Proton-coupled electron transfer in biology: results from synergistic studies in natural and model systems

Hydrogen bond network between amino acid radical intermediates on the proton-coupled electron transfer pathway of E. coli α2 ribonucleotide reductase

Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides in all organisms. In all Class Ia RNRs, initiation of nucleotide diphosphate (NDP) reduction requires a reversible oxidation over 35 Å by a tyrosyl radical (Y122•, Escherichia coli) in subunit β of a cysteine (C439) in the active site of subunit α. This radical transfer (RT) occurs by a specific pathway involving redox active tyrosines (Y122 ⇆ Y356 in β to Y731 ⇆ Y730 ⇆ C439 in α); each oxidation necessitates loss of a proton coupled to loss of an electron (PCET). To study these steps, 3-aminotyrosine was site-specifically incorporated in place of Y356-β, Y731- and Y730-α, and each protein was incubated with the appropriate second subunit β(α), CDP and effector ATP to trap an amino tyrosyl radical (NH2Y•) in the active α2β2 complex. High-frequency (263 GHz) pulse electron paramagnetic resonance (EPR) of the NH2Y•s reported the gx values with unprecedented resolution and revealed strong electrostatic effects caused by the protein environment. (2)H electron-nuclear double resonance (ENDOR) spectroscopy accompanied by quantum chemical calculations provided spectroscopic evidence for hydrogen bond interactions at the radical sites, i.e., two exchangeable H bonds to NH2Y730•, one to NH2Y731• and none to NH2Y356•. Similar experiments with double mutants α-NH2Y730/C439A and α-NH2Y731/Y730F allowed assignment of the H bonding partner(s) to a pathway residue(s) providing direct evidence for colinear PCET within α. The implications of these observations for the PCET process within α and at the interface are discussed.

Catalytic Oxygen Evolution by Cobalt Oxido Thin Films

The contemporary demand to generate fuels from solar energy has stimulated intense effort to develop water splitting catalysts that can be coupled to light-absorbing materials. Cobalt oxido catalyst (Co-OECs) films deposited from buffered Co(II) solutions have emerged as arguably the most studied class of heterogeneous oxygen evolution catalysts. The interest in these materials stems from their formation by self-assembly, their self-healing properties, and their promising catalytic activity under a variety of conditions. The structure and function of these catalysts are reviewed here together with studies of molecular Co-O cluster compounds, which have proven invaluable in elucidating the chemistry of the Co-OECs.

Kinetics of hydrogen atom abstraction from substrate by an active site thiyl radical in ribonucleotide reductase

Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides in all organisms. Active E. coli class Ia RNR is an α₂β₂ complex that undergoes reversible, long-range proton-coupled electron transfer (PCET) over a pathway of redox active amino acids (β-Y₁₂₂ → [β-W₄₈] → β-Y₃₅₆ → α-Y₇₃₁ → α-Y₇₃₀ → α-C₄₃₉) that spans ∼35 Å. To unmask PCET kinetics from rate-limiting conformational changes, we prepared a photochemical RNR containing a [Re^I] photooxidant site-specifically incorporated at position 355 ([Re]-β₂), adjacent to PCET pathway residue Y₃₅₆ in β. [Re]-β₂ was further modified by replacing Y₃₅₆ with 2,3,5-trifluorotyrosine to enable photochemical generation and spectroscopic observation of chemically competent tyrosyl radical(s). Using transient absorption spectroscopy, we compare the kinetics of Y· decay in the presence of substrate and wt-α₂, Y₇₃₁F-α₂ ,or C₄₃₉S-α₂, as well as with 3′-[²H]-substrate and wt-α₂. We find that only in the presence of wt-α₂ and the unlabeled substrate do we observe an enhanced rate of radical decay indicative of forward radical propagation. This observation reveals that cleavage of the 3′-C–H bond of substrate by the transiently formed C₄₃₉· thiyl radical is rate-limiting in forward PCET through α and has allowed calculation of a lower bound for the rate constant associated with this step of (1.4 ± 0.4) × 10⁴ s^–1. Prompting radical propagation with light has enabled observation of PCET events heretofore inaccessible, revealing active site chemistry at the heart of RNR catalysis.

