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1.  Theory of Proton-Coupled Electron Transfer in Energy Conversion Processes 
Accounts of chemical research  2009;42(12):1881-1889.
Proton-coupled electron transfer (PCET) reactions play an essential role in a broad range of energy conversion processes, including photosynthesis and respiration. These reactions also form the basis of many types of solar fuel cells and electrochemical devices. Recent advances in the theory of PCET enable the prediction of the impact of system properties on the reaction rates. These predictions may guide the design of more efficient catalysts for energy production, including those based on artificial photosynthesis and solar energy conversion. This Account summarizes the theoretically predicted dependence of PCET rates on system properties and illustrates potential approaches for tuning the reaction rates in chemical systems.
A general theoretical formulation for PCET reactions has been developed over the past decade. In this theory, PCET reactions are described in terms of nonadiabatic transitions between the reactant and product electron-proton vibronic states. A series of nonadiabatic rate constant expressions for both homogeneous and electrochemical PCET reactions have been derived in various well-defined limits. Recently this theory has been extended to include the effects of solvent dynamics and to describe ultrafast interfacial PCET. Analysis of the rate constant expressions provides insight into the underlying physical principles of PCET and enables the prediction of the dependence of the rates on the physical properties of the system. Moreover, the kinetic isotope effect, which is the ratio of the rates for hydrogen and deuterium, provides a useful mechanistic probe. Typically the PCET rate will increase as the electronic coupling and temperature increase and as the total reorganization energy and equilibrium proton donor-acceptor distance decrease. The rate constant is predicted to increase as the driving force becomes more negative, rather than exhibit turnover behavior in the inverted region, because excited vibronic product states associated with low free energy barriers and relatively large vibronic couplings become accessible. The physical basis for the experimentally observed pH dependence of PCET reactions has been debated in the literature. When the proton acceptor is a buffer species, the pH dependence may arise from the protonation equilibrium of the buffer. It could also arise from kinetic complexity of competing concerted and sequential PCET reaction pathways. In electrochemical PCET, the heterogeneous rate constants and current densities depend strongly on the overpotential. The change in equilibrium proton donor-acceptor distance upon electron transfer may lead to asymmetries in the Tafel plots and deviations of the transfer coefficient from the standard value of one-half at zero overpotential.
Applications of this theory to experimentally studied systems illustrate approaches that can be utilized to tune the PCET rate. For example, the rate can be tuned by changing the pH or using different buffer species as proton acceptors. The rate can also be tuned with site-specific mutagenesis in biological systems or chemical modifications that vary the substituents on the redox species in chemical systems. Understanding the impact of these changes on the PCET rate may assist experimental efforts to enhance energy conversion processes.
PMCID: PMC2841513  PMID: 19807148
2.  Analysis of Kinetic Isotope Effects for Proton-Coupled Electron Transfer Reactions 
The journal of physical chemistry. A  2009;113(10):2117-2126.
A series of rate constant expressions for nonadiabatic proton-coupled electron transfer (PCET) reactions are analyzed and compared. The approximations underlying each expression are enumerated, and the regimes of validity for each expression are illustrated by calculations on model systems. In addition, the kinetic isotope effects (KIEs) for a series of model PCET reactions are analyzed to elucidate the fundamental physical principles dictating the magnitude of the KIE and the dependence of the KIE on the physical properties of the system, including temperature, reorganization energy, driving force, equilibrium proton donor-acceptor distance, and effective frequency of the proton donor-acceptor mode. These calculations lead to three physical insights that are directly relevant to experimental data. First, these calculations provide an explanation for a decrease in the KIE as the proton donor-acceptor distance increases, even though typically the KIE will increase with increasing equilibrium proton donor-acceptor distance if all other parameters remain fixed. Often the proton donor-acceptor frequency decreases as the proton donor-acceptor distance increases, and these two effects impact the KIE in opposite directions, so either trend could be observed. Second, these calculations provide an explanation for an increase in the KIE as the temperature increases, even though typically the KIE will decrease with increasing temperature if all other parameters remain fixed. The combination of a rigid hydrogen bond, which corresponds to a high proton donor-acceptor frequency, and low solvent polarity, which corresponds to small solvent reorganization energy, allows the KIE to either increase or decrease with temperature, depending on the other properties of the system. Third, these calculations provide insight into the dependence of the rate constant and KIE on the driving force, which has been studied experimentally for a wide range of PCET systems. The rate constant increases as the driving force becomes more negative because excited vibronic product states associated with low free energy barriers and relatively large vibronic couplings become accessible. The ln[KIE] has a maximum near zero driving force and decreases significantly as the driving force becomes more positive or negative because the contributions from excited vibronic states increase as the reaction becomes more asymmetric, and contributions from excited vibronic states decrease the KIE. These calculations and analyses lead to experimentally testable predictions of trends in the KIEs for PCET systems.
