Monitoring nanobubble nucleation at early-stage within a sub-9 nm solid-state nanopore

Nanobubble nucleation study is important for understanding the dynamic behavior of nanobubble growth, which is instructive for the nanobubble applications. Benefiting from nanopore fabrication, herein, we fabricated a sub-9 nm SiN_X nanopore with the comparable size to nanobubbles at early-stage. The confined nanopore interface serves as a generator for producing nanobubbles by the chemical reaction between NaBH₄ and H₂ O and as an ultra-sensitive sensor for monitoring the H₂ nanobubble nucleation process. By carrying out the NaBH₄ concentration-dependent experiments, we found the life-time of nanobubbles decreased 250 times and the frequency of nanobubble generation increased 38 times with the NaBH₄ concentration increasing from 6 to 100 mM. The long-time equilibrium between gas molecules inward flux and outward flux could prolong the life-time of nanobubbles to hundreds of milliseconds at low NaBH₄ concentration. The raw current trace depicted that the transient accumulation and dissolution of cavity occurred during all the life-time of nanobubbles. Therefore, the sub-9 nm SiN_X nanopore shows a strong ability for real-time monitoring the nanobubble nucleation at early-stage with high temporal and spatial resolution. This work provides a guide to study the dynamic and stochastic characteristics of nanobubbles.

Revealing the transient conformations of a single flavin adenine dinucleotide using an aerolysin nanopore

Flavin adenine dinucleotide (FAD) as a cofactor is involved in numerous important metabolic pathways where the biological function is intrinsically related to its transient conformations. The confined space of enzymes requires FAD set in its specific intermediate conformation. However, conventional methods only detect stable conformations of FAD molecules, while transient intermediates are hidden in ensemble measurements. There still exists a challenge to uncover the transient conformation of each FAD molecule, which hinders the understanding of the structure-activity relationship of the FAD mechanism. Here, we employ the electrochemically confined space of an aerolysin nanopore to directly characterize a series of transient conformations of every individual FAD. Based on distinguishable current blockages, the "stack", "open", and four quasi-stacked FADs are clearly determined in solution, which is further confirmed by temperature-dependent experiments and mutant aerolysin assay. Combined with molecular dynamics simulations, we achieved a direct correlation between the residual current ratio (I/I ₀) and FAD backbone angle. These results would facilitate further understanding of the structure-activity relationship in the flavoprotein.

Ion-Specific Effects on Hydrogen Bond Network at a Submicropore Confined Liquid-Vacuum Interface: An in Situ Liquid ToF-SIMS Study

The hydrogen bond (HB), one of the essential properties of water, tends to link water molecules to form dynamic water clusters. Extrinsic ions could change the size distribution of water clusters by influencing HBs. But the mechanism, especially the influence range of ions on HBs, is still in dispute due to limitation of analytical methods. Herein, we use in situ liquid ToF-SIMS analysis combined with density functional theory calculation to study the influence of different halide anions on HBs at a submicropore confined liquid-vacuum interface. Our experimental results demonstrated that anions show synchronous local and long-range effects on HBs. Specifically, the larger the anion is, the greater degree the long-range HB network and the local hydration number of anions are influenced. More importantly, we found that the long-range effect on the HB network is influenced by nuclear quantum effects, whereas the local effect on water molecules in the first hydration shell is not.

Single Molecule Study of Hydrogen Bond Interactions Between Single Oligonucleotide and Aerolysin Sensing Interface

The aerolysin nanopore displays a charming sensing capability for single oligonucleotide discrimination. When reading from the electrochemical signal, stronger interaction between the aerolysin nanopore and oligonucleotide represent prolonged duration time, thereby amplifying the hidden but intrinsic signal thus improving the sensitivity. In order to further understand and optimize the performance of the aerolysin nanopore, we focus on the investigation of the hydrogen bond interaction between nanopore, and analytes. Taking advantage of site-direct mutagenesis, single residue is replaced. According to whole protein sequence screening, the region near K238 is one of the key sensing regions. Such a positively charged amino acid is then mutagenized into cysteine and tyrosine denoted as K238C, and K238Y. As (dA)₄ traverses the pores, K238C dramatically produces a six times longer duration time than the WT aerolysin nanopore at the voltage of +120 mV. However, K238Y shortens the dwell time which suggests the acceleration of the translocation causing poor sensitivity. Referring to our previous findings in K238G, and K238F, our results suggest that the hydrogen bond does not dominate the dynamic translocation process, but enhances the interaction between pores and analytes confined in such nanopore space. These insights give detailed information for the rational design of the sensing mechanism of the aerolysin nanopore, thereby providing further understanding for the weak interactions between biomolecules and the confined space for nanopore sensing.