Preparation, structural characterization, and thermochemistry of an isolable 4-arylphenoxyl radical

The preparation and full characterization of the 4-(nitrophenyl)phenoxyl radical, 2,6-di-(t)butyl-4-(4'-nitrophenyl) phenoxyl radical ((t)Bu2NPArO(•)) is described. This is a rare example of an isolable and crystallographically characterized phenoxyl radical and is the only example in which the parent phenol is also crystallographically well-defined. Analysis of EPR spectra indicates some spin delocalization onto the secondary aromatic ring and nitro group. Equilibrium studies show that the corresponding phenol has an O-H bond dissociation free energy (BDFE) of 77.8 ± 0.5 kcal mol(-1) in MeCN (77.5 ± 0.5 kcal mol(-1) in toluene). This value is higher than related isolated phenoxyl radicals, making this a useful reagent for hydrogen atom transfer (HAT) studies. Additional thermochemical and spectroscopic parameters are also discussed.

Role of pendant proton relays and proton-coupled electron transfer on the hydrogen evolution reaction by nickel hangman porphyrins

The hangman motif provides mechanistic insights into the role of pendant proton relays in governing proton-coupled electron transfer (PCET) involved in the hydrogen evolution reaction (HER). We now show improved HER activity of Ni compared with Co hangman porphyrins. Cyclic voltammogram data and simulations, together with computational studies using density functional theory, implicate a shift in electrokinetic zone between Co and Ni hangman porphyrins due to a change in the PCET mechanism. Unlike the Co hangman porphyrin, the Ni hangman porphyrin does not require reduction to the formally metal(0) species before protonation by weak acids in acetonitrile. We conclude that protonation likely occurs at the Ni(I) state followed by reduction, in a stepwise proton transfer-electron transfer pathway. Spectroelectrochemical and computational studies reveal that upon reduction of the Ni(II) compound, the first electron is transferred to a metal-based orbital, whereas the second electron is transferred to a molecular orbital on the porphyrin ring.

Hydrogen bonding networks tune proton-coupled redox steps during the enzymatic six-electron conversion of nitrite to ammonia

Multielectron multiproton reactions play an important role in both biological systems and chemical reactions involved in energy storage and manipulation. A key strategy employed by nature in achieving such complex chemistry is the use of proton-coupled redox steps. Cytochrome c nitrite reductase (ccNiR) catalyzes the six-electron seven-proton reduction of nitrite to ammonia. While a catalytic mechanism for ccNiR has been proposed on the basis of studies combining computation and crystallography, there have been few studies directly addressing the nature of the proton-coupled events that are predicted to occur along the nitrite reduction pathway. Here we use protein film voltammetry to directly interrogate the proton-coupled steps that occur during nitrite reduction by ccNiR. We find that conversion of nitrite to ammonia by ccNiR adsorbed to graphite electrodes is defined by two distinct phases; one is proton-coupled, and the other is not. Mutation of key active site residues (H257, R103, and Y206) modulates these phases and specifically alters the properties of the detected proton-dependent step but does not inhibit the ability of ccNiR to conduct the full reduction of nitrite to ammonia. We conclude that the active site residues examined are responsible for tuning the protonation steps that occur during catalysis, likely through an extensive hydrogen bonding network, but are not necessarily required for the reaction to proceed. These results provide important insight into how enzymes can specifically tune proton- and electron transfer steps to achieve high turnover numbers in a physiological pH range.

Photochemical tyrosine oxidation in the structurally well-defined α3Y protein: proton-coupled electron transfer and a long-lived tyrosine radical

