Determination of Ag[I] and NADH Using Single-Molecule Conductance Ratiometric Probes

Frontiers in Single-Molecule Junction Detection: A Review of Recent Innovations and Breakthroughs

Single-molecule junction techniques offer powerful tools for studying physical and chemical properties at the single-molecule level, while enabling groundbreaking advances in ultrasensitive sensing. This review encapsulates the latest progress made in tracking chemical reactions and intermolecular interactions by employing single-molecule junction techniques. Additionally, we explore their practical applications in detection and sensing of trace chemical substances and biomolecules. Single-molecule electrical measurements, such as mechanically controllable break junctions (MCBJs), scanning tunneling microscopy break junctions (STM-BJs), and graphene-molecule-graphene single-molecule junctions (GMG-SMJ), exhibit exceptional sensitivity and resolution. These techniques allow for precise control and detection at the molecular scale, providing powerful tools for research across disciplines such as chemistry, biology, and physics while also driving new discoveries and advancements in related fields. Furthermore, we highlight the applications of single-molecule junction-based sensing techniques in identifying small molecules and ions in various media, thus contributing noteworthy insights into the design of ultrasensitive single-molecule sensors.

Interpretable Identification of Single-Molecule Charge Transport via Fusion Attention-Based Deep Learning

Interpretability is fundamental in the precise identification of single-molecule charge transport, and its absence in deep learning models is currently the major barrier to the usage of such powerful algorithms in the field. Here, we have pioneered a novel identification method employing fusion attention-based deep learning technologies. Central to our approach is the innovative neural network architecture, SingleFACNN, which integrates convolutional neural networks with a fusion of multihead self-attention and spatial attention mechanisms. Our findings demonstrate that SingleFACNN accurately classifies the three-type and four-type STM-BJ data sets, leveraging the convolutional layers' robust feature extraction and the attention layers' capacity to capture long-range interactions. Through comprehensive gradient-weighted class activation mapping and ablation studies, we identified and analyzed the critical features impacting classification outcomes with remarkable accuracy, thus enhancing the interpretability of our deep learning model. Furthermore, SingleFACNN's application was extended to mixed samples with varying proportions, achieving commendable prediction performance at low computational cost. Our study underscores the potential of SingleFACNN in advancing the interpretability and credibility of deep learning applications in single-molecule charge transport, opening new avenues for single-molecule detection in complex systems.

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

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

Insight of Employing Molecular Junctions for Sensor Applications

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

From Molecular Electronics to Molecular Intelligence

Molecular electronics is a field that explores the ultimate limits of electronic device dimensions by using individual molecules as operable electronic devices. Over the past five decades since the proposal of a molecular rectifier by Aviram and Ratner in 1974 ( Chem. Phys. Lett.1974,29, 277-283), researchers have developed various fabrication and characterization techniques to explore the electrical properties of molecules. With the push of electrical characterizations and data analysis methodologies, the reproducibility issues of the single-molecule conductance measurement have been chiefly resolved, and the origins of conductance variation among different devices have been investigated. Numerous prototypical molecular electronic devices with external physical and chemical stimuli have been demonstrated based on the advances of instrumental and methodological developments. These devices enable functions such as switching, logic computing, and synaptic-like computing. However, as the goal of molecular electronics, how can molecular-based intelligence be achieved through single-molecule electronic devices? At the fiftieth anniversary of molecular electronics, we try to answer this question by summarizing recent progress and providing an outlook on single-molecule electronics. First, we review the fabrication methodologies for molecular junctions, which provide the foundation of molecular electronics. Second, the preliminary efforts of molecular logic devices toward integration circuits are discussed for future potential intelligent applications. Third, some molecular devices with sensing applications through physical and chemical stimuli are introduced, demonstrating phenomena at a single-molecule scale beyond conventional macroscopic devices. From this perspective, we summarize the current challenges and outlook prospects by describing the concepts of "AI for single-molecule electronics" and "single-molecule electronics for AI".

