Deciphering the Roles of Interfacial Amino Acids in Inter-Protein Charge Transport.

Elucidating charge transport (CT) through proteins is critical for gaining insights into ubiquitous CT chain reactions in biological systems and developing high-performance bioelectronic devices. While intra-protein CT has been extensively studied, crucial knowledge about inter-protein CT via interfacial amino acids is still absent due to the structural complexity. Herein, by loading cytochrome c (Cyt c) on well-defined peptide self-assembled monolayers to mimic the protein-protein interface, we provide a precisely controlled platform for identifying the roles of interfacial amino acids in solid-state CT via peptide-Cyt c junctions. The terminal amino acid of peptides serves as a fine-tuning factor for both the interfacial interaction between peptides and Cyt c and the immobilized Cyt c orientation, resulting in a nearly 10-fold difference in current through peptide-Cyt c junctions with varied asymmetry. This work provides a valuable platform for studying CT across proteins and contributes to the understanding of fundamental principles governing inter-protein CT.

Scalable Synthesis of Bilayer Graphene at Ambient Temperature.

In this work, we develop for the first time a facile chemical lithiation-assisted exfoliation approach to the controllable and scalable preparation of bilayer graphene. Biphenyl lithium (Bp-Li), a strong reducing reagent, is selected to realize the spontaneous Li-intercalation into graphite at ambient temperature, forming lithium graphite intercalation compounds (Li-GICs). The potential of Bp-Li (0.11 V vs Li/Li+), which is just lower than the potential of stage-2 lithium intercalation (0.125 V), enables the precise lithiation of graphite to stage-2 Li-GICs (LiC12). Intriguingly, the exfoliation of LiC12 leads to the bilayer-favored production of graphene, giving a high selectivity of 78%. Furthermore, the mild intercalation-exfoliation procedure yields high-quality graphene with negligible structural deterioration. The obtained graphene exhibits ultralow defect density (ID/IG ∼ 0.14) and a considerably high C/O ratio (∼29.7), superior to most current state-of-the-art techniques. This simple and scalable strategy promotes the understanding of chemical Li-intercalation methods for preparing high-quality graphene and shows great potential for layer-controlled engineering.

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.

Specific Small-Molecule Detection Using Designed Nucleic Acid Nanostructure Carriers and Nanopores.

In the realm of nanopore sensor technology, an enduring challenge lies in achieving the discerning detection of small biomolecules with a sufficiently high signal-to-noise ratio. This study introduces a method for reliably quantifying the concentration of target small molecules, utilizing tetrahedral DNA nanostructures as surrogates for the captured molecules through a magnetic-bead-based competition substitution mechanism. Magnetic Fe3O4-DNA tetrahedron nanoparticles (MNPs) are incorporated into a nanopore electrochemical system for small-molecule sensing. In the presence of the target, the DNA tetrahedron, featuring an aptamer tail acting as a molecular carrier, detaches from the MNPs due to aptamer deformation. Following removal of the MNPs, the DNA tetrahedron bound to the target traversed the nanopore by applying a positive potential. This approach exhibits various advantages, including heightened sensitivity, selectivity, an improved signal-to-noise ratio (SNR), and robust anti-interference capabilities. Our findings demonstrate that this innovative methodology has the potential to significantly enhance the sensing of various small-molecule targets by nanopores, thereby advancing the sensitivity and dynamic range. This progress holds promise for the development of precise clinical diagnostic tools.

Enhancing Effect of Fullerene Guest and Counterion on the Structural Stability and Electrical Conductivity of Octahedral Metallo-Supramolecular Cages.