PMCID: PMC2880663  PMID: 19182970
3.  Theoretical Analysis of the Unusual Temperature Dependence of the Kinetic Isotope Effect in Quinol Oxidation 
This paper presents theoretical calculations on model biomimetic systems for quinol oxidation. In these model systems, an excited-state [Ru(bpy)2(pbim)]+ complex (bpy = 2,2’-dipyridyl, pbim = 2-(2-pyridyl)benzimidazolate) oxidizes a ubiquinol or plastoquinol analogue in acetonitrile. The charge transfer reaction occurs via a proton-coupled electron transfer (PCET) mechanism, in which an electron is transferred from the quinol to the Ru and a proton is transferred from the quinol to the pbim− ligand. The experimentally measured average kinetic isotope effects (KIEs) at 296 K are 1.87 and 3.45 for the ubiquinol and plastoquinol analogues, respectively, and the KIE decreases with temperature for plastoquinol but increases with temperature for ubiquinol. The present calculations provide a possible explanation for the differences in magnitudes and temperature dependences of the KIEs for the two systems and, in particular, an explanation for the unusual inverse temperature dependence of the KIE for the ubiquinol analogue. These calculations are based on a general theoretical formulation for PCET reactions that includes quantum mechanical effects of the electrons and transferring proton, as well as the solvent reorganization and proton donor-acceptor motion. The physical properties of the system that enable the inverse temperature dependence of the KIE are a stiff hydrogen bond, which corresponds to a high-frequency proton donor-acceptor motion, and small inner-sphere and solvent reorganization energies. The inverse temperature dependence of the KIE may be observed if the (0/0) pair of reactant/product vibronic states is in the inverted Marcus region, while the (0/1) pair of reactant/product vibronic states is in the normal Marcus region and is the dominant contributor to the overall rate. In this case, the free energy barrier for the dominant transition is lower for deuterium than for hydrogen because of the smaller splittings between the vibronic energy levels for deuterium, and the KIE increases with increasing temperature. The temperature dependence of the KIE is found to be very sensitive to the interplay among the driving force, the reorganization energy, and the vibronic coupling in this regime.
PMCID: PMC2710000  PMID: 19351186
4.  Concerted Proton-Electron Transfer in a Ruthenium Terpyridyl-Benzoate System with a Large Separation between the Redox and Basic Sites 
In order to understand how the separation between the electron and proton-accepting sites affects proton-coupled electron transfer (PCET) reactivity, we have prepared ruthenium complexes with 4′-(4-carboxyphenyl)terpyridine ligands, and studied reactivity with hydrogen atom donors (H-X). RuII(pydic)(tpy-PhCOOH) (RuIIPhCOOH), was synthesized in one pot from [(p-cymene)RuCl2]2, sodium 4′-(4-carboxyphenyl)-2,2′:6′,2″-terpyridine ([Na+]tpy-PhCOO−), and disodium pyridine-2,6-dicarboxylate (Na2pydic). RuIIPhCOOH plus nBu4NOH in DMF yields the deprotonated Ru(II) complex, nBu4N[RuII(pydic)(tpy-PhCOO)] (RuIIPhCOO−). The Ru(III) complex (RuIIIPhCOO) has been isolated by one-electron oxidation of RuIIPhCOO− with triarylaminium radical cations (NAr3•+). The bond dissociation free energy (BDFE) of the O–H bond in RuIIPhCOOH is calculated from pKa and E1/2 measurements as 87 kcal mol-1, making RuIIIPhCOO a strong hydrogen atom acceptor. There are 10 bonds and ca. 11.2 Å separating the metal from the carboxylate basic site in RuIIIPhCOO. Even with this separation, RuIIIPhCOO oxidizes the hydrogen atom donor TEMPOH (BDFE = 66.5 kcal mol-1, ΔG°rxn = -21 kcal mol-1) by removal of an electron and a proton to form RuIIPhCOOH and TEMPO radical in a concerted proton-electron transfer (CPET) process. The second order rate constant for this reaction is (1.1 ± 0.1) × 105 M-1 s-1 with kH/kD = 2.1 ± 0.2, similar to the observed kinetics in an analogous system without the phenyl spacer, RuIII(pydic)(tpy-COO) (RuIIICOO−). In contrast, hydrogen transfer from 2,6-di-tert-butyl-p-methoxyphenol [tBu2(OMe)ArOH] to RuIIIPhCOO is several orders of magnitude slower than the analogous reaction with RuIIICOO.
PMCID: PMC2765064  PMID: 19569636
5.  Proton-coupled electron transfer in solution, proteins, and electrochemistry 
The journal of physical chemistry. B  2008;112(45):14108-14123.
Recent advances in the theoretical treatment of proton-coupled electron transfer (PCET) reactions are reviewed. These reactions play an important role in a wide range of biological processes, as well as in fuel cells, solar cells, chemical sensors, and electrochemical devices. A unified theoretical framework has been developed to describe both sequential and concerted PCET, as well as hydrogen atom transfer (HAT). A quantitative diagnostic has been proposed to differentiate between HAT and PCET in terms of the degree of electronic nonadiabaticity, where HAT corresponds to electronically adiabatic proton transfer and PCET corresponds to electronically nonadiabatic proton transfer. In both cases, the overall reaction is typically vibronically nonadiabatic. A series of rate constant expressions have been derived in various limits by describing the PCET reactions in terms of nonadiabatic transitions between electron-proton vibronic states. These expressions account for the solvent response to both electron and proton transfer and the effects of the proton donor-acceptor vibrational motion. The solvent and protein environment can be represented by a dielectric continuum or described with explicit molecular dynamics. These theoretical treatments have been applied to numerous PCET reactions in solution and proteins. Expressions for heterogeneous rate constants and current densities for electrochemical PCET have also been derived and applied to model systems.
PMCID: PMC2720037  PMID: 18842015
6.  The Third Dimension of a More O’Ferrall-Jencks Diagram for Hydrogen Atom Transfer in the Isoelectronic Hydrogen Exchange Reactions of (PhX)2H• with X = O, NH, and CH2 
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)2H•, where X = O, NH, and CH2, 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 PhNH2 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.