Peptide-Based Electrical Array Sensor for Discriminating Heavy Metal Ions

Charge transport in molecular junctions provides an excellent way to investigate the response of molecules to intrinsic changes and external stimuli, exhibiting powerful potential for developing sensors. However, achieving multianalyte recognition remains a challenge. Herein, we innovatively developed an electrical array sensor based on peptide self-assembled layers for discriminating various heavy metal ions. Three peptide sequences were designed as sensing units with varying binding affinities for different metal ions. Electrical measurements demonstrated that different metal ions diversely affect the charge transport of peptide junctions. By using principal component analysis, a clear discrimination between the five kinds of heavy metal ions can be achieved. In the analysis of real samples, the array sensor showed a reliable anti-interference capability. The array sensor offers possibilities for large-area molecular junctions to construct functional molecular sensing devices.

Tuning charge transport by manipulating concentration dependent single-molecule absorption configurations

Understanding and tuning charge transport in molecular junctions is pivotal for crafting molecular devices with tailored functionalities. Here, we report a novel approach to manipulate the absorption configuration within a 4,4'-bipyridine (4,4'-BPY) molecular junction, utilizing the scanning tunneling microscope break junction technique in a concentration-dependent manner. Single-molecule conductance measurements demonstrate that the molecular junctions exhibit a significant concentration dependence, with a transition from high conductance (HC) to low conductance (LC) states as the concentration decreases. Moreover, we identified an additional conductance state in the molecular junctions besides already known HC and LC states. Flicker noise analysis and theoretical calculations provided valuable insights into the underlying charge transport mechanisms and single-molecule absorption configurations concerning varying concentrations. These findings contribute to a fundamental comprehension of charge transport in concentration-dependent molecular junctions. Furthermore, they offer promising prospects for controlling single-molecule adsorption configurations, thereby paving the way for future molecular devices.

Supramolecular Radical Electronics

Supramolecular radical chemistry is an emerging area bridging supramolecular chemistry and radical chemistry, and the integration of radicals into the supramolecular architecture offers a new dimension for tuning their structures and functions. Although various efforts have been devoted to the fabrication of supramolecular junctions, the charge transport characterization through the supramolecular radicals remained unexplored due to the challenges in creating supramolecular radicals at the single-molecule level. Here, we demonstrate the fabrication and charge transport investigation of a supramolecular radical junction using the electrochemical scanning tunneling microscope-based break junction (EC-STM-BJ) technique. We found that the conductance of a supramolecular radical junction was more than 1 order of magnitude higher than that of a supramolecular junction without a radical and even higher than that of a fully conjugated oligophenylenediamine molecule with a similar length. The combined experimental and theoretical investigations revealed that the radical increased the binding energy and decreased the energy gap in the supramolecular radical junction, which leads to the near-resonant transport through the supramolecular radical. Our work demonstrated that the supramolecular radical can provide not only strong binding but also efficient electrical coupling between building blocks, which provides new insights into supramolecular radical chemistry and new materials with supramolecular radicals.

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.

Direct biomolecule discrimination in mixed samples using nanogap-based single-molecule electrical measurement

In single-molecule measurements, metal nanogap electrodes directly measure the current of a single molecule. This technique has been actively investigated as a new detection method for a variety of samples. Machine learning has been applied to analyze signals derived from single molecules to improve the identification accuracy. However, conventional identification methods have drawbacks, such as the requirement of data to be measured for each target molecule and the electronic structure variation of the nanogap electrode. In this study, we report a technique for identifying molecules based on single-molecule measurement data measured only in mixed sample solutions. Compared with conventional methods that require training classifiers on measurement data from individual samples, our proposed method successfully predicts the mixing ratio from the measurement data in mixed solutions. This demonstrates the possibility of identifying single molecules using only data from mixed solutions, without prior training. This method is anticipated to be particularly useful for the analysis of biological samples in which chemical separation methods are not applicable, thereby increasing the potential for single-molecule measurements to be widely adopted as an analytical technique.

