Electron Flow through Proteins

Protein Electronic Energy Transport Levels Derived from High-Sensitivity Near-UV and Constant Final State Yield Photoemission Spectroscopy

Proteins are attractive as functional components in molecular junctions. However, controlling the electronic charge transport via proteins, held between two electrodes, requires information on their frontier orbital energy level alignment relative to the electrodes' Fermi level (EF), which normally requires studies of UV Photoemission Spectroscopy (UPS) with HeI excitation. Such excitation is problematic for proteins, which can denature under standard measuring conditions. Here high-sensitivity soft UV photoemission spectroscopy (HS-UPS) combined with Constant Final State Yield Spectroscopy (CFS-YS) is used to get this information for electrode/protein contacts. Monolayers of the redox protein Azurin, (Az) and its Apo-form on Au substrates, have HOMO onset energies, obtained from CFS-YS, differ by ≈0.2 eV, showing the crucial role of the Cu redox centre in the electron transport process. It is found that combined HS-UPS/CFS-YS measurements agree with the Photoelectron Yield Spectroscopy (PYS), showing potential of the HS-UPS + CFS-YS as a powerful tool to characterize and map the energetics of a protein-electrode interfaces, which will aid optimizing design of devices with targeted electronic properties, as well as for novel applications.

An Expansion of Polarization Control Using Semiconductor-Liquid Junctions

This report examines the concept of independent control over current and applied potential in electrocatalysis, as a means of improving control over product selectivity. Previous work, while permitting separate modulation of current and potentiostat bias, precluded independent control over the current flow and applied cell potential. This study seeks to resolve that limitation by exploiting the Schottky diode behavior inherent to semiconductor-electrolyte interfaces. Light is explored as a prospective second degree of freedom for controlling polarization in a suitably designed, photoelectrochemical (PEC) device, enabling the arbitrary selection of current with respect to an applied cell potential. In contrast to metal electrodes, the property of light-dependent carrier concentrations in semiconductors forms the operative means of controlling charge fluxes at some arbitrary applied potential in PEC devices featuring a semiconductor-liquid junction. This functionality enables exploration of polarization states distinct from those accessible with a dark cell, with implications for improved control over electrochemical reactions.

Overview of Injectable Hydrogels for the Treatment of Myocardial Infarction

Myocardial infarction (MI) triggers adverse remodeling mechanisms, thus leading to heart failure. Since the application of biomaterial-based scaffolds emerged as a viable approach for providing mechanical support and promoting cell growth, injectable hydrogels have garnered substantial attention in MI treatment because of their minimally invasive administration through injection and diminished risk of infection. To fully understand the interplay between injectable hydrogels and infarcted myocardium repair, this review provides an overview of recent advances in injectable hydrogel-mediated MI therapy, including: I) material designs for repairing the infarcted myocardium, considering the pathophysiological mechanism of MI and design principles for biomaterials in MI treatment; II) the development of injectable functional hydrogels for MI treatment, including conductive, self-healing, drug-loaded, and stimulus-responsive hydrogels; and III) research progress in using injectable hydrogels to restore cardiac function in infarcted myocardium by promoting neovascularization, enhancing cardiomyocyte proliferation, decreasing myocardial fibrosis, and inhibiting excessive inflammation. Overall, this review presents the current state of injectable hydrogel research in MI treatment, offering valuable information to facilitate interdisciplinary knowledge transfer and enable the development of prognostic markers for suitable injectable materials.

A bacteriorhodopsin-based biohybrid solar cell using carbon-based electrolyte and cathode components

There is currently a high demand for energy production worldwide, mainly producing renewable and sustainable energy. Bio-sensitized solar cells (BSCs) are an excellent option in this field due to their optical and photoelectrical properties developed in recent years. One of the biosensitizers that shows promise in simplicity, stability and quantum efficiency is bacteriorhodopsin (bR), a photoactive, retinal-containing membrane protein. In the present work, we have utilized a mutant of bR, D96N, in a photoanode-sensitized TiO2 solar cell, integrating low-cost, carbon-based components, including a cathode composed of PEDOT (poly(3,4-ethylenedioxythiophene) functionalized with multi-walled carbon nanotubes (CNT) and a hydroquinone/benzoquinone (HQ/BQ) redox electrolyte. The photoanode and cathode were characterized morphologically and chemically (SEM, TEM, and Raman). The electrochemical performance of the bR-BSCs was investigated using linear sweep voltammetry (LSV), open circuit potential decay (VOC), and impedance spectroscopic analysis (EIS). The champion device yielded a current density (JSC) of 1.0 mA/cm2, VOC of -669 mV, a fill factor of ~24 %, and a power conversion efficiency (PCE) of 0.16 %. This bR device is one of the first bio-based solar cells utilizing carbon-based alternatives for the photoanode, cathode, and electrolyte. This may decrease the cost and significantly improve the device's sustainability.

Exploring π-π interactions and electron transport in complexes involving a hexacationic host and PAH guest: a promising avenue for molecular devices

Single isolated molecules and supramolecular host-guest systems, which consist of π-π stacking interactions, are emerging as promising building blocks for creating molecular electronic devices. In this article, we have investigated the noncovalent π-π interaction and intermolecular electron charge transport involved in a series of host-guest complexes formed between a cage-like host (H6+) and polycyclic aromatic hydrocarbon (PAH) guests (G1-G7) using different quantum chemical approaches. The host (H6+) consists of two triscationic π-electron-deficient trispyridiniumtriazine (TPZ3+) units that are bridged face-to-face by three ethylene-triazole-ethylene. Our theoretical calculations show that the perylene and naphthalene inclusion complexes G7⊂H and G1⊂H have the highest and lowest interaction energies, respectively. In addition, energy decomposition analysis (EDA) indicated that the dispersion interaction term, ΔEdisp, significantly contributes to the host-guest interaction and is correlated with the existence of π-π van der Waals interaction. Using the nonequilibrium Greens function (NEGF) method in combination with density functional theory (DFT), the current-voltage (I-V) curves of the complexes were estimated. The conductance values increased when the guests were embedded inside the host cavity. Notably, the complex G7⊂H has the maximum conductance value. Overall, this study provided the electron transport of the PAH inclusion host-guest complex through π-π interaction and provided a direction for the fabrication of future supramolecular molecular devices.

