Biochemistry and theory of proton-coupled electron transfer

Evidence for a Proton-Coupled Electron Transfer Mechanism in a Biomimetic System for Monoamine Oxidase B Catalysis

Mechanistic studies with 5-ethyl-3-methyllumiflavinium (Fl⁺ ) perchlorate, a biomimetic model for flavoenzyme monoamine oxidase B (MAO-B) catalysis, and the tertiary, allyl amine 1-methyl-4-(1-methyl-1 H-pyrrol-2-yl)-1,2,3,6-tetrahydropyridine (MMTP) reveal that proton-coupled electron transfer (PCET) may be an important pathway for MAO catalysis. The first step involves a single-electron transfer (SET) leading to the free radicals Fl^. and MMTP^. , the latter produced by deprotonation of the initially formed and highly acidic MMTP^.+ . Molecular oxygen (O₂ ) is found to play a hitherto unrecognized role in the early steps of the oxidation. MMTP and several structurally similar tertiary amines are the only tertiary amines oxidized by MAO, and their structural/electronic properties provide the key to understanding this behavior. A general hypothesis about the role of SET in MAO catalysis, and the recognition that PCET occurs with appropriately substituted substrates is presented.

Charge separation and successive reconfigurations of electronic and protonic states in a water-splitting catalytic cycle with the Mn4CaO5 cluster. On the mechanism of water splitting in PSII

Charge separation, reloading of electrons and protons, and O₂ generation in a catalytic cycle for water splitting with Mn₄CaO₅ in PSII.

Redox-Active Guanidines in Proton-Coupled Electron-Transfer Reactions: Real Alternatives to Benzoquinones?

Guanidino-functionalized aromatics (GFAs) are readily available, stable organic redox-active compounds. In this work we apply one particular GFA compound, 1,2,4,5-tetrakis(tetramethylguanidino)benzene, in its oxidized form in a variety of oxidation/oxidative coupling reactions to demonstrate the scope of its proton-coupled electron transfer (PCET) reactivity. Addition of an excess of acid boosts its oxidation power, enabling the oxidative coupling of substrates with redox potentials of at least +0.77 V vs. Fc⁺ /Fc. The green recyclability by catalytic re-oxidation with dioxygen is also shown. Finally, a direct comparison indicates that GFAs are real alternatives to toxic halo- or cyano-substituted benzoquinones.

Mediation of Electron Transfer by Quadrupolar Interactions: The Constitutional, Electronic, and Energetic Complementarities in Supramolecular Chemistry

Studies of intermolecular interactions enhance our knowledge of chemistry across molecular and supramolecular levels. Here, we show that host-guest quadrupolar interaction has a profound influence on the molecular system. With covalently bonded dimolybdenum complex units as the electron donor (D) and acceptor (A) and a thienylene group (C₄H₂S) as the bridge (B), the mixed-valence D-B-A complexes are shaped with clefts in the middle of the molecule. Interestingly, in aromatic solvents, the D-A electronic coupling constants (H_ab) and electron transfer rates (k_et) are dramatically reduced. Theoretical computations indicate that an aromatic molecule is encapsulated in the cleft of the D-B-A array; quadrupole-quadrupole interaction between the guest molecule and the C₄H₂S bridge evokes a charge redistribution, which increases the HOMO-LUMO energy gap, intervening in the through-bond electron transfer. These results demonstrate that a supramolecular system is unified underlying the characteristics of the assembled molecules through constitutional, electronic, and energetic complementarities.

Correlations between Spectra and Resistivity in Transition Metal Oxides

A comparison between photoconductivity spectra and resistivity in two transition metal oxides, La_2-xSr_xCuO₄ and La_1-xSr_xVO₃, is presented. The resistivities ρ(T) for x < 0.05 in the cuprate and x < 0.28 in the vanadate are typical for single electron transfer. For T > 100 K, ρ(T) - ρ(0) ∼ T^3/2. For higher dopings (x) the cuprate is a superconductor (x < 0.25) and the vanadate an ordinary metal. This tallies with the number of oxidation states and their spins when the electrons transfer locally. The insulator-metal transition and the vanishing of Cooper pairs are discussed in the conclusion.