Synthesis of a quinoxaline-hydrazinobenzothiazole based probe-single point detection of Cu2+, Co2+, Ni2+ and Hg2+ ions in real water samples

A novel quinoxaline-hydrazinobenzothiazole based sensor was synthesized and characterized using NMR, FTIR, and Mass spectroscopy techniques. The sensor achieves the distinct "single-point" colorimetric and fluorescent detection of Cu²⁺, Co²⁺, Ni²⁺ and Hg²⁺ ions with distinguishable color changes from yellow to red, pale red, pale brown and orange, respectively. The UV-visible and fluorescence emission spectral investigation revealed the excellent single-point sensing ability of the probe towards four different heavy metal ions with a ratiometric response. Nanomolar levels of detection of about 1.16 × 10^-7 M, 9.92 × 10^-8 M, 8.21 × 10^-8 M, and 1.14 × 10^-7 M for Cu²⁺, Co²⁺, Ni²⁺ and Hg²⁺ ions, respectively, were achieved using our sensor, which are below the US-EPA permissible limits. Additionally, the sensor was utilized for naked eye detection under normal daylight. Quantitative determination of the metal ions in real water samples was also demonstrated.

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.

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.

Fluorescence-Responsive Detection of Ag(I), Al(III), and Cr(III) Ions Using Cd(II) Based Pillared-Layer Frameworks

Two Cd(II) based coordination polymers, {Cd₃(btc)₂(BTD-bpy)₂]∙1.5MeOH∙4H₂O}_n (1) and [Cd₂(1,4-ndc)₂(BTD-bpy)₂]_n (2), where BTD-bpy = bis(pyridin-4-yl)benzothiadiazole, btc = benzene-1,3,5-tricarboxylate, and 1,4-ndc = naphthalene-1,4-dicarboxylate, were hydro(solvo)thermally synthesized. Compound 1 has a three-dimensional non-interpenetrating pillared-bilayer open framework with sufficient free voids of 25.1%, which is simplified to show a topological (4,6,8)-connected net with the point symbol of (3²4²56)(3⁴4⁴5⁴6²8)(3⁴4²6¹⁹7²8). Compound 2 has a three-dimensional two-fold interpenetrating bipillared-layer condense framework regarded as a 6-connected primitive cubic (pcu) net topology. Compounds 1 and 2 both exhibited good water stability and high thermal stability approaching 350 °C. Upon excitation, compounds 1 and 2 both emitted blue light fluorescence at 471 and 479 nm, respectively, in solid state and at 457 and 446 nm, respectively, in the suspension phase of H₂O. Moreover, compounds 1 and 2 in the suspension phase of H₂O both exhibited a fluorescence quenching effect in sensing Ag⁺, attributed to framework collapse, and a fluorescence enhancement response in sensing Al³⁺ and Cr³⁺, ascribed to weak ion-framework interactions, with high selectivity and sensitivity and low detection limit.

Novel electrochemical and electrochemiluminescence dual-modality sensing platform for sensitive determination of antimicrobial peptides based on probe encapsulated liposome and nanochannel array electrode

With the increasing application of antimicrobial peptides (AMPs) to replace antibiotics in medicine, food and agriculture, it is highly desired to develop a fast, reliable, and convenient strategy for sensitive detection of AMPs. Herein, a novel electrochemical (EC) and electrochemiluminescence (ECL) dual-modality sensing platform was developed based on probe encapsulated liposomes and nanochannel array modified electrodes, which enables sensitive determination of nisin in food samples. The bifunctional probe with both EC and ECL signals, tris(2,2-bipyridyl) dichlororuthenium (II) (Ru(bpy)₃²⁺), was chosen to be easily encapsulated in liposomes (Ru(bpy)₃²⁺@liposome). Based on the unique sterilization mechanism that AMPs can disrupt cell membranes, Ru(bpy)₃²⁺@liposome can be destroyed by nisin and release a large number of Ru(bpy)₃²⁺ probes. Vertically-ordered mesoporous silica-nanochannel film (VMSF) modified ITO electrodes (VMSF/ITO) prepared by electrochemically assisted self-assembly (EASA) method were applied as the sensing electrode. Due to the efficient enrichment of Ru(bpy)₃²⁺ by the negatively charged nanochannel arrays, VMSF/ITO enables detection of the EC/ECL signals of the released Ru(bpy)₃²⁺ probes with ultrahigh sensitivity. In consequence, sensitive dual-modality detection of nisin was achieved by the combination of Ru(bpy)₃²⁺@liposome and VMSF/ITO. The developed sensing system can realize sensitive determination of nisin in ECL mode in the concentration range of 10 ng/ml to 50 μg/ml with a limit of detection (LOD) of 9.3 ng/ml, or in EC mode from 800 ng/ml to 100 μg/ml with a LOD of 70 ng/ml. Combined with the excellent anti-fouling and anti-interference performance of VMSF, rapid and sensitive detection of nisin in milk or egg white was also achieved by the sensor.