n → π* Interaction Enabling Transient Inversion of Chirality

This study reports the observation and characterization of two isomers of the acrolein dimer by using high-resolution rotational spectroscopy in pulsed jets. The first isomer is stabilized by two hydrogen bonds, adopting a planar configuration, and is energetically favored over the second isomer, which exhibits a dominant n → π* interaction in a nearly orthogonal arrangement. Surprisingly, the n → π* interaction was revealed to enable a concerted tunneling motion of two moieties along the carbonyl group. This motion leads to the inversion of transient chirality associated with the exchange of donor-acceptor roles, as revealed by the spectral feature of quadruplets. Inversion of transient chirality is a fundamental phenomenon in quantum mechanics and commonly observed for only inversional motions of protons. It is the first discovery, to the best of our knowledge, that such heavy moieties can also undergo chirality inversion.

Stereoselective amino acid synthesis by synergistic photoredox-pyridoxal radical biocatalysis

Developing synthetically useful enzymatic reactions that are not known in biochemistry and organic chemistry is an important challenge in biocatalysis. Through the synergistic merger of photoredox catalysis and pyridoxal 5'-phosphate (PLP) biocatalysis, we developed a pyridoxal radical biocatalysis approach to prepare valuable noncanonical amino acids, including those bearing a stereochemical dyad or triad, without the need for protecting groups. Using engineered PLP enzymes, either enantiomeric product could be produced in a biocatalyst-controlled fashion. Synergistic photoredox-pyridoxal radical biocatalysis represents a powerful platform with which to discover previously unknown catalytic reactions and to tame radical intermediates for asymmetric catalysis.

Electronic coupling and electron transfer in hydrogen-bonded mixed-valence compounds

Electron transfer provided by hydrogen bonds represents a unique and highly significant area of research, as it has a crucial role to play in a wide variety of chemical and biological systems. The hydrogen-bonded mixed-valence system, in the form of donor-hydrogen bond-acceptor, provides an ideal platform for exploring thermally-induced electron transfer across this non-covalent unit. Over the past decades, ongoing progress has been made in this field. Here we critically assess some studies on the qualitative and quantitative evaluation of electronic coupling and thermal electron transfer across hydrogen bond interface. Additionally, selected experimental examples are discussed in terms of intervalence charge transfer, with particular attention paid to the proton-coupled and often overlooked proton-uncoupled electron transfer pathway in hydrogen-bonded mixed-valence systems. We further highlight the major limitations of this research area and suggest potential directions for future exploration.

Protein Orientation Defines Rectification of Electronic Current via Solid-State Junction of Entire Photosystem-1 Complex

We demonstrate that the direction of current rectification via one of nature's most efficient light-harvesting systems, the photosystem 1 complex (PS1), can be controlled by its orientation on Au substrates. Molecular self-assembly of the PS1 complex using four different linkers with distinct functional head groups that interact by electrostatic and hydrogen bonds with different surface parts of the entire protein PS1 complex was used to tailor the PS1 orientation. We observe an orientation-dependent rectification in the current-voltage characteristics for linker/PS1 molecule junctions. Results of an earlier study using a surface two-site PS1 mutant complex having its orientation set by covalent binding to the Au substrate supports our conclusion. Current-voltage-temperature measurements on the linker/PS1 complex indicate off-resonant tunneling as the main electron transport mechanism. Our ultraviolet photoemission spectroscopy results highlight the importance of the protein orientation for the energy level alignment and provide insight into the charge transport mechanism via the PS1 transport chain.

Chances and challenges of long-distance electron transfer for cellular redox reactions

Biological redox reactions often use a set-up in which final redox partners are localized in different compartments and electron transfer (ET) among them is mediated by redox-active molecules. In enzymes, these ET processes occur over nm distances, whereas multi-protein filaments bridge μm ranges. Electrons are transported over cm ranges in cable bacteria, which are formed by thousands of cells. In this review, we describe molecular mechanisms that explain how respiration in a compartmentalized set-up ensures redox homeostasis. We highlight mechanistic studies on ET through metal-free peptides and proteins demonstrating that long-distance ET is possible because amino acids Tyr, Trp, Phe, and Met can act as relay stations. This cuts one long ET into several short reaction steps. The chances and challenges of long-distance ET for cellular redox reactions are then discussed.

Cofactor Dynamics Couples the Protein Surface to the Heme in Cytochrome c, Facilitating Electron Transfer

Electron transport through biomolecules and in biological transport networks is of great importance to bioenergetics and biocatalysis. More generally, it is of crucial importance to understand how the pathways that connect buried metallocofactors to other cofactors, and to protein surfaces, affect the biological chemistry of metalloproteins. In terms of electron transfer (ET), the strongest coupling pathways usually comprise covalent and hydrogen bonded networks, with a limited number of through-space contacts. Herein, we set out to determine the relative roles of hydrogen bonds involved in ET via an established heme-to-surface tunneling pathway in cytochrome (cyt) c (i.e., heme-W59-D60-E61-N62). A series of cyt c variants were produced where a ruthenium tris(diimine) photooxidant was placed at position 62 via covalent modification of the N62C residue. Surprisingly, variants where the H-bonding residues W59 and D60 were replaced (i.e., W59F and D60A) showed no change in ET rate from the ferrous heme to Ru(III). In contrast, changing the composition of an alternative tunneling pathway (i.e., heme-M64-N63-C62) with the M64L substitution shows a factor of 2 decrease in the rate of heme-to-Ru ET. This pathway involves a through-space tunneling step between the heme and M64 residue, and such steps are usually disfavored. To rationalize why the heme-M64-N63-C62 is preferred, molecular dynamics (MD) simulations and Pathways analysis were employed. These simulations show that the change in heme-Ru ET rates is attributed to different conformations with compressed donor-acceptor distances, by ∼2 Å in pathway distance, in the M64-containing protein as compared to the M64L protein. The change in distance is correlated with changes in the electronic coupling that are in accord with the experimentally observed heme-Ru ET rates. Remarkably, the M64L variation at the core of the protein translates to changes in cofactor dynamics at the protein surface. The surface changes identified by MD simulations include dynamic anion-π and dipole-dipole interactions. These interactions influence the strength of tunneling pathways and ET rates by facilitating decreases in through-space tunneling distances in key coupling pathways.

