Direct observation of single-molecule hydrogen-bond dynamics with single-bond resolution

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.

Rotaxane-Functionalized Dyes for Charge-Rectification in p-Type Photoelectrochemical Devices

A supramolecular photovoltaic strategy is applied to enhance power conversion efficiencies (PCE) of photoelectrochemical devices by suppressing electron-hole recombination after photoinduced electron transfer (PET). Here, the author exploit supramolecular localization of the redox mediator-in close proximity to the dye-through a rotaxane topology, reducing electron-hole recombination in p-type dye-sensitized solar cells (p-DSSCs). Dye PRotaxane features 1,5-dioxynaphthalene recognition sites (DNP-arms) with a mechanically-interlocked macrocyclic redox mediator naphthalene diimide macrocycle (3-NDI-ring), stoppering synthetically via click chemistry. The control molecule PStopper has stoppered DNP-arms, preventing rotaxane formation with the 3-NDI-ring. Transient absorption and time-resolved fluorescence spectroscopy studies show ultrafast (211 ± 7 fs and 2.92 ± 0.05 ps) PET from the dye-moiety of PRotaxane to its mechanically interlocked 3-NDI-ring-acceptor, slowing down the electron-hole recombination on NiO surfaces compared to the analogue . p-DSSCs employing PRotaxane (PCE = 0.07%) demonstrate a 30% PCE increase compared to PStopper (PCE = 0.05%) devices, combining enhancements in both open-circuit voltages (VOC = 0.43 vs 0.36 V) and short-circuit photocurrent density (JSC = -0.39 vs -0.34 mA cm-2 ). Electrochemical impedance spectroscopy shows that PRotaxane devices exhibit hole lifetimes (τh ) approaching 1 s, a 16-fold improvement compared to traditional I- /I3 - -based systems (τh = 50 ms), demonstrating the benefits obtained upon nanoengineering of interfacial dye-regeneration at the photocathode.

Multiple hydrogen bonding driven supramolecular architectures and their biomedical applications

Supramolecular chemistry combines the strength of molecular assembly via various molecular interactions. Hydrogen bonding facilitated self-assembly with the advantages of directionality, specificity, reversibility, and strength is a promising approach for constructing advanced supramolecules. There are still some challenges in hydrogen bonding based supramolecular polymers, such as complexity originating from tautomerism of the molecular building modules, the assembly process, and structure versatility of building blocks. In this review, examples are selected to give insights into multiple hydrogen bonding driven emerging supramolecular architectures. We focus on chiral supramolecular assemblies, multiple hydrogen bonding modules as stimuli responsive sources, interpenetrating polymer networks, multiple hydrogen bonding assisted organic frameworks, supramolecular adhesives, energy dissipators, and quantitative analysis of nano-adhesion. The applications in biomedical materials are focused with detailed examples including drug design evolution for myotonic dystrophy, molecular assembly for advanced drug delivery, an indicator displacement strategy for DNA detection, tissue engineering, and self-assembly complexes as gene delivery vectors for gene transfection. In addition, insights into the current challenges and future perspectives of this field to propel the development of multiple hydrogen bonding facilitated supramolecular materials are proposed.

Evaluation of wound healing active principles in the transdermal patch formulated with crude bio wastes and plant extracts against GSK-3 beta - an in silico study

The wound-healing process is accelerated by inhibiting proteins that decelerate the wound-healing pathway. One of the active proteins involved in enhancing healing at the nuclear level and in gene expression is catenin. Inhibition of Glycogen Synthase Kinase 3β (GSK3 β) phosphorylates and degrades catenin via the downstream Wnt signalling pathway, thereby stabilizing catenin. A medicated wound dressing transdermal patch designed with fusion of bio wastes, viz. physiologically clotted fibrin, fish scale collagen, and the ethanolic extract of Mangifera indica (L.) and spider web, was analysed against GSK3β to enhance healing. In our earlier studies, the compounds present in the transdermal patch were identified using GC-MS analysis; 12 compounds exhibiting the wound healing mechanism were analyzed using PASS software and filtered out. From these 12 compounds, 6 compounds that possessed drug-likeness were screened by SwissADME and vNN-ADMET to dock against GSK3β in the present work. The PyRx results confirmed the binding of the six ligands to the active site of the target protein. Though the remaining filtered ligands also exhibited inhibitory activity, Molecular dynamics simulation studies were carried out with 100 ns on a complex of 10,12 Tricosadiyonic acid, Nopyl acetate and 2 Methyl 4 Heptanol as they showed binding affinity of -6.2Kcal/mol, -5.7Kcal/mol and -5.1Kcal/mol respectively. The stability of the complex was validated using MD simulation parameters RMSD, RMSF, Rg, and Number of Hydrogen bonds. These results implied that the transdermal patch would be efficient in accelerating the wound healing process through the inactivation of GSK3β.Communicated by Ramaswamy H. Sarma.

