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

Electric Field-Induced Sequential Prototropic Tautomerism in Enzyme-like Nanopocket Created by Single Molecular Break Junction

Mastering the control of external stimuli-induced chemical transformations with detailed insights into the mechanistic pathway is the key for developing efficient synthetic strategies and designing functional molecular systems. Enzymes, the most potent biological catalysts, efficiently utilize their built-in electric field to catalyze and control complex chemical reactions within the active site. Herein, we have demonstrated the interfacial electric field-induced prototropic tautomerization reaction in acylhydrazone entities by creating an enzymatic-like nanopocket within the atomically sharp gold electrodes using a mechanically controlled break junction (MCBJ) technique. In addition to that, the molecular system used here contains two coupled acylhydrazone reaction centers, hence demonstrating a cooperative stepwise electric field-induced reaction realized at the single molecular level. Furthermore, the mechanistic studies revealed a proton relay-assisted tautomerization showing the importance of external factors such as solvent in such electric field-driven reactions. Finally, single-molecule charge transport and energetics calculations of different molecular species at various applied electric fields using a polarizable continuum solvent model confirm and support our experimental findings. Thus, this study demonstrates that mimicking an enzymatic pocket using a single molecular junction's interfacial electric field as a trigger for chemical reactions can open new avenues to the field of synthetic chemistry.

Flexible Crossbar Molecular Devices with Patterned EGaIn Top Electrodes for Integrated All-Molecule-Circuit Implementation

Here, a unique crossbar architecture is designed and fabricated, incorporating vertically integrated self-assembled monolayers in electronic devices. This architecture is used to showcase 100 individual vertical molecular junctions on a single chip with a high yield of working junctions and high device uniformity. The study introduces a transfer approach for patterned liquid-metal eutectic alloy of gallium and indium top electrodes, enabling the creation of fully flexible molecular devices with electrical functionalities. The devices exhibit excellent charge transport performance, sustain a high rectification ratio (>103), and stable endurance and retention properties, even when the devices are significantly bent. Furthermore, Boolean logic gates, including OR and AND gates, as well as half-wave and full-wave rectifying circuits, are successfully implemented. The unique design of the flexible molecular device represents a significant step in harnessing the potential of molecular devices for high-density integration and possible molecule-based computing.

Programmed Heterostructures for Enhanced Electrical Conductivity

Interfacial electron transport in multicomponent systems plays a crucial role in controlling electrical conductivity. Organic-inorganic heterostructures electronic devices where all the entities are covalently bonded to each other can reduce interfacial electrical resistance, thus suitable for low-power consumption electronic operations. Programmed heterostructures of covalently bonded interfaces between ITO-ethynylbenzene (EB) and EB-zinc ferrite (ZF) nanoparticles, a programmed structure showing 67 978-fold enhancement of electrical current as compared to pristine NPs-based two terminal devices are created. An electrochemical approach is adopted to prepare nearly π-conjugated EB oligomer films of thickness ≈26 nm on ITO-electrode on which ZF NPs are chemically attached. A "flip-chip" method is employed to combine two EB-ZnFe2O4 NPs-ITO to probe electrical conductivity and charge conduction mechanism. The EB-ZnFe2O4 NPs exhibit strong electronic coupling at ITO-EB and EB-NPs with an energy barrier of 0.13 eV between the ITO Fermi level and the LUMO of EB-ZF NPs for efficient charge transport. Both the DC and AC-based electrical measurements manifest a low resistance at ITO-EB and EB-ZF NPs, revealing enhanced electrical current at ± 1.5 V. The programmed heterostructure devices can meet a strategy to create well-controlled molecular layers for electronic applications toward miniaturized components that shorten charge carrier distance, and interfacial resistance.

