Tunnel conductance of Watson-Crick nucleoside-base pairs from telegraph noise

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.

Chemical Sensors using Single-Molecule Electrical Measurements

Driven by the digitization and informatization of contemporary society, electrical sensors are developing toward minimal structure, intelligent function, and high detection resolution. Single-molecule electrical measurement techniques have been proven to be capable of label-free molecular recognition and detection, which opens a new strategy for the design of efficient single-molecule detection sensors. In this review, we outline the main advances and potentials of single-molecule electronics for qualitative identification and recognition assays at the single-molecule level. Strategies for single-molecule electro-sensing and its main applications are reviewed, mainly in the detection of ions, small molecules, oligomers, genetic materials, and proteins. This review summarizes the remaining challenges in the current development of single-molecule electrical sensing and presents some potential perspectives for this field.

Intermolecular and Electrode-Molecule Bonding in a Single Dimer Junction of Naphthalenethiol as Revealed by Surface-Enhanced Raman Scattering Combined with Transport Measurements

Electron transport through noncovalent interaction is of fundamental and practical importance in nanomaterials and nanodevices. Recent single-molecule studies employing single-molecule junctions have revealed unique electron transport properties through noncovalent interactions, especially those through a π-π interaction. However, the relationship between the junction structure and electron transport remains elusive due to the insufficient knowledge of geometric structures. In this article, we employ surface-enhanced Raman scattering (SERS) synchronized with current-voltage (I-V) measurements to characterize the junction structure, together with the transport properties, of a single dimer and monomer junction of naphthalenethiol, the former of which was formed by the intermolecular π-π interaction. The correlation analysis of the vibrational energy and electrical conductance enables identifying the intermolecular and molecule-electrode interactions in these molecular junctions and, consequently, addressing the transport properties exclusively associated with the π-π interaction. In addition, the analysis achieved discrimination of the interaction between the NT molecule and the Au electrode of the junction, i.e., Au-π interactions through-π coupling and though-space coupling. The power density spectra support the noncovalent character at the interfaces in the molecular junctions. These results demonstrate that the simultaneous SERS and I-V technique provides a unique means for the structural and electrical investigation of noncovalent interactions.

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.

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.

Selective Anchoring Groups for Molecular Electronic Junctions with ITO Electrodes

Indium tin oxide (ITO) is an attractive substrate for single-molecule electronics since it is transparent while maintaining electrical conductivity. Although it has been used before as a contacting electrode in single-molecule electrical studies, these studies have been limited to the use of carboxylic acid terminal groups for binding molecular wires to the ITO substrates. There is thus the need to investigate other anchoring groups with potential for binding effectively to ITO. With this aim, we have investigated the single-molecule conductance of a series of eight tolane or "tolane-like" molecular wires with a variety of surface binding groups. We first used gold-molecule-gold junctions to identify promising targets for ITO selectivity. We then assessed the propensity and selectivity of carboxylic acid, cyanoacrylic acid, and pyridinium-squarate to bind to ITO and promote the formation of molecular heterojunctions. We found that pyridinium squarate zwitterions display excellent selectivity for binding to ITO over gold surfaces, with contact resistivity comparable to that of carboxylic acids. These single-molecule experiments are complemented by surface chemical characterization with X-ray photoelectron spectroscopy, quartz crystal microbalance, contact angle determination, and nanolithography using an atomic force miscroscope. Finally, we report the first density-functional theory calculations involving ITO electrodes to model charge transport through ITO-molecule-gold heterojunctions.

Observing Host-Guest Interactions at Molecular Interfaces by Monitoring the Electrochemical Current

Macrocyclic cucurbit[n]uril (CB[n]) molecules have triggered renewed interest because of their outstanding capabilities as host molecules to selectively interact with a wide range of small guest molecules. Here, CB[7]-based host-guest interactions were investigated for a guest-modified nanoelectrode by monitoring the electrochemical current. A ferrocene (Fc)-terminated molecule immobilized on a gold nanoelectrode (GNE) showed suitable affinity with CB[7] when the effective exposing area of the GNE was between 5.3 and 12 μm² and the bias applied on the GNE was -500 mV. Monitoring the dynamics of nanoparticles (NPs) on a nanoelectrode provides new insights into the host-guest interactions at molecular interfaces.

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.