Learning Shapelets for Improving Single-Molecule Nanopore Sensing

The nanopore technique employs a nanoscale cavity to electrochemically confine individual molecules, achieving ultrasensitive single-molecule analysis based on evaluating the amplitude and duration of the ionic current. However, each nanopore sensing interface has its own intrinsic sensing ability, which does not always efficiently generate distinctive blockade currents for multiple analytes. Therefore, analytes that differ at only a single site often exhibit similar blockade currents or durations in nanopore experiments, which often produces serious overlap in the resulting statistical graphs. To improve the sensing ability of nanopores, herein we propose a novel shapelet-based machine learning approach to discriminate mixed analytes that exhibit nearly identical blockade current amplitudes and durations. DNA oligomers with a single-nucleotide difference, 5'-AAAA-3' and 5'-GAAA-3', are employed as model analytes that are difficult to identify in aerolysin nanopores at 100 mV. First, a set of the most informative and discriminative segments are learned from the time-series data set of blockade current signals using the learning time-series shapelets (LTS) algorithm. Then, the shapelet-transformed representation of the signals is obtained by calculating the minimum distance between the shapelets and the original signals. A simple logistic classifier is used to identify the two types of DNA oligomers in accordance with the corresponding shapelet-transformed representation. Finally, an evaluation is performed on the validation data set to show that our approach can achieve a high F₁ score of 0.933. In comparison with the conventional statistical methods for the analysis of duration and residual current, the shapelet-transformed representation provides clearly discriminated distributions for multiple analytes. Taking advantage of the robust LTS algorithm, one could anticipate the real-time analysis of nanopore events for the direct identification and quantification of multiple biomolecules in a complex real sample (e.g., serum) without labels and time-consuming mutagenesis.

Simultaneous single-molecule discrimination of cysteine and homocysteine with a protein nanopore

Discrimination between cysteine and homocysteine at the single-molecule level is achieved within a K238Q mutant aerolysin nanopore, which provides a confined space for high spatial resolution to identify the amino acid difference with a 5'-benzaldehyde poly(dA)₄ probe. Our strategy allows potential detection and characterization of various amino acids and their modifications, and provides a crucial step towards developing nanopore protein sequencing devices.

Correlated Anodic-Cathodic Nanocollision Events Reveal Redox Behaviors of Single Silver Nanoparticles

We reported a novel method to real-time monitor the redox behaviors of single Ag nanoparticles (AgNPs) at a Au ultramicroelectrode between oxidizing and reducing pulse potentials using the nanocollision electrochemical method. At fast pulse potentials, the instantaneous anodic-cathodic current transients of a single AgNP were observed for the electrooxidation of AgNP, followed by the electroreduction of the newborn silver oxide (AgO) NP in alkaline media via switching of redox potentials; however, only anodic oxidation signals of individual AgNPs were observed in neutral solution. Through this study, we have revealed the substantial different dynamic nanocollision electrochemical behaviors of single AgNPs on the electrode surface in various media. Our study offers a new view for clearly clarifying in situ tracking of the electron-transfer process of single NPs by correlating electrochemical oxidation and reduction behaviors with the complementary information.