Tyrosine oxidation–reduction involves proton-coupled electron transfer (PCET) and a reactive radical state. These properties are effectively controlled in enzymes that use tyrosine as a high-potential, one-electron redox cofactor. The α₃Y model protein contains Y32, which can be reversibly oxidized and reduced in voltammetry measurements. Structural and kinetic properties of α₃Y are presented. A solution NMR structural analysis reveals that Y32 is the most deeply buried residue in α₃Y. Time-resolved spectroscopy using a soluble flash-quench generated [Ru(2,2′-bipyridine)₃]³⁺ oxidant provides high-quality Y32–O• absorption spectra. The rate constant of Y32 oxidation (k_PCET) is pH dependent: 1.4 × 10⁴ M^–1 s^–1 (pH 5.5), 1.8 × 10⁵ M^–1 s^–1 (pH 8.5), 5.4 × 10³ M^–1 s^–1 (pD 5.5), and 4.0 × 10⁴ M^–1 s^–1 (pD 8.5). k^H/k^D of Y32 oxidation is 2.5 ± 0.5 and 4.5 ± 0.9 at pH(D) 5.5 and 8.5, respectively. These pH and isotope characteristics suggest a concerted or stepwise, proton-first Y32 oxidation mechanism. The photochemical yield of Y32–O• is 28–58% versus the concentration of [Ru(2,2′-bipyridine)₃]³⁺. Y32–O• decays slowly, t_1/2 in the range of 2–10 s, at both pH 5.5 and 8.5, via radical–radical dimerization as shown by second-order kinetics and fluorescence data. The high stability of Y32–O• is discussed relative to the structural properties of the Y32 site. Finally, the static α₃Y NMR structure cannot explain (i) how the phenolic proton released upon oxidation is removed or (ii) how two Y32–O• come together to form dityrosine. These observations suggest that the dynamic properties of the protein ensemble may play an essential role in controlling the PCET and radical decay characteristics of α₃Y.

Stacking of metal chelating rings with π-systems in mononuclear complexes of copper(II) with 3,6-dichloro-2,5-dihydroxy-1,4-benzoquinone (chloranilic acid) and 2,2'-bipyridine ligands

A series of four novel mononuclear complexes of copper(II) with chloranilic acid and 2,2'-bipyridine were prepared and structurally characterised by X-ray structure analysis and IR spectroscopy. The complexes exhibit square-planar, square-pyramidal and octahedral coordination. The chloranilate dianion coordinates the Cu(II) atom in a terminal bidentate o-quinone-like mode forming a mononuclear complex species. The crystal packing of the aqua complex and the complexes with crystal water molecules are defined by hydrogen bonds. However, significant contributions are from interactions involving five-membered chelate rings with both types of ligands and intermolecular π-systems (bipyridine and chloranilate rings). The crystal packing of the complex with square planar Cu(II) coordination is dominated by interactions of the chelate rings with π-delocalised bonds and intermolecular π-systems. The occurrence of dimorphism could be related to the different types of these interactions in the stacks. The crystal packing of the octahedral complexes of the mono- and dihydrate solvates reveal 3D-networks with pores occupied by non-coordinated bipyridine molecules.

Concerted proton-electron transfers: fundamentals and recent developments

Proton-coupled electron transfers (PCET) are ubiquitous in natural and synthetic processes. This review focuses on reactions where the two events are concerted. Semiclassical models of such reactions allow their kinetic characterization through activation versus driving force relationships, estimates of reorganization energies, effects of the nature of the proton acceptor, and H/D kinetic isotope effect as well as their discrimination from stepwise pathways. Several homogeneous reactions (through stopped-flow and laser flash-quench techniques) and electrochemical processes are discussed in this framework. Once the way has been rid of the improper notion of pH-dependent driving force, water appears as a remarkable proton acceptor in terms of reorganization energy and pre-exponential factor, thanks to its H-bonded and H-bonding properties, similarly to purposely synthesized "H-bond train" molecules. The most recent developments are in modeling and description of emblematic concerted proton-electron transfer (CPET) reactions associated with the breaking of a heavy-atom bond in an all-concerted process.

Electrochemical evidence for intermolecular proton-coupled electron transfer through a hydrogen bond complex in a p-phenylenediamine-based urea. Introduction of the "wedge scheme" as a useful means to describe reactions of this type