Cellular sentience as the primary source of biological order and evolution

All life is cellular, starting some 4 billion years ago with the emergence of the first cells. In order to survive their early evolution in the face of an extremely challenging environment, the very first cells invented cellular sentience and cognition, allowing them to make relevant decisions to survive through creative adaptations in a continuously running evolutionary narrative. We propose that the success of cellular life has crucially depended on a biological version of Maxwell's demons which permits the extraction of relevant sensory information and energy from the cellular environment, allowing cells to sustain anti-entropic actions. These sensor-effector actions allowed for the creative construction of biological order in the form of diverse organic macromolecules, including crucial polymers such as DNA, RNA, and cytoskeleton. Ordered biopolymers store analogue (structures as templates) and digital (nucleotide sequences of DNA and RNA) information that functioned as a form memory to support the development of organisms and their evolution. Crucially, all cells are formed by the division of previous cells, and their plasma membranes are physically and informationally continuous across evolution since the beginning of cellular life. It is argued that life is supported through life-specific principles which support cellular sentience, distinguishing life from non-life. Biological order, together with cellular cognition and sentience, allow the creative evolution of all living organisms as the authentic authors of evolutionary novelty.

On the roles of methionine and the importance of its microenvironments in redox metalloproteins

The amino acid residue methionine (Met) is commonly thought of as a ligand in redox metalloproteins, for example in cytochromes c and in blue copper proteins. However, the roles of Met can go beyond a simple ligand. The thioether functional group of Met allows it to be considered as a hydrophobic residue as well as one that is capable of weak dipolar interactions. In addition, the lone pairs on sulphur allow Met to interact with other groups, inluding the aforementioned metal ions. Because of its properties, Met can play diverse roles in metal coordination, fine tuning of redox reactions, or supporting protein structures. These roles are strongly influenced by the nature of the surrounding medium. Herein, we describe several common interactions between Met and surrounding aromatic amino acids and how they affect the physical properties of both copper and iron metalloproteins. While the importance of interactions between Met and other groups is established in biological systems, less is known about their roles in redox metalloproteins and our view is that this is an area that is ready for greater attention.

Efficient Intermolecular Charge Transport in π-Stacked Pyridinium Dimers Using Cucurbit[8]uril Supramolecular Complexes

Intermolecular charge transport through π-conjugated molecules plays an essential role in biochemical redox processes and energy storage applications. In this work, we observe highly efficient intermolecular charge transport upon dimerization of pyridinium molecules in the cavity of a synthetic host (cucurbit[8]uril, CB[8]). Stable, homoternary complexes are formed between pyridinium molecules and CB[8] with high binding affinity, resulting in an offset stacked geometry of two pyridiniums inside the host cavity. The charge transport properties of free and dimerized pyridiniums are characterized using a scanning tunneling microscope-break junction (STM-BJ) technique. Our results show that π-stacked pyridinium dimers exhibit comparable molecular conductance to isolated, single pyridinium molecules, despite a longer transport pathway and a switch from intra- to intermolecular charge transport. Control experiments using a CB[8] homologue (cucurbit[7]uril, CB[7]) show that the synthetic host primarily serves to facilitate dimer formation and plays a minimal role on molecular conductance. Molecular modeling using density functional theory (DFT) reveals that pyridinium molecules are planarized upon dimerization inside the host cavity, which facilitates charge transport. In addition, the π-stacked pyridinium dimers possess large intermolecular LUMO-LUMO couplings, leading to enhanced intermolecular charge transport. Overall, this work demonstrates that supramolecular assembly can be used to control intermolecular charge transport in π-stacked molecules.

Photophysical Properties of BODIPY Derivatives for the Implementation of Organic Solar Cells: A Computational Approach

Solar cells based on organic compounds are a proven emergent alternative to conventional electrical energy generation. Here, we provide a computational study of power conversion efficiency optimization of boron dipyrromethene (BODIPY) derivatives by means of their associated open-circuit voltage, short-circuit density, and fill factor. In doing so, we compute for the derivatives' geometrical structures, energy levels of frontier molecular orbitals, absorption spectra, light collection efficiencies, and exciton binding energies via density functional theory (DFT) and time-dependent (TD)-DFT calculations. We fully characterize four D-π-A (BODIPY) molecular systems of high efficiency and improved J _sc that are well suited for integration into bulk heterojunction (BHJ) organic solar cells as electron-donor materials in the active layer. Our results are twofold: we found that molecular complexes with a structural isoxazoline ring exhibit a higher power conversion efficiency (PCE), a useful result for improving the BHJ current, and, on the other hand, by considering the molecular systems as electron-acceptor materials, with P3HT as the electron donor in the active layer, we found a high PCE compound favorability with a pyrrolidine ring in its structure, in contrast to the molecular systems built with an isoxazoline ring. The theoretical characterization of the electronic properties of the BODIPY derivatives provided here, computed with a combination of ab initio methods and quantum models, can be readily applied to other sets of molecular complexes to hierarchize optimal power conversion efficiency.