Single Nanoparticle Electrochemistry

Experimental techniques to monitor and visualize the behaviors of single nanoparticles have not only revealed the significant spatial and temporal heterogeneity of those individuals, which are hidden in ensemble methods, but more importantly, they have also enabled researchers to elucidate the origin of such heterogeneity. In pursuing the intrinsic structure-function relations of single nanoparticles, the recently developed stochastic collision approach demonstrated some early promise. However, it was later realized that the appropriate sizing of a single nanoparticle by an electrochemical method could be far more challenging than initially expected owing to the dynamic motion of nanoparticles in electrolytes and complex charge-transfer characteristics at electrode surfaces. This clearly indicates a strong necessity to integrate single nanoparticle electrochemistry with high-resolution optical microscopy. Hence, this review aims to give a timely update of the latest progress for both electrochemically sensing and seeing single nanoparticles. A major focus is on collision-based measurements, where nanoparticles or single entities in solution impact on a collector electrode and the electrochemical response is recorded. These measurements are further enhanced with optical measurements in parallel. For completeness, advances in other related methods for single nanoparticle electrochemistry are also included.

Wireless nanopore electrodes for analysis of single entities

Measurements of a single entity underpin knowledge of the heterogeneity and stochastics in the behavior of molecules, nanoparticles, and cells. Electrochemistry provides a direct and fast method to analyze single entities as it probes electron/charge-transfer processes. However, a highly reproducible electrochemical-sensing nanointerface is often hard to fabricate because of a lack of control of the fabrication processes at the nanoscale. In comparison with conventional micro/nanoelectrodes with a metal wire inside, we present a general and easily implemented protocol that describes how to fabricate and use a wireless nanopore electrode (WNE). Nanoscale metal deposition occurs at the tip of the nanopipette, providing an electroactive sensing interface. The WNEs utilize a dynamic ionic flow instead of a metal wire to sense the interfacial redox process. WNEs provide a highly controllable interface with a 30- to 200-nm diameter. This protocol presents the construction and characterization of two types of WNEs-the open-type WNE and closed-type WNE-which can be used to achieve reproducible electrochemical measurements of single entities. Combined with the related signal amplification mechanisms, we also describe how WNEs can be used to detect single redox molecules/ions, analyze the metabolism of single cells, and discriminate single nanoparticles in a mixture. This protocol is broadly applicable to studies of living cells, nanomaterials, and sensors at the single-entity level. The total time required to complete the protocol is ~10-18 h. Each WNE costs ~$1-$3.

On-surface synthesis of planar dendrimers via divergent cross-coupling reaction

Dendrimers are homostructural and highly branched macromolecules with unique dendritic effects and extensive use in multidisciplinary fields. Although thousands of dendrimers have been synthesized in solution, the on-surface synthetic protocol for planar dendrimers has never been explored, limiting the elucidation of the mechanism of dendritic effects at the single-molecule level. Herein, we describe an on-surface synthetic approach to planar dendrimers, in which exogenous palladium is used as a catalyst to address the divergent cross-coupling of aryl bromides with isocyanides. This reaction enables one aryl bromide to react with two isocyanides in sequential steps to generate the divergently grown product composed of a core and two branches with high selectivity and reactivity. Then, a dendron with four branches and dendrimers with eight or twelve branches in the outermost shell are synthesized on Au(111). This work opens the door for the on-surface synthesis of various planar dendrimers and relevant macromolecular systems.

Although many strategies exist to synthesize dendrimers in solution, the synthesis of planar dendrimers on a surface has proven challenging. Here, the authors produce planar dendrimers through a divergent on-surface cross-coupling reaction between one aryl bromide and two isocyanides, which enables the growth of branches from a single reactive site.

Detection of Single Proteins with a General Nanopore Sensor

Single protein sensing based on solid-state nanopores is promising but challenging, because the fast translocation velocity of a protein is beyond the bandwidth of nanopore instruments. To decelerate the translocation speed, here, we employed a common protein cross-link interaction to achieve a general and robust nanopore sensing platform for single-molecule detection of protein. Benefiting from the EDC/NHS coupling interaction between nanopore and proteins, a 10-fold decrease in speed has been achieved. The clearly distinguishable current signatures further reveal that the anisotropic translocation of a protein, which are horizontal, vertical, and flipping transit inside nanopore confinement. This strategy provides a general platform for rapid detection of proteins as well as exploring fundamental protein dynamics at the single-molecule level.

Revisiting a classical redox process on a gold electrode by operando ToF-SIMS: where does the gold go?