The electrochemistry of several p-phenylenediamine derivatives, in which one of the amino groups is part of an urea functional group, has been investigated in methylene chloride and acetonitrile. The ureas are abbreviated U(R)R', where R' indicates the substituent on the N that is part of the phenylenediamine redox couple and R indicates the substituent on the other urea N. Cyclic voltammetry and UV-vis spectroelectrochemical studies indicate that U(Me)H and U(H)H undergo an apparent 1e(-) oxidation that actually corresponds to 2e(-) oxidation of half the ureas to a quinoidal-diimine cation, U(R)(+). This is accompanied by proton transfer to the other half of the ureas to make the electroinactive cation HU(R)H(+). This explains the observed irreversibility of the oxidation of U(Me)H in both solvents and U(H)H in acetonitrile. However, the oxidation of U(H)H in methylene chloride is reversible at higher concentrations and slower scan rates. Several lines of evidence suggest that the most likely reason for this is the accessibility of a H-bond complex between U(H)(+) and HU(H)H(+) in methylene chloride. Reduction of the H-bond complex occurs at a less negative potential than that of U(H)(+), leading to reversible behavior. This conclusion is strongly supported by the appearance of a more negative reduction peak at lower concentrations and faster scan rates, conditions in which the H-bond complex is less favored. The overall reaction mechanism is conveniently described by a "wedge scheme", which is a more general version of the square scheme typically used to describe redox processes in which proton transfer accompanies electron transfer.

Reversible, long-range radical transfer in E. coli class Ia ribonucleotide reductase

Ribonucleotide reductases (RNRs) catalyze the conversionof nucleotides to 2'-deoxynucleotides and are classified on the basis of the metallo-cofactor used to conduct this chemistry. The class Ia RNRs initiate nucleotide reduction when a stable diferric-tyrosyl radical (Y•, t1/2 of 4 days at 4 °C) cofactor in the β2 subunit transiently oxidizes a cysteine to a thiyl radical (S•) in the active site of the α2 subunit. In the active α2β2 complex of the class Ia RNR from E. coli , researchers have proposed that radical hopping occurs reversibly over 35 Å along a specific pathway comprised of redox-active aromatic amino acids: Y122• ↔ [W48?] ↔ Y356 in β2 to Y731 ↔ Y730 ↔ C439 in α2. Each step necessitates a proton-coupled electron transfer (PCET). Protein conformational changes constitute the rate-limiting step in the overall catalytic scheme and kinetically mask the detailed chemistry of the PCET steps. Technology has evolved to allow the site-selective replacement of the four pathway tyrosines with unnatural tyrosine analogues. Rapid kinetic techniques combined with multifrequency electron paramagnetic resonance, pulsed electron-electron double resonance, and electron nuclear double resonance spectroscopies have facilitated the analysis of stable and transient radical intermediates in these mutants. These studies are beginning to reveal the mechanistic underpinnings of the radical transfer (RT) process. This Account summarizes recent mechanistic studies on mutant E. coli RNRs containing the following tyrosine analogues: 3,4-dihydroxyphenylalanine (DOPA) or 3-aminotyrosine (NH2Y), both thermodynamic radical traps; 3-nitrotyrosine (NO2Y), a thermodynamic barrier and probe of local environmental perturbations to the phenolic pKa; and fluorotyrosines (FnYs, n = 2 or 3), dual reporters on local pKas and reduction potentials. These studies have established the existence of a specific pathway spanning 35 Å within a globular α2β2 complex that involves one stable (position 122) and three transient (positions 356, 730, and 731) Y•s. Our results also support that RT occurs by an orthogonal PCET mechanism within β2, with Y122• reduction accompanied by proton transfer from an Fe1-bound water in the diferric cluster and Y356 oxidation coupled to an off-pathway proton transfer likely involving E350. In α2, RT likely occurs by a co-linear PCET mechanism, based on studies of light-initiated radical propagation from photopeptides that mimic the β2 subunit to the intact α2 subunit and on [(2)H]-ENDOR spectroscopic analysis of the hydrogen-bonding environment surrounding a stabilized NH2Y• formed at position 730. Additionally, studies on the thermodynamics of the RT pathway reveal that the relative reduction potentials decrease according to Y122 < Y356 < Y731 ≈ Y730 ≤ C439, and that the pathway in the forward direction is thermodynamically unfavorable. C439 oxidation is likely driven by rapid, irreversible loss of water during the nucleotide reduction process. Kinetic studies of radical intermediates reveal that RT is gated by conformational changes that occur on the order of >100 s(-1) in addition to the changes that are rate-limiting in the wild-type enzyme (∼10 s(-1)). The rate constant of one of the PCET steps is ∼10(5) s(-1), as measured in photoinitiated experiments.