Metallo-supramolecular cages have garnered tremendous attention for their diverse yet molecular-level precision structures. However, physical properties of these supramolecular ensembles, which are of potential significance in molecular electronics, remain largely unexplored. We herein constructed a series of octahedral metallo-cages and cage-fullerene complexes with notably enhanced structural stability. As such, we could systematically evaluate the electrical conductivity of these ensembles at both single-molecule level and aggregated bulk state (as well-defined films). Our findings reveal that counteranions and fullerene guests play a pivotal role in determining the electrical conductivity of aggregated state, while such effects are less significant for single-molecule conductance. Both counteranions and fullerenes effectively tune the electronic structures and packing density of metallo-supramolecular assemblies, and facilitate efficient charge transfer between the cage hosts and fullerenes, resulting in a notable one order of magnitude increase in electrical conductivity of the aggregated state.

Base Pair Stacking Modulates Solid-State Charge Transport in DNA Hairpins.

Particular interest has been focused on modulation of solid-state charge transport (CT) in DNA. Nevertheless, it remains challenging to do so in a sensitive and predictive manner due to the lack of a definite relationship between DNA base pair stacking and DNA CT. The challenges can be mainly attributed to the ill-defined systems, which may lead to ambiguous and even contradictory conclusions. Here, we use DNA hairpins to construct the well-defined self-assembled monolayers. We reveal nearly positive-linear correlations between DNA conformation and CT in the DNA hairpins regulated with metal ion chelation and DNA sequence. The correlations have been confirmed by the solid-state current-voltage characteristics and circular dichroism in solution. The enhanced CT via metal ion chelated DNA hairpins is mainly from the improved DNA energy coupling to electrodes, not the almost unchanged energy barrier when Hg ion-induced DNA conformational switches toward the canonical B-form.

Nanoconfinement-Guided Construction of Nanozymes for Determining H2 O2 Produced by Sonication.

Nanomaterials with enzyme-like activities, termed as nanozymes, have found wide applications in various fields. It has been a long-term aim to rationally design and synthesize highly active nanozymes and thus to further improve their application performance. Guided by the nanoconfinement effect, we confine cytochrome c (Cyt c) within a mesoporous metal-organic framework (MOF), PCN-222 nanoparticle (NP), forming a protein/MOF hybrid nanozyme, termed as Cyt c@PCN-222 NP. The confined Cyt c exhibits around 3-4-fold higher peroxidase-like activity than free Cyt c. Due to the increase in the activity of Cyt c, the Cyt c@PCN-222 NPs exhibit a quite low limit of detection (≈0.13 µM) towards H2 O2 . Sonication-induced H2 O2 formation in water by using a lab-quipped ultrasonic cleaner can be sensitively probed, which suggests that H2 O2 -sensitive materials should be carefully handled during the utilization of ultrasonic equipment. We speculate that this nanoconfinement strategy can broaden our synthetic methodology for the rational design of nanozymes.

Supramolecular Enhancement of Charge Transport through Pillar[5]arene-Based Self-Assembled Monolayers.

Intermolecular charge transport is one of the essential modes for modulating charge transport in molecular electronic devices. Supermolecules are highly promising candidates for molecular devices because of their abundant structures and easy functionalization. Herein, we report an efficient strategy to enhance charge transport through pillar[5]arene self-assembled monolayers (SAMs) by introducing cationic guests. The current density of pillar[5]arene SAMs can be raised up to about 2.1 orders of magnitude by inserting cationic molecules into the cavity of pillar[5]arenes in SAMs. Importantly, we have also observed a positive correlation between the charge transport of pillar[5]arene-based complex SAMs and the binding affinities of the pillar[5]arene-based complexation. Such an enhancement of charge transport is attributed to the efficient host-guest interactions that stabilize the supramolecular complexes and lower the energy gaps for charge transport. This work provides a predictive pattern for the regulation of intermolecular charge transport in guiding the design of next generation switches and functional sensors in supramolecular electronics.

Electron transport via tyrosine-doped oligo-alanine peptide junctions: role of charges and hydrogen bonding.