Our results indicated that a gold electrode participates in the redox reaction of [Fe(CN)₆]^3/4– by competing with it to form Au(CN)₂^–.

Electrochemical redox conversion between ferricyanide and ferrocyanide on a gold electrode is one of the most classical reactions in electrochemistry. In textbooks, the gold electrode is seen as chemically inert, on which only the adsorption/desorption of [Fe(CN)₆]^3/4– and electron transfer take place. Here, the electrochemical process of [Fe(CN)₆]^3/4– on a gold electrode was revisited using a vacuum-compatible microfluidic electrochemical cell in combination with operando liquid ToF-SIMS. An intermediate, Au(CN)₂^–, was observed in the cyclic voltammetry of ferricyanide with an interesting periodic potential-dependent variation trend. It was demonstrated that the gold electrode participated in the redox reaction of [Fe(CN)₆]^3/4– by competing with it to form Au(CN)₂^–, since the formation constant was Fe(CN)₆^3– > Au(CN)₂^– > Fe(CN)₆^4–. The formation and evolution of Au(CN)₂^– depends on the ratio of Fe(iii) and Fe(ii) on the surface of the gold electrode, which was determined by the redox conversion between Fe(iii) and Fe(ii) as well as the electric field force-based attraction or repulsion between the gold electrode and [Fe(CN)₆]^3/4–. Both of these factors were potential-dependent, resulting in the periodic change of Au(CN)₂^– in the dynamic potential scan of [Fe(CN)₆]^3/4–. These results provided solid molecular evidence for the participation of the gold electrode in the [Fe(CN)₆]^3/4– redox system, which will deepen mechanistic understandings of related electrochemical applications.

Toward Precision Measurement and Manipulation of Single-Molecule Reactions by a Confined Space

All chemical reactions can be divided into a series of single molecule reactions (SMRs), the elementary steps that involve only isomerization of, dissociation from, and addition to an individual molecule. Analyzing SMRs is of paramount importance to identify the intrinsic molecular mechanism of a complex chemical reaction, which is otherwise implausible to reveal in an ensemble fashion, owing to the significant static and dynamic heterogeneity of real-world chemical systems. The single-molecule measurement and manipulation methods developed recently are playing an increasingly irreplaceable role to detect and recognize short-lived intermediates, visualize their transient existence, and determinate the kinetics and dynamics of single bond breaking and formation. Notably, none of the above SMRs characterizations can be realized without the aid of a confined space. Therefore, this Review aims to highlight the recent progress in the development of confined space enabled single-molecule sensing, imaging, and tuning methods to study chemical reactions. Future prospects of SMRs research are also included, including a push toward the physical limit on transduction of information to signals and vice versa, transmission and recording of signals, computational modeling and simulation, and rational design of a confined space for precise SMRs.

Simultaneous Removal of Multiple Heavy Metal Ions from River Water Using Ultrafine Mesoporous Magnetite Nanoparticles

The exploration of simultaneous removal of co-existing or multiple pollutants from water by the means of nanomaterials paves a new avenue that is free from secondary pollution and inexpensive. In the aquatic environment, river water contains a mixture of ions, which can influence the adsorption process. In this respect, removing heavy metal ions becomes a true challenge. Here, four heavy metal ions, namely, Pb²⁺, Cd²⁺, Cu²⁺, and Ni²⁺, have been successfully removed simultaneously from river water using ultrafine mesoporous magnetite (Fe₃O₄) nanoparticles (UFMNPs) based on the affinity of these metal ions toward the UFMNP surfaces as well as their unique mesoporous structure, promoting the easy adsorption. The individual removal efficiencies of Pb²⁺, Cd²⁺, Cu²⁺, and Ni²⁺ ions from river water were 98, 87, 90, and 78%, respectively, whereas the removal efficiencies of the mixed Pb²⁺, Cd²⁺, Cu²⁺, and Ni²⁺ ions were 86, 80, 84, and 54%, respectively, in the same river water. Thus, the data clearly indicate the complex removal of heavy metal ions in multi-ion systems. This study has demonstrated the huge potential of UFMNPs to be effective for their use in wastewater treatment, especially to simultaneously remove multiple heavy metal ions from aqueous media.