A rapid freeze-quench setup for multi-frequency EPR spectroscopy of enzymatic reactions

Electron paramagnetic resonance (EPR) spectroscopy in combination with the rapid freeze-quench (RFQ) technique is a well-established method to trap and characterize intermediates in chemical or enzymatic reactions at the millisecond or even shorter time scales. The method is particularly powerful for mechanistic studies of enzymatic reactions when combined with high-frequency EPR (ν≥90 GHz), which permits the identification of substrate or protein radical intermediates by their electronic g values. In this work, we describe a new custom-designed micro-mix rapid freeze-quench apparatus, for which reagent volumes for biological samples as small as 20 μL are required. The apparatus was implemented with homemade sample collectors appropriate for 9, 34, and 94 GHz EPR capillaries (4, 2, and 0.87 mm outer diameter, respectively) and the performance was evaluated. We demonstrate the application potential of the RFQ apparatus by following the enzymatic reaction of PpoA, a fungal dioxygenase producing hydro(pero)xylated fatty acids. The larger spectral resolution at 94 GHz allows the discernment of structural changes in the EPR spectra, which are not detectable in the same samples at the standard 9 GHz frequency.

Targeting ribonucleotide reductase for cancer therapy

INTRODUCTION

Ribonucleotide reductase (RR) is a unique enzyme, because it is responsible for reducing ribonucleotides to their corresponding deoxyribonucleotides, which are the building blocks required for DNA replication and repair. Dysregulated RR activity is associated with genomic instability, malignant transformation and cancer development. The use of RR inhibitors, either as a single agent or combined with other therapies, has proven to be a promising approach for treating solid tumors and hematological malignancies.

AREAS COVERED

This review covers recent publications in the area of RR, which include: i) the structure, function and regulation of RR; ii) the roles of RR in cancer development; iii) the classification, mechanisms and clinical application of RR inhibitors for cancer therapy and iv) strategies for developing novel RR inhibitors in the future.

EXPERT OPINION

Exploring the possible nonenzymatic roles of RR subunit proteins in carcinogenesis may lead to new rationales for developing novel anticancer drugs. Updated information about the structure and holoenzyme models of RR will help in identifying potential sites in the protein that could be targets for novel RR inhibitors. Determining RR activity and subunit levels in clinical samples will provide a rational platform for developing personalized cancer therapies that use RR inhibitors.

Modulation of Y356 photooxidation in E. coli class Ia ribonucleotide reductase by Y731 across the α2:β2 interface

Substrate turnover in class Ia ribonucleotide reductase (RNR) requires reversible radical transport across two subunits over 35 Å, which occurs by a multistep proton-coupled electron-transfer mechanism. Using a photooxidant-labeled β2 subunit of Escherichia coli class Ia RNR, we demonstrate photoinitiated oxidation of a tyrosine in an α2:β2 complex, which results in substrate turnover. Using site-directed mutations of the redox-active tyrosines at the subunit interface, Y356F(β) and Y731F(α), this oxidation is identified to be localized on Y356. The rate of Y356 oxidation depends on the presence of Y731 across the interface. This observation supports the proposal that unidirectional PCET across the Y356(β)-Y731(α)-Y730(α) triad is crucial to radical transport in RNR.

Extra-low-frequency magnetic fields alter cancer cells through metabolic restriction

BACKGROUND

Biological effects of extra-low-frequency (ELF) magnetic fields (MFs) have lacked a credible mechanism of interaction between MFs and living material.

OBJECTIVES

To examine the effect of ELF-MFs on cancer cells.

METHODS

Five cancer cell lines were exposed to ELF-MFs within the range of 0.025-5 µT, and the cells were examined for karyotype changes after 6 d.

RESULTS

All cancer cells lines lost chromosomes from MF exposure, with a mostly flat dose-response. Constant MF exposures for three weeks allow a rising return to the baseline, unperturbed karyotypes. From this point, small MF increases or decreases are again capable of inducing karyotype contractions (KCs). Our data suggest that the KCs are caused by MF interference with mitochondria's adenosine triphosphate synthase (ATPS), compensated by the action of adenosine monophosphate-activated protein kinase (AMPK). The effects of MFs are similar to those of the ATPS inhibitor, oligomycin. They are amplified by metformin, an AMPK stimulator, and attenuated by resistin, an AMPK inhibitor. Over environmental MFs, KCs of various cancer cell lines show exceptionally wide and flat dose-responses, except for those of erythroleukemia cells, which display a progressive rise from 0.025 to 0.4 µT.