PMCID: PMC3516191  PMID: 23226989
7.  Kinetic Effects Of Increased Proton Transfer Distance On Proton-Coupled Oxidations Of Phenol-Amines 
Journal of the American Chemical Society  2011;133(43):17341-17352.
To test the effect of varying the proton donor-acceptor distance in proton-coupled electron transfer (PCET) reactions, the oxidation of a bicyclic amino-indanol (2) is compared with that of a closely related phenol with an ortho CPh2NH2 substituent (1). Spectroscopic, structural, thermochemical and computational studies show that the two amino-phenols are very similar, except that the O⋯N distance (dON) is >0.1 Å longer in 2 than in 1. The difference in dON is 0.13 ± 0.03 Å from X-ray crystallography and 0.165 Å from DFT calculations. Oxidations of these phenols by outer-sphere oxidants yield distonic radical cations •OAr–NH3+ by concerted proton-electron transfer (CPET). Simple tunneling and classical kinetic models both predict that the longer donor-acceptor distance in 2 should lead to slower reactions, by ca. two orders of magnitude, as well as larger H/D kinetic isotope effects (KIEs). However, kinetic studies show that the compound with the longer proton-transfer distance, 2, exhibits smaller KIEs and has rate constants that are quite close to those of 1. For example, the oxidation of 2 by the triarylamminium radical cation N(C6H4OMe)3•+ (3a+) occurs at (1.4 ± 0.1) × 104 M-1 s-1, only a factor of two slower than the closely related reaction of 1 with N(C6H4OMe)2(C6H4Br)•+ (3b+). This difference in rate constants is well accounted for by the slightly different free energies of reaction: ΔG°(2 + 3a+) = +0.078 V vs. ΔG°(1 + 3b+) = +0.04 V. The two phenol-amines do display some subtle kinetic differences: for instance, compound 2 has a shallower dependence of CPET rate constants on driving force (Brønsted α, Δln(k)/Δln(Keq)). These results show that the simple tunneling model is not a good predictor of the effect of proton donor-acceptor distance on concerted-electron transfer reactions involving strongly hydrogen-bonded systems. Computational analysis of the observed similarity of the two phenols emphasizes the importance of the highly anharmonic O⋯H⋯N potential energy surface and the influence of proton vibrational excited states.
PMCID: PMC3228417  PMID: 21919508
8.  Proton-coupled electron transfer: the mechanistic underpinning for radical transport and catalysis in biology 
Charge transport and catalysis in enzymes often rely on amino acid radicals as intermediates. The generation and transport of these radicals are synonymous with proton-coupled electron transfer (PCET), which intrinsically is a quantum mechanical effect as both the electron and proton tunnel. The caveat to PCET is that proton transfer (PT) is fundamentally limited to short distances relative to electron transfer (ET). This predicament is resolved in biology by the evolution of enzymes to control PT and ET coordinates on highly different length scales. In doing so, the enzyme imparts exquisite thermodynamic and kinetic controls over radical transport and radical-based catalysis at cofactor active sites. This discussion will present model systems containing orthogonal ET and PT pathways, thereby allowing the proton and electron tunnelling events to be disentangled. Against this mechanistic backdrop, PCET catalysis of oxygen–oxygen bond activation by mono-oxygenases is captured at biomimetic porphyrin redox platforms. The discussion concludes with the case study of radical-based quantum catalysis in a natural biological enzyme, class I Escherichia coli ribonucleotide reductase. Studies are presented that show the enzyme utilizes both collinear and orthogonal PCET to transport charge from an assembled diiron-tyrosyl radical cofactor to the active site over 35 Å away via an amino acid radical-hopping pathway spanning two protein subunits.
PMCID: PMC1647304  PMID: 16873123
proton-coupled electron transfer; amino acid radicals; tunnelling; tyrosine; catalysis; ribonucleotide reductase
ACS chemical biology  2010;5(12):1157-1168.
Tyrosine side chains are involved in proton coupled electron transfer reactions (PCET) in many complex proteins, including photosystem II (PSII) and ribonucleotide reductase. For example, PSII contains two redox-active tyrosines, TyrD (Y160D2) and TyrZ (Y161D1), which have different protein environments, midpoint potentials, and roles in catalysis. TyrD has a lower midpoint potential than TyrZ, and its protein environment is distinguished by potential pi-cation interactions with arginine residues. Designed biomimetic peptides provide a system that can be used to investigate how the protein matrix controls PCET reactions. As a model for the redox-active tyrosines in PSII, we are employing a designed, 18 amino acid beta hairpin peptide in which PCET reactions occur between a tyrosine (Tyr5) and a cross-strand histidine (His14). In this peptide, the single tyrosine is hydrogen bonded to an arginine residue, Arg16, and a second arginine, Arg12, has a pi-cation interaction with Tyr5. In this report, the effect of these hydrogen bonding and electrostatic interactions on the PCET reactions is investigated. Electrochemical titrations show that histidine substitutions change the nature of PCET reactions, and optical titrations show that Arg16 substitution changes the pK of Tyr5. Removal of Arg16 or Arg12 increases the midpoint potential for tyrosine oxidation. The effects of Arg12 substitution are consistent with the midpoint potential difference, which is observed for the PSII redox-active tyrosine residues. Our results demonstrate that a pi-cation interaction, hydrogen bonding, and PCET reactions alter redox-active tyrosine function. These interactions can contribute equally to the control of midpoint potential and reaction rate.