Single-Molecule Conductance of Intramolecular Hydrogen Bonding in Histamine on Gold

We perform single-molecule conductance measurements and DFT calculations on histamine, a biogenic amine that contains a flexible aliphatic linker and several nitrogen moieties with a potential for hydrogen bonding. Our study determines that junctions containing the free-base form of histamine can bridge through a molecular structure containing an intramolecular hydrogen bond. Conductance of this structure is higher than that through the saturated aliphatic linker. Flicker noise analysis of junction conductance confirms that transport occurs through the hydrogen bond and establishes a benchmark for noise measurements in hydrogen-bonded junctions. Overall, our work provides insights into the formation and conduction of intramolecular hydrogen bonding in single-molecule conductance measurements and into the conformations of the neurotransmitter histamine on noble metal surfaces.

Robust Single-Supermolecule Switches Operating in Response to Two Different Noncovalent Interactions

Supramolecular electronics provide an opportunity to introduce molecular assemblies into electronic devices through a combination of noncovalent interactions such as [π···π] and hydrogen-bonding interactions. The fidelity and dynamics of noncovalent interactions hold considerable promise when it comes to building devices with controllable and reproducible switching functions. Here, we demonstrate a strategy for building electronically robust switches by harnessing two different noncovalent interactions between a couple of pyridine derivatives. The single-supermolecule switch is turned ON when compressing the junction enabling [π···π] interactions to dominate the transport, while the switch is turned OFF by stretching the junction to form hydrogen-bonded dimers, leading to a dramatic decrease in conductance. The robustness and reproducibility of these single-supermolecule switches were achieved by modulating the junction with Ångström precision at frequencies of up to 190 Hz while obtaining high ON/OFF ratios of ∼600. The research presented herein opens up an avenue for designing robust bistable mechanoresponsive devices which will find applications in the building of integrated circuits for microelectromechanical systems.

Research on Electric Field-Induced Catalysis Using Single-Molecule Electrical Measurement

The role of catalysis in controlling chemical reactions is crucial. As an important external stimulus regulatory tool, electric field (EF) catalysis enables further possibilities for chemical reaction regulation. To date, the regulation mechanism of electric fields and electrons on chemical reactions has been modeled. The electric field at the single-molecule electronic scale provides a powerful theoretical weapon to explore the dynamics of individual chemical reactions. The combination of electric fields and single-molecule electronic techniques not only uncovers new principles but also results in the regulation of chemical reactions at the single-molecule scale. This perspective focuses on the recent electric field-catalyzed, single-molecule chemical reactions and assembly, and highlights promising outlooks for future work in single-molecule catalysis.

Voltage-driven control of single-molecule keto-enol equilibrium in a two-terminal junction system

Keto-enol tautomerism, describing an equilibrium involving two tautomers with distinctive structures, provides a promising platform for modulating nanoscale charge transport. However, such equilibria are generally dominated by the keto form, while a high isomerization barrier limits the transformation to the enol form, suggesting a considerable challenge to control the tautomerism. Here, we achieve single-molecule control of a keto-enol equilibrium at room temperature by using a strategy that combines redox control and electric field modulation. Based on the control of charge injection in the single-molecule junction, we could access charged potential energy surfaces with opposite thermodynamic driving forces, i.e., exhibiting a preference for the conducting enol form, while the isomerization barrier is also significantly reduced. Thus, we could selectively obtain desired and stable tautomers, which leads to significant modulation of the single-molecule conductance. This work highlights the concept of single-molecule control of chemical reactions on more than one potential energy surface.