Single-Molecule Tunneling Sensors for Nitrobenzene Explosives

The tunneling current through the single-molecule junctions principally offers the ultimate solution for chemical and biochemical sensing via the interactions between probes and target analytes at the single-molecule level. However, it remains unexplored to achieve the sensitive and selective detection of targeted analytes using single-molecule junction techniques due to the challenge in quantitative evaluation of sensing sensitivity and selectivity. Herein, we demonstrate a single-molecule tunneling sensor for the highly sensitive and selective detection of nitrobenzene explosives using scanning tunneling microscope break junction (STM-BJ). Taking advantage of π-π stacking interactions between the molecular probes and nitrobenzene explosives, we use a spectral clustering algorithm to assign the signal of probes and π-stacked probes for sensitively detecting the targeted analytes and the distinguishable conductance change of probes when interacting with different nitroaromatic explosive compounds for selective detection. We find that pronounced conductance changes up to 0.8 orders of magnitude when the probes interact with TNT. Also, we obtain a sensitivity of up to ∼10 pM for TNT and high sensitivity for eight TNT analogues. Combined with theoretical calculations, we discover that the harness of the destructive quantum interference of the probe M1OH after interacting with TNT leads to high selectivity in sensing with TNT. Our work demonstrates the great potential of the single-molecule tunneling current for environmental sensing molecules with high selectivity and sensitivity.

Recent Advances in Single-Molecule Sensors Based on STM Break Junction Measurements

Single-molecule recognition and detection with the highest resolution measurement has been one of the ultimate goals in science and engineering. Break junction techniques, originally developed to measure single-molecule conductance, recently have also been proven to have the capacity for the label-free exploration of single-molecule physics and chemistry, which paves a new way for single-molecule detection with high temporal resolution. In this review, we outline the primary advances and potential of the STM break junction technique for qualitative identification and quantitative detection at a single-molecule level. The principles of operation of these single-molecule electrical sensing mainly in three regimes, ion, environmental pH and genetic material detection, are summarized. It clearly proves that the single-molecule electrical measurements with break junction techniques show a promising perspective for designing a simple, label-free and nondestructive electrical sensor with ultrahigh sensitivity and excellent selectivity.

Nanosensors Based on Structural Memory Carbon Nanodots for Ag+ Fluorescence Determination

Ag⁺ pollution is of great harm to the human body and environmental biology. Therefore, there is an urgent need to develop inexpensive and accurate detection methods. Herein, lignin-derived structural memory carbon nanodots (C_SM-dots) with outstanding fluorescence properties were fabricated via a green method. The mild preparation process allowed the C_SM-dots to remain plentiful phenol, hydroxyl, and methoxy groups, which have a specific interaction with Ag⁺ through the reduction of silver ions. Further, the sulfur atoms doped on C_SM-dots provided more active sites on their surface and the strong interaction with Ag nanoparticles. The C_SM-dots can specifically bind Ag⁺, accompanied by a remarkable fluorescence quenching response. This “turn-off” fluorescence behavior was used for Ag⁺ determination in a linear range of 5–290 μM with the detection limit as low as 500 nM. Furthermore, findings showed that this sensing nano-platform was successfully used for Ag⁺ determination in real samples and intracellular imaging, showing great potential in biological and environmental monitoring applications.