PMCID: PMC3042127  PMID: 20919724
EPR spectroscopy; photosystem II; square wave voltammetry; circular dichroism; redox-active tyrosine. pi-cation; hydrogen bond
10.  Driving force dependence of rates for nonadiabatic proton and proton-coupled electron transfer: Conditions for inverted region behavior 
The journal of physical chemistry. B  2009;113(44):14545-14548.
The driving force dependence of the rate constants for nonadiabatic electron transfer (ET), proton transfer (PT), and proton-coupled electron transfer (PCET) reactions are examined. Inverted region behavior, where the rate constant decreases as the reaction becomes more exoergic (i.e., as ΔG0 becomes more negative), has been observed experimentally for ET and PT. This behavior was predicted theoretically for ET but is not well understood for PT and PCET. The objective of this Letter is to predict the experimental conditions that could lead to observation of inverted region behavior for PT and PCET. The driving force dependence of the rate constant is qualitatively different for PT and PCET than for ET because of the high proton vibrational frequency and substantial shift between the reactant and product proton vibrational wavefunctions. As a result, inverted region behavior is predicted to be experimentally inaccessible for PT and PCET if only the driving force is varied. This behavior may be observed for PT over a limited range of rates and driving forces if the solvent reorganization energy is low enough to cause observable oscillations. Moreover, this behavior may be observed for PT or PCET if the proton donor-acceptor distance increases as ΔG0 becomes more negative. Thus, a plausible explanation for experimentally observed inverted region behavior for PT or PCET is that varying the driving force also impacts other properties of the system, such as the proton donor-acceptor distance.
PMCID: PMC2783471  PMID: 19795899
11.  Redox-Linked Conformational Control of Proton Coupled Electron Transfer: Y122 in the Ribonucleotide Reductase β2 Subunit 
The journal of physical chemistry. B  2013;117(28):8457-8468.
Tyrosyl radicals play essential roles in biological proton coupled electron transfer (PCET) reactions. Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides and is vital in DNA replication in all organisms. Class Ia RNRs consist of α2 and β2 homodimeric subunits. In class 1a RNR, such as the E. coli enzyme, an essential tyrosyl radical (Y122O•)-diferric cofactor is located in β2. While Y122O• is extremely stable in free β2, Y122O• is highly reactive in the quaternary substrate-α2β2 complex and serves as a radical initiator in catalytic PCET between β2 and α2. In this report, we investigate the structural interactions that control the reactivity of Y122O• in a model system, isolated E. coli β2. Y122O• was reduced with hydroxyurea (HU), a radical scavenger that quenches the radical in a clinically relevant reaction. In the difference FT-IR spectrum, associated with this PCET reaction, amide I (CO) and amide II (CN/NH) bands were observed. Specific 13C-labeling of the tyrosine C1 carbon assigned a component of these bands to the Y122-T123 amide bond. Comparison to density functional calculations on a model dipeptide, tyrosine-threonine, and structural modeling demonstrated that PCET is associated with a Y122 rotation and a 7.2 Å translation of the Y122 phenolic oxygen. To test for the functional consequences of this structural change, a proton inventory defined the origin of the large solvent isotope effect (SIE=16.7±1.0 at 25°C) on this reaction. These data suggest that the one electron, HU-mediated reduction of Y122O• is associated with two, rate-limiting (full or partial) proton transfer reactions. One is attributable to HU oxidation (SIE=11.9, net H atom transfer), and the other is attributable to coupled, hydrogen-bonding changes in the Y122O•-diferric cofactor (SIE=1.4). These results illustrate the importance of redox-linked changes to backbone and ring dihedral angles in high potential PCET and provide evidence for rate-limiting, redox-linked hydrogen-bonding interactions between Y122O• and the iron cluster.
PMCID: PMC3757525  PMID: 23822111
tyrosyl radical; proton coupled electron transfer; vibrational spectroscopy; proton inventory; conformational dynamics; density functional theory
12.  Proton-Coupled Electron Transfer of Ruthenium(III)-Pterin Complexes: A Mechanistic Insight 
Journal of the American Chemical Society  2009;131(32):11615-11624.
Ruthenium(II) complexes having pterins of redox-active heteroaromatic coenzymes as ligands were demonstrated to perform multistep proton transfer (PT), electron transfer (ET), and proton-coupled electron transfer (PCET) processes. Thermodynamic parameters including pKa, bond dissociation energy (BDE) of multistep PCET processes in acetonitrile (MeCN) were determined for ruthenium-pterin complexes, [RuII(Hdmp)(TPA)](ClO4)2 (1), [RuII(Hdmdmp)(TPA)](ClO4)2 (2), [RuII(dmp−)(TPA)]ClO4 (3) and [RuII(dmdmp−)(TPA)]ClO4 (4) (Hdmp = 6,7-dimethylpterin, Hdmdmp = N,N-dimethyl-6,7-dimethylpterin, TPA = tris(2-pyridylmethyl)amine), all of which had been isolated and characterized before. The BDE difference between 1 and one-electron oxidized species, [RuIII(dmp−)(TPA)]2+, was determined to be 89 kcal mol−1, which was large enough to achieve hydrogen atom transfer (HAT) from phenol derivatives. In the HAT reactions from phenol derivatives to [RuIII(dmp−)(TPA)]2+, the second-order rate constants (k) were determined to exhibit a linear relationship with BDE values of phenol derivatives with a slope (−0.4), suggesting that this HAT is simultaneous proton and electron transfer. As for HAT reaction from 2,4,6-tri-tert-buthylphenol (TBP; BDE = 79.15 kcal mol−1) to [RuIII(dmp−)(TPA)]2+, the activation parameters were determined to be ΔH‡ = 1.6 ± 0.2 kcal mol−1 and ΔS‡ = −36 ± 2 cal K−1 mol−1. This small activation enthalpy suggests a hydrogen-bonded adduct formation prior to HAT. Actually, in the reaction of 4-nitrophenol with [RuIII(dmp−)(TPA)]2+, the second-order rate constants exhibited saturation behavior at higher concentrations of the substrate and low-temperature ESI-MS allowed us to detect the hydrogen-bonding adduct. This also lends credence to an associative mechanism of the HAT involving intermolecular hydrogen bonding between the deprotonated dmp ligand and the phenolic O-H to facilitate the reaction. In particular, a two-point hydrogen bonding between the complex and the substrate involving the 2-amino group of the deprotonated pterin ligand effectively facilitates the HAT reaction from the substrate to the Ru(III)-pterin complex.
