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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Solid-State Protein Junctions: Cross- Laboratory Study Shows Preservation of Mechanism at Varying Electronic Coupling.

Successful integration of proteins in solid-state electronics requires contacting them in a non-invasive fashion, with a solid conducting surface for immobilization as one such contact. The contacts can affect and even dominate the measured electronic transport. Often substrates, substrate treatments, protein immobilization, and device geometries differ between laboratories. Thus the question arises how far results from different laboratories and platforms are comparable and how to distinguish genuine protein electronic transport properties from platform-induced ones. We report a systematic comparison of electronic transport measurements between different laboratories, using all commonly used large-area schemes to contact a set of three proteins of largely different types. Altogether we study eight different combinations of molecular junction configurations, designed so that Ageoof junctions varies from 105 to 10-3 µm2. Although for the same protein, measured with similar device geometry, results compare reasonably well, there are significant differences in current densities (an intensive variable) between different device geometries. Likely, these originate in the critical contact-protein coupling (∼contact resistance), in addition to the actual number of proteins involved, because the effective junction contact area depends on the nanometric roughness of the electrodes and at times, even the proteins may increase this roughness. On the positive side, our results show that understanding what controls the coupling can make the coupling a design knob. In terms of extensive variables, such as temperature, our comparison unanimously shows the transport to be independent of temperature for all studied configurations and proteins. Our study places coupling and lack of temperature activation as key aspects to be considered in both modeling and practice of protein electronic transport experiments.

Backbone-Constrained Peptides: Temperature and Secondary Structure Affect Solid-State Electron Transport.

The primary sequence and secondary structure of a peptide are crucial to charge migration, not only in solution (electron transfer, ET), but also in the solid-state (electron transport, ETp). Hence, understanding the charge migration mechanisms is fundamental to the development of biomolecular devices and sensors. We report studies on four Aib-containing helical peptide analogues: two acyclic linear peptides with one and two electron-rich alkene-based side chains, respectively, and two peptides that are further rigidified into a macrocycle by a side bridge constraint, containing one or no alkene. ETp was investigated across Au/peptide/Au junctions, between 80 and 340 K in combination with the molecular dynamic (MD) simulations. The results reveal that the helical structure of the peptide and electron-rich side chain both facilitate the ETp. As temperature increases, the loss of helical structure, change of monolayer tilt angle, and increase of thermally activated fluctuations affect the conductance of peptides. Specifically, room temperature conductance across the peptide monolayers correlates well with previously observed ET rate constants, where an interplay between backbone rigidity and electron-rich side chains was revealed. Our findings provide new means to manipulate electronic transport across solid-state peptide junctions.

Orientation of Oligopeptides in Self-Assembled Monolayers Inferred from Infrared Reflection-Absorption Spectroscopy.

A series of a single tryptophan containing oligo-alanine peptides were recently characterized as conductive molecules that enable electron transport between electrodes. IR reflection-absorption of self-assembled monolayers of such peptides on gold surfaces revealed that the relative intensities of amide I and II bands in the respective spectra depend on the tryptophan residue position in the oligopeptide sequence. This indicates different average peptide orientations with respect to the normal onto the carrying gold surface. We developed a model which calculates the polarized reflectivities of the amide I and II bands as function of the angle of the incident light, the average peptide orientation and the relative orientations of peptide group at the N-terminal. The orientation and strength of vibrational transition dipole moments were calculated by employing an excitonic coupling approach which considers probable conformational distributions of the disordered peptides. Our results revealed that the position of the tryptophan can affect the effective tilt angle of the peptide as well as the orientation of transition dipole moments with respect to the reflection plane. We have also calculated the average end to end distances of the examined peptides and found them to be in reasonable agreement with experimental values determined by ellipsometry. Some evidence is obtained for the notion that increasing the tilt angle of the investigated peptides reduces their conductivity.

Transistor configuration yields energy level control in protein-based junctions.

The incorporation of proteins as functional components in electronic junctions has received much interest recently due to their diverse bio-chemical and physical properties. However, information regarding the energies of the frontier orbitals involved in their electron transport (ETp) has remained elusive. Here we employ a new method to quantitatively determine the energy position of the molecular orbital, nearest to the Fermi level (EF) of the electrode, in the electron transfer protein Azurin. The importance of the Cu(ii) redox center of Azurin is demonstrated by measuring gate-controlled conductance switching which is absent if Azurin's copper ions are removed. Comparing different electrode materials, a higher conductance and a lower gate-induced current onset is observed for the material with smaller work function, indicating that ETp via Azurin is LUMO-mediated. We use the difference in work function to calibrate the difference in gate-induced current onset for the two electrode materials, to a specific energy level shift and find that ETp via Azurin is near resonance. Our results provide a basis for mapping and studying the role of energy level positions in (bio)molecular junctions.

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.