A way of modulating the solid-state electron transport (ETp) properties of oligopeptide junctions is presented by charges and internal hydrogen bonding, which affect this process markedly. The ETp properties of a series of tyrosine (Tyr)-containing hexa-alanine peptides, self-assembled in monolayers and sandwiched between gold electrodes, are investigated in response to their protonation state. Inserting a Tyr residue into these peptides enhances the ETp carried via their junctions. Deprotonation of the Tyr-containing peptides causes a further increase of ETp efficiency that depends on this residue's position. Combined results of molecular dynamics simulations and spectroscopic experiments suggest that the increased conductance upon deprotonation is mainly a result of enhanced coupling between the charged C-terminus carboxylate group and the adjacent Au electrode. Moreover, intra-peptide hydrogen bonding of the Tyr hydroxyl to the C-terminus carboxylate reduces this coupling. Hence, the extent of such a conductance change depends on the Tyr-carboxylate distance in the peptide's sequence.

Tuning electronic transport via hepta-alanine peptides junction by tryptophan doping.

Charge migration for electron transfer via the polypeptide matrix of proteins is a key process in biological energy conversion and signaling systems. It is sensitive to the sequence of amino acids composing the protein and, therefore, offers a tool for chemical control of charge transport across biomaterial-based devices. We designed a series of linear oligoalanine peptides with a single tryptophan substitution that acts as a "dopant," introducing an energy level closer to the electrodes' Fermi level than that of the alanine homopeptide. We investigated the solid-state electron transport (ETp) across a self-assembled monolayer of these peptides between gold contacts. The single tryptophan "doping" markedly increased the conductance of the peptide chain, especially when its location in the sequence is close to the electrodes. Combining inelastic tunneling spectroscopy, UV photoelectron spectroscopy, electronic structure calculations by advanced density-functional theory, and dc current-voltage analysis, the role of tryptophan in ETp is rationalized by charge tunneling across a heterogeneous energy barrier, via electronic states of alanine and tryptophan, and by relatively efficient direct coupling of tryptophan to a Au electrode. These results reveal a controlled way of modulating the electrical properties of molecular junctions by tailor-made "building block" peptides.

Electronic structure of dipeptides in the gas-phase and as an adsorbed monolayer.

Peptide-based molecular electronic devices are promising due to the large diversity and unique electronic properties of biomolecules. These electronic properties can change considerably with peptide structure, allowing diverse design possibilities. In this work, we explore the effect of the side-chain of the peptide on its electronic properties, by using both experimental and computational tools to detect the electronic energy levels of two model peptides. The peptides include 2Ala and 2Trp as well as their 3-mercaptopropionic acid linker which is used to form monolayers on an Au surface. Specifically, we compare experimental ultraviolet photoemission spectroscopy measurements with density functional theory based computational results. By analyzing differences in frontier energy levels and molecular orbitals between peptides in gas-phase and in a monolayer on gold, we find that the electronic properties of the peptide side-chain are maintained during binding of the peptide to the gold substrate. This indicates that the energy barrier for the peptide electron transport can be tuned by the amino acid compositions, which suggests a route for structural design of peptide-based electronic devices.

High-resolution probing heparan sulfate-antithrombin interaction on a single endothelial cell surface: single-molecule AFM studies.

Heparan sulfate (HS) plays diverse functions in multiple biological processes by interacting with a wide range of important protein ligands, such as the key anticoagulant factor, antithrombin (AT). The specific interaction of HS with a protein ligand is determined mainly by the sulfation patterns on the HS chain. Here, we reported the probing single-molecule interaction of AT and HS (both wild type and mutated) expressed on the endothelial cell surface under near-physiological conditions by atomic force microscopy (AFM). Functional AFM imaging revealed the uneven distribution of HS on the endothelial cell surface though they are highly expressed. Force spectroscopy measurements using an AT-functionalized AFM tip revealed that AT interacts with endothelial HS on the cell surface through multiple binding sites. The interaction essentially requires HS to be N-, 2-O- and/or 6-O-sulfated. This work provides a new tool to probe the HS-protein ligand interaction at a single-molecular level on the cell surface to elucidate the functional roles of HS.