PMCID: PMC3201791  PMID: 19722655
13.  Theoretical Studies of Proton-Coupled Electron Transfer: Models and Concepts Relevant to Bioenergetics 
Coordination chemistry reviews  2008;252(3-4):384-394.
Theoretical studies of proton-coupled electron transfer (PCET) reactions for model systems provide insight into fundamental concepts relevant to bioenergetics. A dynamical theoretical formulation for vibronically nonadiabatic PCET reactions has been developed. This theory enables the calculation of rates and kinetic isotope effects, as well as the pH and temperature dependences, of PCET reactions. Methods for calculating the vibronic couplings for PCET systems have also been developed and implemented. These theoretical approaches have been applied to a wide range of PCET reactions, including tyrosyl radical generation in a tyrosine-bound rhenium polypyridyl complex, phenoxyl/phenol and benzyl/toluene self-exchange reactions, and hydrogen abstraction catalyzed by the enzyme lipoxygenase. These applications have elucidated some of the key underlying physical principles of PCET reactions. The tools and concepts derived from these theoretical studies provide the foundation for future theoretical studies of PCET in more complex bioenergetic systems such as Photosystem II.
PMCID: PMC2971562  PMID: 21057592
proton-coupled electron transfer; proton transfer; electron transfer; hydrogen transfer
14.  Synthesis and Structural Characterization of a Series of Mn(III)-OR Complexes, Including a Water-Soluble Mn(III)-OH that Promotes Aerobic Hydrogen Atom Transfer 
Inorganic chemistry  2013;52(21):10.1021/ic401234t.
Hydrogen atom transfer reactions (HAT) are a class of proton-coupled electron transfer (PCET) reactions used in biology to promote substrate oxidation. The driving force for such reactions depend on both the oxidation potential of the catalyst and the pKa of the proton acceptor site. Both high-valent transition-metal oxo M(IV)=O (M= Fe, Mn) and lower-valent transition-metal hydroxo compounds M(III)–OH (M= Fe, Mn) have been shown to promote these reactions. Herein we describe the synthesis, structure and reactivity properties of a series of Mn(III)-OR compounds (R= pNO2Ph(5), Ph(6), Me(7), H(8)), some of which abstract H-atoms. The Mn(III)-OH complex 8 is water-soluble and represents a rare example of a stable mononuclear Mn(III)-OH. In water, the redox potential of 8 was found to be pH-dependent and the Pourbaix (Ep,c vs pH) diagram has a slope (52 mV/pH) that is indicative of the transfer a single proton with each electron (ie, PCET). The two compounds with the lowest oxidation potential, hydroxide and methoxide-bound 7 and 8 are found to oxidize TEMPOH, whereas the compounds with the highest oxidation potential, phenol-ligated 5 and 6, are shown to be unreactive. Hydroxide-bound 8 reacts with TEMPOH an order of magnitude faster than methoxide-bound 7. Kinetic data (kH/kD= 3.1 (8), kH/kD= 2.1 (7)) are consistent with concerted H-atom abstraction. The reactive species 8 can be aerobically regenerated in H2O, and at least 10 turnovers can be achieved without significant degradation of the “catalyst”. The linear correlation between redox potential and pH, obtained from the Pourbaix diagram, was used to calculate the BDFE= 74.0±0.5 kcal/mol for Mn(II)-OH2 in water, and in MeCN its BDFE was estimated to be (70.1 kcal/mol). The reduced protonated derivative of 8, [MnII(SMe2N4(tren))(H2O)]+ (9), was estimated to have a pKa of 21.2 in MeCN. The ability (7) and inability (5 and 6) of the other members of the series to abstract a H-atom from TEMPOH was used to estimate either an upper or lower limit to the Mn(II)-O(H)R pKa based on their experimentally determined redox potentials. The trend in pKa (21.2(R=H) > 16.2(R=Me) > 13.5(R=Ph) > 12.2(R=pNO2Ph)) is shown to oppose that of oxidation potential Ep,c (−220(R= pNO2Ph) > −300(R= Ph) > −410(R= Me) > −600(R= H) mV vs Fc+/0) for this particular series.
PMCID: PMC3885356  PMID: 24156315
15.  Proton-Coupled Electron Transfer in Photosystem II: Proton Inventory of a Redox Active Tyrosine 
Journal of the American Chemical Society  2009;131(30):10567-10573.
