Can One Define the Conductance of Amino Acids?

Single-molecule detection of modified amino acid regulating transcriptional activity

Acetylation of lysine, a component of histones, regulates transcriptional activity. Simple detection methods for acetyl lysine are essential for early diagnosis of diseases and understanding of the physiological effects. We have detected and recognized acetyl lysine at the single-molecule level by combining MCBJ measurement and machine learning.

Electron transport through two interacting channels in Azurin-based solid-state junctions

The fundamental question of "what is the transport path of electrons through proteins?" initially introduced while studying long-range electron transfer between localized redox centers in proteins in vivo is also highly relevant to the transport properties of solid-state, dry metal-protein-metal junctions. Here, we report conductance measurements of such junctions, Au-(Azurin monolayer ensemble)-Bismuth (Bi) ones, with well-defined nanopore geometry and ~103 proteins/pore. Our results can be understood as follows. (1) Transport is via two interacting conducting channels, characterized by different spatial and time scales. The slow and spatially localized channel is associated with the Cu center of Azurin and the fast delocalized one with the protein's polypeptide matrix. Transport via the slow channel is by a sequential (noncoherent) process and in the second one by direct, off-resonant tunneling. (2) The two channels are capacitively coupled. Thus, with a change in charge occupation of the weakly coupled (metal center) channel, the broad energy level manifold, responsible for off-resonance tunneling, shifts, relative to the electrodes' Fermi levels. In this process, the off-resonance (fast) channel dominates transport, and the slow (redox) channel, while contributing only negligibly directly, significantly affects transport by intramolecular gating.

Benchmarking break-junction techniques: electric and thermoelectric characterization of naphthalenophanes

Break-junction techniques provide the possibility to study electric and thermoelectric properties of single-molecule junctions in great detail. These techniques rely on the same principle of controllably breaking metallic contacts in order to create single-molecule junctions, whilst keeping track of the junction's conductance. Here, we compare results from mechanically controllable break junction (MCBJ) and scanning tunneling microscope (STM) methods, while characterizing conductance properties of the same novel mechanosensitive para- and meta-connected naphtalenophane compounds. In addition, thermopower measurements are carried out for both compounds using the STM break junction (STM-BJ) technique. For the conductance experiments, the same data processing using a clustering analysis is performed. We obtain to a large extent similar results for both methods, although values of conductance and stretching lengths for the STM-BJ technique are slightly larger in comparison with the MCBJ. STM-BJ thermopower experiments show similar Seebeck coefficients for both compounds. An increase in the Seebeck coefficient is revealed, whilst the conductance decreases, after which it saturates at around 10 μV K-1. This phenomenon is studied theoretically using a tight binding model. It shows that changes of molecule-electrode electronic couplings combined with shifts of the resonance energies explain the correlated behavior of conductance and Seebeck coefficient.

Electron-Sponge Nature of Polyoxometalates for Next-Generation Electrocatalytic Water Splitting and Nonvolatile Neuromorphic Devices

Designing next-generation molecular devices typically necessitates plentiful oxygen-bearing sites to facilitate multiple-electron transfers. However, the theoretical limits of existing materials for energy conversion and information storage devices make it inevitable to hunt for new competitors. Polyoxometalates (POMs), a unique class of metal-oxide clusters, have been investigated exponentially due to their structural diversity and tunable redox properties. POMs behave as electron-sponges owing to their intrinsic ability of reversible uptake-release of multiple electrons. In this review, numerous POM-frameworks together with desired features of a contender material and inherited properties of POMs are systematically discussed to demonstrate how and why the electron-sponge-like nature of POMs is beneficial to design next-generation water oxidation/reduction electrocatalysts, and neuromorphic nonvolatile resistance-switching random-access memory devices. The aim is to converge the attention of scientists who are working separately on electrocatalysts and memory devices, on a point that, although the application types are different, they all hunt for a material that could exhibit electron-sponge-like feature to realize boosted performances and thus, encouraging the scientists of two completely different fields to explore POMs as imperious contenders to design next-generation nanodevices. Finally, challenges and promising prospects in this research field are also highlighted.

