Radical initiation in the class I ribonucleotide reductase: long-range proton-coupled electron transfer?

Radicals as hydrogen bond donors and acceptors

High-level quantum chemical techniques were used to study the hydrogen bonding interactions in dimers of simple hydrogen bond donors and acceptors. The dimers studied were formed from combinations of CH(4), NH(3), OH(2) with each other and with the *CH(3), *NH(2), and *OH radicals. It was found that complexes in which a radical serves as a hydrogen bond donor, i.e. *AH(x)-BH(y), are more strongly bound than dimers in which the hydrogen bond donor is the analogous parent molecule, i.e. AH(x+1)-BH(y). Complexes in which a radical serves as a hydrogen bond acceptor, i.e. BH(y) (-) *AH(x), are more weakly bound than dimers in which the hydrogen bond acceptor is the analogous parent molecule, i.e. BH(y)-AH(x+1). The differences in these binding properties are attributable to the facts that, in radicals, the A-H bonds are more polar and the A atoms have less negative partial charges than in molecules. Detailed analyses of spin densities revealed that spin delocalization from a radical to a molecule is negligible. Therefore, spin delocalization plays no role in the binding within the complexes studied in this work. Density functional theory methods were also used to calculate the binding energies of the complexes. It was found that the PBE0 and B971 functionals predict binding energies that are in good agreement with the high-level wavefunction data, whereas the performance of the common B3LYP method is not as good. Correcting the functionals for their ability to treat dispersion interactions in carbon-containing compounds improves the binding energies computed with the B3LYP and PBE0 functionals but results in over-binding with B971.

Characterization of a peroxodiiron(III) intermediate in the T201S variant of toluene/o-xylene monooxygenase hydroxylase from Pseudomonas sp. OX1

We report the observation of a novel intermediate in the reaction of a reduced toluene/o-xylene monooxygenase hydroxylase (ToMOH(red)) T201S variant, in the presence of a regulatory protein (ToMOD), with dioxygen. This species is the first oxygenated intermediate with an optical band in any toluene monooxygenase. The UV-vis and Mossbauer spectroscopic properties of the intermediate allow us to assign it as a peroxodiiron(III) species, T201S(peroxo), similar to H(peroxo) in methane monooxygenase. Although T201S generates T201S(peroxo) in addition to optically transparent ToMOH(peroxo), previously observed in wild-type ToMOH, this conservative variant is catalytically active in steady-state catalysis and single-turnover experiments and displays the same regiospecificity for toluene and slightly different regiospecificity for o-xylene oxidation.

Slow hydrogen atom transfer reactions of oxo- and hydroxo-vanadium compounds: the importance of intrinsic barriers

Reactions are described that interconvert vanadium(IV) oxo-hydroxo complexes [V(IV)O(OH)(R(2)bpy)(2)]BF(4) (1a-c) and vanadium(V) dioxo complexes [V(V)O(2)(R(2)bpy)(2)]BF(4) (2a-c) [R(2)bpy = 4,4'-di-tert-butyl-2,2'-bipyridine ((t)Bu(2)bpy), a; 4,4'-dimethyl-2,2'-bipyridine (Me(2)bpy), b; 2,2'-bipyridine (bpy), c]. These are rare examples of pairs of isolated, sterically unencumbered, first-row metal-oxo/hydroxo complexes that differ by a hydrogen atom (H(+) + e(-)). The V(IV)-(t)Bu(2)bpy derivative 1a has a useful (1)H NMR spectrum, despite being paramagnetic. Complex 2a abstracts H(*) from organic substrates with weak O-H and C-H bonds, converting 2,6-(t)Bu(2)-4-MeO-C(6)H(2)OH (ArOH) and 2,2,6,6-tetramethyl-N-hydroxypiperidine (TEMPOH) to their corresponding radicals ArO(*) and TEMPO, hydroquinone to benzoquinone, and dihydroanthracene to anthracene. The equilibrium constant for 2a + ArOH <==> 1a + ArO(*) is (4 +/- 2) x 10(-3), implying that the VO-H bond dissociation free energy (BDFE) is 70.6 +/- 1.2 kcal mol(-1). Consistent with this value, 1a is oxidized by 2,4,6-(t)Bu(3)C(6)H(2)O(*). All of these reactions are surprisingly slow, typically occurring over hours at ambient temperatures. The net hydrogen-atom pseudo-self-exchange 1a + 2b <==> 2a + 1b, using the (t)Bu- and Me-bpy substituents as labels, also occurs slowly, with k(se) = 1.3 x 10(-2) M(-1) s(-1) at 298 K, DeltaH(double dagger) = 15 +/- 2 kcal mol(-1), and DeltaS(double dagger) = 16 +/- 5 cal mol(-1) K. Using this k(se) and the BDFE, the vanadium reactions are shown to follow the Marcus cross relation moderately well, with calculated rate constants within 10(2) of the observed values. The vanadium self-exchange reaction is ca. 10(6) slower than that for the related Ru(IV)O(py)(bpy)(2)(2+)/Ru(III)OH(py)(bpy)(2)(2+) self-exchange. The origin of this dramatic difference has been probed with DFT calculations on the self-exchange reactions of 1c + 2c and on monocationic ruthenium complexes with pyrrolate or fluoride in place of the py ligands. The calculations reproduce the difference in barrier heights and show that transfer of a hydrogen atom involves more structural reorganization for vanadium than the Ru analogues. The vanadium complexes have larger changes in the metal-oxo and metal-hydroxo bond lengths, which is traced to the difference in d-orbital occupancy in the two systems. This study thus highlights the importance of intrinsic barriers in the transfer of a hydrogen atom, in addition to the thermochemical (bond strength) factors that have been previously emphasized.

