B) are known. Single-molecule conductance measurements made with a series of α,ω-substituted oligoynes (X-{(CC)_N}-X, N = 1, 2, 3, 4), functionalised by terminal groups, X (4-thioanisole (C₆H₄SMe), 5-(3,3-dimethyl-2,3-dihydrobenzo[b]thiophene) (DMBT), 4-aniline (C₆H₄NH₂), 4-pyridine (Py), capable of serving as 'anchor groups' to contact the oligoyne fragment within a molecular junction, have shown the expected exponential dependence of molecular conductance, G, with the number of alkyne repeating units. In turn, this allows estimation of the anchor (a_i) and backbone (b_i) parameters. Using these values, together with previously determined parameters for other molecular fragments, the QCR is found to accurately estimate the junction conductance of more complex molecular circuits formed from smaller components assembled in series.

Learning Conductance: Gaussian Process Regression for Molecular Electronics

Experimental studies of charge transport through single molecules often rely on break junction setups, where molecular junctions are repeatedly formed and broken while measuring the conductance, leading to a statistical distribution of conductance values. Modeling this experimental situation and the resulting conductance histograms is challenging for theoretical methods, as computations need to capture structural changes in experiments, including the statistics of junction formation and rupture. This type of extensive structural sampling implies that even when evaluating conductance from computationally efficient electronic structure methods, which typically are of reduced accuracy, the evaluation of conductance histograms is too expensive to be a routine task. Highly accurate quantum transport computations are only computationally feasible for a few selected conformations and thus necessarily ignore the rich conformational space probed in experiments. To overcome these limitations, we investigate the potential of machine learning for modeling conductance histograms, in particular by Gaussian process regression. We show that by selecting specific structural parameters as features, Gaussian process regression can be used to efficiently predict the zero-bias conductance from molecular structures, reducing the computational cost of simulating conductance histograms by an order of magnitude. This enables the efficient calculation of conductance histograms even on the basis of computationally expensive first-principles approaches by effectively reducing the number of necessary charge transport calculations, paving the way toward their routine evaluation.

Topological Radical Pairs Produce Ultrahigh Conductance in Long Molecular Wires

Molecular one-dimensional topological insulators (1D TIs), which conduct through energetically low-lying topological edge states, can be extremely highly conducting and exhibit a reversed conductance decay, affording them great potential as building blocks for nanoelectronic devices. However, these properties can only be observed at the short length limit. To extend the length at which these anomalous effects can be observed, we design topological oligo[n]emeraldine wires using short 1D TIs as building blocks. As the wire length increases, the number of topological states increases, enabling an increased electronic transmission along the wire; specifically, we show that we can drive over a microampere current through a single ∼5 nm molecular wire, appreciably more than what has been observed in other long wires reported to date. Calculations and experiments show that the longest oligo[7]emeraldine with doped topological states has over 10⁶ enhancements in the transmission compared to its pristine form. The discovery of these highly conductive, long organic wires helps overcome a fundamental hurdle to implementing molecules in complex, nanoscale circuitry: their structures become too insulating at lengths that are useful in designing nanoscale circuits.

Cleavage of non-polar C(sp2)‒C(sp2) bonds in cycloparaphenylenes via electric field-catalyzed electrophilic aromatic substitution

Electrophilic aromatic substitution (EAS) is one of the most fundamental reactions in organic chemistry. Using an oriented external electric field (OEEF) instead of traditional reagents to tune the EAS reactivity can offer an environmentally friendly method to synthesize aromatic compounds and hold the promise of broadening its scope. Despite these advantages, OEEF catalysis of EAS is difficult to realize, due to the challenge of microscopically orienting OEEF along the direction of electron reorganizations. In this work, we demonstrate OEEF-catalyzed EAS reactions in a series of cycloparaphenylenes (CPPs) using the scanning tunneling microscope break junction (STM-BJ) technique. Crucially, the unique radial π-conjugation of CPPs enables a desired alignment for the OEEF to catalyze the EAS with Au STM tip (or substrate) acting as an electrophile. Under mild conditions, the OEEF-catalyzed EAS reactions can cleave the inherently inert C(sp²)-C(sp²) bond, leading to high-yield (~97%) formation of linear oligophenylenes terminated with covalent Au-C bonds. These results not only demonstrate the feasibility of OEEF catalysis of EAS, but also offer a way of exploring new mechanistic principles of classic organic reactions aided by OEEF.

Helical Molecule as an Efficient Rectifier: Effects of Molecular Conformation and Transverse Electric Field

The phenomenon of charge current rectification is critically investigated using a single stranded helical molecule in presence of transverse electric field. Two different helical molecules, DNA and protein, are taken into account to explore the specific roles of molecular conformation on rectification, which have not been addressed so far to the best of our concern. Sandwiching the molecular system within source and drain electrodes, we compute charge currents for two bias polarities and the degree of current rectification based on non-equilibrium Green's function formalism within a tight-binding framework. At non-zero electric field, site energies of the molecule are modulated in a cosine form, similar to the well known Aubry-André-Harper relation, resulting an atypical and fragmented energy band spectrum. The appearance of non-uniform site energies plays the central role for generating different currents in two bias polarities, and thus, the current rectification. We find that a high degree of current rectification can be established using the helical system and it becomes more effective for the protein molecule than the DNA one. At the end, the rectification operation considering a more general helical structure is discussed to make the present communication a self-contained one. Our proposition may provide a new route of getting controlled current rectification using similar kind of biological molecules and other tailor made helical geometries.