Single-molecular protein-based bioelectronics via electronic transport: fundamentals, devices and applications

Biomolecular electronics is a rapidly growing multidisciplinary field that combines biology, nanoscience, and engineering to bridge the two important fields of life sciences and molecular electronics. Proteins are remarkable for their ability to recognize molecules and transport electrons, making the integration of proteins into electronic devices a long sought-after goal and leading to the emergence of the field of protein-based bioelectronics, also known as proteotronics. This field seeks to design and create new biomolecular electronic platforms that allow for the understanding and manipulation of protein-mediated electronic charge transport and related functional applications. In recent decades, there have been numerous reports on protein-based bioelectronics using a variety of nano-gapped electrical devices and techniques at the single molecular level, which are not achievable with conventional ensemble approaches. This review focuses on recent advances in physical electron transport mechanisms, device fabrication methodologies, and various applications in protein-based bioelectronics. We discuss the most recent progress of the single or few protein-bridged electrical junction fabrication strategies, summarise the work on fundamental and functional applications of protein bioelectronics that enable high and dynamic electron transport, and highlight future perspectives and challenges that still need to be addressed. We believe that this specific review will stimulate the interdisciplinary research of topics related to protein-related bioelectronics, and open up new possibilities for single-molecule biophysics and biomedicine.

Electronic Conductance and Thermopower of Cross-Conjugated and Skipped-Conjugated Molecules in Single-Molecule Junctions

We report a combined experimental and theoretical study of a series of thiomethyl (SMe) anchored cross-conjugated molecules featuring an acyclic central bridging ketone and their analogous skipped-conjugated alcohol derivatives. Studies of these molecules in a gold|single-molecule|gold junction using scanning tunneling microscopy-break junction techniques reveal a similar conductance (G) value for both the cross-conjugated molecules and their skipped-conjugated partners. Theoretical studies based on density functional theory of the molecules in their optimum geometries in the junction reveal the reason for this similarity in conductance, as the predicted conductance for the alcohol series of compounds varies more with the tilt angle. Thermopower measurements reveal a higher Seebeck coefficient (S) for the cross-conjugated ketone molecules relative to the alcohol derivatives, with a particularly high S for the biphenyl derivative 3a (-15.6 μV/K), an increase of threefold compared to its alcohol analog. The predicted behavior of the quantum interference (QI) in this series of cross-conjugated molecules is found to be constructive, though the appearance of a destructive QI feature for 3a is due to the degeneracy of the HOMO orbital and may explain the enhancement of the value of S for this molecule.

Computational evaluation of transport parameters and logic circuit designing of L-Lysine amino acid stringed to Au, Ag, Cu, Pt, and Pd electrodes

The integrants of proteins, i.e., amino acids, have grossed exceptional recognition for their applications towards designing imminent switching devices. Among 20 amino acids, L-Lysine (i.e., positively charged) has the highest number of CH₂ chains, and such chains affect the rectification ratio in several biomolecules. Towards molecular rectification, we investigate the transport parameters of L-Lysine in conjunction with five different coinage metal electrodes, i.e., Au, Ag, Cu, Pt and Pd to form five distinct devices. We deputize the NEGF-DFT formulism for computing conductance, frontier molecular orbitals, current-voltage, and molecular projected self-Hamiltonian calculations using a self-consistent function. We focus on the most widely used electron exchange correlation combination, i.e., the PBE version of GGA with DZDP basis set. The molecular devices under inquisition exhibit phenomenal rectification ratios (RR) in conjunction with negative differential resistance (NDR) regimes. The nominated molecular device offers a substantial rectification ratio of 45.6 with platinum electrodes and a prominent peak to valley current ratio of 1.78 with copper electrodes. We deduce from these findings that L-Lysine based molecular devices would implicit in future bio-nanoelectronic devices. The OR and AND logic gates are also proposed hinged on highest rectification ratio of L-Lysine-based devices.