Molecular Electronics: Creating and Bridging Molecular Junctions and Promoting Its Commercialization

Molecular electronics is driven by the dream of expanding Moore's law to the molecular level for next-generation electronics through incorporating individual or ensemble molecules into electronic circuits. For nearly 50 years, numerous efforts have been made to explore the intrinsic properties of molecules and develop diverse fascinating molecular electronic devices with the desired functionalities. The flourishing of molecular electronics is inseparable from the development of various elegant methodologies for creating nanogap electrodes and bridging the nanogap with molecules. This review first focuses on the techniques for making lateral and vertical nanogap electrodes by breaking, narrowing, and fixed modes, and highlights their capabilities, applications, merits, and shortcomings. After summarizing the approaches of growing single molecules or molecular layers on the electrodes, the methods of constructing a complete molecular circuit are comprehensively grouped into three categories: 1) directly bridging one-molecule-electrode component with another electrode, 2) physically bridging two-molecule-electrode components, and 3) chemically bridging two-molecule-electrode components. Finally, the current state of molecular circuit integration and commercialization is discussed and perspectives are provided, hoping to encourage the community to accelerate the realization of fully scalable molecular electronics for a new era of integrated microsystems and applications.

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.

Graphene-molecule-graphene single-molecule junctions to detect electronic reactions at the molecular scale

The ability to measure the behavior of a single molecule during a reaction implies the detection of inherent dynamic and static disordered states, which may not be represented when measuring ensemble averages. Here, we describe the building of devices with graphene-molecule-graphene single-molecule junctions integrated into an electrical circuit. These devices are simple to build and are stable, showing tolerance to mechanical changes, solution environment and voltage stimulation. The design of a conductive channel based on a single molecule enables single-molecule detection and is sensitive to variations in physical properties and chemical structures of the detected molecules. The on-chip setup of single-molecule junctions further offers complementary metal-oxide-semiconductor (CMOS) compatibility, enabling logic functions in circuit elements, as well as deciphering of reaction intermediates. We detail the experimental procedure to prepare graphene transistor arrays as a basis for single-molecule junctions and the preparation of nanogapped carboxyl-terminal graphene electrodes by using electron-beam lithography and oxygen plasma etching. We describe the basic design of a molecular bridge with desired functions and terminals to form covalent bonds with electrode arrays, via a chemical reaction, to construct stably integrated single-molecule devices with a yield of 30-50% per chip. The immobilization of the single molecules is then characterized by using inelastic electron tunneling spectra, single-molecule imaging and fluorescent spectra. The whole protocol can be implemented within 2 weeks and requires users trained in using ultra-clean laboratory facilities and the aforementioned instrumentation.

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.

Quantitative Microscopic Observation of Base-Ligand Interactions via Hydrogen Bonds by Single-Molecule Counting

Chemical properties have been based on statistical averages since the introduction of Avogadro's number. The lack of suitable methods for counting identified single molecules has posed challenges to counting statistics. The selectivity, affinity, and mode of hydrogen bonding between base and small molecules that make up DNA, which is vital for living organisms, have not yet been revealed at the single molecule level. Here, we show the quantitation of the above-mentioned parameters via single-molecule counting based on the combination of single-molecule electrical measurements and AI. The binding selectivity values of five ligands to four different base molecules were evaluated quantitatively by determining the ratio of the number of aggregates in a solution mixture of base molecules and a ligand. In addition, we show the ligand dependence of the mode and number of microscopic hydrogen bonds via single-molecule counting and quantum chemical calculations.

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.

Single-molecule nano-optoelectronics: insights from physics

Single-molecule optoelectronic devices promise a potential solution for miniaturization and functionalization of silicon-based microelectronic circuits in the future. For decades of its fast development, this field has made significant progress in the synthesis of optoelectronic materials, the fabrication of single-molecule devices and the realization of optoelectronic functions. On the other hand, single-molecule optoelectronic devices offer a reliable platform to investigate the intrinsic physical phenomena and regulation rules of matters at the single-molecule level. To further realize and regulate the optoelectronic functions toward practical applications, it is necessary to clarify the intrinsic physical mechanisms of single-molecule optoelectronic nanodevices. Here, we provide a timely review to survey the physical phenomena and laws involved in single-molecule optoelectronic materials and devices, including charge effects, spin effects, exciton effects, vibronic effects, structural and orbital effects. In particular, we will systematically summarize the basics of molecular optoelectronic materials, and the physical effects and manipulations of single-molecule optoelectronic nanodevices. In addition, fundamentals of single-molecule electronics, which are basic of single-molecule optoelectronics, can also be found in this review. At last, we tend to focus the discussion on the opportunities and challenges arising in the field of single-molecule optoelectronics, and propose further potential breakthroughs.

