Self-Aligning Nanojunctions for Integrated Single-Molecule Circuits.

Robust, high-yield integration of nanoscale components such as graphene nanoribbons, nanoparticles, or single-molecules with conventional electronic circuits has proven to be challenging. This difficulty arises because the contacts to these nanoscale devices must be precisely fabricated with angstrom-level resolution to make reliable connections, and at manufacturing scales this cannot be achieved with even the highest-resolution lithographic tools. Here we introduce an approach that circumvents this issue by precisely creating nanometer-scale gaps between metallic carbon electrodes by using a self-aligning, solution-phase process, which allows facile integration with conventional electronic systems with yields approaching 50%. The electrode separation is controlled by covalently binding metallic single-walled carbon nanotube (mCNT) electrodes to individual DNA duplexes to create mCNT-DNA-mCNT nanojunctions, where the gap is precisely matched to the DNA length. These junctions are then integrated with top-down lithographic techniques to create single-molecule circuits that have electronic properties dominated by the DNA in the junction, have reproducible conductance values with low dispersion, and are stable and robust enough to be utilized as active, high-specificity electronic biosensors for dynamic single-molecule detection of specific oligonucleotides, such as those related to the SARS-CoV-2 genome. This scalable approach for high-yield integration of nanometer-scale devices will enable opportunities for manufacturing of hybrid electronic systems for a wide range of applications.

Mapping DNA Conformations Using Single-Molecule Conductance Measurements.

DNA is an attractive material for a range of applications in nanoscience and nanotechnology, and it has recently been demonstrated that the electronic properties of DNA are uniquely sensitive to its sequence and structure, opening new opportunities for the development of electronic DNA biosensors. In this report, we examine the origin of multiple conductance peaks that can occur during single-molecule break-junction (SMBJ)-based conductance measurements on DNA. We demonstrate that these peaks originate from the presence of multiple DNA conformations within the solutions, in particular, double-stranded B-form DNA (dsDNA) and G-quadruplex structures. Using a combination of circular dichroism (CD) spectroscopy, computational approaches, sequence and environmental controls, and single-molecule conductance measurements, we disentangle the conductance information and demonstrate that specific conductance values come from specific conformations of the DNA and that the occurrence of these peaks can be controlled by controlling the local environment. In addition, we demonstrate that conductance measurements are uniquely sensitive to identifying these conformations in solutions and that multiple configurations can be detected in solutions over an extremely large concentration range, opening new possibilities for examining low-probability DNA conformations in solutions.

Structure-Dependent Electrical Conductance of DNA Origami Nanowires.

Exploring the structural and electrical properties of DNA origami nanowires is an important endeavor for the advancement of DNA nanotechnology and DNA nanoelectronics. Highly conductive DNA origami nanowires are a desirable target for creating low-cost self-assembled nanoelectronic devices and circuits. In this work, the structure-dependent electrical conductance of DNA origami nanowires is investigated. A silicon nitride (Si3 N4 ) on silicon semiconductor chip with gold electrodes was used for collecting electrical conductance measurements of DNA origami nanowires, which are found to be an order of magnitude less electrically resistive on Si3 N4 substrates treated with a monolayer of hexamethyldisilazane (HMDS) (∼1013 ohms) than on native Si3 N4 substrates without HMDS (∼1014 ohms). Atomic force microscopy (AFM) measurements of the height of DNA origami nanowires on mica and Si3 N4 substrates reveal that DNA origami nanowires are ∼1.6 nm taller on HMDS-treated substrates than on the untreated ones indicating that the DNA origami nanowires undergo increased structural deformation when deposited onto untreated substrates, causing a decrease in electrical conductivity. This study highlights the importance of understanding and controlling the interface conditions that affect the structure of DNA and thereby affect the electrical conductance of DNA origami nanowires.

Review of Dielectrophoretic Manipulation of Micro and Nanomaterials: Fundamentals, Recent Developments, and Challenges.

This paper reviews the state-of-the-art methods of dielectrophoresis for micro- and nanomaterial manipulation. Dielectrophoresis is a well-known technique for material manipulation using a nonuniform electric field. This field can apply a force to dielectric materials and move them toward a predefined location. Controlling the pattern of the electric field and its intensity, achieved by a specific arrangement of electrodes or insulators, along with the dielectric properties of the materials allows a variety of manipulation functions including trapping, separation, and transportation. The development of microfabrication techniques has significantly improved the research quality in the field of dielectrophoresis for precisely manipulating micro and nanomaterials. Later, the advent of microfluidic devices provided an excellent platform for reliable and practical devices. Modifying the shape, geometry, and material of the electrodes, isolating the electrodes from the sample, incorporating a particular arrangement of insulators within the electric field, and monitoring the operation in situ are some of the methods utilized for overcoming common problems in dielectrophoretic devices or the problems associated with a specific sample and the manipulation function. The goal of the research in this field is to design practical, high throughput, and inexpensive devices that reliably manipulate micro and nanomaterials. Accordingly, this review aims to represent latest findings and advancements in the field of dielectrophoresis. In particular, the working principles, technical implementation details, current status, and the issues and challenges of dielectrophoretic devices for electrode-based and insulator-based dielectrophoresis in terms of operation and fabrication are discussed.