Photosystem II (PSII) catalyzes the light driven oxidation of water and the reduction of plastoquinone. PSII is a multisubunit membrane protein; the D1 and D2 polypeptides form the heterodimeric core of the PSII complex. Water oxidation occurs at a manganese-containing oxygen evolving complex (OEC). PSII contains two redox active tyrosines, YZ and YD, which form the neutral tyrosyl radicals, Yz • and YD •. YD has been assigned as tyrosine 160 in the D2 polypeptide through isotopic labeling and site-directed mutagenesis. While YD is not directly involved in the oxidation of water, it has been implicated in the formation and stabilization of the OEC. PSII structures have shown YD to be within hydrogen bonding distance of histidine 189 in the D2 polypeptide. Spectroscopic studies have suggested that a proton is transferred between YD and histidine 189 when YD is oxidized and reduced. In our previous work, we used 2H2O solvent exchange to demonstrate that the mechanism of YD proton-coupled electron transfer (PCET) differs at high and low pH (Jenson, D. L.; Evans, A.; Barry, B. A. J. Phys. Chem. B 2007, 111, 12599–12604). In this paper, we utilize the proton inventory technique to obtain more information concerning the PCET mechanism at high pH. The hypercurvature of the proton inventory data provides evidence for the existence of multiple, proton donation pathways to YD •. In addition, at least one of these pathways must involve the transfer of more than one proton.
PMCID: PMC2846377  PMID: 19586025
oxygen evolution; tyrosyl radical; solvent isotope effect; EPR spectroscopy; proton inventory; hypercurvature
16.  Branched Activation- and Catalysis-Specific Pathways for Electron Relay to the Manganese/Iron Cofactor in Ribonucleotide Reductase from Chlamydia trachomatis† 
Biochemistry  2008;47(33):8477-8484.
A conventional class I (subclass a or b) ribonucleotide reductase (RNR) employs a tyrosyl radical (Y•) in its R2 subunit for reversible generation of a 3′-hydrogen-abstracting cysteine radical in its R1 subunit by proton-coupled electron transfer (PCET) through a network of aromatic amino acids spanning the two subunits. The class Ic RNR from the human pathogen Chlamydia trachomatis (Ct) uses a MnIV/FeIII cofactor (specifically, the MnIV ion) in place of the Y• for radical initiation. Ct R2 is activated when its MnII/FeII form reacts with O2 to generate a MnIV/FeIV intermediate, which decays by reduction of the FeIV site to the active MnIV/FeIII state. Here we show that the reduction step in this sequence is mediated by residue Y222. Substitution of Y222 with F retards the intrinsic decay of the MnIV/FeIV intermediate by ∼10-fold and diminishes the ability of ascorbate to accelerate the decay by ∼65-fold but has no detectable effect on the catalytic activity of the MnIV/FeIII–R2 product. By contrast, substitution of Y338, the cognate of the subunit interfacial R2 residue in the R1 ⇔ R2 PCET pathway of the conventional class I RNRs [Y356 in Escherichia coli (Ec) R2], has almost no effect on decay of the MnIV/FeIV intermediate but abolishes catalytic activity. Substitution of W51, the Ct R2 cognate of the cofactor-proximal R1 ⇔ R2 PCET pathway residue in the conventional class I RNRs (W48 in Ec R2), both retards reduction of the MnIV/FeIV intermediate and abolishes catalytic activity. These observations imply that Ct R2 has evolved branched pathways for electron relay to the cofactor during activation and catalysis. Other R2s predicted also to employ the Mn/Fe cofactor have Y or W (also competent for electron relay) aligning with Y222 of Ct R2. By contrast, many R2s known or expected to use the conventional Y•-based system have redox-inactive L or F residues at this position. Thus, the presence of branched activation- and catalysis-specific electron relay pathways may be functionally important uniquely in the Mn/Fe-dependent class Ic R2s.
PMCID: PMC2681183  PMID: 18656954
17.  Probing Nonadiabaticity in the Proton-Coupled Electron Transfer Reaction Catalyzed by Soybean Lipoxygenase 
Proton-coupled electron transfer (PCET) plays a vital role in many biological and chemical processes. PCET rate constant expressions are available for various well-defined regimes, and determining which expression is appropriate for a given system is essential for reliable modeling. Quantitative diagnostics have been devised to characterize the vibronic nonadiabaticity between the electron–proton quantum subsystem and the classical nuclei, as well as the electron–proton nonadiabaticity between the electrons and proton(s) within the quantum subsystem. Herein these diagnostics are applied to a model of the active site of the enzyme soybean lipoxygenase, which catalyzes a PCET reaction that exhibits unusually high deuterium kinetic isotope effects at room temperature. Both semiclassical and electronic charge density diagnostics illustrate vibronic and electron–proton nonadiabaticity for this PCET reaction, supporting the use of the Golden rule nonadiabatic rate constant expression with a specific form of the vibronic coupling. This type of characterization will be useful for theoretical modeling of a broad range of PCET processes.
PMCID: PMC4170820  PMID: 25258676
18.  4-Meth­oxy­benzamidinium hydrogen oxalate monohydrate 
The title hydrated salt, C8H11N2O+·C2HO4 −·H2O, was synthesized by a reaction of 4-meth­oxy­benzamidine (4-amidino­anisole) and oxalic acid in water solution. In the cation, the amidinium group forms a dihedral angle of 15.60 (6)° with the mean plane of the benzene ring. In the crystal, each amidinium unit is bound to three acetate anions and one water mol­ecule by six distinct N—H⋯O hydrogen bonds. The ion pairs of the asymmetric unit are joined by two N—H⋯O hydrogen bonds into ionic dimers in which the carbonyl O atom of the semi-oxalate anion acts as a bifurcated acceptor, thus generating an R 1 2(6) motif. These subunits are then joined through the remaining N—H⋯O hydrogen bonds to adjacent semi-oxalate anions into linear tetra­meric chains running approximately along the b axis. The structure is stabilized by N—H⋯O and O—H⋯O inter­molecular hydrogen bonds. The water mol­ecule plays an important role in the cohesion and the stability of the crystal structure being involved in three hydrogen bonds connecting two semi-oxalate anions as donor and a benzamidinium cation as acceptor.