Stochastic Binding Dynamics of a Photoswitchable Single Supramolecular Complex

In this work, a real-time precise electrical method to directly monitor the stochastic binding dynamics of a single supramolecule based on the host-guest interaction between a cyclodextrin and an azo compound is reported. Different intermolecular binding states during the binding process are distinguished by conductance signals detected from graphene-molecule-graphene single-molecule junctions. In combination with theoretical calculations, the reciprocating and unidirectional motions in the trans form as well as the restrained reciprocating motion in the cis form due to the steric hindrance is observed, which could be reversibly switched by visible and UV irradiation. The integration of individual supramolecules into nanocircuits not only offers a facile and effective strategy to probe the dynamic process of supramolecular systems, but also paves the way to construct functional molecular devices toward real applications such as switches, sensors, and logic devices.

Single-molecule field effect and conductance switching driven by electric field and proton transfer

Single-molecule junctions (SMJs) offer a novel strategy for miniaturization of electronic devices. In this work, we realize a graphene-porphyrin-graphene SMJ driven by electric field and proton transfer in two configurations. In the transistor configuration with ionic liquid gating, an unprecedented field-effect performance is achieved with a maximum on/off ratio of ~4800 and a gate efficiency as high as ~179 mV/decade in consistence with the theoretical prediction. In the other configuration, controllable proton transfer, tautomerization switching, is directly observed with bias dependence. Room temperature proton transfer leads to a two-state conductance switching, and more precise tautomerization is detected, showing a four-state conductance switching at high bias voltages and low temperatures. Such an SMJ in two configurations provides new insights into not only building multifunctional molecular nanocircuits toward real applications but also deciphering the intrinsic properties of matters at the molecular scale.

Single-Molecule Junction: A Reliable Platform for Monitoring Molecular Physical and Chemical Processes

Monitoring and manipulating the physical and chemical behavior of single molecules is an important development direction of molecular electronics that aids in understanding the molecular world at the single-molecule level. The electrical detection platform based on single-molecule junctions can monitor physical and chemical processes at the single-molecule level with a high temporal resolution, stability, and signal-to-noise ratio. Recently, the combination of single-molecule junctions with different multimodal control systems has been widely used to explore significant physical and chemical phenomena because of its powerful monitoring and control capabilities. In this review, we focus on the applications of single-molecule junctions in monitoring molecular physical and chemical processes. The methods developed for characterizing single-molecule charge transfer and spin characteristics as well as revealing the corresponding intrinsic mechanisms are introduced. Dynamic detection and regulation of single-molecule conformational isomerization, intermolecular interactions, and chemical reactions are also discussed in detail. In addition to these dynamic investigations, this review discusses the open challenges of single-molecule detection in the fields of physics and chemistry and proposes some potential applications in this field.

Accurate Single-Molecule Kinetic Isotope Effects

An accurate single-molecule kinetic isotope effect (sm-KIE) was applied to circumvent the inherent limitation of conventional ensemble KIE by using graphene-molecule-graphene single-molecule junctions. In situ monitoring of the single-molecule reaction trajectories in real time with high temporal resolution has the capability to characterize the deeper information brought by KIE. The C-O bond cleavage and the C-C bond formation of the transition state (TS) were observed in the Claisen rearrangement through the secondary kinetic isotope effect, demonstrating the high detection sensitivity and accuracy of this method. More interestingly, this sm-KIE can be used to determine TS structures under different electric fields, revealing the multidimensional regulation of the TS. The detection and manipulation of the TS provide a broad perspective to understand and optimize chemical reactions and biomimetic progress.

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.

Single-Molecule Junctions with Highly Improved Stability

Single-molecule junctions (SMJs) have been fabricated using layers generated by diazonium electroreduction. This process creates a C-Au covalent bond between the molecule and the electrode. Rigid oligomers of variable length, based on porphyrin derivatives in their free base or cobalt complex forms, have been grafted on the surface. The conductance of the oligomers has been studied by a scanning tunneling microscopy break junction (STM-bj) technique and G(t) measurements, and the lifetime of the SMJs has been investigated. The conductance histograms indicate that charge transport in the porphyrins is relatively efficient and influenced by the presence of the cobalt center. With both systems, random telegraph G(t) signals are easily recorded, showing SMJ on/off states. The SMJs then stabilize and exhibit a surprisingly long lifetime around 10 s, and attenuation plots, obtained by both G(t) and STM-bj measurements, give identical values. This work shows that highly stable SMJs can be prepared using a diazonium grafting approach.