Molecular quantum interference effects on thermopower in hybrid 2-dimensional monolayers.

Quantum interference effects in single-molecule devices can significantly enhance the thermoelectric properties of these devices. However, single-molecule systems have limited utility for power conversion. In this work, we study the effects of destructive quantum interference in molecular junctions on the thermoelectric properties of hybrid, 2-dimensional molecule-nanoparticle monolayers. We study two isomers of benzenedithiol molecules, with either a para or meta configuration for the thiol groups, as molecular interlinkers between gold nanoparticles in the structure. The asymmetrical structure in the meta configuration significantly improves the Seebeck coefficient and power factor over the para configuration. These results suggest that thermoelectric performance of engineered, nanostructured material can be enhanced by harnessing quantum interference effects in the substituent components.

A Chirality-Based Quantum Leap.

There is increasing interest in the study of chiral degrees of freedom occurring in matter and in electromagnetic fields. Opportunities in quantum sciences will likely exploit two main areas that are the focus of this Review: (1) recent observations of the chiral-induced spin selectivity (CISS) effect in chiral molecules and engineered nanomaterials and (2) rapidly evolving nanophotonic strategies designed to amplify chiral light-matter interactions. On the one hand, the CISS effect underpins the observation that charge transport through nanoscopic chiral structures favors a particular electronic spin orientation, resulting in large room-temperature spin polarizations. Observations of the CISS effect suggest opportunities for spin control and for the design and fabrication of room-temperature quantum devices from the bottom up, with atomic-scale precision and molecular modularity. On the other hand, chiral-optical effects that depend on both spin- and orbital-angular momentum of photons could offer key advantages in all-optical and quantum information technologies. In particular, amplification of these chiral light-matter interactions using rationally designed plasmonic and dielectric nanomaterials provide approaches to manipulate light intensity, polarization, and phase in confined nanoscale geometries. Any technology that relies on optimal charge transport, or optical control and readout, including quantum devices for logic, sensing, and storage, may benefit from chiral quantum properties. These properties can be theoretically and experimentally investigated from a quantum information perspective, which has not yet been fully developed. There are uncharted implications for the quantum sciences once chiral couplings can be engineered to control the storage, transduction, and manipulation of quantum information. This forward-looking Review provides a survey of the experimental and theoretical fundamentals of chiral-influenced quantum effects and presents a vision for their possible future roles in enabling room-temperature quantum technologies.

Gold Nanoparticle Synthesis.

Gold nanoparticles (Au nanoparticles) that are ~12 nm in diameter were synthesized by rapidly injecting a solution of 150 mg (0.15 mmol) of tetrachloroauric acid in 3.0 g (3.7 mmol, 3.6 mL) of oleylamine (technical grade) and 3.0 mL of toluene into a boiling solution of 5.1 g (6.4 mmol, 8.7 mL) of oleylamine in 147 mL of toluene. While boiling and mixing the reaction solution for 2 hours, the color of the reaction mixture changed from clear, to light yellow, to light pink, and then slowly to dark red. The heat was then turned off, and the solution was allowed to gradually cool down to room temperature for 1 hour. The gold nanoparticles were then collected and separated from the solution using a centrifuge and washed three times; by vortexing and dispersing the gold nanoparticles in 10 mL portions of toluene, and then precipitating the gold nanoparticles by adding 40 mL portions of methanol and spinning them in a centrifuge. The solution was then decanted to remove any remaining byproducts and unreacted starting materials. Drying the gold nanoparticles in a vacuum environment produced a solid black pellet; which could be stored for long periods of time (up to one year) for later use, and then redissolved in organic solvents such as toluene.

A machine learning approach for accurate and real-time DNA sequence identification.