PMCID: PMC3588951  PMID: 23476187
19.  Dichotomous Hydrogen Atom Transfer vs. Proton Coupled Electron Transfer During Activation of X-H Bonds (X = C, N, O) by Nonheme Iron-Oxo Complexes of Variable Basicity 
Journal of the American Chemical Society  2013;135(45):10.1021/ja408073m.
We describe herein the hydrogen-atom transfer (HAT)/ proton-coupled electron-transfer (PCET) reactivity for FeIV-oxo and FeIII-oxo complexes (1–4) that activate C-H, N-H, and O-H bonds in 9,10 dihydroanthracene (S1), dimethylformamide (S2), 1,2 diphenylhydrazine (S3), p-methoxyphenol (S4), and 1,4-cyclohexadiene (S5). In 1–3, the iron is pentacoordinated by tris[N'-tert-butylureaylato)-N-ethylene]aminato ([H3buea]3−) or its derivatives. These complexes are basic, in the order 3 >> 1 > 2. Oxidant 4, [FeIVN4Py(O)]2+ (N4Py: N,N-bis(2-pyridylmethyl)-bis(2-pyridyl) methylamine), is the least basic oxidant. The DFT results match experimental trends and exhibit a mechanistic spectrum ranging from concerted HAT and PCET reactions to concerted-asynchronous proton transfer (PT) / electron transfer (ET) mechanisms, all the way to PT. The singly occupied orbital along the O---H---X (X= C, N, O) moiety in the TS shows clearly that in the PCET cases, the electron is transferred separately from the proton. The Bell-Evans-Polanyi principle does not account for the observed reactivity pattern, as evidenced by the scatter in the plot of calculated barrier vs. reactions driving forces. However, a plot of the deformation energy in the TS vs. the respective barrier provides a clear signature of the HAT/PCET dichotomy. Thus, in all C-H bond activations, the barrier derives from the deformation energy required to create the TS, whereas in N-H/O-H bond activations, the deformation energy is much larger than the corresponding barrier, indicating the presence of stabilizing interaction between the TS fragments. A valence bond model is used to link the observed results with the basicity/acidity of the reactants.
PMCID: PMC3876471  PMID: 24124906
20.  Conserved Hydrogen Bonding Networks of MitoNEET Tune FeS Cluster Binding and Structural Stability 
Biochemistry  2013;52(27):4687-4696.
While its biological function remains unclear, the 3-Cys, 1-His ligated human [2Fe-2S] cluster containing protein mitoNEET is of interest due to its interaction with the anti-diabetes drug pioglitazone. The mitoNEET [2Fe-2S] cluster demonstrates proton coupled-electron transfer (PCET) and marked cluster instability which have both been linked to the single His-ligand. Highly conserved hydrogen bonding networks, which include the His-87 ligand, exist around the [2Fe-2S] cluster. Through a series of site-directed mutations the PCET of the cluster has been examined, demonstrating that multiple sites of protonation exist in addition to the His-ligand, which can influence redox potential. The mutations also demonstrate that while replacement of the His-ligand with cysteine results in a stable cluster, the removal of Lys-55 also greatly stabilizes the cluster. We have also noted for the first time that the oxidation state of the cluster controls stability; the reduced cluster is stable, while the oxidized one is much more labile. Finally, it is shown that upon cluster loss the mitoNEET protein structure becomes less stable, while upon in vitro reconstitution both cluster and secondary structure are recovered. Recently two other proteins have been identified with a 3-Cys(sulfur) 1-His motif, IscR and Grx3/4-Fra2, both of which are sensors of iron and redox homeostatsis. These results lead to a model in which mitoNEET could sense cellular oxidation state and proton concentration and respond through cluster loss and unfolding.
PMCID: PMC3940166  PMID: 23758282
MitoNEET; iron-sulfur protein; protein film voltammetry (PFV); proton coupled-electron transfer (PCET); Circular Dichroism (CD)
21.  Photochemical Tyrosine Oxidation in the Structurally Well-Defined α3Y Protein: Proton-Coupled Electron Transfer and a Long-Lived Tyrosine Radical 
Journal of the American Chemical Society  2014;136(40):14039-14051.
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 (kPCET) 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). kH/kD 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, t1/2 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.
PMCID: PMC4195373  PMID: 25121576
22.  A Structural Element that Facilitates Proton-Coupled Electron Transfer in Oxalate Decarboxylase†,†† 
Biochemistry  2012;51(13):2911-2920.
The conformational properties of an active-site loop segment, defined by residues Ser161-Glu162-Asn163-Ser164, 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 Rad. 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.
PMCID: PMC3319475  PMID: 22404040
Oxalate Decarboxylase; Heavy Atom Isotope Effects; Proton-Coupled Electron Transfer; Enzyme Catalysis
23.  Molecular eyes: proteins that transform light into biological information 
Interface Focus  2013;3(5):20130005.
