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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.  Spectral observation of conversion between ionized vs. non-ionized proton-coupled electron transfer interfaces† 
Two-point hydrogen bonding between acid and base functionalities provides a convenient method for the modular assembly of proton-coupled electron transfer (PCET) networks, especially when that interface comprises an amidinium and two-point anionic partner; a system is presented that permits the proton configuration within the interface to be determined when pKa values of the conjugate acids are known.
PMCID: PMC4625797  PMID: 18473057
3.  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
4.  Proton-Coupled Electron Transfer in Biology: Results from Synergistic Studies in Natural and Model Systems 
Annual review of biochemistry  2009;78:673-699.
Proton-coupled electron transfer (PCET) underpins energy conversion in biology. PCET may occur with the unidirectional or bidirectional transfer of a proton and electron and may proceed synchronously or asynchronously. To illustrate the role of PCET in biology, this review presents complementary biological and model systems that explore PCET in electron transfer (ET) through hydrogen bonds [azurin as compared to donor-acceptor (D–A) hydrogen-bonded networks], the activation of C–H bonds [alcohol dehydrogenase and soybean lipoxygenase (SLO) as compared to Fe(III) metal complexes], and the generation and transport of amino acid radicals [photosystem II (PSII) and ribonucleotide reductase (RNR)as compared to tyrosine-modified photoactive Re(I) and Ru(II) complexes]. In providing these comparisons, the fundamental principles of PCET in biology are illustrated in a tangible way.
PMCID: PMC4625787  PMID: 19344235
amino acid radical; lipoxygenase; photosystem II; ribonucleotide reductase; tyrosine
5.  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
6.  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
7.  Charge Transfer Dynamics at the α/β Subunit Interface of a Photochemical Ribonucleotide Reductase 
Ribonucleotide reductase (RNR) catalyzes the conversion of ribonucleotides to deoxyribonucleotides to provide the monomeric building blocks for DNA replication and repair. Nucleotide reduction occurs by way of multi-step proton-coupled electron transfer (PCET) over a pathway of redox active amino acids spanning ~ 35 Å and two subunits (α2 and β2). Despite the fact that PCET in RNR is rapid, slow conformational changes mask kinetic examination of these steps. As such, we have pioneered methodology in which site-specific incorporation of a [ReI] photooxidant on the surface of the β2 subunit (photoβ2) allows photochemical oxidation of the adjacent PCET pathway residue β-Y356 and time-resolved spectroscopic observation of the ensuing reactivity. A series of photoβ2s capable of performing photoinitiated substrate turnover have been prepared in which four different fluorotyrosines (FnYs) are incorporated in place of β-Y356. The FnYs are deprotonated under biological conditions, undergo oxidation by electron transfer (ET) and provide a means by which to vary the ET driving force (ΔG°) with minimal additional perturbations across the series. We have used these features to map the correlation between ΔG° and kET both with and without the fully assembled photoRNR complex. The photooxidation of FnY356 within the α/β subunit interface occurs within the Marcus inverted region with a reorganization energy of λ ≈ 1 eV. We also observe enhanced electronic coupling between donor and acceptor (HDA) in the presence of an intact PCET pathway. Additionally, we have investigated the dynamics of proton transfer (PT) by a variety of methods including dependencies on solvent isotopic composition, buffer concentration, and pH. We present evidence for the role of α2 in facilitating PT during β-Y356 photooxidation; PT occurs by way of readily exchangeable positions and within a relatively “tight” subunit interface. These findings show that RNR controls ET by lowering λ, raising HDA, and directing PT both within and between individual polypeptide subunits.
Graphical abstract
PMCID: PMC4924928  PMID: 26710997
8.  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
9.  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
10.  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
11.  Kinetics of Hydrogen Atom Abstraction from Substrate by an Active Site Thiyl Radical in Ribonucleotide Reductase 
Journal of the American Chemical Society  2014;136(46):16210-16216.
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 [ReI] 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.
PMCID: PMC4244835  PMID: 25353063
12.  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
13.  ENDOR spectroscopy and DFT calculations: evidence for the hydrogen bond network within α2 in the PCET of E. coli ribonucleotide reductase 
Journal of the American Chemical Society  2012;134(42):17661-17670.
E.coli class I ribonucleotide reductase (RNR) catalyzes the conversion of nucleotides to deoxynucleotides and is composed of two subunits: α2 and β2. β2 contains a stable di-iron tyrosyl radical (Y122•) cofactor required to generate a thiyl radical (C439•) in α2 over a distance of 35 Å, which in turn initiates the chemistry of the reduction process. The radical transfer process is proposed to occur by proton-coupled electron transfer (PCET) via a specific pathway: Y122 ⇆ W48[?] ⇆ Y356 in β2, across the subunit interface to Y731⇆ Y730 ⇆ C439 in α2. Within α2 a co-linear PCET model has been proposed. To obtain evidence for this model, 3-amino tyrosine (NH2Y) replaced Y730 in α2 and this mutant was incubated with β2, CDP and ATP to generate a (NH2Y730•) in D2O. [2H]-Electron-nuclear double resonance (ENDOR) spectra at 94 GHz of this intermediate were obtained and together with DFT models of α2 and quantum chemical calculations allowed assignment of the prominent ENDOR features to two hydrogen bonds likely associated with C439 and Y731. A third proton was assigned to a water molecule in close proximity (2.2 Å O-H---O distance) to residue 730. The calculations also suggest that the unusual g-values measured for NH2Y730• are consistent with the combined effect of the hydrogen bonds to Cys439 and Tyr731, both nearly perpendicular to the ring plane of NH2Y730. The results provide the first experimental evidence for the hydrogen bond network between the pathway residues in α2 of the active RNR complex, for which no structural data is available.