Label-Free Single-Molecule Electrical Sensor for Ultrasensitive and Selective Detection of Iodide Ions in Human Urine

Herein, a label-free single-molecule electrical sensor was first proposed for the ultrasensitive and selective detection of iodide ions in human urine. Single-molecule conductance measurements in different halogen ion solutions via scanning tunneling microscopy break junction (STM-BJ) clearly revealed that I- ions strongly affect the stability and displacement distance (Δz) distribution of molecular junctions. Theoretical calculations prove that the specific adsorption of I- ions modifies the surface properties and weakens the molecular adsorption. Furthermore, the average conductance peak area versus the logarithm of the I- ion concentration has a very good linear relationship in the range of 5 × 10-6 to 5 × 10-10 M, with a correlation coefficient of 0.99. This quantitative analysis remains valid in the presence of interfering ions of SO42-, ClO4-, Br-, and Cl- as well as interfering molecules of ascorbic acid, uric acid, dopamine, and cysteine. A cross-comparison of the human urine detection results of this single-molecule electrical sensor with those of the clinical method of As3+-Ce4+ catalytic spectrophotometry revealed an average difference of 0.9%, which decreased the detection time of 2 h with the traditional method to approximately 15 min. This work proves the promising practical potential of the single-molecule electrical technique for relevant clinical analysis.

Insight of Employing Molecular Junctions for Sensor Applications

Molecular junctions (MJs) exhibit distinct charge transport properties and have the potential to become the next generation of electronic devices. Advancing molecular electronics for practical uses, such as sensors, is crucial to propel its progress to the next level. In this review, we discussed how MJs can serve as a sensor for detecting a wide range of analytes with exceptional sensitivity and specificity. The primary advances and potential of molecular junctions for the various kinds of sensors including photosensors, explosives (DNTs, TNTs), cancer biomarker detection (DNA, mRNA), COVID detection, biogases (CO, NO, NH), environmental pH, practical chemicals, and water pollutants are listed and examined here. The fundamental ideas of molecular junction formation as well as the sensing mechanism have been examined here. This review demonstrates that MJ-based sensors hold significant promise for real-time and on-site detection. It provides valuable insights into current research and outlines potential future directions for advancing molecular junction-based sensors for practical applications.

Single-molecule detection of modified amino acid regulating transcriptional activity

Acetylation of lysine, a component of histones, regulates transcriptional activity. Simple detection methods for acetyl lysine are essential for early diagnosis of diseases and understanding of the physiological effects. We have detected and recognized acetyl lysine at the single-molecule level by combining MCBJ measurement and machine learning.

Making the Most of Nothing: One-Class Classification for Single-Molecule Transport Studies

Single-molecule experiments offer a unique means to probe molecular properties of individual molecules-yet they rest upon the successful control of background noise and irrelevant signals. In single-molecule transport studies, large amounts of data that probe a wide range of physical and chemical behaviors are often generated. However, due to the stochasticity of these experiments, a substantial fraction of the data may consist of blank traces where no molecular signal is evident. One-class (OC) classification is a machine learning technique to identify a specific class in a data set that potentially consists of a wide variety of classes. Here, we examine the utility of two different types of OC classification models on four diverse data sets from three different laboratories. Two of these data sets were measured at cryogenic temperatures and two at room temperature. By training the models solely on traces from a blank experiment, we demonstrate the efficacy of OC classification as a powerful and reliable method for filtering out blank traces from a molecular experiment in all four data sets. On a labeled 4,4'-bipyridine data set measured at 4.2 K, we achieve an accuracy of 96.9 ± 0.3 and an area under the receiver operating characteristic curve of 99.5 ± 0.3 as validated over a fivefold cross-validation. Given the wide range of physical and chemical properties that can be probed in single-molecule experiments, the successful application of OC classification to filter out blank traces is a major step forward in our ability to understand and manipulate molecular properties.

Many-Body Quantum Interference Route to the Two-Channel Kondo Effect: Inverse Design for Molecular Junctions and Quantum Dot Devices

Molecular junctions-whether actual single molecules in nanowire break junctions or artificial molecules realized in coupled quantum dot devices-offer unique functionality due to their orbital complexity, strong electron interactions, gate control, and many-body effects from hybridization with the external electronic circuit. Inverse design involves finding candidate structures that perform a desired function optimally. Here we develop an inverse design strategy for generalized quantum impurity models describing molecular junctions, and as an example, use it to demonstrate that many-body quantum interference can be leveraged to realize the two-channel Kondo critical point in simple 4- or 5-site molecular moieties. We show that remarkably high Kondo temperatures can be achieved, meaning that entropy and transport signatures should be experimentally accessible.