Controlled condensation by liquid contact-induced adaptations of molecular conformations in self-assembled monolayers.

Surface condensation control strategies are crucial but commonly require relatively tedious, time-consuming, and expensive techniques for surface-chemical and topographical engineering. Here we report a strategy to alter surface condensation behavior without resorting to any molecule-type or topographical transmutations. After ultrafast contact of liquids with and removal from surfaces, the condensation rate and density of water droplets on the surfaces decrease, the extent of which is positively correlated with the polarity of the liquid and the duration of contact. The liquid contact-induced condensation rate/density decrease (LCICD) can be attributed to the decrease of nucleation site density resulted from the liquid contact-induced adaption of surface molecular conformation. Based on this, we find that LCICD is applicable to various surfaces, on condition that there are flexible segments capable of shielding at least part of nucleation sites through changing the conformation under liquid contact induction. Leveraging the LCICD effect, we achieve erasable information storage on diverse substrates. Furthermore, our strategy holds promise for controlling condensation of other substances since LCICD is not specific to the water condensation process.

Secondary Structure-Dependent Charge Transport in iLOV Protein Junctions.

The composition and structure of proteins are crucial for charge migration in the solid-state charge transport (CTp). Despite much progress, it is still challenging to explore the relationship between conformational change and CTp in the complex protein system. Herein, we design three improved light-oxygen-voltage (iLOV) domains, and efficiently regulate the CTp of the iLOV self-assembled monolayers (SAMs) by pH induced conformation variation. The current density can be controlled in the range of one order of magnitude. Interestingly, the CTp of iLOV displays negative linear relations with the ß-sheet contents. Single-level Landauer fitting and transition voltage spectroscopy analysis suggest that ß-sheet-dependent CTp would be related to the coupling between iLOV and electrodes. This work proposes a new strategy to explore the CTp in complex molecular system. Our findings deepen the understanding on protein structure-CTp relationship, and provide predictive mode of protein CTp responses for the design of functional bioelectronics.

Revealing the role of double-layer microenvironments in pH-dependent oxygen reduction activity over metal-nitrogen-carbon catalysts.

A standing puzzle in electrochemistry is that why the metal-nitrogen-carbon catalysts generally exhibit dramatic activity drop for oxygen reduction when traversing from alkaline to acid. Here, taking FeCo-N6-C double-atom catalyst as a model system and combining the ab initio molecular dynamics simulation and in situ surface-enhanced infrared absorption spectroscopy, we show that it is the significantly distinct interfacial double-layer structures, rather than the energetics of multiple reaction steps, that cause the pH-dependent oxygen reduction activity on metal-nitrogen-carbon catalysts. Specifically, the greatly disparate charge densities on electrode surfaces render different orientations of interfacial water under alkaline and acid oxygen reduction conditions, thereby affecting the formation of hydrogen bonds between the surface oxygenated intermediates and the interfacial water molecules, eventually controlling the kinetics of the proton-coupled electron transfer steps. The present findings may open new and feasible avenues for the design of advanced metal-nitrogen-carbon catalysts for proton exchange membrane fuel cells.

Hard-soft chemistry guides the adaptable charge transport in lysine-doped heptapeptide junctions.

Counterions always coexist with charged peptides in charge transport processes, which are excellent candidate components for tunable molecular electronic devices. Here, we introduced hard-soft acid base theory to analyze the counterion-modulated peptide charge transport. We demonstrate that the peptide charge transport is improved by enhanced peptide-counterion interactions.

Fluorescent Ag clusters via a protein-directed approach as a Hg(II) ion sensor.