Direct Observation of Amide Bond Formation in a Plasmonic Nanocavity Triggered by Single Nanoparticle Collisions

The real-time observation of chemical bond formation at the single-molecule level is one of the great challenges in the fields of organic and biomolecular chemistry. Valuable information can be gleaned that is not accessible using ensemble-average measurements. Although remarkably sophisticated techniques for monitoring chemical reactions have been developed, the ability to detect the specific formation of a chemical bond in situ at the single-molecule level has remained an elusive goal. Amide bonds are routinely formed from the aminolysis of N-hydroxysuccinimide (NHS) esters by primary amines, and the protocol is widely used for the synthesis, cross-linking, and labeling of peptides and proteins. Herein, a plasmonic nanocavity was applied to study aminolysis reaction for amide bond formation, which was initiated by single nanoparticle collision events between suitably functionalized free-moving gold nanoparticles and a gold nanoelectrode in an aqueous buffer. By means of simultaneous surface enhanced Raman spectroscopy (SERS) and single-entity electrochemistry (EC) measurements, we have probed the dynamic evolution of amide bond formation in the aminolysis reaction with 10 s of millisecond time resolution. Hence, we demonstrate that single-entity EC-SERS is a valuable and sensitive technique by which chemical reactions can be studied at the single-molecule level.

Atomically Precise Engineering of Single-Molecule Stereoelectronic Effect

Charge transport in a single-molecule junction is extraordinarily sensitive to both the internal electronic structure of a molecule and its microscopic environment. Two distinct conductance states of a prototype terphenyl molecule are observed, which correspond to the bistability of outer phenyl rings at each end. An azobenzene unit is intentionally introduced through atomically precise side-functionalization at the central ring of the terphenyl, which is reversibly isomerized between trans and cis forms by either electric or optical stimuli. Both experiment and theory demonstrate that the azobenzene side-group delicately modulates charge transport in the backbone via a single-molecule stereoelectronic effect. We reveal that the dihedral angle between the central and outer phenyl ring, as well as the corresponding rotation barrier, is subtly controlled by isomerization, while the behaviors of the phenyl ring away from the azobenzene are hardly affected. This tunability offers a new route to precisely engineer multiconfigurational single-molecule memories, switches, and sensors.

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.

Environmental Control of Single-Molecule Junction Evolution and Conductance: A Case Study of Expanded Pyridinium Wiring

Environmental control of single-molecule junction evolution and conductance was demonstrated for expanded pyridinium molecules by scanning tunneling microscopy break junction method and interpreted by quantum transport calculations including solvent molecules explicitly. Fully extended and highly conducting molecular junctions prevail in water environment as opposed to short and less conducting junctions formed in non-solvating mesitylene. A theoretical approach correctly models single-molecule conductance values considering the experimental junction length. Most pronounced difference in the molecular junction formation and conductance was identified for a molecule with the highest stabilization energy on the gold substrate confirming the importance of molecule-electrode interactions. Presented concept of tuning conductance through molecule-electrode interactions in the solvent-driven junctions can be used in the development of new molecular electronic devices.

Electric field-catalyzed single-molecule Diels-Alder reaction dynamics

Precise time trajectories and detailed reaction pathways of the Diels-Alder reaction were directly observed using accurate single-molecule detection on an in situ label-free single-molecule electrical detection platform. This study demonstrates the well-accepted concerted mechanism and clarifies the role of charge transfer complexes with endo or exo configurations on the reaction path. An unprecedented stepwise pathway was verified at high temperatures in a high-voltage electric field. Experiments and theoretical results revealed an electric field-catalyzed mechanism that shows the presence of a zwitterionic intermediate with one bond formation and variation of concerted and stepwise reactions by the strength of the electric field, thus establishing a previously unidentified approach for mechanistic control by electric field catalysis.

Multi-Interactions in Ionic Liquids for Natural Product Extraction

Natural products with a variety of pharmacological effects are important sources for commercial drugs, and it is very crucial to develop effective techniques to selectively extract and isolate bioactive natural components from the plants against the background of sustainable development. Ionic liquids (ILs) are a kind of designable material with unique physicochemical properties, including good thermal stability, negligible vapor pressure, good solvation ability, etc. ILs have already been used in pharmaceuticals for extraction, purification, drug delivery, etc. It has been reported that multi-interactions, like hydrogen bonding, hydrophobic interactions, play important roles in the extraction of bioactive components from the plants. In this review, recent progress in the understanding of scientific essence of hydrogen bonding, the special interaction, in ILs was summarized. The extraction of various natural products, one important area in pharmaceutical, by conventional and functional ILs as well as the specific roles of multi-interactions in this process were also reviewed. Moreover, problems existing in bioactive compound extraction by ILs and the future developing trends of this area are given, which might be helpful for scientists, especially beginners, in this field.