A Mycobacterium tuberculosis ligand-binding Mn/Fe protein reveals a new cofactor in a remodeled R2-protein scaffold

Chlamydia trachomatis R2c is the prototype for a recently discovered group of ribonucleotide reductase R2 proteins that use a heterodinuclear Mn/Fe redox cofactor for radical generation and storage. Here, we show that the Mycobacterium tuberculosis protein Rv0233, an R2 homologue and a potential virulence factor, contains the heterodinuclear manganese/iron-carboxylate cofactor but displays a drastic remodeling of the R2 protein scaffold into a ligand-binding oxidase. The first structural characterization of the heterodinuclear cofactor shows that the site is highly specific for manganese and iron in their respective positions despite a symmetric arrangement of coordinating residues. In this protein scaffold, the Mn/Fe cofactor supports potent 2-electron oxidations as revealed by an unprecedented tyrosine-valine crosslink in the active site. This wolf in sheep's clothing defines a distinct functional group among R2 homologues and may represent a structural and functional counterpart of the evolutionary ancestor of R2s and bacterial multicomponent monooxygenases.

Role of the AcsF protein in Chloroflexus aurantiacus

The green phototrophic bacteria contain a unique complement of chlorophyll pigments, which self-assemble efficiently into antenna structures known as chlorosomes with little involvement of protein. The few proteins found in chlorosomes have previously been thought to have a primarily structural function. The biosynthetic pathway of the chlorosome pigments, bacteriochlorophylls c, d, and e, is not well understood. In this report, we used spectroscopic, proteomic, and gene expression approaches to investigate the chlorosome proteins of the green filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus. Surprisingly, Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase, AcsF, was identified under anaerobic growth conditions. The AcsF protein was found in the isolated chlorosome fractions, and the proteomics analysis suggested that significant portions of the AcsF proteins are not accessible to protease digestion. Additionally, quantitative real-time PCR studies showed that the transcript level of the acsF gene is not lower in anaerobic growth than in semiaerobic growth. Since the proposed enzymatic activity of AcsF requires molecular oxygen, our studies suggest that the roles of AcsF in C. aurantiacus need to be investigated further.

Trends in ground-state entropies for transition metal based hydrogen atom transfer reactions

Reported herein are thermochemical studies of hydrogen atom transfer (HAT) reactions involving transition metal H-atom donors M(II)LH and oxyl radicals. [Fe(II)(H(2)bip)(3)](2+), [Fe(II)(H(2)bim)(3)](2+), [Co(II)(H(2)bim)(3)](2+), and Ru(II)(acac)(2)(py-imH) [H(2)bip = 2,2'-bi-1,4,5,6-tetrahydropyrimidine, H(2)bim = 2,2'-bi-imidazoline, acac = 2,4-pentandionato, py-imH = 2-(2'-pyridyl)imidazole)] each react with TEMPO (2,2,6,6-tetramethyl-1-piperidinoxyl) or (t)Bu(3)PhO(*) (2,4,6-tri-tert-butylphenoxyl) to give the deprotonated, oxidized metal complex M(III)L and TEMPOH or (t)Bu(3)PhOH. Solution equilibrium measurements for the reaction of [Co(II)(H(2)bim)(3)](2+) with TEMPO show a large, negative ground-state entropy for hydrogen atom transfer, -41 +/- 2 cal mol(-1) K(-1). This is even more negative than the DeltaS(o)(HAT) = -30 +/- 2 cal mol(-1) K(-1) for the two iron complexes and the DeltaS(o)(HAT) for Ru(II)(acac)(2)(py-imH) + TEMPO, 4.9 +/- 1.1 cal mol(-1) K(-1), as reported earlier. Calorimetric measurements quantitatively confirm the enthalpy of reaction for [Fe(II)(H(2)bip)(3)](2+) + TEMPO, thus also confirming DeltaS(o)(HAT). Calorimetry on TEMPOH + (t)Bu(3)PhO(*) gives DeltaH(o)(HAT) = -11.2 +/- 0.5 kcal mol(-1) which matches the enthalpy predicted from the difference in literature solution BDEs. A brief evaluation of the literature thermochemistry of TEMPOH and (t)Bu(3)PhOH supports the common assumption that DeltaS(o)(HAT) approximately 0 for HAT reactions of organic and small gas-phase molecules. However, this assumption does not hold for transition metal based HAT reactions. The trend in magnitude of |DeltaS(o)(HAT)| for reactions with TEMPO, Ru(II)(acac)(2)(py-imH) << [Fe(II)(H(2)bip)(3)](2+) = [Fe(II)(H(2)bim)(3)](2+) < [Co(II)(H(2)bim)(3)](2+), is surprisingly well predicted by the trends for electron transfer half-reaction entropies, DeltaS(o)(ET), in aprotic solvents. This is because both DeltaS(o)(ET) and DeltaS(o)(HAT) have substantial contributions from vibrational entropy, which varies significantly with the metal center involved. The close connection between DeltaS(o)(HAT) and DeltaS(o)(ET) provides an important link between these two fields and provides a starting point from which to predict which HAT systems will have important ground-state entropy effects.