Functional and protective hole hopping in metalloenzymes

Electrons can tunnel through proteins in microseconds with a modest release of free energy over distances in the 15 to 20 Å range. To span greater distances, or to move faster, multiple charge transfers (hops) are required. When one of the reactants is a strong oxidant, it is convenient to consider the movement of a positively charged "hole" in a direction opposite to that of the electron. Hole hopping along chains of tryptophan (Trp) and tyrosine (Tyr) residues is a critical function in several metalloenzymes that generate high-potential intermediates by reactions with O2 or H2O2, or by activation with visible light. Examination of the protein structural database revealed that Tyr/Trp chains are common protein structural elements, particularly among enzymes that react with O2 and H2O2. In many cases these chains may serve a protective role in metalloenzymes by deactivating high-potential reactive intermediates formed in uncoupled catalytic turnover.

Prediction of the standard potentials for one-electron oxidation of N,N,N',N' tetrasubstituted p-phenylenediamines by calculation

The formal potentials for the reversible one-electron oxidation of N,N,N',N' tetrasubstituted p-phenylenediamines in acetonitrile have been applied as a test set for benchmarking computational methods for a series of compounds with only small structural differences. The aim of the study is to propose a simple method for calculating the standard oxidation potentials, and therefore, the protocol is progressively developed by adding more terms in the energy expression. In addition, the effect of including implicit solvation models (IEFPCM, CPCM, and SMD), larger basis sets, and correlation methods are investigated. The oxidation potentials calculated using the G3MP2B3 approach with IEFPCM resulted in the best fit (R² = 0.9624), but the slope of the correlation line, 0.74, is far from the optimal value, 1.00. B3LYP/6-311++G(d,p) and TPSSh/6-311++G(2d,p) yielded only slightly less consistent data (R² = 0.9388 and R² = 0.9425), but with much better slopes, 1.00 and 0.94, respectively. We conclude that it is important to investigate the basis set size and treatment of electron correlation when calculating oxidation potentials for N,N,N',N' tetrasubstituted p-phenylenediamines.

Atomic and Electronic Structure of Pilus from Geobacter sulfurreducens through QM/MM Calculations: Evidence for Hole Transfer in Aromatic Residues

Long-range electron transport has been widely and experimentally reported in Geobacter sulfurreducens pilus protein. However, a better understanding of the still undefined molecular arrangement can bring to light the role of key residues in this phenomenon. We propose a theoretical investigation of the electronic structure of aromatic residue groups in the protein through a classical molecular dynamics (MD) simulation, followed by a quantum mechanics/molecular mechanics (QM/MM) electronic study of different frames sampled from MD trajectories, an electrostatic potential and electron density analysis, an analysis of the density of states, and an investigation of hole formation through Dyson orbital calculations. We observe a highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy gap in the ranges of 1.4-2.3 eV and 2.9-3.3 eV and a less intense dipole moment along the aromatic residues in the presence of water in comparison to the system in vacuum. HOMO and LUMO electron densities highlight the occupation of one tyrosine residue in every representation for HOMO and a delocalization along two to three rings for LUMO. The results show how the electronic structure of the aromatic residues is sensitive to the ring arrangement and the surrounding environment. In our study, we observe that slight rearrangements in the fiber geometry can create temporary conditions for hole transfer.

Nickel-Sulfonate Mode of Substrate Binding for Forward and Reverse Reactions of Methyl-SCoM Reductase Suggest a Radical Mechanism Involving Long-Range Electron Transfer

Methyl-coenzyme M reductase (MCR) catalyzes both the synthesis and the anaerobic oxidation of methane (AOM). Its catalytic site contains Ni at the core of cofactor F430. The Ni ion, in its low-valent Ni(I) state, lights the fuse leading to homolysis of the C-S bond of methyl-coenzyme M (methyl-SCoM) to generate a methyl radical, which abstracts a hydrogen atom from coenzyme B (HSCoB) to generate methane and the mixed disulfide CoMSSCoB. Direct reversal of this reaction activates methane to initiate anaerobic methane oxidation. On the basis of the crystal structures, which reveal a Ni-thiol interaction between Ni(II)-MCR and inhibitor CoMSH, a Ni(I)-thioether complex with substrate methyl-SCoM has been transposed to canonical MCR mechanisms. Similarly, a Ni(I)-disulfide with CoMSSCoB is proposed for the reverse reaction. However, this Ni(I)-sulfur interaction poses a conundrum for the proposed hydrogen-atom abstraction reaction because the >6 Å distance between the thiol group of SCoB and the thiol of SCoM observed in the structures appears to be too long for such a reaction. The spectroscopic, kinetic, structural, and computational studies described here establish that both methyl-SCoM and CoMSSCoB bind to the active Ni(I) state of MCR through their sulfonate groups, forming a hexacoordinate Ni(I)-N/O complex, not Ni(I)-S. These studies rule out direct Ni(I)-sulfur interactions in both substrate-bound states. As a solution to the mechanistic conundrum, we propose that both the forward and the reverse MCR reactions emanate through long-range electron transfer from the Ni(I)-sulfonate complexes with methyl-SCoM and CoMSSCoB, respectively.