Tuning Radical Relay Residues by Proton Management Rescues Protein Electron Hopping

Transient tyrosine and tryptophan radicals play key roles in the electron transfer (ET) reactions of photosystem (PS) II, ribonucleotide reductase (RNR), photolyase, and many other proteins. However, Tyr and Trp are not functionally interchangeable, and the factors controlling their reactivity are often unclear. Cytochrome c peroxidase (CcP) employs a Trp191^•+ radical to oxidize reduced cytochrome c (Cc). Although a Tyr191 replacement also forms a stable radical, it does not support rapid ET from Cc. Here we probe the redox properties of CcP Y191 by non-natural amino acid substitution, altering the ET driving force and manipulating the protic environment of Y191. Higher potential fluorotyrosine residues increase ET rates marginally, but only addition of a hydrogen bond donor to Tyr191^• (via Leu232His or Glu) substantially alters activity by increasing the ET rate by nearly 30-fold. ESR and ESEEM spectroscopies, crystallography, and pH-dependent ET kinetics provide strong evidence for hydrogen bond formation to Y191^• by His232/Glu232. Rate measurements and rapid freeze quench ESR spectroscopy further reveal differences in radical propagation and Cc oxidation that support an increased Y191^• formal potential of ∼200 mV in the presence of E232. Hence, Y191 inactivity results from a potential drop owing to Y191^•+ deprotonation. Incorporation of a well-positioned base to accept and donate back a hydrogen bond upshifts the Tyr^• potential into a range where it can effectively oxidize Cc. These findings have implications for the Y_Z/Y_D radicals of PS II, hole-hopping in RNR and cryptochrome, and engineering proteins for long-range ET reactions.

Stabilizing Low-Coordinated O Ions To Operate Cationic and Anionic Redox Chemistry of Li-Ion Battery Materials

Conventional electrochemical processes are mainly operated by cationic redox chemistry. Developing cumulative cationic and anionic redox chemistry offers a transformative approach to increase the energy storage capacity of Li-ion batteries and active sites of catalysts. However, realizing the reversible anionic redox reaction to increase the specific capacity in Li-ion battery materials is a large challenge because uncontrollable anion-anion combination and gas evolutions cause poor cyclic performance. Here, we use open-framework metal-fluorides (FeF₃·0.33H₂O) to demonstrate cumulative cationic and anionic redox reactions to be realized through O substitution. Experimental studies verified that O substitution could form reductive O ions, and stabilizing this reductive low-coordinated O by p-d orbital hybridization and hydrogen-transfer-mediated O-H bond formation plays an important role in operating anionic electrochemistry. O substitution also exhibits an improved cyclic performance beyond the insertion-reaction capacity (150 mA h/g) of FeF₃·0.33H₂O (225 and 300 mA h/g). Theoretical calculations show that FeF_2.67O_0.33·0.33H₂O exhibits a 50% higher insertion-reaction capacity (225 mA h/g) than FeF₃·0.33H₂O (150 mA h/g) before structural collapse, which is attributed to cumulative cationic (Fe³⁺ ↔ Fe²⁺) and anionic (O^- ↔ O^2-) redox reactions based on our electronic structure analysis. The present study opens a new avenue to develop cationic and anionic electrochemistry to improve the storage capacity and cyclic performance through stabilizing low-coordinated O ions.

Ultrafast Oxidation of a Tyrosine by Proton-Coupled Electron Transfer Promotes Light Activation of an Animal-like Cryptochrome

The animal-like cryptochrome of Chlamydomonas reinhardtii (CraCRY) is a recently discovered photoreceptor that controls the transcriptional profile and sexual life cycle of this alga by both blue and red light. CraCRY has the uncommon feature of efficient formation and longevity of the semireduced neutral form of its FAD cofactor upon blue light illumination. Tyrosine Y₃₇₃ plays a crucial role by elongating , as fourth member, the electron transfer (ET) chain found in most other cryptochromes and DNA photolyases, which comprises a conserved tryptophan triad. Here, we report the full mechanism of light-induced FADH^• formation in CraCRY using transient absorption spectroscopy from hundreds of femtoseconds to seconds. Electron transfer starts from ultrafast reduction of excited FAD to FAD^•- by the proximal tryptophan (0.4 ps) and is followed by delocalized migration of the produced WH^•+ radical along the tryptophan triad (∼4 and ∼50 ps). Oxidation of Y₃₇₃ by coupled ET to WH^•+ and deprotonation then proceeds in ∼800 ps, without any significant kinetic isotope effect, nor a pH effect between pH 6.5 and 9.0. The FAD^•-/Y₃₇₃^• pair is formed with high quantum yield (∼60%); its intrinsic decay by recombination is slow (∼50 ms), favoring reduction of Y₃₇₃^• by extrinsic agents and protonation of FAD^•- to form the long-lived, red-light absorbing FADH^• species. Possible mechanisms of tyrosine oxidation by ultrafast proton-coupled ET in CraCRY, a process about 40 times faster than the archetypal tyrosine-Z oxidation in photosystem II, are discussed in detail.