Proteins have proven to be particularly attractive as effective ligands in the synthesis of nano- and subnanoscaled materials because of their multiple chelating and functional groups imparting unique functionalities. However, protein-directed fluorescent metal cluster synthesis is still a challenge but a promising area of research. Here, we report on the synthesis of new water-soluble, stable, fluorescent Ag clusters via a facile, green method using denatured bovine serum albumin (dBSA) as a stabilizing agent. The dBSA with its 35 free cysteine residues could contribute to polyvalent interactions with the Ag clusters and serve as effective stabilizing agents for these clusters. The as-prepared Ag clusters showed high fluorescence emission at ∼637 nm and were stable even in 1 M NaCl. The fluorescent Ag clusters were then used in the detection of Hg(2+) with high sensitivity and selectivity. The detection limit was 10 nM in the linear range from 10 nM to 5 µM.

Interaction between DNA and microcystin-LR studied by spectra analysis and atomic force microscopy.

Microcystin-LR (MC-LR) is one of the hepatotoxins produced by cyanobacteria in the eutrophicated fresh water. In this work, the minor groove binding mode of MC-LR to plasmid DNA was explored by using UV and fluorescence spectra, and the binding characteristics of MC-LR for plasmid DNA were calculated via the fluorescence quenching of ethidium bromide (EB) and mole ratio method. Furthermore, atomic force microscopy (AFM) was used to observe DNA morphology change in the presence of MC-LR. With the increasing concentration of MC-LR, circle DNA strands twined gradually to rod condensates. The possible reason for the condensation might be the masking of the electrostatic repulsion between DNA double strands by MC-LR. The present study might provide useful information for the pathopoiesis mechanism of MC-LR. More, because the condensation of DNA could affect the progresses of gene expression and protein transcription, it may implicate another trend to explore the nosogenesis of MC-LR.

Conformation-dependent charge transport through short peptides.

We report on charge transport across single short peptides using the Mechanically Controlled Break Junction (MCBJ) method. We record thousands of electron transport events across single-molecule junctions and with an unsupervised machine learning algorithm, we identify several classes of traces with multifarious conductance values that may correspond to different peptide conformations. Data analysis shows that very short peptides, which are more rigid, show conductance plateaus at low conductance values of about 10-3G0 and below, with G0 being the conductance quantum, whereas slightly longer, more flexible peptides also show plateaus at higher values. Fully stretched peptide chains exhibit conductance values that are of the same order as that of alkane chains of similar length. The measurements show that in the case of short peptides, different compositions and molecular lengths offer a wide range of junction conformations. Such information is crucial to understand mechanism(s) of charge transport in and across peptide-based biomolecules.

Details of Single-Molecule Force Spectroscopy Data Decoded by a Network-Based Automatic Clustering Algorithm.

Atomic force microscopy-single-molecule force spectroscopy (AFM-SMFS) is a powerful methodology to probe intermolecular and intramolecular interactions in biological systems because of its operability in physiological conditions, facile and rapid sample preparation, versatile molecular manipulation, and combined functionality with high-resolution imaging. Since a huge number of AFM-SMFS force-distance curves are collected to avoid human bias and errors and to save time, numerous algorithms have been developed to analyze the AFM-SMFS curves. Nevertheless, there is still a need to develop new algorithms for the analysis of AFM-SMFS data since the current algorithms cannot specify an unbinding force to a corresponding/each binding site due to the lack of networking functionality to model the relationship between the unbinding forces. To address this challenge, herein, we develop an unsupervised method, i.e., a network-based automatic clustering algorithm (NASA), to decode the details of specific molecules, e.g., the unbinding force of each binding site, given the input of AFM-SMFS curves. Using the interaction of heparan sulfate (HS)-antithrombin (AT) on different endothelial cell surfaces as a model system, we demonstrate that NASA is able to automatically detect the peak and calculate the unbinding force. More importantly, NASA successfully identifies three unbinding force clusters, which could belong to three different binding sites, for both Ext1f/f and Ndst1f/f cell lines. NASA has great potential to be applied either readily or slightly modified to other AFM-based SMFS measurements that result in "saw-tooth"-shaped force-distance curves showing jumps related to the force unbinding, such as antibody-antigen interaction and DNA-protein interaction.