Lone-Pair-Induced Structural Ordering in the Mixed-Valent 0D Metal-Halides Rb23BiIII x SbIII 7-x SbV 2Cl54 (0 ≤ x ≤ 7)

Mixed-valent metal-halides containing ns² lone pairs may exhibit intense visible absorption, while zero-dimensional (0D) ns²-based metal-chlorides are generally colorless but have demonstrated promising optoelectronic properties suitable for thermometry and radiation detection. Here, we report solvothermally synthesized mixed-valent 0D metal-halides Rb₂₃Bi^III _x Sb^III _7-x Sb^V ₂Cl₅₄ (0 ≤ x ≤ 7). Rb₂₃Sb^III ₇Sb^V ₂Cl₅₄ crystallizes in an orthorhombic space group (Cmcm) with a unique, layered 0D structure driven by the arrangement of the 5s² lone pairs of the Sb^IIICl₆ octahedra. This red material is likely the true structure of a previously reported monoclinic "Rb_2.67SbCl₆" phase, the structure of which was not determined. Partially or fully substituting Sb^III with isoelectronic Bi^III yields the series Rb₂₃Bi^III _x Sb^III _7-x Sb^V ₂Cl₅₄ (0 < x ≤ 7), which exhibits a similar layered 0D structure but with additional disorder that yields a trigonal crystal system with an enantiomorphic space group (R32). Second harmonic generation of 532 nm light from a 1064 nm laser using Rb₂₃Bi^III ₇Sb^V ₂Cl₅₄ powder confirms the noncentrosymmetry of this space group. As with the prototypical mixed-valent pnictogen halides, the visible absorption bands of the Rb₂₃Bi^III _x Sb^III _7-x Sb^V ₂Cl₅₄ family are the result of intervalent Sb^III-Sb^V and mixed-valent Bi^III-Sb^V charge transfer bands (CTB), with a blueshift of the absorption edge as Bi^III substitution increases. No PL is observed from this family of semiconductors, but a crystal of Rb₂₃Bi^III ₇Sb^V ₂Cl₅₄ exhibits a high resistivity of 1.0 × 10¹⁰ Ω·cm and X-ray photoconductivity with a promising μτ product of 8.0 × 10^-5 cm² s^-1 V^-1. The unique 0D layered structures of the Rb₂₃Bi^III _x Sb^III _7-x Sb^V ₂Cl₅₄ family highlight the versatility of the ns² lone pair in semiconducting metal-halides, pointing the way toward new functional 0D metal-halide compounds.

Theoretical Study of Shallow Distance Dependence of Proton-Coupled Electron Transfer in Oligoproline Peptides

Long-range electron transfer is coupled to proton transfer in a wide range of chemically and biologically important processes. Recently the proton-coupled electron transfer (PCET) rate constants for a series of biomimetic oligoproline peptides linking Ru(bpy)₃²⁺ to tyrosine were shown to exhibit a substantially shallower dependence on the number of proline spacers compared to the analogous electron transfer (ET) systems. The experiments implicated a concerted PCET mechanism involving intramolecular electron transfer from tyrosine to Ru(bpy)₃³⁺ and proton transfer from tyrosine to a hydrogen phosphate dianion. Herein these PCET systems, as well as the analogous ET systems, are studied with microsecond molecular dynamics, and the ET and PCET rate constants are calculated with the corresponding nonadiabatic theories. The molecular dynamics simulations illustrate that smaller ET donor-acceptor distances are sampled by the PCET systems than by the analogous ET systems. The shallower dependence of the PCET rate constant on the ET donor-acceptor distance is explained in terms of an additional positive, distance-dependent electrostatic term in the PCET driving force, which attenuates the rate constant at smaller distances. This electrostatic term depends on the change in the electrostatic interaction between the charges on each end of the bridge and can be modified by altering these charges. On the basis of these insights, this theory predicted a less shallow distance dependence of the PCET rate constant when imidazole rather than hydrogen phosphate serves as the proton acceptor, even though their pK_a values are similar. This theoretical prediction was subsequently validated experimentally, illustrating that long-range electron transfer processes can be tuned by modifying the nature of the proton acceptor in concerted PCET processes. This level of control has broad implications for the design of more effective charge-transfer systems.

Shallow Distance Dependence for Proton-Coupled Tyrosine Oxidation in Oligoproline Peptides

We have explored the kinetic effect of increasing electron transfer (ET) distance in a biomimetic, proton-coupled electron-transfer (PCET) system. Biological ET often occurs simultaneously with proton transfer (PT) in order to avoid the high-energy, charged intermediates resulting from the stepwise transfer of protons and electrons. These concerted proton-electron-transfer (CPET) reactions are implicated in numerous biological ET pathways. In many cases, PT is coupled to long-range ET. While many studies have shown that the rate of ET is sensitive to the distance between the electron donor and acceptor, extensions to biological CPET reactions are sparse. The possibility of a unique ET distance dependence for CPET reactions deserves further exploration, as this could have implications for how we understand biological ET. We therefore explored the ET distance dependence for the CPET oxidation of tyrosine in a model system. We prepared a series of metallopeptides with a tyrosine separated from a Ru(bpy)32+ complex by an oligoproline bridge of increasing length. Rate constants for intramolecular tyrosine oxidation were measured using the flash-quench transient absorption technique in aqueous solutions. The rate constants for tyrosine oxidation decreased by 125-fold with three added proline residues between tyrosine and the oxidant. By comparison, related intramolecular ET rate constants in very similar constructs were reported to decrease by 4-5 orders of magnitude over the same number of prolines. The observed shallow distance dependence for tyrosine oxidation is proposed to originate in part from the requirement for stronger oxidants, leading to a smaller hole-transfer effective tunneling barrier height. The shallow distance dependence observed here and extensions to distance-dependent CPET reactions have potential implications for long-range charge transfers.

Catalysis and Electron Transfer in De Novo Designed Helical Scaffolds

The relationship between protein structure and function is one of the greatest puzzles within biochemistry. De novo metalloprotein design is a way to wipe the board clean and determine what is required to build in function from the ground up in an unrelated structure. This Review focuses on protein design efforts to create de novo metalloproteins within alpha-helical scaffolds. Examples of successful designs include those with carbonic anhydrase or nitrite reductase activity by incorporating a ZnHis3 or CuHis3 site, or that recapitulate the spectroscopic properties of unique electron-transfer sites in cupredoxins (CuHis2 Cys) or rubredoxins (FeCys4 ). This work showcases the versatility of alpha helices as scaffolds for metalloprotein design and the progress that is possible through careful rational design. Our studies cover the invariance of carbonic anhydrase activity with different site positions and scaffolds, refinement of our cupredoxin models, and enhancement of nitrite reductase activity up to 1000-fold.