Characterization of perdeuterated high-potential iron-sulfur protein with high-resolution X-ray crystallography

Perdeuteration in neutron crystallography is an effective method for determining the positions of hydrogen atoms in proteins. However, there is shortage of evidence that the high-resolution details of perdeuterated proteins are consistent with those of the nondeuterated proteins. In this study, we determined the X-ray structure of perdeuterated high-potential iron-sulfur protein (HiPIP) at a high resolution of 0.85 å resolution. The comparison of the nondeuterated and perdeuterated structures of HiPIP revealed slight differences between the two structures. The spectroscopic and spectroelectrochemical studies also showed that perdeuterated HiPIP has approximately the same characteristics as nondeuterated HiPIP. These results further emphasize the suitability of using perdeuterated proteins in the high-resolution neutron crystallography.

Zero-field nuclear magnetic resonance of chemically exchanging systems

Zero- to ultralow-field (ZULF) nuclear magnetic resonance (NMR) is an emerging tool for precision chemical analysis. In this work, we study dynamic processes and investigate the influence of chemical exchange on ZULF NMR J-spectra. We develop a computational approach that allows quantitative calculation of J-spectra in the presence of chemical exchange and apply it to study aqueous solutions of [¹⁵N]ammonium (¹⁵N\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathrm{H}}_4^ +$$\end{document}H4+) as a model system. We show that pH-dependent chemical exchange substantially affects the J-spectra and, in some cases, can lead to degradation and complete disappearance of the spectral features. To demonstrate potential applications of ZULF NMR for chemistry and biomedicine, we show a ZULF NMR spectrum of [2-¹³C]pyruvic acid hyperpolarized via dissolution dynamic nuclear polarization (dDNP). We foresee applications of affordable and scalable ZULF NMR coupled with hyperpolarization to study chemical exchange phenomena in vivo and in situations where high-field NMR detection is not possible to implement.

Zero-field nuclear magnetic resonance can identify species and collective behaviors in mixtures without applied magnetic fields. Here the authors demonstrate its use for resolving proton exchange in ammonium and for the detection of hyperpolarized pyruvic acid, an important imaging biomarker.

Mechanistic Studies of Proton-Coupled Electron Transfer in a Calorimetry Cell

Mechanistic studies of proton-coupled electron-transfer (PCET) reactions in proteins are complicated by the challenge of following proton transfer (PT) in these large molecules. Herein we describe the use of isothermal titration calorimetry (ITC) to establish proton involvement in protein redox reactions and the identity of PT sites. We validate this approach with three variants of a heme protein cytochrome c (cyt c) and show that the method yields a wealth of thermodynamic information that is important for characterizing PCET reactions, including reduction potentials, redox-dependent p K_a values, and reaction enthalpies for both electron-transfer (ET) and PT steps. We anticipate that this facile and label-free ITC approach will find widespread applications in studies of other redox proteins and enhance our knowledge of PCET reaction mechanisms.

1H high field electron-nuclear double resonance spectroscopy at 263 GHz/9.4 T

We present and discuss the performance of ¹H electron-nuclear double resonance (ENDOR) at 263 GHz/9.4 T by employing a prototype, commercial quasi optical spectrometer. Basic instrumental features of the setup are described alongside a comprehensive characterization of the new ENDOR probe head design. The performance of three different ENDOR pulse sequences (Davies, Mims and CP-ENDOR) is evaluated using the ¹H BDPA radical. A key feature of 263 GHz spectroscopy - the increase in orientation selectivity in comparison with 94 GHz experiments - is discussed in detail. For this purpose, the resolution of ¹H ENDOR spectra at 263 GHz is verified using a representative protein sample containing approximately 15 picomoles of a tyrosyl radical. Davies ENDOR spectra recorded at 5 K reveal previously obscured spectral features, which are interpreted by spectral simulations aided by DFT calculations. Our analysis shows that seven internal proton couplings are detectable for this specific radical if sufficient orientation selectivity is achieved. The results prove the fidelity of 263 GHz experiments in reporting orientation-selected ¹H ENDOR spectra and demonstrate that new significant information can be uncovered in complex molecular systems, owing to the enhanced resolution combined with high absolute sensitivity and no compromise in acquisition time.