Nanopipettes: a potential tool for DNA detection

As the information in DNA is of practical value for clinical diagnosis, it is important to develop efficient and rapid methods for DNA detection. In the past decades, nanopores have been extensively explored for DNA detection due to their low cost and high efficiency. As a sub-group of the solid-state nanopore, nanopipettes exhibit great potential for DNA detection which is ascribed to their stability, ease of fabrication and good compatibility with other technologies, compared with biological and traditional solid-state nanopores. Herein, the review systematically summarizes the recent progress in DNA detection with nanopipettes and highlights those studies dedicated to improve the performance of DNA detection using nanopipettes through different approaches, including reducing the rate of DNA translocation, improving the spatial resolution of sensing nanopipettes, and controlling DNA molecules through novel techniques. Besides, some new perspectives of the integration of nanopipettes with other technologies are reviewed.

Monitoring the Dynamic Process of Formation of Plasmonic Molecular Junctions during Single Nanoparticle Collisions

The capability to study the dynamic formation of plasmonic molecular junction is of fundamental importance, and it will provide new insights into molecular electronics/plasmonics, single-entity electrochemistry, and nanooptoelectronics. Here, a facile method to form plasmonic molecular junctions is reported by utilizing single gold nanoparticle (NP) collision events at a highly curved gold nanoelectrode modified with a self-assembled monolayer. By using time-resolved electrochemical current measurement and surface-enhanced Raman scattering spectroscopy, the current changes and the evolution of interfacial chemical bonding are successfully observed in the newly formed molecular tunnel junctions during and after the gold NP "hit-n-stay" and "hit-n-run" collision events. The results lead to an in-depth understanding of the single NP motion and the associated molecular level changes during the formation of the plasmonic molecular junctions in a single NP collision event. This method also provides a new platform to study molecular changes at the single molecule level during electron transport in a dynamic molecular tunnel junction.

Charge transport at a molecular GaAs nanoscale junction

The use of semiconducting electrodes in molecular junctions is an elegant way to impart new properties to nanodevices. Here we report metal-molecule(s)–metal Schottky photodiodes whose behaviour can be tuned by appropriate choice of molecule and doping density, giving further insights into the molecule–semiconductor interface.

Single-Molecule Transport at a Rectifying GaAs Contact

In most single- or few-molecule devices, the contact electrodes are simple ohmic resistors. Here we describe a new type of single-molecule device in which metal and semiconductor contact electrodes impart a function, namely, current rectification, which is then modified by a molecule bridging the gap. We study junctions with the structure Au STM tip/X/n-GaAs substrate, where "X" is either a simple alkanedithiol or a conjugated unit bearing thiol/methylthiol contacts, and we detect current jumps corresponding to the attachment and detachment of single molecules. From the magnitudes of the current jumps we can deduce values for the conductance decay constant with molecule length that agree well with values determined from Au/molecule/Au junctions. The ability to impart functionality to a single-molecule device through the properties of the contacts as well as through the properties of the molecule represents a significant extension of the single-molecule electronics "tool-box".

Single-Molecule Electronics: Chemical and Analytical Perspectives

It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance.

Fabrication and characterization of nanopores with insulated transverse nanoelectrodes for DNA sensing in salt solution

We report on the fabrication, simulation, and characterization of insulated nanoelectrodes aligned with nanopores in low-capacitance silicon nitride membrane chips. We are exploring these devices for the transverse sensing of DNA molecules as they are electrophoretically driven through the nanopore in a linear fashion. While we are currently working with relatively large nanopores (6-12 nm in diameter) to demonstrate the transverse detection of DNA, our ultimate goal is to reduce the size sufficiently to resolve individual nucleotide bases, thus sequencing DNA as it passes through the pore. We present simulations and experiments that study the impact of insulating these electrodes, which is important to localize the sensing region. We test whether the presence of nanoelectrodes or insulation affects the stability of the ionic current flowing through the nanopore, or the characteristics of DNA translocation. Finally, we summarize the common device failures and challenges encountered during fabrication and experiments, explore the causes of these failures, and make suggestions on how to overcome them in the future.

Chemical recognition and binding kinetics in a functionalized tunnel junction

4(5)-(2-mercaptoethyl)-1H-imidazole-2-carboxamide is a molecule that has multiple hydrogen bonding sites and a short flexible linker. When tethered to a pair of electrodes, it traps target molecules in a tunnel junction. Surprisingly large recognition-tunneling signals are generated for all naturally occurring DNA bases A, C, G, T and 5-methyl-cytosine. Tunnel current spikes are stochastic and broadly distributed, but characteristic enough so that individual bases can be identified as a tunneling probe is scanned over DNA oligomers. Each base yields a recognizable burst of signal, the duration of which is controlled entirely by the probe speed, down to speeds of 1 nm s -1, implying a maximum off-rate of 3 s -1 for the recognition complex. The same measurements yield a lower bound on the on-rate of 1 M -1 s -1. Despite the stochastic nature of the signals, an optimized multiparameter fit allows base calling from a single signal peak with an accuracy that can exceed 80% when a single type of nucleotide is present in the junction, meaning that recognition-tunneling is capable of true single-molecule analysis. The accuracy increases to 95% when multiple spikes in a signal cluster are analyzed.