Technologies for investigating single-molecule chemical reactions

Single molecules, the smallest independently stable units in the material world, serve as the fundamental building blocks of matter. Among different branches of single-molecule sciences, single-molecule chemical reactions, by revealing the behavior and properties of individual molecules at the molecular scale, are particularly attractive because they can advance the understanding of chemical reaction mechanisms and help to address key scientific problems in broad fields such as physics, chemistry, biology and materials science. This review provides a timely, comprehensive overview of single-molecule chemical reactions based on various technical platforms such as scanning probe microscopy, single-molecule junction, single-molecule nanostructure, single-molecule fluorescence detection and crossed molecular beam. We present multidimensional analyses of single-molecule chemical reactions, offering new perspectives for research in different areas, such as photocatalysis/electrocatalysis, organic reactions, surface reactions and biological reactions. Finally, we discuss the opportunities and challenges in this thriving field of single-molecule chemical reactions.

Charge Transport through Single-Molecule Junctions with σ-Delocalized Systems

Single-molecule junctions, formed by a single molecule bridging a gap between two metal electrodes, are attracting attention as basic models of ultrasmall electronic devices. Although charge transport through π-conjugated molecules with π-delocalized system has been widely studied for a number of molecular junctions, there has been almost no research on charge transport through molecular junctions with a σ-delocalized orbital system. Compounds with hexa-selenium-substituted benzene form a σ-delocalized orbital system on the periphery of the benzene ring. In this study, we fabricated single-molecule junctions with the σ-delocalized orbital systems arising from lone-pair interactions of selenium atoms and clarified their electronic properties using the break-junction method. The single-molecule junctions with the σ-orbital systems show efficient charge transport properties and can be one of the alternatives to those with conventional π-orbital systems as minute electronic conductors.

Biosensors for Public Health and Environmental Monitoring: The Case for Sustainable Biosensing

Climate change is a profound crisis that affects every aspect of life, including public health. Changes in environmental conditions can promote the spread of pathogens and the development of new mutants and strains. Early detection is essential in managing and controlling this spread and improving overall health outcomes. This perspective article introduces basic biosensing concepts and various biosensors, including electrochemical, optical, mass-based, nano biosensors, and single-molecule biosensors, as important sustainability and public health preventive tools. The discussion also includes how the sustainability of a biosensor is crucial to minimizing environmental impacts and ensuring the long-term availability of vital technologies and resources for healthcare, environmental monitoring, and beyond. One promising avenue for pathogen screening could be the electrical detection of biomolecules at the single-molecule level, and some recent developments based on single-molecule bioelectronics using the Scanning Tunneling Microscopy-assisted break junctions (STM-BJ) technique are shown here. Using this technique, biomolecules can be detected with high sensitivity, eliminating the need for amplification and cell culture steps, thereby enhancing speed and efficiency. Furthermore, the STM-BJ technique demonstrates exceptional specificity, accurately detects single-base mismatches, and exhibits a detection limit essentially at the level of individual biomolecules. Finally, a case is made here for sustainable biosensors, how they can help, the paradigm shift needed to achieve them, and some potential applications.

High-bandwidth low-current measurement system for automated and scalable probing of tunnel junctions in liquids

Tunnel junctions have long been used to immobilize and study the electronic transport properties of single molecules. The sensitivity of tunneling currents to entities in the tunneling gap has generated interest in developing electronic biosensors with single molecule resolution. Tunnel junctions can, for example, be used for sensing bound or unbound DNA, RNA, amino acids, and proteins in liquids. However, manufacturing technologies for on-chip integrated arrays of tunnel junction sensors are still in their infancy, and scalable measurement strategies that allow the measurement of large numbers of tunneling junctions are required to facilitate progress. Here, we describe an experimental setup to perform scalable, high-bandwidth (>10 kHz) measurements of low currents (pA-nA) in arrays of on-chip integrated tunnel junctions immersed in various liquid media. Leveraging a commercially available compact 100 kHz bandwidth low-current measurement instrument, we developed a custom two-terminal probe on which the amplifier is directly mounted to decrease parasitic probe capacitances to sub-pF levels. We also integrated a motorized three-axis stage, which could be powered down using software control, inside the Faraday cage of the setup. This enabled automated data acquisition on arrays of tunnel junctions without worsening the noise floor despite being inside the Faraday cage. A deliberately positioned air gap in the fluidic path ensured liquid perfusion to the chip from outside the Faraday cage without coupling in additional noise. We demonstrate the performance of our setup using rapid current switching observed in electromigrated gold tunnel junctions immersed in deionized water.

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.