Most biological photoreceptors are protein/cofactor complexes that induce a physiological reaction upon absorption of a photon. Therefore, these proteins represent signal converters that translate light into biological information. Researchers use this property to stimulate and study various biochemical processes conveniently and non-invasively by the application of light, an approach known as optogenetics. Here, we summarize the recent experimental progress on the family of blue light receptors using FAD (BLUF) receptors. Several BLUF photoreceptors modulate second messenger levels and thus represent highly interesting tools for optogenetic application. In order to activate a coupled effector protein, the flavin-binding pocket of the BLUF domain undergoes a subtle rearrangement of the hydrogen network upon blue light absorption. The hydrogen bond switch is facilitated by the ultrafast light-induced proton-coupled electron transfer (PCET) between a tyrosine and the flavin in less than a nanosecond and remains stable on a long enough timescale for biochemical reactions to take place. The cyclic nature of the photoinduced reaction makes BLUF domains powerful model systems to study protein/cofactor interaction, protein-modulated PCET and novel mechanisms of biological signalling. The ultrafast nature of the photoconversion as well as the subtle structural rearrangement requires sophisticated spectroscopic and molecular biological methods to study and understand this highly intriguing signalling process.
PMCID: PMC3915823  PMID: 24511384
photoreceptor; flavin; proton-coupled electron transfer; spectroscopy
24.  Hybrid Quantum/Classical Molecular Dynamics Simulations of the Proton Transfer Reactions Catalyzed by Ketosteroid Isomerase: Analysis of Hydrogen Bonding, Conformational Motions, and Electrostatics 
Biochemistry  2009;48(44):10608-10619.
Hybrid quantum/classical molecular dynamics simulations of the two proton transfer reactions catalyzed by ketosteroid isomerase are presented. The potential energy surfaces for the proton transfer reactions are described with the empirical valence bond method. Nuclear quantum effects of the transferring hydrogen increase the rates by a factor of ~8, and dynamical barrier recrossings decrease the rates by a factor of 3–4. For both proton transfer reactions, the donor-acceptor distance decreases substantially at the transition state. The carboxylate group of the Asp38 side chain, which serves as the proton acceptor and donor in the first and second steps, respectively, rotates significantly between the two proton transfer reactions. The hydrogen bonding interactions within the active site are consistent with the hydrogen bonding of both Asp99 and Tyr14 to the substrate. The simulations suggest that a hydrogen bond between Asp99 and the substrate is present from the beginning of the first proton transfer step, whereas the hydrogen bond between Tyr14 and the substrate is virtually absent in the first part of this step but forms nearly concurrently with the formation of the transition state. Both hydrogen bonds are present throughout the second proton transfer step until partial dissociation of the product. The hydrogen bond between Tyr14 and Tyr55 is present throughout both proton transfer steps. The active site residues are more mobile during the first step than during the second step. The van der Waals interaction energy between the substrate and the enzyme remains virtually constant along the reaction pathway, but the electrostatic interaction energy is significantly stronger for the dienolate intermediate than for the reactant and product. Mobile loop regions distal to the active site exhibit significant structural rearrangements and, in some cases, qualitative changes in the electrostatic potential during the catalytic reaction. These results suggest that relatively small conformational changes of the enzyme active site and substrate strengthen the hydrogen bonds that stabilize the intermediate, thereby facilitating the proton transfer reactions. Moreover, the conformational and electrostatic changes associated with these reactions are not limited to the active site but rather extend throughout the entire enzyme.
PMCID: PMC2783618  PMID: 19799395
25.  Site-specific incorporation of 3-nitrotyrosine as a probe of pKa perturbation of redox-active tyrosines in ribonucleotide reductase 
E. coli ribonucleotide reductase catalyzes the reduction of nucleoside 5′-diphosphates into 2′-deoxynucleotides and is composed of two subunits: α2 and β2. During turnover, a stable tyrosyl radical (Y·) at Y122-β2 reversibly oxidizes C439 in the active site of α2. This radical propagation step is proposed to occur over 35 Å, to use specific redox-active tyrosines (Y122 and Y356 in β2, Y731 and Y730 in α2), and to involve proton-coupled electron transfer (PCET). 3-Nitrotyrosine (NO2Y, pKa 7.1) has been incorporated in place of Y122, Y731 and Y730 to probe how the protein environment perturbs each pKa in the presence of the second subunit, substrate (S), and allosteric effector (E). The activity of each mutant is < 4 × 10−3 that of the wt subunit. The [NO2Y730]-α2 and [NO2Y731]-α2 each exhibits a pKa of 7.8 – 8.0 with E and E/β2. The pKa of [NO2Y730]-α2 is elevated to 8.2 - 8.3 in the S/E/β2 complex, while no further perturbation is observed for [NO2Y731]-α2. Mutations in pathway residues adjacent to the NO2Y that disrut H bonding minimally perturb its Ka. The pKa of NO2Y122-β2 alone or with α2/S/E is > 9.6. X-ray crystal structures have been obtained for all NO2Y-α2 mutants (2.1 – 3.1 Å resolution), which show minimal structural perturbation compared to wt-α2. Together with the pKa of the previously reported NO2Y356-β2 (7.5 in the α2/S/E complex, Yee, C. et al, Biochemistry 2003, 42, 14541-14552.), these studies provide a picture of the protein environment of the ground state at each Y in the PCET pathway and are the starting point for understanding differences in PCET mechanisms at each residue in the pathway.
PMCID: PMC2905227  PMID: 20518462

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