On the Elementary Chemical Mechanisms of Unidirectional Proton Transfers: A Nonadiabatic Electron-Wavepacket Dynamics Study

We propose a set of chemical reaction mechanisms of unidirectional proton transfers, which may possibly work as an elementary process in chemical and biological systems. Being theoretically derived based on our series of studies on charge separation dynamics in water splitting by Mn oxides, the present mechanisms have been constructed after careful exploration over the accumulated biological studies on cytochrome c oxidase (CcO) and bacteriorhodopsin. In particular, we have focused on the biochemical findings in the literature that unidirectional transfers of approximately two protons are driven by one electron passage through the reaction center (binuclear center) in CcO, whereas no such dissipative electron transfer is believed to be demanded in the proton transport in bacteriorhodopsin. The proposed basic mechanisms of unidirectional proton transfers are further reduced to two elementary dynamical processes, namely, what we call the coupled proton and electron-wavepacket transfer (CPEWT) and the inverse CPEWT. To show that the proposed mechanisms can indeed be materialized in a molecular level, we construct model systems with possible molecules that are rather familiar in biological chemistry, for which we perform the ab initio calculations of full-dimensional nonadiabatic electron-wavepacket dynamics coupled with all nuclear motions including proton transfers.

Efficient electron transfer across hydrogen bond interfaces by proton-coupled and -uncoupled pathways

Thermal electron transfer through hydrogen bonds remains largely unexplored. Here we report the study of electron transfer through amide-amide hydrogen bonded interfaces in mixed-valence complexes with covalently bonded Mo₂ units as the electron donor and acceptor. The rate constants for electron transfer through the dual hydrogen bonds across a distance of 12.5 Å are on the order of ∼ 10¹⁰ s^-1, as determined by optical analysis based on Marcus-Hush theory and simulation of ν(NH) vibrational band broadening, with the electron transfer efficiencies comparable to that of π conjugated bridges. This work demonstrates that electron transfer across a hydrogen bond may proceed via the known proton-coupled pathway, as well as an overlooked proton-uncoupled pathway that does not involve proton transfer. A mechanistic switch between the two pathways can be achieved by manipulation of the strengths of electronic coupling and hydrogen bonding. The knowledge of the non-proton coupled pathway has shed light on charge and energy transport in biological systems.

Probing the Proton-Coupled Electron-Transfer (PCET) Reactivity of a Cross-Conjugated Cruciform Chromophore by Redox-State-Dependent Fluorescence

Proton-coupled electron transfer (PCET) reactions are of great importance in synthetic chemistry and in biology, but the acquisition of kinetic information for these reactions is often difficult. Herein, we report the synthesis of a new PCET reagent, showing redox-state dependent fluorescence, by merging the concept of cross-conjugated cruciform chromophores with the strategy of imposing redox activity and Brønsted basicity to aromatic compounds by substitution with guanidino groups. The compound is isolated and characterized in all stable states-reduced, twofold and fourfold protonated and twofold oxidized-and then applied in PCET reactions by using its redox-state dependent fluorescence signal for kinetic measurements.

Thermal Activation of CH4 and H2 as Mediated by the Ruthenium Oxide Cluster Ions [RuOx ]+ (x=1-3): On the Influence of Oxidation States