Understanding Emergent Complexity from a Single-Molecule Perspective

Molecules, with structural, scaling, and interaction diversities, are crucial for the emergence of complex behaviors. Interactions are essential prerequisites for complex systems to exhibit emergent properties that surpass the sum of individual component characteristics. Tracing the origin of complex molecular behaviors from interactions is critical to understanding ensemble emergence, and requires insights at the single-molecule level. Electrical signals from single-molecule junctions enable the observation of individual molecular behaviors, as well as intramolecular and intermolecular interactions. This technique provides a foundation for bottom-up explorations of emergent complexity. This Perspective highlights investigations of various interactions via single-molecule junctions, including intramolecular orbital and weak intermolecular interactions and interactions in chemical reactions. It also provides potential directions for future single-molecule junctions in complex system research.

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.

Emerging sensing platforms based on Cucurbit[n]uril functionalized gold nanoparticles and electrodes

Cucurbit[n]urils (CB[n]s, n = 5-8, 10, and 14), synthetic macrocycles with unique host-guest properties, have triggered increasing research interest in recent years. Gold nanoparticles (Au NPs) and electrodes stand out as exceptional substrates for sensing due to their remarkable physicochemical characteristics. Coupling the CB[n]s with Au NPs and electrodes has enabled the development of emerging sensing platforms for various promising applications. However, monitoring the behavior of analytes at the single-molecule level is currently one of the most challenging topics in the field of CB[n]-based sensing. Constructing supramolecular junctions in a sensing platform provides an ideal structure for single-molecule analysis, which can provide insights for a fundamental understanding of supramolecular interactions and chemical reactions and guide the design of sensing applications. This feature article outlines the progress in the preparation of the CB[n] functionalized Au NPs and Au electrodes, as well as the construction and application of supramolecular junctions in sensing platforms, based on the methods of recognition tunneling (RT), surface-enhanced Raman spectroscopy (SERS), single-molecule force spectroscopy (SMFS), and electrochemical sensing (ECS). A brief perspective on the future development of and challenges in CB[n] mediated sensing platforms is also covered.

Thickness-Dependent Charge Transport in Three Dimensional Ru(II)- Tris(phenanthroline)-Based Molecular Assemblies

We describe here the fabrication of large-area molecular junctions with a configuration of ITO/[Ru(Phen)3]/Al to understand temperature- and thickness-dependent charge transport phenomena. Thanks to the electrochemical technique, thin layers of electroactive ruthenium(II)-tris(phenanthroline) [Ru(Phen)3] with thicknesses of 4-16 nm are covalently grown on sputtering-deposited patterned ITO electrodes. The bias-induced molecular junctions exhibit symmetric current-voltage (j-V) curves, demonstrating highly efficient long-range charge transport and weak attenuation with increased molecular film thickness (β = 0.70 to 0.79 nm-1). Such a lower β value is attributed to the accessibility of Ru(Phen)3 molecular conduction channels to Fermi levels of both the electrodes and a strong electronic coupling at ITO-molecules interfaces. The thinner junctions (d = 3.9 nm) follow charge transport via resonant tunneling, while the thicker junctions (d = 10-16 nm) follow thermally activated (activation energy, Ea ∼ 43 meV) Poole-Frenkel charge conduction, showing a clear "molecular signature" in the nanometric junctions.

The role of halogens in Au-S bond cleavage for energy-differentiated catalysis at the single-bond limit

The transformation from one compound to another involves the breaking and formation of chemical bonds at the single-bond level, especially during catalytic reactions that are of great significance in broad fields such as energy conversion, environmental science, life science and chemical synthesis. The study of the reaction process at the single-bond limit is the key to understanding the catalytic reaction mechanism and further rationally designing catalysts. Here, we develop a method to monitor the catalytic process from the perspective of the single-bond energy using high-resolution scanning tunneling microscopy single-molecule junctions. Experimental and theoretical studies consistently reveal that the attack of a halogen atom on an Au atom can reduce the breaking energy of Au-S bonds, thereby accelerating the bond cleavage reaction and shortening the plateau length during the single-molecule junction breaking. Furthermore, the distinction in catalytic activity between different halogen atoms can be compared as well. This study establishes the intrinsic relationship among the reaction activation energy, the chemical bond breaking energy and the single-molecule junction breaking process, strengthening our mastery of catalytic reactions towards precise chemistry.