BACKGROUND: The all-electronic Single Molecule Break Junction (SMBJ) method is an emerging alternative to traditional polymerase chain reaction (PCR) techniques for genetic sequencing and identification. Existing work indicates that the current spectra recorded from SMBJ experimentations contain unique signatures to identify known sequences from a dataset. However, the spectra are typically extremely noisy due to the stochastic and complex interactions between the substrate, sample, environment, and the measuring system, necessitating hundreds or thousands of experimentations to obtain reliable and accurate results. RESULTS: This article presents a DNA sequence identification system based on the current spectra of ten short strand sequences, including a pair that differs by a single mismatch. By employing a gradient boosted tree classifier model trained on conductance histograms, we demonstrate that extremely high accuracy, ranging from approximately 96 % for molecules differing by a single mismatch to 99.5 % otherwise, is possible. Further, such accuracy metrics are achievable in near real-time with just twenty or thirty SMBJ measurements instead of hundreds or thousands. We also demonstrate that a tandem classifier architecture, where the first stage is a multiclass classifier and the second stage is a binary classifier, can be employed to boost the single mismatched pair's identification accuracy to 99.5 %. CONCLUSIONS: A monolithic classifier, or more generally, a multistage classifier with model specific parameters that depend on experimental current spectra can be used to successfully identify DNA strands.

Role of intercalation in the electrical properties of nucleic acids for use in molecular electronics.

Intercalating ds-DNA/RNA with small molecules can play an essential role in controlling the electron transmission probability for molecular electronics applications such as biosensors, single-molecule transistors, and data storage. However, its applications are limited due to a lack of understanding of the nature of intercalation and electron transport mechanisms. We addressed this long-standing problem by studying the effect of intercalation on both the molecular structure and charge transport along the nucleic acids using molecular dynamics simulations and first-principles calculations coupled with the Green's function method, respectively. The study on anthraquinone and anthraquinone-neomycin conjugate intercalation into short nucleic acids reveals some universal features: (1) the intercalation affects the transmission by two mechanisms: (a) inducing energy levels within the bandgap and (b) shifting the location of the Fermi energy with respect to the molecular orbitals of the nucleic acid, (2) the effect of intercalation was found to be dependent on the redox state of the intercalator: while oxidized anthraquinone decreases, reduced anthraquinone increases the conductance, and (3) the sequence of the intercalated nucleic acid further affects the transmission: lowering the AT-region length was found to enhance the electronic coupling of the intercalator with GC bases, hence yielding an increase of more than four times in conductance. We anticipate our study to inspire designing intercalator-nucleic acid complexes for potential use in molecular electronics via creating a multi-level gating effect.

Multidimensional Characterization of Single-Molecule Dynamics in a Plasmonic Nanocavity.

Nanoscale manipulation and characterization of individual molecules is necessary to understand the intricacies of molecular structure, which governs phenomena such as reaction mechanisms, catalysis, local effective temperatures, surface interactions, and charge transport. Here we utilize Raman enhancement between two nanostructured electrodes in combination with direct charge transport measurements to allow for simultaneous characterization of the electrical, optical, and mechanical properties of a single molecule. This multi-dimensional information yields repeatable, self-consistent, verification of single-molecule resolution, and allows for detailed analysis of structural and configurational changes of the molecule in situ. These experimental results are supported by a machine-learning based statistical analysis of the spectral information and calculations to provide insight into the correlation between structural changes in a single-molecule and its charge-transport properties.

Temperature-Dependent Tunneling in Furan Oligomer Single-Molecule Junctions.

Two commonly observed charge transport mechanisms in single-molecule junctions are coherent tunneling and incoherent hopping. It has been generally believed that tunneling processes yield temperature-independent conductance behavior and hopping processes exhibit increasing conductance with increasing temperature. However, it has recently been proposed that tunneling can also yield temperature-dependent transport due to the thermal broadening of the Fermi energy of the contacts. In this work, we examine a series of rigid, planar furan oligomers that are free from a rotational internal degree of freedom to examine the temperature dependence of tunneling transport directly over a wide temperature range (78-300 K). Our results demonstrate conductance transition from a temperature-independent regime to a temperature-dependent regime. By examining various hopping and tunneling models and the correlation between the temperature dependence of conductance and molecular orbital energy offset from the Fermi level, we conclude thermally assisted tunneling is the dominant cause for the onset of temperature-dependent conductance in these systems.

Conductance and configuration of molecular gold-water-gold junctions under electric fields.

Water molecules can mediate charge transfer in biological and chemical reactions by forming electronic coupling pathways. Understanding the mechanism requires a molecular-level electrical characterization of water. Here, we describe the measurement of single water molecular conductance at room temperature, characterize the structure of water molecules using infrared spectroscopy, and perform theoretical studies to assist in the interpretation of the experimental data. The study reveals two distinct states of water, corresponding to a parallel and perpendicular orientation of the molecules. Water molecules switch from parallel to perpendicular orientations on applying an electric field, producing switching from high to low conductance states, thus enabling the determination of single water molecular dipole moments. The work further shows that water-water interactions affect the atomic scale configuration and conductance of water molecules. These findings demonstrate the importance of the discrete nature of water molecules in electron transfer and set limits on water-mediated electron transfer rates.