Single-Molecule Chemical Reactions Unveiled in Molecular Junctions

Understanding chemical processes at the single-molecule scale represents the ultimate limit of analytical chemistry. Single-molecule detection techniques allow one to reveal the detailed dynamics and kinetics of a chemical reaction with unprecedented accuracy. It has also enabled the discoveries of new reaction pathways or intermediates/transition states that are inaccessible in conventional ensemble experiments, which is critical to elucidating their intrinsic mechanisms. Thanks to the rapid development of single-molecule junction (SMJ) techniques, detecting chemical reactions via monitoring the electrical current through single molecules has received an increasing amount of attention and has witnessed tremendous advances in recent years. Research efforts in this direction have opened a new route for probing chemical and physical processes with single-molecule precision. This review presents detailed advancements in probing single-molecule chemical reactions using SMJ techniques. We specifically highlight recent progress in investigating electric-field-driven reactions, reaction dynamics and kinetics, host–guest interactions, and redox reactions of different molecular systems. Finally, we discuss the potential of single-molecule detection using SMJs across various future applications.

Molecular Rectifiers with a Very High Rectification Ratio Enabled by Oxidative Damage in Double-Stranded DNA

In this work, we report a novel strategy to construct highly efficient molecular diodes using oxidatively damaged DNA molecules. Being exposed to several endogenous and exogenous events, DNA suffers from constant oxidative damage, leading to the oxidation of guanine to 8-oxoguanine (8oxoG). Here, we study the charge migration properties of native and oxidatively damaged DNA using a multiscale multiconfigurational methodology comprising molecular dynamics, density functional theory, and kinetic Monte Carlo simulations. We perform a comprehensive study to understand the effect of different concentrations and locations of 8oxoG in a dsDNA sequence on its charge-transport properties and find tunable rectifier properties having potential applications in molecular electronics such as molecular switches and molecular rectifiers. We also discover the negative differential resistance properties of the fully oxidized Drew-Dickerson sequence. The presence of 8oxoG guanine leads to the trapping of charge, thus operating as a charge sink, which reveals how oxidized guanine saves the rest of the genome from further oxidative damage.

Trusting our machines: validating machine learning models for single-molecule transport experiments

In this tutorial review, we will describe crucial aspects related to the application of machine learning to help users avoid the most common pitfalls. The examples we present will be based on data from the field of molecular electronics, specifically single-molecule electron transport experiments, but the concepts and problems we explore will be sufficiently general for application in other fields with similar data. In the first part of the tutorial review, we will introduce the field of single-molecule transport, and provide an overview of the most common machine learning algorithms employed. In the second part of the tutorial review, we will show, through examples grounded in single-molecule transport, that the promises of machine learning can only be fulfilled by careful application. We will end the tutorial review with a discussion of where we, as a field, could go from here.

In this tutorial review, we will describe crucial aspects related to the application of machine learning to help users avoid the most common pitfalls.

Redox-Addressable Single-Molecule Junctions Incorporating a Persistent Organic Radical

Integrating radical (open-shell) species into non-cryogenic nanodevices is key to unlocking the potential of molecular electronics. While many efforts have been devoted to this issue, in the absence of a chemical/electrochemical potential the open-shell character is generally lost in contact with the metallic electrodes. Herein, single-molecule devices incorporating a 6-oxo-verdazyl persistent radical have been fabricated using break-junction techniques. The open-shell character is retained at room temperature, and electrochemical gating permits in situ reduction to a closed-shell anionic state in a single-molecule transistor configuration. Furthermore, electronically driven rectification arises from bias-dependent alignment of the open-shell resonances. The integration of radical character, transistor-like switching, and rectification in a single molecular component paves the way to further studies of the electronic, magnetic, and thermoelectric properties of open-shell species.

Interpolating Nonadiabatic Molecular Dynamics Hamiltonian with Inverse Fast Fourier Transform

Nonadiabatic (NA) molecular dynamics (MD) allows one to investigate far-from-equilibrium processes in nanoscale and molecular materials at the atomistic level and in the time domain, mimicking time-resolved spectroscopic experiments. Ab initio NAMD is limited to about 100 atoms and a few picoseconds, due to computational cost of excitation energies and NA couplings. We develop a straightforward methodology that can extend ab initio quality NAMD to nanoseconds and thousands of atoms. The ab initio NAMD Hamiltonian is sampled and interpolated along a trajectory using a Fourier transform, and then, it is used to perform NAMD with known algorithms. The methodology relies on the classical path approximation, which holds for many materials and processes. To achieve a complete ab initio quality description, the trajectory can be obtained using an ab initio trained machine learning force field. The method is demonstrated with charge carrier trapping and relaxation in hybrid organic-inorganic and all-inorganic metal halide perovskites that exhibit complex dynamics and are actively studied for optoelectronic applications.