CONCLUSIONS

The biological effects of MFs are connected to an alteration in the structure of water that impedes the flux of protons in ATPS channels. These results may be environmentally important, in view of the central roles played in human physiology by ATPS and AMPK, particularly in their links to diabetes, cancer and longevity.

Catalytic ketyl-olefin cyclizations enabled by proton-coupled electron transfer

Concerted proton-coupled electron transfer is a key mechanism of substrate activation in biological redox catalysis. However, its applications in organic synthesis remain largely unexplored. Herein, we report the development of a new catalytic protocol for ketyl-olefin coupling and present evidence to support concerted proton-coupled electron transfer being the operative mechanism of ketyl formation. Notably, reaction outcomes were correctly predicted by a simple thermodynamic formalism relating the oxidation potentials and pKa values of specific Brønsted acid/reductant combinations to their capacity to act jointly as a formal hydrogen atom donor.

Randomness and multilevel interactions in biology

The dynamic instability of living systems and the "superposition" of different forms of randomness are viewed, in this paper, as components of the contingently changing, or even increasing, organization of life through ontogenesis or evolution. To this purpose, we first survey how classical and quantum physics define randomness differently. We then discuss why this requires, in our view, an enriched understanding of the effects of their concurrent presence in biological systems' dynamics. Biological randomness is then presented not only as an essential component of the heterogeneous determination and intrinsic unpredictability proper to life phenomena, due to the nesting of, and interaction between many levels of organization, but also as a key component of its structural stability. We will note as well that increasing organization, while increasing "order", induces growing disorder, not only by energy dispersal effects, but also by increasing variability and differentiation. Finally, we discuss the cooperation between diverse components in biological networks; this cooperation implies the presence of constraints due to the particular nature of bio-entanglement and bio-resonance, two notions to be reviewed and defined in the paper.

Reversible phenol oxidation and reduction in the structurally well-defined 2-Mercaptophenol-α₃C protein

2-Mercaptophenol-α₃C serves as a biomimetic model for enzymes that use tyrosine residues in redox catalysis and multistep electron transfer. This model protein was tailored for electrochemical studies of phenol oxidation and reduction with specific emphasis on the redox-driven protonic reactions occurring at the phenol oxygen. This protein contains a covalently modified 2-mercaptophenol-cysteine residue. The radical site and the phenol compound were specifically chosen to bury the phenol OH group inside the protein. A solution nuclear magnetic resonance structural analysis (i) demonstrates that the synthetic 2-mercaptophenol-α₃C model protein behaves structurally as a natural protein, (ii) confirms the design of the radical site, (iii) reveals that the ligated phenol forms an interhelical hydrogen bond to glutamate 13 (phenol oxygen-carboxyl oxygen distance of 3.2 ± 0.5 Å), and (iv) suggests a proton-transfer pathway from the buried phenol OH (average solvent accessible surface area of 3 ± 5%) via glutamate 13 (average solvent accessible surface area of the carboxyl oxygens of 37 ± 18%) to the bulk solvent. A square-wave voltammetry analysis of 2-mercaptophenol-α₃C further demonstrates that (v) the phenol oxidation-reduction cycle is reversible, (vi) formal phenol reduction potentials can be obtained, and (vii) the phenol-O(•) state is long-lived with an estimated lifetime of ≥180 millisecond. These properties make 2-mercaptophenol-α₃C a unique system for characterizing phenol-based proton-coupled electron transfer in a low-dielectric and structured protein environment.

The Third Dimension of a More O'Ferrall-Jencks Diagram for Hydrogen Atom Transfer in the Isoelectronic Hydrogen Exchange Reactions of (PhX)(2)H(•) with X = O, NH, and CH(2)