Ionogel-Electrode for the Study of Protein Tunnel Junctions under Physiologically Relevant Conditions

The study of charge transport through proteins is essential for understanding complicated electrochemical processes in biological activities while the reasons for the coexistence of tunneling and hopping phenomena in protein junctions still remain unclear. In this work, a flexible and conductive ionogel electrode is synthesized and is used as a top contact to form highly reproducible protein junctions. The junctions of proteins, including human serum albumin, cytochrome C and hemoglobin, show temperature-independent electron tunneling characteristics when the junctions are in solid states while with a different mechanism of temperature-dependent electron hopping when junctions are hydrated under physiologically relevant conditions. It is demonstrated that the solvent reorganization energy plays an important role in the electron-hopping process and experimentally shown that it requires ≈100 meV for electron hopping through one heme group inside a hydrated protein molecule connected between two electrodes.

Thermoelectric Enhancement in Single Organic Radical Molecules

Organic thermoelectric materials have potential for wearable heating, cooling, and energy generation devices at room temperature. For this to be technologically viable, high-conductance (G) and high-Seebeck-coefficient (S) materials are needed. For most semiconductors, the increase in S is accompanied by a decrease in G. Here, using a combined experimental and theoretical investigation, we demonstrate that a simultaneous enhancement of S and G can be achieved in single organic radical molecules, thanks to their intrinsic spin state. A counterintuitive quantum interference (QI) effect is also observed in stable Blatter radical molecules, where constructive QI occurs for a meta-connected radical, leading to further enhancement of thermoelectric properties. Compared to an analogous closed-shell molecule, the power factor is enhanced by more than 1 order of magnitude in radicals. These results open a new avenue for the development of organic thermoelectric materials operating at room temperature.

Single-Molecule Junction Formation in Break-Junction Measurements

The scanning tunneling microscope-based break-junction (STM-BJ) technique is the most common method used to study the electronic properties of single-molecule junctions. It relies on repeatedly forming and rupturing a Au contact in an environment of the target molecules. The probability of junction formation is typically very high (∼70-95%), prompting questions relating to how the nanoscale structure of the Au electrode before the metal point contact ruptures alters junction formation. Here we analyze conductance traces measured with the STM-BJ setup by combining correlation analysis and multiple machine learning tools, including gradient-boosted trees and neural networks. We show that two key features describing the Au-Au contact prior to rupture determine the extent of contact relaxation (snapback) and the probability of junction formation. Importantly, our data strongly indicate that molecular junctions are formed prior to the rupture of the Au-Au contact, explaining the high probability of junction formation observed in room-temperature solution measurements.

Molecular electronics behaviour of L-aspartic acid using symmetrical metal electrodes

Protein-based electronics is one of the growing areas of bio-nanoelectronics, where novel electronic devices possessing distinctive properties are being fabricated using specific proteins. Furthermore, if the bio-molecule is analysed amidst different electrodes, intriguing properties are elucidated. This research article investigates the electron transport properties of L-aspartic acid (i.e. L-amino acid) bound to symmetrical electrodes of gold, silver, copper, platinum and palladium employing NEGF-DFT approach using self-consistent function. The theoretical work function of different electrodes is calculated using local density approximation and generalized gradient approximation approach. The calculated work function correlates well with the hole tunneling barrier and conductance of the molecular device, which further authenticate the coupling strength between molecule and electrode. Molecule under consideration also exhibits negative differential resistance region and rectification ratio with all the different electrodes, due to its asymmetrical structure. The molecular device using platinum electrodes exhibits the highest peak to valley ratio of 1.38 and rectification ratio of 3.20, at finite bias. The switching characteristics of different molecular device are justified with detailed transmission spectra and MPSH. These results indicate that L-aspartic acid and similar biomolecule can be vital to the growth of Proteotronics.

The Role of Metal Ions in the Electron Transport through Azurin-Based Junctions

We studied the coherent electron transport through metal–protein–metal junctions based on a blue copper azurin, in which the copper ion was replaced by three different metal ions (Co, Ni and Zn). Our results show that neither the protein structure nor the transmission at the Fermi level change significantly upon metal replacement. The discrepancy with previous experimental observations suggests that the transport mechanism taking place in these types of junctions is probably not fully coherent.