Unravelling electron transfer in peptide-cation complexes: a model for mimicking redox centres in proteins

We provide evidence that bound zinc promotes electron transfer in a peptide by changing the electronic properties of the peptide.

Soil solid-phase organic matter-mediated microbial reduction of iron minerals increases with land use change sequence from fallow to paddy fields

The microbial reduction of Fe(III) minerals (MRF) is an important process in paddy soil because it can affect the biogeochemical cycles of many major and trace elements. Natural organic matter (NOM) that mainly exists in the form of solid phase in soil can mediate MRF through electron shuttling functionality. However, whether a link exists between solid-phase NOM-mediated MRF in soil and the age of paddy field since the reclamation on fallow is unclear. Here, we use microbial reduction method to assess the solid-phase NOM-mediated MRF of paddy soils with different reclamation ages. The results show that solid-phase NOM-mediated MRF exhibits a positive response to land use change sequence from fallow to paddy field, indicating that the long-term natural development of paddy field favors the electron shuttling of NOM between cells and Fe(III) minerals. This increase in the electron shuttling of NOM is not due to the increase in the redox functional groups of NOM, but may be attributed to the formation of NOM-mineral complex through the synergistic increases in NOM content and transformation of soil texture from clay loam to loam. The decrease in the redox potential of Fe(III) minerals in soil caused by decreased pH and the increase in Fe content in the organic matter-complexed form may also partly facilitate electron transfer from NOM to Fe(III) minerals. Our work is useful in predicting the role of soil solid-phase NOM in mediating MRF in the context of long-term reclamation of paddy field and provides guidance for the environmental management of paddy fields.

Assessing Possible Mechanisms of Micrometer-Scale Electron Transfer in Heme-Free Geobacter sulfurreducens Pili

The electrically conductive pili of Geobacter sulfurreducens are of both fundamental and practical interest. They facilitate extracellular and interspecies electron transfer (ET) and also provide an electrical interface between living and nonliving systems. We examine the possible mechanisms of G. sulfurreducens electron transfer in regimes ranging from incoherent to coherent transport. For plausible ET parameters, electron transfer in G. sulfurreducens bacterial nanowires mediated only by the protein is predicted to be dominated by incoherent hopping between phenylalanine (Phe) and tyrosine (Tyr) residues that are 3 to 4 Å apart, where Phe residues in the hopping pathways may create delocalized "islands." This mechanism could be accessible in the presence of strong oxidants that are capable of oxidizing Phe and Tyr residues. We also examine the physical requirements needed to sustain biological respiration via nanowires. We find that the hopping regimes with ET rates on the order of 10⁸ s^-1 between Phe islands and Tyr residues, and conductivities on the order of mS/cm, can support ET fluxes that are compatible with cellular respiration rates, although sustaining this delocalization in the heterogeneous protein environment may be challenging. Computed values of fully coherent electron fluxes through the pili are orders of magnitude too low to support microbial respiration. We suggest experimental probes of the transport mechanism based on mutant studies to examine the roles of aromatic amino acids and yet to be identified redox cofactors.

Repeat proteins as versatile scaffolds for arrays of redox-active FeS clusters

Molecular string of beads: modular extension of a protein backbone builds a chain of electroactive clusters.

Arrays of one, two and four electron-transfer active [4Fe–4S] clusters were constructed on modular tetratricopeptide repeat protein scaffolds, with the number of clusters determined solely by the size of the scaffold. The constructs show reversible redox activity and transient charge stabilization necessary to facilitate charge transfer.

How a cofactor-free protein environment lowers the barrier to O2 reactivity

Molecular oxygen (O₂)-utilizing enzymes are among the most important in biology. The abundance of O₂, its thermodynamic power, and the benign nature of its end products have raised interest in oxidases and oxygenases for biotechnological applications. Although most O₂-dependent enzymes have an absolute requirement for an O₂-activating cofactor, several classes of oxidases and oxygenases accelerate direct reactions between substrate and O₂ using only the protein environment. Nogalamycin monooxygenase (NMO) from Streptomyces nogalater is a cofactor-independent enzyme that catalyzes rate-limiting electron transfer between its substrate and O₂ Here, using enzyme-kinetic, cyclic voltammetry, and mutagenesis methods, we demonstrate that NMO initially activates the substrate, lowering its pK_a by 1.0 unit (ΔG* = 1.4 kcal mol^-1). We found that the one-electron reduction potential, measured for the deprotonated substrate both inside and outside the protein environment, increases by 85 mV inside NMO, corresponding to a ΔΔG ⁰' of 2.0 kcal mol^-1 (0.087 eV) and that the activation barrier, ΔG ^‡, is lowered by 4.8 kcal mol^-1 (0.21 eV). Applying the Marcus model, we observed that this suggests a sizable decrease of 28 kcal mol^-1 (1.4 eV) in the reorganization energy (λ), which constitutes the major portion of the protein environment's effect in lowering the reaction barrier. A similar role for the protein has been proposed in several cofactor-dependent systems and may reflect a broader trend in O₂-utilizing proteins. In summary, NMO's protein environment facilitates direct electron transfer, and NMO accelerates rate-limiting electron transfer by strongly lowering the reorganization energy.