A critical element in theoretical characterization of the mechanism of proton-coupled electron transfer (PCET) reactions, including hydrogen atom transfer (HAT), is the formulation of the electron and proton localized diabatic states, based on which a More O'Ferrall-Jencks diagram can be represented to determine the step-wise and concerted nature of the reaction. Although the More O'Ferrall-Jencks diabatic states have often been used empirically to develop theoretical models for PCET reactions, the potential energy surfaces for these states have never been determined directly based on first principles calculations using electronic structure theory. The difficulty is due to a lack of practical method to constrain electron and proton localized diabatic states in wave function or density functional theory calculations. Employing a multistate density functional theory (MSDFT), in which the electron and proton localized diabatic configurations are constructed through block-localization of Kohn-Sham orbitals, we show that distinction between concerted proton-electron transfer (CPET) and HAT, which are not distinguishable experimentally from phenomenological kinetic data, can be made by examining the third dimension of a More O'Ferrall-Jencks diagram that includes both the ground and excited state potential surfaces. In addition, we formulate a pair of effective two-state valence bond models to represent the CPET and HAT mechanisms. We found that the lower energy of the CPET and HAT effective diabatic states at the intersection point can be used as an energetic criterion to distinguish the two mechanisms. In the isoelectronic series of hydrogen exchange reaction in (PhX)(2)H(•), where X = O, NH, and CH(2), there is a continuous transition from a CPET mechanism for the phenoxy radical-phenol pair to a HAT process for benzyl radical and toluene, while the reaction between PhNH(2) and PhNH(•) has a mechanism intermediate of CPET and HAT. The electronically nonadiabatic nature of the CPET mechanism in the phenol system can be attributed to the overlap interactions between the ground and excited state surfaces, resulting in roughly orthogonal minimum energy paths on the adiabatic ground and excited state potential energy surfaces. On the other hand, the minimum energy path on the adiabatic ground state for the HAT mechanism coincides with that on the excited state, producing a large electronic coupling that separates the two surfaces by more than 120 kcal/mol.

Spanning four mechanistic regions of intramolecular proton-coupled electron transfer in a Ru(bpy)3(2+)-tyrosine complex

Proton-coupled electron transfer (PCET) from tyrosine (TyrOH) to a covalently linked [Ru(bpy)(3)](2+) photosensitizer in aqueous media has been systematically reinvestigated by laser flash-quench kinetics as a model system for PCET in radical enzymes and in photochemical energy conversion. Previous kinetic studies on Ru-TyrOH molecules (Sjödin et al. J. Am. Chem. Soc. 2000, 122, 3932; Irebo et al. J. Am. Chem. Soc. 2007, 129, 15462) have established two mechanisms. Concerted electron-proton (CEP) transfer has been observed when pH < pK(a)(TyrOH), which is pH-dependent but not first-order in [OH(-)] and not dependent on the buffer concentration when it is sufficiently low (less than ca. 5 mM). In addition, the pH-independent rate constant for electron transfer from tyrosine phenolate (TyrO(-)) was reported at pH >10. Here we compare the PCET rates and kinetic isotope effects (k(H)/k(D)) of four Ru-TyrOH molecules with varying Ru(III/II) oxidant strengths over a pH range of 1-12.5. On the basis of these data, two additional mechanistic regimes were observed and identified through analysis of kinetic competition and kinetic isotope effects (KIE): (i) a mechanism dominating at low pH assigned to a stepwise electron-first PCET and (ii) a stepwise proton-first PCET with OH(-) as proton acceptor that dominates around pH = 10. The effect of solution pH and electrochemical potential of the Ru(III/II) oxidant on the competition between the different mechanisms is discussed. The systems investigated may serve as models for the mechanistic diversity of PCET reactions in general with water (H(2)O, OH(-)) as primary proton acceptor.

Reversible voltammograms and a Pourbaix diagram for a protein tyrosine radical

Reversible voltammograms and a voltammetry half-wave potential versus solution pH diagram are described for a protein tyrosine radical. This work required a de novo designed tyrosine-radical protein displaying a unique combination of structural and electrochemical properties. The α(3)Y protein is structurally stable across a broad pH range. The redox-active tyrosine Y32 resides in a desolvated and well-structured environment. Y32 gives rise to reversible square-wave and differential pulse voltammograms at alkaline pH. The formal potential of the Y32-O(•)/Y32-OH redox couple is determined to 918 ± 2 mV versus the normal hydrogen electrode at pH 8.40 ± 0.01. The observation that Y32 gives rise to fully reversible voltammograms translates into an estimated lifetime of ≥30 ms for the Y32-O(•) state. This illustrates the range of tyrosine-radical stabilization that a structured protein can offer. Y32 gives rise to quasireversible square-wave and differential pulse voltammograms at acidic pH. These voltammograms represent the Y32 species at the upper edge of the quasirevesible range. The square-wave net potential closely approximates the formal potential of the Y32-O(•)/Y32-OH redox couple to 1,070 ± 1 mV versus the normal hydrogen electrode at pH 5.52 ± 0.01. The differential pulse voltammetry half-wave potential of the Y32-O(•)/Y32-OH redox pair is measured between pH 4.7 and 9.0. These results are described and analyzed.