Electrochemical tunnelling sensors and their potential applications

The quantum-mechanical tunnelling effect allows charge transport across nanometre-scale gaps between conducting electrodes. Application of a voltage between these electrodes leads to a measurable tunnelling current, which is highly sensitive to the gap size, the voltage applied and the medium in the gap. Applied to liquid environments, this offers interesting prospects of using tunnelling currents as a sensitive tool to study fundamental interfacial processes, to probe chemical reactions at the single-molecule level and to analyse the composition of biopolymers such as DNA, RNA or proteins. This offers the possibility of a new class of sensor devices with unique capabilities.

Insulated gold scanning tunneling microscopy probes for recognition tunneling in an aqueous environment

Chemically functionalized probes are required for tunneling measurements made via chemical contacts ("Recognition Tunneling"). Here, we describe the etching of gold STM probes suitable for chemical functionalization with moieties bearing thiol groups. Insulated with high density polyethylene, these probes may be used in aqueous electrolytes with sub pA leakage currents. The area of the exposed probe surface was characterized via the saturation current in an electroactive solution (0.1 M K(3)Fe(CN)(6)). Twenty five percent of the probes had an exposed region of 10 nm radius or less.

Identifying diversity in nanoscale electrical break junctions

The realization of molecular-scale electronic devices will require the development of novel strategies for controlling electrical properties of metal/molecule/metal junctions, down to the single molecule level. Here, we show that it is possible to exert chemical control over the formation of metal/molecule...molecule/metal junctions in which the molecules interact by pi-stacking. The tip of an STM is used to form one contact, and the substrate the other; the molecules are conjugated oligophenyleneethynylenes (OPEs). Supramolecular pi-pi interactions allow current to flow through the junction, but not if bulky tert-butyl substituents on the phenyl rings prevent such interactions. For the first time, we find evidence that pi-stacked junctions can form even for OPEs with two thiol contacts. Furthermore, we find evidence for metal|molecule|metal junctions involving oligophenyleneethynylene monothiols, in which the second contact must be formed by the interaction of the pi-electrons of the terminal phenyl ring with the metal surface.

Recognition tunneling

Single molecules in a tunnel junction can now be interrogated reliably using chemically functionalized electrodes. Monitoring stochastic bonding fluctuations between a ligand bound to one electrode and its target bound to a second electrode ('tethered molecule-pair' configuration) gives insight into the nature of the intermolecular bonding at a single molecule-pair level, and defines the requirements for reproducible tunneling data. Simulations show that there is an instability in the tunnel gap at large currents, and this results in a multiplicity of contacts with a corresponding spread in the measured currents. At small currents (i.e. large gaps) the gap is stable, and functionalizing a pair of electrodes with recognition reagents (the 'free-analyte' configuration) can generate a distinct tunneling signal when an analyte molecule is trapped in the gap. This opens up a new interface between chemistry and electronics with immediate implications for rapid sequencing of single DNA molecules.

Nanopore Sequencing: Electrical Measurements of the Code of Life

Sequencing a single molecule of deoxyribonucleic acid (DNA) using a nanopore is a revolutionary concept because it combines the potential for long read lengths (>5 kbp) with high speed (1 bp/10 ns), while obviating the need for costly amplification procedures due to the exquisite single molecule sensitivity. The prospects for implementing this concept seem bright. The cost savings from the removal of required reagents, coupled with the speed of nanopore sequencing places the $1000 genome within grasp. However, challenges remain: high fidelity reads demand stringent control over both the molecular configuration in the pore and the translocation kinetics. The molecular configuration determines how the ions passing through the pore come into contact with the nucleotides, while the translocation kinetics affect the time interval in which the same nucleotides are held in the constriction as the data is acquired. Proteins like α-hemolysin and its mutants offer exquisitely precise self-assembled nanopores and have demonstrated the facility for discriminating individual nucleotides, but it is currently difficult to design protein structure ab initio, which frustrates tailoring a pore for sequencing genomic DNA. Nanopores in solid-state membranes have been proposed as an alternative because of the flexibility in fabrication and ease of integration into a sequencing platform. Preliminary results have shown that with careful control of the dimensions of the pore and the shape of the electric field, control of DNA translocation through the pore is possible. Furthermore, discrimination between different base pairs of DNA may be feasible. Thus, a nanopore promises inexpensive, reliable, high-throughput sequencing, which could thrust genomic science into personal medicine.