The Dynamical Emergence of Biology From Physics: Branching Causation via Biomolecules

Biology differs fundamentally from the physics that underlies it. This paper proposes that the essential difference is that while physics at its fundamental level is Hamiltonian, in biology, once life has come into existence, causation of a contextual branching nature occurs at every level of the hierarchy of emergence at each time. The key feature allowing this to happen is the way biomolecules such as voltage-gated ion channels can act to enable branching logic to arise from the underlying physics, despite that physics per se being of a deterministic nature. Much randomness occurs at the molecular level, which enables higher level functions to select lower level outcomes according to higher level needs. Intelligent causation occurs when organisms engage in deduction, enabling prediction and planning. This is possible because ion channels enable action potentials to propagate in axons. The further key feature is that such branching biological behavior acts down to cause the underlying physical interactions to also exhibit a contextual branching behavior.

Optical and Electronic Properties of Molecular Systems Derived from Rhodanine

Push-pull functional compounds consisting of dicyanorhodanine derivatives have attracted a lot of interest because their optical, electronic, and charge transport properties make them useful as building blocks for organic photovoltaic implementations. The analysis of the frontier molecular orbitals shows that the vertical transitions of electronic absorption are characterized as intramolecular charge transfer; furthermore, we show that the analyzed compounds exhibit bathochromic displacements when comparing the presence (or absence) of solvent as an interacting medium. In comparison with materials defined by their energy of reorganization of electrons (holes) as electron (hole) transporters, we find a transport hierarchy whereby the molecule ( Z)-2-(1,1-dicyanomethylene)-5-[(4-dimethylamino)benzylidene]-1,3-thiazol-4 is better at transporting holes than molecule ( Z)-2-(1,1-dicyanomethylene)-5-(tetrathiafulvalene-2-ylidene)-1,3-thiazol-4.

Stable Mixed-Valent Complexes Formed by Electron Delocalization Across Hydrogen Bonds of Pyrimidinone-Linked Metal Clusters

Electron transfer across a mixed-valent hydrogen-bonded self-dimer of oxo-centered triruthenium clusters bridged by a pair of 4(3 H)-pyrimidinones is reported. Spectroelectrochemical studies in methylene chloride reveal that 1 rapidly self-dimerizes upon one-electron reduction, forming the strongly coupled mixed-valent hydrogen-bonded dimer (1₂)^-. In the mixed-valent state, significantly broadened, partially coalesced ν(CO) bands are observed, allowing estimation of the electron transfer rate ( k_ET) by an optical Bloch line shape analysis. Simulation of the FTIR line shapes provides an estimate of k_ET on the order of 10¹¹ s^-1, indicating a highly delocalized electronic structure across the hydrogen bonds. These findings are supported by the determination of the formation constant ( K_MV) for (1₂)^-, which is found to be on the order of 10⁶ M^-1, or nearly 4 orders of magnitude higher than that for the neutral isovalent dimer (1₂). This represents a stabilization of approximately 5.7 kcal/mol (1980 cm^-1) arising from electron exchange across the hydrogen bonds in the mixed-valent state. Significantly, an enormous intensity enhancement of the amide ν(NH) band (3300 cm^-1) of (1₂)^- is observed, supporting strong mixing of the bridging ligand vibrational modes with the electronic wave function of the mixed-valent state. These findings demonstrate strong donor-bridge-acceptor coupling and that highly delocalized electronic structures can be attained in hydrogen-bonded systems, which are often considered to be too weakly bound to support strong electronic communication.

Tunneling explains efficient electron transport via protein junctions

Metalloproteins, proteins containing a transition metal ion cofactor, are electron transfer agents that perform key functions in cells. Inspired by this fact, electron transport across these proteins has been widely studied in solid-state settings, triggering the interest in examining potential use of proteins as building blocks in bioelectronic devices. Here, we report results of low-temperature (10 K) electron transport measurements via monolayer junctions based on the blue copper protein azurin (Az), which strongly suggest quantum tunneling of electrons as the dominant charge transport mechanism. Specifically, we show that, weakening the protein-electrode coupling by introducing a spacer, one can switch the electron transport from off-resonant to resonant tunneling. This is a consequence of reducing the electrode's perturbation of the Cu(II)-localized electronic state, a pattern that has not been observed before in protein-based junctions. Moreover, we identify vibronic features of the Cu(II) coordination sphere in transport characteristics that show directly the active role of the metal ion in resonance tunneling. Our results illustrate how quantum mechanical effects may dominate electron transport via protein-based junctions.

Amide Neighbouring-Group Effects in Peptides: Phenylalanine as Relay Amino Acid in Long-Distance Electron Transfer

In nature, proteins serve as media for long-distance electron transfer (ET) to carry out redox reactions in distant compartments. This ET occurs either by a single-step superexchange or through a multi-step charge hopping process, which uses side chains of amino acids as stepping stones. In this study we demonstrate that Phe can act as a relay amino acid for long-distance electron hole transfer through peptides. The considerably increased susceptibility of the aromatic ring to oxidation is caused by the lone pairs of neighbouring amide carbonyl groups, which stabilise the Phe radical cation. This neighbouring-amide-group effect helps improve understanding of the mechanism of extracellular electron transfer through conductive protein filaments (pili) of anaerobic bacteria during mineral respiration.

Microbial nanowires - Electron transport and the role of synthetic analogues

Electron transfer is central to cellular life, from photosynthesis to respiration. In the case of anaerobic respiration, some microbes have extracellular appendages that can be utilised to transport electrons over great distances. Two model organisms heavily studied in this arena are Shewanella oneidensis and Geobacter sulfurreducens. There is some debate over how, in particular, the Geobacter sulfurreducens nanowires (formed from pilin nanofilaments) are capable of achieving the impressive feats of natural conductivity that they display. In this article, we outline the mechanisms of electron transfer through delocalised electron transport, quantum tunnelling, and hopping as they pertain to biomaterials. These are described along with existing examples of the different types of conductivity observed in natural systems such as DNA and proteins in order to provide context for understanding the complexities involved in studying the electron transport properties of these unique nanowires. We then introduce some synthetic analogues, made using peptides, which may assist in resolving this debate. Microbial nanowires and the synthetic analogues thereof are of particular interest, not just for biogeochemistry, but also for the exciting potential bioelectronic and clinical applications as covered in the final section of the review.