Thermal gas-phase reactions of the ruthenium-oxide clusters [RuO_x ]⁺ (x=1-3) with methane and dihydrogen have been explored by using FT-ICR mass spectrometry complemented by high-level quantum chemical calculations. For methane activation, as compared to the previously studied [RuO]⁺ /CH₄ couple, the higher oxidized Ru systems give rise to completely different product distributions. [RuO₂ ]⁺ brings about the generations of [Ru,O,C,H₂ ]⁺ /H₂ O, [Ru,O,C]⁺ /H₂ /H₂ O, and [Ru,O,H₂ ]⁺ /CH₂ O, whereas [RuO₃ ]⁺ exhibits a higher selectivity and efficiency in producing formaldehyde and syngas (CO+H₂ ). Regarding the reactions with H₂ , as compared to CH₄ , both [RuO]⁺ and [RuO₂ ]⁺ react similarly inefficiently with oxygen-atom transfer being the main reaction channel; in contrast, [RuO₃ ]⁺ is inert toward dihydrogen. Theoretical analysis reveals that the reduction of the metal center drives the overall oxidation of methane, whereas the back-bonding orbital interactions between the cluster ions and dihydrogen control the H-H bond activation. Furthermore, the reactivity patterns of [RuO_x ]⁺ (x=1-3) with CH₄ and H₂ have been compared with the previously reported results of Group 8 analogues [OsO_x ]⁺ /CH₄ /H₂ (x=1-3) and the [FeO]⁺ /H₂ system. The electronic origins for their distinctly different reaction behaviors have been addressed.

Microsolvation of the Redox-Active Tyrosine-D in Photosystem II: Correlation of Energetics with EPR Spectroscopy and Oxidation-Induced Proton Transfer

Photosystem II (PSII) of oxygenic photosynthesis captures sunlight to drive the catalytic oxidation of water and the reduction of plastoquinone. Among the several redox-active cofactors that participate in intricate electron transfer pathways there are two tyrosine residues, YZ and YD. They are situated in symmetry-related electron transfer branches but have different environments and play distinct roles. YZ is the immediate oxidant of the oxygen-evolving Mn4CaO5 cluster, whereas YD serves regulatory and protective functions. The protonation states and hydrogen-bond network in the environment of YD remain debated, while the role of microsolvation in stabilizing different redox states of YD and facilitating oxidation or mediating deprotonation, as well the fate of the phenolic proton, is unclear. Here we present detailed structural models of YD and its environment using large-scale quantum mechanical models and all-atom molecular dynamics of a complete PSII monomer. The energetics of water distribution within a hydrophobic cavity adjacent to YD are shown to correlate directly with electron paramagnetic resonance (EPR) parameters such as the tyrosyl g-tensor, allowing us to map the correspondence between specific structural models and available experimental observations. EPR spectra obtained under different conditions are explained with respect to the mode of interaction of the proximal water with the tyrosyl radical and the position of the phenolic proton within the cavity. Our results revise previous models of the energetics and build a detailed view of the role of confined water in the oxidation and deprotonation of YD. Finally, the model of microsolvation developed in the present work rationalizes in a straightforward way the biphasic oxidation kinetics of YD, offering new structural insights regarding the function of the radical in biological photosynthesis.

Grand-canonical approach to density functional theory of electrocatalytic systems: Thermodynamics of solid-liquid interfaces at constant ion and electrode potentials

Properties of solid-liquid interfaces are of immense importance for electrocatalytic and electrochemical systems, but modeling such interfaces at the atomic level presents a serious challenge and approaches beyond standard methodologies are needed. An atomistic computational scheme needs to treat at least part of the system quantum mechanically to describe adsorption and reactions, while the entire system is in thermal equilibrium. The experimentally relevant macroscopic control variables are temperature, electrode potential, and the choice of the solvent and ions, and these need to be explicitly included in the computational model as well; this calls for a thermodynamic ensemble with fixed ion and electrode potentials. In this work, a general framework within density functional theory (DFT) with fixed electron and ion chemical potentials in the grand canonical (GC) ensemble is established for modeling electrocatalytic and electrochemical interfaces. Starting from a fully quantum mechanical description of multi-component GC-DFT for nuclei and electrons, a systematic coarse-graining is employed to establish various computational schemes including (i) the combination of classical and electronic DFTs within the GC ensemble and (ii) on the simplest level a chemically and physically sound way to obtain various (modified) Poisson-Boltzmann (mPB) implicit solvent models. The detailed and rigorous derivation clearly establishes which approximations are needed for coarse-graining as well as highlights which details and interactions are omitted in vein of computational feasibility. The transparent approximations also allow removing some of the constraints and coarse-graining if needed. We implement various mPB models within a linear dielectric continuum in the GPAW code and test their capabilities to model capacitance of electrochemical interfaces as well as study different approaches for modeling partly periodic charged systems. Our rigorous and well-defined DFT coarse-graining scheme to continuum electrolytes highlights the inadequacy of current linear dielectric models for treating properties of the electrochemical interface.