Unveiling the Intrinsic Catalytic Activities of Single-Gold-Nanoparticle-Based Enzyme Mimetics

Gold nanoparticles (AuNPs) have been demonstrated to serve as effective nanomaterial-based enzyme mimetics (nanozymes) for a number of enzymatic reactions under mild conditions. The intrinsic glucose oxidase and peroxidase activities of single AuNPs and Ag-Au nanohybrids, respectively, were investigated by single NP collision electrochemical measurements. A significantly high turnover number of nanozymes was obtained from individual catalytic events compared with the results from the classical, ensemble-averaged measurements. The unusual enhancement of catalytic activity of single nanozymes is believed to originate from the high accessible surface area of monodispersed NPs and the high activities of carbon-supported NPs during single-particle collision at a carbon ultramicroelectrode. This work introduces a new method for the precise characterization of the intrinsic catalytic activities of nanozymes, giving further insights to the design of high-efficiency nanomaterial catalysts.

A Closed-Type Wireless Nanopore Electrode for Analyzing Single Nanoparticles

Measuring the intrinsic features of single nanoparticles by nanoelectrochemistry holds deep fundamental importance and has potential impacts in nanoscience. However, electrochemically analyzing single nanoparticles is challenging, as the sensing nanointerface is uncontrollable. To address this challenge, we describe here the fabrication and characterization of a closed-type wireless nanopore electrode (WNE) that exhibits a highly controllable morphology and outstanding reproducibility. The facile fabrication of WNE enables the preparation of well-defined nanoelectrodes in a general chemistry laboratory without the use of a clean room and expensive equipment. One application of a 30 nm closed-type WNE in analysis of single gold nanoparticles in the mixture is also highlighted, which shows a high current resolution of 0.6 pA and high temporal resolution of 0.01 ms. Accompanied by their excellent morphology and small diameters, more potential applications of closed-type WNEs can be expanded from nanoparticle characterization to single molecule/ion detection and single-cell probing.

Direct Molecular Evidence of Proton Transfer and Mass Dynamics at the Electrode-Electrolyte Interface

Proton transfer has been widely regarded as a key step in many electrochemical and biological processes. However, direct molecular evidence has long been lacking. In this work, we chose the electrochemical oxidation of acetaminophen (APAP) as a model system and utilized in situ liquid time-of-flight secondary ion mass spectroscopy (ToF-SIMS) to molecularly examine proton solvation and transfer in this process. In addition, we successfully captured and identified the transient radical intermediate, providing solid molecular evidence to resolve an important debate in electron transfer-proton transfer oxidation mechanism of APAP. Moreover, the potential-dependent behaviors of both inert ions and electroactive species during the dynamic potential scanning were chemically monitored in real time and the mass diffusion mechanism regarding the electroactive and nonelectroactive species was revealed under polarized conditions. The results are consistent with our computer simulations. The observations in this work greatly improved our understanding of proton transfer and mass dynamics occurring at the electrode-electrolyte interface in complex electrochemical processes.

A lithium-ion-active aerolysin nanopore for effectively trapping long single-stranded DNA

Wild-type aerolysin (AeL) nanopores allow direct single nucleotide discrimination of very short oligonucleotides (≤10 nt) without labelling, which shows great potential for DNA sensing. To achieve real applications, one major obstacle of AeL is its poor capture ability of long single-stranded DNA (ssDNA, >10 nt). Here, we have proposed a novel and robust strategy for the electrostatic focusing of long ssDNA into a lithium-chloride (LiCl)-active AeL. By using this method, for the first time we have demonstrated AeL detection of ssDNA longer than 100 nt. Due to screening more negative charges, LiCl improves AeL capture ability of long ssDNA (i.e. 60 nt) by 2.63- to 10.23-fold compared to KCl. Further calculations and molecular dynamics simulations revealed that strong binding between Li+ and the negatively charged residue neutralized the AeL, leading to a reduction in the energy barrier for ssDNA capture. These findings facilitate the future high-throughput applications of AeL in genetic and epigenetic diagnostics.