STATEMENT OF SIGNIFICANCE

Some microbes have extracellular appendages that transport electrons over vast distances in order to respire, such as the dissimilatory metal-reducing bacteria Geobacter sulfurreducens. There is significant debate over how G. sulfurreducens nanowires are capable of achieving the impressive feats of natural conductivity that they display: This mechanism is a fundamental scientific challenge, with important environmental and technological implications. Through outlining the techniques and outcomes of investigations into the mechanisms of such protein-based nanofibrils, we provide a platform for the general study of the electronic properties of biomaterials. The implications are broad-reaching, with fundamental investigations into electron transfer processes in natural and biomimetic materials underway. From these studies, applications in the medical, energy, and IT industries can be developed utilising bioelectronics.

An internal electron reservoir enhances catalytic CO2 reduction by a semisynthetic enzyme

The development of an artificial metalloenzyme for CO2 reduction is described. The small-molecule catalyst [Ni(II)(cyclam)](2+) has been incorporated within azurin. Selectivity for CO generation over H(+) reduction is enhanced within the protein environment, while the azurin active site metal impacts the electrochemical overpotential and photocatalytic activity. The enhanced catalysis observed for copper azurin suggests an important role for intramolecular electron transfer, analogous to native CO2 reducing enzymes.

Effects of electron transfer on the stability of hydrogen bonds

The measurement of the dimerization constants of hydrogen-bonded ruthenium complexes (1₂, 2₂, 3₂) linked by a self-complementary pair of 4-pyridylcarboxylic acid ligands in different redox states is reported.

The measurement of the dimerization constants of hydrogen-bonded ruthenium complexes (1₂, 2₂, 3₂) linked by a self-complementary pair of 4-pyridylcarboxylic acid ligands in different redox states is reported. Using a combination of FTIR and UV/vis/NIR spectroscopies, the dimerization constants (K_D) of the isovalent, neutral states, 1₂, 2₂, 3₂, were found to range from 75 to 130 M^–1 (ΔG⁰ = –2.56 to –2.88 kcal mol^–1), while the dimerization constants (K_2–) of the isovalent, doubly-reduced states, (1₂)^2–, (2₂)^2–, (3₂)^2–, were found to range from 2000 to 2500 M^–1 (ΔG⁰ = –4.5 to –4.63 kcal mol^–1). From the aforementioned values and the comproportionation constant for the mixed-valent dimers, the dimerization constants (K_MV) of the mixed-valent, hydrogen-bonded dimers, (1₂)^–, (2₂)^–, (3₂)^–, were found to range from 0.5 × 10⁶ to 1.2 × 10⁶ M^–1 (ΔG⁰ = –7.78 to –8.31 kcal mol^–1). On average, the hydrogen-bonded, mixed-valent states are stabilized by –5.27 (0.04) kcal mol^–1 relative to the isovalent, neutral, hydrogen-bonded dimers and –3.47 (0.06) kcal mol^–1 relative to the isovalent, dianionic hydrogen bonded dimers. Electron exchange in the mixed valence states imparts significant stability to hydrogen bonding. This is the first quantitative measurement of the strength of hydrogen bonds in the presence and absence of electronic exchange.

Intramolecular Photogeneration of a Tyrosine Radical in a Designed Protein

Long-distance biological electron transfer occurs through a hopping mechanism and often involves tyrosine as a high potential intermediate, for example in the early charge separation steps during photosynthesis. Protein design allows for the development of minimal systems to study the underlying principles of complex systems. Herein, we report the development of the first ruthenium-linked designed protein for the photogeneration of a tyrosine radical by intramolecular electron transfer.

A π-π conjugation-containing soft and conductive injectable polymer hydrogel highly efficiently rebuilds cardiac function after myocardial infarction

Previous studies suggested that a stiffer hydrogel system exhibited a better performance to promote heart function after myocardial infarction (MI). However, the nature of myocardium, a tissue that alternately contracts and relaxes with electrical impulses, leads us to hypothesize that a soft and conductive hydrogel may be in favor of mechanical and electrical signals transmission to enhance heart function after MI. In this work, π-π conjugation interaction was first employed to produce a soft injectable hydrogel with conductive property. Melamine with π-π conjugation ring was used as a core to synthesize a multi-armed crosslinker PEGDA700-Melamine (PEG-MEL), which could crosslink with thiol-modified hyaluronic acid (HA-SH) to form an injectable hydrogel rapidly. By incorporating graphene oxide (GO), the injectable PEG-MEL/HA-SH/GO hydrogel exhibited a soft (G' = 25 Pa) and anti-fatigue mechanical property and conductive property (G = 2.84 × 10^-4 S/cm). The hydrogel encapsulating adipose tissue-derived stromal cells (ADSCs) was injected into MI area of rats. The significant increase in α-Smooth Muscle Actin (α-SMA) and Connexin 43 (Cx43) expression confirmed that the gel efficiently promoted the transmission of mechanical and electrical signals. Meanwhile, a significant improvement of heart functions, such as distinct increase of ejection fraction (EF), smaller infarction size, less fibrosis area, and higher vessel density, was achieved.

Genetically encoded conductive protein nanofibers secreted by engineered cells

Bacterial biofilms are promising tools for functional applications as bionanomaterials.

{Ru(CO)x}-Core complexes with benzimidazole ligands: synthesis, X-ray structure and evaluation of anticancer activity in vivo

fac-[Ru^II(CO)₃Cl₂(MBI)] and -[Ru^II(CO)₃Cl₂(DMBI)] are CO-releasing materials able to link histidines of proteins, and the latter showed antitumor effects in murine colon cancer.