A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase

The conformational properties of an active-site loop segment, defined by residues Ser(161)-Glu(162)-Asn(163)-Ser(164), have been shown to be important for modulating the intrinsic reactivity of Mn(II) in the active site of Bacillus subtilis oxalate decarboxylase. We now detail the functional and structural consequences of removing a conserved Arg/Thr hydrogen-bonding interaction by site-specific mutagenesis. Hence, substitution of Thr-165 by a valine residue gives an OxDC variant (T165V) that exhibits impaired catalytic activity. Heavy-atom isotope effect measurements, in combination with the X-ray crystal structure of the T165V OxDC variant, demonstrate that the conserved Arg/Thr hydrogen bond is important for correctly locating the side chain of Glu-162, which mediates a proton-coupled electron transfer (PCET) step prior to decarboxylation in the catalytically competent form of OxDC. In addition, we show that the T165V OxDC variant exhibits a lower level of oxalate consumption per dioxygen molecule, consistent with the predictions of recent spin-trapping experiments [Imaram et al. (2011) Free Radicals Biol. Med. 50, 1009-1015]. This finding implies that dioxygen might participate as a reversible electron sink in two putative PCET steps and is not merely used to generate a protein-based radical or oxidized metal center.

Mechanism of light induced water splitting in Photosystem II of oxygen evolving photosynthetic organisms

The reactions of light induced oxidative water splitting were analyzed within the framework of the empirical rate constant-distance relationship of non-adiabatic electron transfer in biological systems (C. C. Page, C. C. Moser, X. Chen , P. L. Dutton, Nature 402 (1999) 47-52) on the basis of structure information on Photosystem II (PS II) (A. Guskov, A. Gabdulkhakov, M. Broser, C. Glöckner, J. Hellmich, J. Kern, J. Frank, W. Saenger, A. Zouni, Chem. Phys. Chem. 11 (2010) 1160-1171, Y. Umena, K. Kawakami, J-R Shen, N. Kamiya, Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9Å. Nature 47 (2011) 55-60). Comparison of these results with experimental data leads to the following conclusions: 1) The oxidation of tyrosine Y(z) by the cation radical P680(+·) in systems with an intact water oxidizing complex (WOC) is kinetically limited by the non-adiabatic electron transfer step and the extent of this reaction is thermodynamically determined by relaxation processes in the environment including rearrangements of hydrogen bond network(s). In marked contrast, all Y(z)(ox) induced oxidation steps in the WOC up to redox state S(3) are kinetically limited by trigger reactions which are slower by orders of magnitude than the rates calculated for non-adiabatic electron transfer. 3) The overall rate of the triggered reaction sequence of Y(z)(ox) reduction by the WOC in redox state S(3) eventually leading to formation and release of O(2) is kinetically limited by an uphill electron transfer step. Alternative models are discussed for this reaction. The protein matrix of the WOC and bound water molecules provide an optimized dynamic landscape of hydrogen bonded protons for catalyzing oxidative water splitting energetically driven by light induced formation of the cation radical P680(+·). In this way the PS II core acts as a molecular machine formed during a long evolutionary process. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.

Energy transfer mediated by asymmetric hydrogen-bonded interfaces

Amidine-appended ferrocene derivatives form a supramolecular assembly with Ru(ii)(bpy-COOH) (L)22+ complexes (bpy-COOH is 4-CO2H-4'-CH3-bpy and L = bpy, 2,2'-bipyridine or btfmbpy, 4,4'-bis (trifluoromethyl)-2,2'-bipyridine). Steady-state, time-resolved spectroscopy and kinetic isotope effects establish that the metal-to-ligand charge transfer excited states of the Ru(ii) complexes are quenched by proton-coupled energy transfer (PCEnT). These results show that proton motion can be effective in mediating not only electron transfer (ET) but energy transfer (EnT) as well.