PMCID: PMC4516058  PMID: 23072506
RNR; proton-coupled electron transfer; high-field ENDOR; DFT; hydrogen bond network
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
15.  Dependence of Vibronic Coupling on Molecular Geometry and Environment: Bridging Hydrogen Atom Transfer and Electron–Proton Transfer 
Journal of the American Chemical Society  2015;137(42):13545-13555.
The rate constants for typical concerted proton-coupled electron transfer (PCET) reactions depend on the vibronic coupling between the diabatic reactant and product states. The form of the vibronic coupling is different for electronically adiabatic and nonadiabatic reactions, which are associated with hydrogen atom transfer (HAT) and electron–proton transfer (EPT) mechanisms, respectively. Most PCET rate constant expressions rely on the Condon approximation, which assumes that the vibronic coupling is independent of the nuclear coordinates of the solute and the solvent or protein. Herein we test the Condon approximation for PCET vibronic couplings. The dependence of the vibronic coupling on molecular geometry is investigated for an open and a stacked transition state geometry of the phenoxyl-phenol self-exchange reaction. The calculations indicate that the open geometry is electronically nonadiabatic, corresponding to an EPT mechanism that involves significant electronic charge redistribution, while the stacked geometry is predominantly electronically adiabatic, corresponding primarily to an HAT mechanism. Consequently, a single molecular system can exhibit both HAT and EPT character. The dependence of the vibronic coupling on the solvent or protein configuration is examined for the soybean lipoxygenase enzyme. The calculations indicate that this PCET reaction is electronically nonadiabatic with a vibronic coupling that does not depend significantly on the protein environment. Thus, the Condon approximation is shown to be valid for the solvent and protein nuclear coordinates but invalid for the solute nuclear coordinates in certain PCET systems. These results have significant implications for the calculation of rate constants, as well as mechanistic interpretations, of PCET reactions.
PMCID: PMC4629534  PMID: 26412613
16.  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
17.  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
18.  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
19.  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. 2H 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.
PMCID: PMC4304443  PMID: 25516424
20.  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
21.  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
22.  Crystal structure of bis­(N-tert-butyl­benzamidinium) hexa­chlorido­zirconate(IV) di­chloro­methane disolvate 
In the crystal of the title complex salt, the amidinium cations and the centrosymmetric ZrIV complex anions are linked by N—H⋯Cl hydrogen bonds, forming a two-dimensional network extending along the b-axis direction.
In the ZrIV complex anion of the title complex salt, [(C4H9)HNC(C6H5)NH2]2[ZrCl6]·2CH2Cl2, the ZrIV cation, located on an inversion centre, is coordinated by six Cl− anions in a distorted octa­hedral geometry with Zr—Cl distances in the range 2.433 (2)–2.4687 (19) Å; in the amidinium cation, the dihedral angle between the aromatic ring and [NCN] plane is 43.3 (4)°. In the crystal, the amidinium cations and [ZrCl6]2− anions are linked by N—H⋯Cl hydrogen bonds, forming a two-dimensional network extending along the b axis; two di­chloro­methane solvent mol­ecules are linked by a pair of weak C—H⋯Cl hydrogen bonds, forming a centrosymmetric [CHCl]2 six-membered ring.
PMCID: PMC4910352  PMID: 27375857
crystal structure; benzamidinium; zirconate; N—H⋯Cl hydrogen bonds
23.  Direct Interfacial Y731 Oxidation in α2 by a Photoβ2 Subunit of E. coli Class Ia Ribonucleotide Reductase 
Proton-coupled electron transfer (PCET) is a fundamental mechanism important in a wide range of biological processes including the universal reaction catalysed by ribonucleotide reductases (RNRs) in making de novo, the building blocks required for DNA replication and repair. These enzymes catalyse the conversion of nucleoside diphosphates (NDPs) to deoxynucleoside diphosphates (dNDPs). In the class Ia RNRs, NDP reduction involves a tyrosyl radical mediated oxidation occurring over 35 Å across the interface of the two required subunits (β2 and α2) involving multiple PCET steps and the conserved tyrosine triad [Y356(β2)–Y731(α2)–Y730(α2)]. We report the synthesis of an active photochemical RNR (photoRNR) complex in which a Re(I)-tricarbonyl phenanthroline ([Re]) photooxidant is attached site-specifically to the Cys in the Y356C-(β2) subunit and an ionizable, 2,3,5-trifluorotyrosine (2,3,5-F3Y) is incorporated in place of Y731 in α2. This intersubunit PCET pathway is investigated by ns laser spectroscopy on [Re356]-β2:2,3,5-F3Y731-α2 in the presence of substrate, CDP, and effector, ATP. This experiment has allowed analysis of the photoinjection of a radical into α2 from β2 in the absence of the interfacial Y356 residue. The system is competent for light-dependent substrate turnover. Time-resolved emission experiments reveal an intimate dependence of the rate of radical injection on the protonation state at position Y731(α2), which in turn highlights the importance of a well-coordinated proton exit channel involving the key residues, Y356 and Y731, at the subunit interface.
PMCID: PMC4618407  PMID: 26504513
24.  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
25.  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

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