Unravelling Structural Dynamics within a Photoswitchable Single Peptide: A Step Towards Multimodal Bioinspired Nanodevices

The majority of the protein structures have been elucidated under equilibrium conditions. The aim herein is to provide a better understanding of the dynamic behavior inherent to proteins by fabricating a label-free nanodevice comprising a single-peptide junction to measure real-time conductance, from which their structural dynamic behavior can be inferred. This device contains an azobenzene photoswitch for interconversion between a well-defined cis, and disordered trans isomer. Real-time conductance measurements revealed three distinct states for each isomer, with molecular dynamics simulations showing each state corresponds to a specific range of hydrogen bond lengths within the cis isomer, and specific dihedral angles in the trans isomer. These insights into the structural dynamic behavior of peptides may rationally extend to proteins. Also demonstrated is the capacity to modulate conductance which advances the design and development of bioinspired electronic nanodevices.

Constructing Dual-Molecule Junctions to Probe Intermolecular Crosstalk

Understanding and controlling charge transport across multiple parallel molecules are fundamental to the creation of innovative functional electronic components, as future molecular devices will likely be multimolecular. The smallest possible molecular ensemble to address this challenge is a dual-molecule junction device, which has potential to unravel the effects of intermolecular crosstalk on electronic transport at the molecular level that cannot be elucidated using either conventional single-molecule or self-assembled monolayer (SAM) techniques. Herein, we demonstrate the fabrication of a scanning tunneling microscopy (STM) dual-molecule junction device, which utilizes noncovalent interactions and allows for direct comparison to the conventional STM single-molecule device. STM-break junction (BJ) measurements reveal a decrease in conductance of 10% per molecule from the dual-molecule to the single-molecule junction device. Quantum transport simulations indicate that this decrease is attributable to intermolecular crosstalk (i.e., intermolecular π-π interactions), with possible contributions from substrate-mediated coupling (i.e., molecule-electrode). This study provides the first experimental evidence to interpret intermolecular crosstalk in electronic transport at the STM-BJ level and translates the experimental observations into meaningful molecular information to enhance our fundamental knowledge of this subject matter. This approach is pertinent to the design and development of future multimolecular electronic components and also to other dual-molecular systems where such crosstalk is mediated by various noncovalent intermolecular interactions (e.g., electrostatic and hydrogen bonding).

Solvent-molecule interaction induced gating of charge transport through single-molecule junctions

To explore solvent gating of single-molecule electrical conductance due to solvent-molecule interactions, charge transport through single-molecule junctions with different anchoring groups in various solvent environments was measured by using the mechanically controllable break junction technique. We found that the conductance of single-molecule junctions can be tuned by nearly an order of magnitude by varying the polarity of solvent. Furthermore, gating efficiency due to solvent-molecule interactions was found to be dependent on the choice of the anchor group. Theoretical calculations revealed that the polar solvent shifted the molecular-orbital energies, based on the coupling strength of the anchor groups. For weakly coupled molecular junctions, the polar solvent-molecule interaction was observed to reduce the energy gap between the molecular orbital and the Fermi level of the electrode and shifted the molecular orbitals. This resulted in a more significant gating effect than that of the strongly coupled molecules. This study suggested that solvent-molecule interaction can significantly affect the charge transport through single-molecule junctions.

In situ formation of H-bonding imidazole chains in break-junction experiments

As a small molecule possessing both strong H-bond donor and acceptor functions, 1H-imidazole can participate in extensive homo- or heteromolecular H-bonding networks. These properties are important in Nature, as imidazole moieties are incorporated in many biologically-relevant compounds. Imidazole also finds applications ranging from corrosion inhibition to fire retardants and photography. We have found a peculiar behaviour of imidazole during scanning tunnelling microscopy-break junction (STM-BJ) experiments, in which oligomeric chains connect the two electrodes and allow efficient charge transport. We attributed this behaviour to the formation of hydrogen-bonding networks, as no evidence of such behaviour was found in 1-methylimidazole (incapable of participating in intramolecular hydrogen bonding). The results are supported by DFT calculations, which confirmed our hypothesis. These findings pave the road to the use of hydrogen-bonding networks for the fabrication of dynamic junctions based on supramolecular interactions.