Analysis of kinetic isotope effects for proton-coupled electron transfer reactions

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.

myo-Inositol oxygenase: a radical new pathway for O(2) and C-H activation at a nonheme diiron cluster

The enzyme myo-inositol oxygenase (MIOX) catalyzes conversion of myo-inositol (cyclohexan-1,2,3,5/4,6-hexa-ol or MI) to d-glucuronate (DG), initiating the only known pathway in humans for catabolism of the carbon skeleton of cell-signaling inositol (poly)phosphates and phosphoinositides. Recent kinetic, spectroscopic and crystallographic studies have shown that the enzyme activates its substrates, MI and O(2), at a carboxylate-bridged nonheme diiron(ii/iii) cluster, making it the first of many known nonheme diiron oxygenases to employ the mixed-valent form of its cofactor. Evidence suggests that: (1) the Fe(iii) site coordinates MI via its C1 and C6 hydroxyl groups; (2) the Fe(ii) site reversibly coordinates O(2) to produce a superoxo-diiron(iii/iii) intermediate; and (3) the pendant oxygen atom of the superoxide ligand abstracts hydrogen from C1 to initiate the unique C-C-bond-cleaving, four-electron oxidation reaction. This review recounts the studies leading to the recognition of the novel cofactor requirement and catalytic mechanism of MIOX and forecasts how remaining gaps in our understanding might be filled by additional experiments.

Electron transfer in peptides and proteins

Electron transfer (ET) processes in proteins drive the energy conversion processes in cells and are also involved in metabolic catalysis. In this tutorial review, the models explaining ET through peptides and proteins are discussed and the biological relevance of ET is elucidated.

Protein engineering of redox-active enzymes

Redox-active enzymes perform many key biological reactions. The electron transfer process is complex, not only because of its versatility, but also because of the intricate and delicate modulation exerted by the protein scaffold on the redox properties of the catalytic sites. Nowadays, there is a wealth of information available about the catalytic mechanisms of redox-active enzymes and the time is propitious for the development of projects based on the protein engineering of redox-active enzymes. In this review, we aim to provide an updated account of the available methods used for protein engineering, including both genetic and chemical tools, which are usually reviewed separately. Specific applications to redox-active enzymes are mentioned within each technology, with emphasis on those cases where the generation of novel functionality was pursued. Finally, we focus on two emerging fields in the protein engineering of redox-active enzymes: the construction of novel nucleic acid-based catalysts and the remodeling of intra-molecular electron transfer networks. We consider that the future development of these areas will represent fine examples of the concurrence of chemical and genetic tools.

Structure of the nucleotide radical formed during reaction of CDP/TTP with the E441Q-alpha2beta2 of E. coli ribonucleotide reductase

The Escherichia coli ribonucleotide reductase (RNR) catalyzes the conversion of nucleoside diphosphates to deoxynucleotides and requires a diferric-tyrosyl radical cofactor for catalysis. RNR is composed of a 1:1 complex of two homodimeric subunits: alpha and beta. Incubation of the E441Q-alpha mutant RNR with substrate CDP and allosteric effector TTP results in loss of the tyrosyl radical and formation of two new radicals on the 200 ms to min time scale. The first radical was previously established by stopped flow UV/vis spectroscopy and pulsed high field EPR spectroscopy to be a disulfide radical anion. The second radical was proposed to be a 4'-radical of a 3'-keto-2'-deoxycytidine 5'-diphosphate. To identify the structure of the nucleotide radical [1'-(2)H], [2'-(2)H], [4'-(2)H], [5'-(2)H], [U-(13)C, (15)N], [U-(15)N], and [5,6 -(2)H] CDP and [beta-(2)H] cysteine-alpha were synthesized and incubated with E441Q-alpha2beta2 and TTP. The nucleotide radical was examined by 9 GHz and 140 GHz pulsed EPR spectroscopy and 35 GHz ENDOR spectroscopy. Substitution of (2)H at C4' and C1' altered the observed hyperfine interactions of the nucleotide radical and established that the observed structure was not that predicted. DFT calculations (B3LYP/IGLO-III/B3LYP/TZVP) were carried out in an effort to recapitulate the spectroscopic observations and lead to a new structure consistent with all of the experimental data. The results indicate, unexpectedly, that the radical is a semidione nucleotide radical of cytidine 5'-diphosphate. The relationship of this radical to the disulfide radical anion is discussed.