Moving Electrons Purposefully through Single Molecules and Nanostructures: A Tribute to the Science of Professor Nongjian Tao (1963-2020).

Electrochemistry intersected nanoscience 25 years ago when it became possible to control the flow of electrons through single molecules and nanostructures. Many surprises and a wealth of understanding were generated by these experiments. Professor Nongjian Tao was among the pioneering scientists who created the methods and technologies for advancing this new frontier. Achieving a deeper understanding of charge transport in molecules and low-dimensional materials was the first priority of his experiments, but he also succeeded in discovering applications in chemical sensing and biosensing for these novel nanoscopic systems. In parallel with this work, the investigation of a range of phenomena using novel optical microscopic methods was a passion of his and his students. This article is a review and an appreciation of some of his many contributions with a view to the future.

A Memristive Element Based on an Electrically Controlled Single-Molecule Reaction.

The exponential proliferation of data during the information age has required the continuous exploration of novel storage paradigms, materials, and devices with increasing data density. As a step toward the ultimate limits in data density, the development of an electrically controllable single-molecule memristive element is reported. In this device, digital information is encoded through switching between two isomer states by applying a voltage signal to the molecular junction, and the information is read out by monitoring the electrical conductance of each isomer. The two states are cycled using an electrically controllable local-heating mechanism for the forward reaction and catalyzed by a single charge-transfer process for the reverse switching. This single-molecule device can be modulated in situ, is fully reversible, and does not display stochastic switching. The I-V curves of this single-molecule system also exhibit memristive character. These features suggest a new approach for the development of molecular switching systems and storage-class memories.

Highly uniform monolayer graphene synthesis via a facile pretreatment of copper catalyst substrates using an ammonium persulfate solution.

The demand for large-area, high-quality synthesis of graphene with chemical vapor deposition (CVD) has increased for the realization of next-generation transparent and flexible optoelectronic applications. In conventional CVD processes, various synthesis parameters can strongly affect the quality of the resultant graphene. In particular, surface engineering of a copper catalyst substrate is one of the most promising pathways for achieving high-quality graphene with excellent reproducibility. For this purpose, simple wet chemical etching of a catalyst substrate without toxic fume byproducts or metal ion residues is desired. Here, we suggest a facile method for preparing a pretreated copper catalyst substrate for highly uniform, large-area CVD graphene growth. This pretreatment method involves a wet copper etchant, ammonium persulfate (APS) solution, and gentle ultrasonication (100 W), which do not produce unwanted or toxic fume byproducts during their reaction. Moreover, this approach does not leave metal ion residue on the cleaned copper substrates that serves as residual nucleation sites and leads to multilayer graphene growth. To evaluate the quality of the synthesized monolayer graphene on the cleaned copper catalyst substrates, we used various characterization techniques, such as Raman spectroscopy and sheet resistance, optical transmittance, and FET characterization.

Potential Dependence of Mechanical Stability and Electronic Coupling of Single S-Au Bonds.

Providing a mechanically stable and electronically efficient coupling between a molecule and an electrode is critical to the study of charge transfer and conductance of the molecule. A common method is to link the molecule to Au electrodes via a linker (e.g., thiol terminal of the molecule). Here we study the mechanical stability and electronic coupling of a S-Au bond in single-molecule junctions over a broad range of electrode potentials. Our results show that the mechanical and electromechanical properties of molecule-electrode contact undergo a systematic change with the potential involving Au oxidation at positive potentials and S protonation at negative potentials. The study establishes the potential range for a stable S-Au bond and determines the potential dependence of the mechanical and electromechanical properties of the molecule-electrode contact, which is crucial to the interpretation of potential-dependent charge transfer in electrochemistry and electrochemical gating of charge transport in molecular electronics.

Detection and identification of genetic material via single-molecule conductance.

The ongoing discoveries of RNA modalities (for example, non-coding, micro and enhancer) have resulted in an increased desire for detecting, sequencing and identifying RNA segments for applications in food safety, water and environmental protection, plant and animal pathology, clinical diagnosis and research, and bio-security. Here, we demonstrate that single-molecule conductance techniques can be used to extract biologically relevant information from short RNA oligonucleotides, that these measurements are sensitive to attomolar target concentrations, that they are capable of being multiplexed, and that they can detect targets of interest in the presence of other, possibly interfering, RNA sequences. We also demonstrate that the charge transport properties of RNA:DNA hybrids are sensitive to single-nucleotide polymorphisms, thus enabling differentiation between specific serotypes of Escherichia coli. Using a combination of spectroscopic and computational approaches, we determine that the conductance sensitivity primarily arises from the effects that the mutations have on the conformational structure of the molecules, rather than from the direct chemical substitutions. We believe that this approach can be further developed to make an electrically based sensor for diagnostic purposes.

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

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