Understanding Short-Range Electron-Transfer Dynamics in Proteins

Short-range electron-transfer (ET) reactions in biological systems are usually ultrafast, having transfer rates comparable to or even faster than corresponding environmental fluctuations, and often display nonexponential behaviors. To understand these nonequilibrium ET dynamics, we carried out detailed theoretical analyses based on the Sumi-Marcus model. It is shown that the ET dynamics is largely determined by the relative time scales of the ET reaction and its surrounding motions. Significantly, different environmental fluctuations can produce a variety of apparent ET dynamics even with the same driving force, Δ G^o, and reorganization energy, λ. We applied our analyses to an ultrafast ET process in DNA repair by (6-4) photolyase and directly obtained the inner and outer reorganization energies (λ_i and λ_o) as well as the free energy Δ G^o of various mutants, providing mechanical insight into ultrafast short-range ET reactions in proteins.

Why Are DNA and Protein Electron Transfer So Different?

The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free of mechanistic bombshells? I suggest that this difference originates in the distinct electronic energy landscapes for the two classes of reactions. In proteins, the donor/acceptor-to-bridge energy gap is typically several-fold larger than in NAs. NA ET can access tunneling, hopping, and resonant transport among the bases, and fluctuations can enable switching among mechanisms; protein ET is restricted to tunneling among redox active cofactors and, under strongly oxidizing conditions, a few privileged amino acid side chains. This review aims to provide conceptual unity to DNA and protein ET reaction mechanisms. The establishment of a unified mechanistic framework enabled the successful design of NA experiments that switch electronic coherence effects on and off for ET processes on a length scale of multiple nanometers and promises to provide inroads to directing and detecting charge flow in soft-wet matter.

Significance of hydrogen bonding networks in the proton-coupled electron transfer reactions of photosystem II from a quantum-mechanics perspective

All quantum-mechanical calculations provide insights into the effect of the hydrogen bonding network on the proton-coupled electron transfer at Y_Z and Y_D in photosystem II.

Electron bifurcation: progress and grand challenges

Electron bifurcation moves electrons from a two-electron donor to reduce two spatially separated one-electron acceptors.

Proton-coupled electron transfer in the reduction of diiron hexacarbonyl complexes and its enhancement on the electrocatalytic reduction of protons by a pendant basic group

The pendant basic groups in a diiron complex acted as proton relay to ease the kinetic resistance in proton reduction and enhance proton-coupled electron transfer (PCET).

Recent advances in bioinspired proton-coupled electron transfer

Fundamental aspects of PCET continue to attract attention. Understanding this reaction type is desirable for small-molecule activation and solar energy conversion.

Excited state structural dynamics of 4-cyano-4′-hydroxystilbene: deciphering the signatures of proton-coupled electron transfer using ultrafast Raman loss spectroscopy

The photo-initiated proton-coupled electron transfer process in the 4-cyano-4′-hydroxystilbene–tert-butylamine adduct strongly affects the excited-state structural dynamics of CHSB.

Photochemical reactivity of phenyl (methyl-tetrazolyl) ketone – hydrogen atom transfer vs. electron transfer

A novel photochemical electron transfer step is observed when a heteroaromatic substituent is present in an aromatic ketone.

Intrinsic Reactivity of Diatomic 3d Transition-Metal Carbides in the Thermal Activation of Methane: Striking Electronic Structure Effects

Mechanistic aspects of the C-H bond activation of methane by metal-carbide cations MC⁺ of the 3d transition-metals Sc-Zn were elucidated by NEVPT2//CASSCF quantum-chemical calculations and verified experimentally for M = Ti, V, Fe, and Cu by using Fourier transform ion-cyclotron resonance mass spectrometry. While MC⁺ species with M = Sc, Ti, V, Cr, Cu, and Zn activate CH₄ at ambient temperature, this is prevented with carbide cations of M = Mn, Fe, and Co by high apparent barriers; NiC⁺ has a small apparent barrier. Hydrogen-atom transfers from methane to metal-carbide cations were found to proceed via a proton-coupled electron transfer mechanism for M = Sc-Co; wherein the doubly occupied π_xz/yz-orbitals between metal and carbon at the carbon site serve as electron donors and the corresponding metal-centered vacant π*_xz/yz-orbitals as electron acceptors. Classical hydrogen-atom transfer transpires only in the case of NiC⁺, while ZnC⁺ follows a mechanistic scenario, in which a formally hydridic hydrogen is transferred. CuC⁺ reacts by a synchronous activation of two C-H bonds. While spin density is often so crucial for the reactions of numerous MO⁺/CH₄ couples, it is much less important for the C-H bond activation by carbide cations of the 3d transition-metals, in which one notes large changes in bond dissociation energies, spin states, number of d-electrons, and charge distributions. All these factors jointly affect both the reactivity of the metal carbides and their mechanisms of C-H bond activation.

Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function

Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.

Solvent-dependent transition from concerted electron-proton to proton transfer in photoinduced reactions between phenols and polypyridine Ru complexes with proton-accepting sites

The bimolecular rate coefficients (kobsq) for quenching the metal-to-ligand charge transfer excited states of two Ru polypyridine complexes containing H-bond accepting sites by six p-substituted phenols exhibit abrupt deviations from the expected linear correlations of log kobsq with phenol's Hammett σp constant. This pattern is attributed to a transition of the quenching mechanism from a concerted electron-proton transfer (EPT) to a proton transfer (PT); the latter becomes predominant for the most acidic phenols in acetonitrile, but not in dichloromethane. This assertion is supported by a detailed thermochemical analysis, which also excludes the quenching pathways involving electron transfer from phenols with or without deprotonation of phenols to the solvent, either concerted or sequential. The transition from EPT to PT upon the σp increase is consistent/supported by the magnitudes of the measured and computed PhOH/OD kinetic isotope effects and by the observed reduction of the EPT product yields upon replacing the low σp methoxyphenol by the high σp nitrophenol. In addition to modulating the relative contribution of the EPT and PT quenching pathways, the solvent strongly affects the bimolecular rate coefficients for the EPT quenching proper. Unlike with H-atom transfer reactions, this kinetic solvent effect could not be quantitatively accounted for by the phenol-solvent H-bonding alone, which suggests a solvent effect on the H-bonding constants in the phenol-Ru complex precursor exciplexes and/or on the unimolecular EPT rate coefficients within these exciplexes.

Theoretical study of proton coupled electron transfer reaction in the light state of the AppA BLUF photoreceptor

The BLUF (blue light sensor using flavin adenine dinucleotide) domain is widely studied as a prototype for proton coupled electron transfer (PCET) reactions in biological systems. In this work, the photo-induced concerted PCET reaction from the light state of the AppA BLUF domain is investigated. To model the simultaneous transfer of two protons in the reaction, two-dimensional potential energy surfaces for the double proton transfer are first calculated for the locally excited and charge transfer states, which are then used to obtain the vibrational wave function overlaps and the vibrational energy levels. Contributions to the PCET rate constant from each pair of vibronic states are then analyzed using the theory based on the Fermi's golden rule. We show that, the recently proposed light state structure of the BLUF domain with a tautomerized Gln63 residue is consistent with the concerted transfer of one electron and two protons. It is also found that, thermal fluctuations of the protein structure, especially the proton donor-acceptor distances, play an important role in determining the PCET reaction rate. © 2018 Wiley Periodicals, Inc.

Selective C-O Coupling Hidden in the Thermal Reaction of [Al2 CuO5 ]+ with Methane

The thermal gas-phase reaction of [Al₂ CuO₅ ]⁺ with methane has been explored by using FT-ICR mass spectrometry complemented by high-level quantum chemical calculations. The generation of atomic [Cu]⁺ from the [Al₂ CuO₅ ]⁺ /CH₄ couple corresponds to the only reaction channel. Labeling experiments and computational studies strongly suggest that methane activation is indeed involved in the production of [Cu]⁺ , and generation of CH₂ O prevails. Mechanistic aspects and the associated doping effects are discussed.