Biomolecular and bioanalytical applications of infrared spectroscopy - A review

Infrared (IR; or mid-infrared, MIR; 4000-400 cm^-1; 2500-25,000 nm) spectroscopy has become one of the most powerful and versatile tools at the disposal of modern bioscience. Because of its high molecular specificity, applicability to wide variety of samples, rapid measurement and non-invasivity, IR spectroscopy forms a potent approach to elucidate qualitative and quantitative information from various kinds of biological material. For these reasons, it became an established bioanalytical technique with diverse applications. This work aims to be a comprehensive and critical review of the recent accomplishments in the field of biomolecular and bioanalytical IR spectroscopy. That progress is presented on a wider background, with fundamental characteristics, the basic principles of the technique outlined, and its scientific capability directly compared with other methods being used in similar fields (e.g. near-infrared, Raman, fluorescence). The article aims to present a complete examination of the topic, as it touches the background phenomena, instrumentation, spectra processing and data analytical methods, spectra interpretation and related information. To suit this goal, the article includes a tutorial information essential to obtain a thorough perspective of bio-related applications of the reviewed methodologies. The importance of the fundamental factors to the final performance and applicability of IR spectroscopy in various areas of bioscience is explained. This information is interpreted in critical way, with aim to gain deep understanding why IR spectroscopy finds extraordinarily intensive use in this remarkably diverse and dynamic field of research and utility. The major focus is placed on the diversity of the applications in which IR biospectroscopy has been established so far and those onto which it is expanding nowadays. This includes qualitative and quantitative analytical spectroscopy, spectral imaging, medical diagnosis, monitoring of biophysical processes, and studies of physicochemical properties and dynamics of biomolecules. The application potential of IR spectroscopy in light of the current accomplishments and the future prospects is critically evaluated and its significance in the progress of bioscience is comprehensively presented.

Fabrication and functions of graphene-molecule-graphene single-molecule junctions

The past two decades have witnessed increasingly rapid advances in the field of single-molecule electronics, which are expected to overcome the limitation of the miniaturization of silicon-based microdevices, thus promoting the development of device manufacturing technologies and characterization means. In addition to this, they can enable us to investigate the intrinsic properties of materials at the atomic- or molecular-length scale and probe new phenomena that are inaccessible in ensemble experiments. In this perspective, we start from a brief introduction on the manufacturing method of graphene-molecule-graphene single-molecule junctions (GMG-SMJs). Then, we make a description on the remarkable functions of GMG-SMJs, especially on the investigation of single-molecule charge transport and dynamics. Finally, we conclude by discussing the main challenges and future research directions of molecular electronics.

Single-Molecule Electrical Detection: A Promising Route toward the Fundamental Limits of Chemistry and Life Science

The ultimate limit of analytical chemistry is single-molecule detection, which allows one to visualize the dynamic processes of chemical/biological interactions with single-molecule or single-event sensitivity and hence enables the study of stochastic fluctuations under equilibrium conditions and the observation of time trajectories and reaction pathways of individual species in nonequilibrated systems. In addition, such studies may also allow the direct observation of novel microscopic quantum effects and fundamental discoveries of underlying molecular mechanisms in organic reactions and biological processes that are not accessible in ensemble experiments, thus providing unique opportunities to solve the key problems of physical, chemical, and life sciences. Consequently, the field of single-molecule detection has received considerable attention and has witnessed tremendous advances in different directions in combination with other disciplines. This Account describes our ongoing work on the development of groundbreaking methods (termed "single-molecule electrical approaches") of translating the detailed processes of chemical reactions or biological functions into detectable electrical signals at the single-event level on the platform of single-molecule electronic devices, with a particular focus on graphene-molecule-graphene single-molecule junctions (GMG-SMJs) and silicon-nanowire-based single-molecule electrical nanocircuits. These nanocircuit-based architectures are complementary to conventional optical or mechanical techniques but exhibit obvious advantages such as the absence of problems associated with bleaching and fluorescent labeling. Dash-line lithography (DLL) is an efficient lithographic method of cutting graphene and forming carboxylic-acid-functionalized nanogapped graphene point contact arrays developed to address the formidable challenges of molecular device fabrication difficulty and poor stability. Molecules of interest terminated by amines on both ends can be covalently sandwiched between graphene point contacts to create high-throughput robust GMG-SMJs containing only one molecule as the conductive element. In conjunction with the ease of device fabrication and device stability, this feature distinguishes GMG-SMJs as a new testbed platform for single-molecule analysis characterized by high temporal resolution and superior signal-to-noise ratios. By exploiting the DLL method, we have fabricated molecular devices that are sensitive to external stimuli and are capable of transducing chemical/biochemical events into electrical signals at the single-molecule level, with notable examples including host-guest interaction, hydrogen bond dynamics, DNA intercalation, photoinduced conformational transition, carbocation formation, nucleophilic addition, and stereoelectronic effect. In addition to GMG-SMJs and considering compatibility with the silicon-based industry, we have also developed a reliable method of point-functionalizing silicon-nanowire-based nanotransistors to afford single-molecule electrical nanocircuits. This approach proved to be a robust platform for single-molecule electrical analysis capable of probing fast dynamic processes such as single-protein detection, DNA hybridization/polymorphism, and motor rotation dynamics. The above systematic investigations emphasize the importance and unique advantages of universal single-molecule electrical approaches for realizing direct, label-free, real-time electrical measurements of reaction dynamics with single-event sensitivity. These approaches promise a fascinating mainstream platform to explore the dynamics of stochastic processes in chemical/biological systems as well as gain information in fields ranging from reaction chemistry for elucidating the intrinsic mechanisms to genomics or proteomics for accurate molecular and even point-of-care clinical diagnoses.