Influence of the Contact Geometry and Counterions on the Current Flow and Charge Transfer in Polyoxometalate Molecular Junctions: A Density Functional Theory Study

Polyoxometalates (POMs) are promising candidates for molecular electronic applications because (1) they are inorganic molecules, which have better CMOS compatibility compared to organic molecules; (2) they are easily synthesized in a one-pot reaction from metal oxides (MO _x ) (where the metal M can be, e.g., W, V, or Mo, and x is an integer between 4 and 7); (3) POMs can self-assemble to form various shapes and configurations, and thus the chemical synthesis can be tailored for specific device performance; and (4) they are redox-active with multiple states that have a very low voltage switching between polarized states. However, a deep understanding is required if we are to make commercial molecular devices a reality. Simulation and modeling are the most time efficient and cost-effective methods to evaluate a potential device performance. Here, we use density functional theory in combination with nonequilibrium Green's function to study the transport properties of [W₁₈O₅₄(SO₃)₂]^4-, a POM cluster, in a variety of molecular junction configurations. Our calculations reveal that the transport profile not only is linked to the electronic structure of the molecule but also is influenced by contact geometry and presence of ions. More specifically, the contact geometry and the number of bonds between the POM and the electrodes determine the current flow. Hence, strong and reproducible contact between the leads and the molecule is mandatory to establish a reliable fabrication process. Moreover, although often ignored, our simulations show that the charge balancing counterions activate the conductance channels intrinsic to the molecule, leading to a dramatic increase in the computed current at low bias. Therefore, the role of these counterions cannot be ignored when molecular based devices are fabricated. In summary, this work shows that the current transport in POM junctions is determined by not only the contact geometry between the molecule and the electrode but also the presence of ions around the molecule. This significantly impacts the transport properties in such nanoscale molecular electronic devices.

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.

Long-lived charged states of single porphyrin-tape junctions under ambient conditions

The ability to control the charge state of individual molecules wired in two-terminal single-molecule junctions is a key challenge in molecular electronics, particularly in relation to the development of molecular memory and other computational componentry. Here we demonstrate that single porphyrin molecular junctions can be reversibly charged and discharged at elevated biases under ambient conditions due to the presence of a localised molecular eigenstate close to the Fermi edge of the electrodes. In particular, we can observe long-lived charge-states with lifetimes upwards of 1-10 seconds after returning to low bias and large changes in conductance, in excess of 100-fold at low bias. Our theoretical analysis finds charge-state lifetimes within the same time range as the experiments. The ambient operation demonstrates that special conditions such as low temperatures or ultra-high vacuum are not essential to observe hysteresis and stable charged molecular junctions.

Nonconsensus motif directed chemical synthesis of glutamine-based glycopeptides

Besides the most common sequon of amino acids found in glycopeptides, namely, N-X-S/T, where X can be any amino acid except proline, a small number of nonconsensus motifs have been found in both eukaryotic and prokaryotic organisms, for example, Q-G-T. Because of the importance of glycopeptides in biotechnology and pharmacy, an adequate synthetic approach to these structures is highly important. In this manuscript, we report the efficient chemical batch synthesis of new glutamine-based glycopeptide structures, which can be used to represent cell surface elements in further biological investigations.

Connectivity dependent thermopower of bridged biphenyl molecules in single-molecule junctions

We report measurements on gold|single-molecule|gold junctions, using a modified scanning tunneling microscope-break junction (STM-BJ) technique, of the Seebeck coefficient and electrical conductance of a series of bridged biphenyl molecules, with meta connectivities to pyridyl anchor groups. These data are compared with a previously reported study of para-connected analogues. In agreement with a tight binding model, the electrical conductance of the meta series is relatively low and is sensitive to the nature of the bridging groups, whereas in the para case the conductance is higher and relatively insensitive to the presence of the bridging groups. This difference in sensitivity arises from the presence of destructive quantum interference in the π system of the unbridged aromatic core, which is alleviated to different degrees by the presence of bridging groups. More precisely, the Seebeck coefficient of meta-connected molecules was found to vary between -6.1 μV K^-1 and -14.1 μV K^-1, whereas that of the para-connected molecules varied from -5.5 μV K^-1 and -9.0 μV K^-1.