Beyond the classical thermodynamic contributions to hydrogen atom abstraction reactivity

Hydrogen atom abstraction (HAA) reactions are cornerstones of chemistry. Various (metallo)enzymes performing the HAA catalysis evolved in nature and inspired the rational development of multiple synthetic catalysts. Still, the factors determining their catalytic efficiency are not fully understood. Herein, we define the simple thermodynamic factor η by employing two thermodynamic cycles: one for an oxidant (catalyst), along with its reduced, protonated, and hydrogenated form; and one for the substrate, along with its oxidized, deprotonated, and dehydrogenated form. It is demonstrated that η reflects the propensity of the substrate and catalyst for (a)synchronicity in concerted H⁺/e^- transfers. As such, it significantly contributes to the activation energies of the HAA reactions, in addition to a classical thermodynamic (Bell-Evans-Polanyi) effect. In an attempt to understand the physicochemical interpretation of η, we discovered an elegant link between η and reorganization energy λ from Marcus theory. We discovered computationally that for a homologous set of HAA reactions, λ reaches its maximum for the lowest |η|, which then corresponds to the most synchronous HAA mechanism. This immediately implies that among HAA processes with the same reaction free energy, ΔG ₀, the highest barrier (≡ΔG ^≠) is expected for the most synchronous proton-coupled electron (i.e., hydrogen) transfer. As proof of concept, redox and acidobasic properties of nonheme Fe^IVO complexes are correlated with activation free energies for HAA from C-H and O-H bonds. We believe that the reported findings may represent a powerful concept in designing new HAA catalysts.

Diabatic model for electrochemical hydrogen evolution based on constrained DFT configuration interaction

The accuracy of density functional theory (DFT) based kinetic models for electrocatalysis is diminished by spurious electron delocalization effects, which manifest as uncertainties in the predicted values of reaction and activation energies. In this work, we present a constrained DFT (CDFT) approach to alleviate overdelocalization effects in the Volmer-Heyrovsky mechanism of the hydrogen evolution reaction (HER). This method is applied a posteriori to configurations sampled along a reaction path to correct their relative stabilities. Concretely, the first step of this approach involves describing the reaction in terms of a set of diabatic states that are constructed by imposing suitable density constraints on the system. Refined reaction energy profiles are then recovered by performing a configuration interaction (CDFT-CI) calculation within the basis spanned by the diabatic states. After a careful validation of the proposed method, we examined HER catalysis on open-ended carbon nanotubes and discovered that CDFT-CI increased activation energies and decreased reaction energies relative to DFT predictions. We believe that a similar approach could also be adopted to treat overdelocalization effects in other electrocatalytic proton-coupled electron transfer reactions, e.g., in the oxygen reduction reaction.

Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants

Understanding the regulation mechanism and molecular determinants of the reduction potential of metalloprotein is a major challenge. An ab initio quantum mechanical/molecular mechanical (QM/MM) method combining the minimum free energy path (MFEP) and fractional number of electron (FNE) approaches has been developed in our group to simulate the redox processes of large systems. The FNE scheme provides an efficient unique description for the redox process, while the MFEP method provides improved conformational sampling on complex environments such as protein in the QM/MM calculations. The reduction potentials of wild-type and seven mutants of azurin, a type 1 copper metalloprotein, were simulated with the QM/MM-MFEP+FNE approach in this paper. A range of 350 mV for the variations of the reduction potentials of these azurin proteins was reproduced faithfully with relative errors around 20 mV. The correlation between structural interactions and reduction potentials observed in simulations provides in-depth insight into the regulation of reduction potentials, which potentially can also be very useful to the engineering of metalloprotein-based electrocatalysts in artificial photosynthesis. The excellent accuracy and efficiency of the QM/MM-MFEP+FNE approach demonstrate the potential for simulations of many electron transfer processes in condensed phases and biochemical systems.

Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer

We present a new concept of free energy calculations of chemical reactions by means of extended sampling molecular dynamics simulations. Biasing potentials are applied on partial atomic charges, which may be combined with atomic coordinates either in a single collective variable or in multi-dimensional biasing simulations. The necessary additional gradients are obtained by solving coupled-perturbed equations within the approximative density-functional tight-binding method. The new computational scheme was implemented in a combination of Gromacs and Plumed. As a prospective application, proton-coupled electron transfer in a model molecular system is studied. Two collective variables are introduced naturally, one for the proton transfer and the other for the electron transfer. The results are in qualitative agreement with the extended free simulations performed for reference. Free energy minima as well as the mechanism of the process are identified correctly, while the topology of the transition region and the height of the energy barrier are only reproduced qualitatively. The application also illustrates possible difficulties with the new methodology. These may be inefficient sampling of spatial coordinates when atomic charges are biased exclusively and a decreased stability of the simulations. Still, the new approach represents a viable alternative for free energy calculations of a certain class of chemical reactions, for instance a proton-coupled electron transfer in proteins.