Large amplitude charge noise and random telegraph fluctuations in room-temperature graphene single-electron transistors

We analyze the noise in liquid-gated, room temperature, graphene quantum dots. These devices display extremely large noise amplitudes. The observed noise is explained in terms of a charge noise model by considering fluctuations in the applied source-drain and gate potentials. We show that the liquid environment and substrate have little effect on the observed noise and as such attribute the noise to charge trapping/detrapping at the disordered graphene edges. The trapping/detrapping of individual charges can be tuned by gating the device, which can result in stable two-level fluctuations in the measured current. These results have important implications for the use of electronic graphene nanodevices in single-molecule biosensing.

Tg Confinement Effect of Random Copolymers of 4-tert-Butylstyrene and 4-Acetoxystyrene with Different Compositions

We observe that the T_g confinement effect of polymer films can saturate with polymer-substrate interaction. Thickness dependences of the glass transition temperature, T_g(h₀), of random copolymer films of 4-tert-butylstyrene (TBS) and 4-acetoxystyrene (AS) supported by silica (SiOx) were measured for different TBS concentrations, X_TBS. For 0 ≤ X_TBS ≤ 0.47, T_g(h₀) displays identical enhancements, independent of X_TBS. For X_TBS > ∼0.66; however, T_g(h₀) decreases steadily with X_TBS. The X_TBS > 0.66 result is in keeping with expectations that TBS interacts less strongly with SiOx than AS does, and weaker polymer-substrate interaction renders greater dominance of the air surface over substrate surface on T_g, and thereby T_g reduction. We propose that saturation in T_g(h₀) found for X_TBS ≤ 0.47 is caused by the maximization in polymer-substrate-specific bond formation. Further experiments and a calculation support this proposition.

Modulating and probing the dynamic intermolecular interactions in plasmonic molecule-pair junctions

The intermolecular interactions, including hydrogen bonds, are electromechanically modulated and probed in metal–molecule pair–metal junctions.

Probing Lewis acid-base interactions in single-molecule junctions

A novel strategy to regulate the tunneling mechanism for charge transport through an organoborane wire via Lewis acid-base interactions has been developed. A change from LUMO- to HOMO-dominated charge transport upon the addition of the fluoride is verified both experimentally and theoretically.

Low-Frequency Noise in Graphene Tunnel Junctions

Graphene tunnel junctions are a promising experimental platform for single molecule electronics and biosensing. Ultimately their noise properties will play a critical role in developing these applications. Here we report a study of electrical noise in graphene tunnel junctions fabricated through feedback-controlled electroburning. We observe random telegraph signals characterized by a Lorentzian noise spectrum at cryogenic temperatures (77 K) and a 1/ f noise spectrum at room temperature. To gain insight into the origin of these noise features, we introduce a theoretical model that couples a quantum mechanical tunnel barrier to one or more classical fluctuators. The fluctuators are identified as charge traps in the underlying dielectric, which through random fluctuations in their occupation introduce time-dependent modulations in the electrostatic environment that shift the potential barrier of the junction. Analysis of the experimental results and the tight-binding model indicate that the random trap occupation is governed by Poisson statistics. In the 35 devices measured at room temperature, we observe a 20-60% time-dependent variance of the current, which can be attributed to a relative potential barrier shift of between 6% and 10%. In 10 devices measured at 77 K, we observe a 10% time-dependent variance of the current, which can be attributed to a relative potential barrier shift of between 3% and 4%. Our measurements reveal a high sensitivity of the graphene tunnel junctions to their local electrostatic environment, with observable features of intertrap Coulomb interactions in the distribution of current switching amplitudes.