Replacement of an electron transfer pathway in cytochrome c peroxidase with a surrogate peptide

A proposed electron transfer pathway in cytochrome c peroxidase was previously excised from the structure by design. The engineered channel mutant was shown to bind peptide surrogates without restoration of cyt c oxidation. Here, we report the 1.6 A crystal structure of (N-benzimidazole-propionic acid)-Gly-Ala-Ala bound within the engineered channel. The peptide retains many features of the native electron transfer pathway: placement of benzimidazole at the position of the Trp-191 radical, hydrogen bonding to Asp235, and positioning of the C-terminus near the point where wild type CcP makes closest contact to cyt c. The inability of this surrogate pathway to restore function supports proposals that electron transfer requires the Trp-191 radical.

Formation and function of the Manganese(IV)/Iron(III) cofactor in Chlamydia trachomatis ribonucleotide reductase

The beta(2) subunit of a class Ia or Ib ribonucleotide reductase (RNR) is activated when its carboxylate-bridged Fe(2)(II/II) cluster reacts with O(2) to oxidize a nearby tyrosine (Y) residue to a stable radical (Y(*)). During turnover, the Y(*) in beta(2) is thought to reversibly oxidize a cysteine (C) in the alpha(2) subunit to a thiyl radical (C(*)) by a long-distance ( approximately 35 A) proton-coupled electron-transfer (PCET) step. The C(*) in alpha(2) then initiates reduction of the 2' position of the ribonucleoside 5'-diphosphate substrate by abstracting the hydrogen atom from C3'. The class I RNR from Chlamydia trachomatis (Ct) is the prototype of a newly recognized subclass (Ic), which is characterized by the presence of a phenylalanine (F) residue at the site of beta(2) where the essential radical-harboring Y is normally found. We recently demonstrated that Ct RNR employs a heterobinuclear Mn(IV)/Fe(III) cluster for radical initiation. In essence, the Mn(IV) ion of the cluster functionally replaces the Y(*) of the conventional class I RNR. The Ct beta(2) protein also autoactivates by reaction of its reduced (Mn(II)/Fe(II)) metal cluster with O(2). In this reaction, an unprecedented Mn(IV)/Fe(IV) intermediate accumulates almost stoichiometrically and decays by one-electron reduction of the Fe(IV) site. This reduction is mediated by the near-surface residue, Y222, a residue with no functional counterpart in the well-studied conventional class I RNRs. In this review, we recount the discovery of the novel Mn/Fe redox cofactor in Ct RNR and summarize our current understanding of how it assembles and initiates nucleotide reduction.

The manganese(IV)/iron(III) cofactor of Chlamydia trachomatis ribonucleotide reductase: structure, assembly, radical initiation, and evolution

The catalytic mechanism of a class I ribonucleotide reductase (RNR) is initiated by the generation of a hydrogen-abstracting thiyl radical via a conformationally gated, proton-coupled electron-transfer (PCET) from a cysteine residue in the alpha(2) subunit over approximately 35A to the cofactor in the beta(2) subunit. A chain of aromatic amino acids that spans the two subunits mediates this long-distance PCET by the formation of transient side-chain radicals. Details of the conformational gating, proton coupling, and 'radical-hopping' have, until very recently, been largely obscured by the failure of intermediate states to accumulate to high levels and the absence of sufficiently sensitive spectroscopic handles for intermediates that may accumulate to trace levels. In the most recently recognized subclass (c) of class I, founded by the enzyme from Chlamydia trachomatis (Ct), the stable tyrosyl radical that serves as the PCET acceptor in the conventional (subclass a or b) class I RNRs is functionally replaced by the Mn(IV) ion of a Mn(IV)/Fe(III) cofactor, which assembles in Ct beta(2) in place of the Fe(2)(III/III) cluster of the conventional beta(2)s. The discovery of this novel radical-initiation cofactor and mechanism has raised intriguing questions concerning the evolution of class I RNRs and affords new opportunities for understanding the gated PCET step that initiates their catalytic mechanism.

Proton-coupled electron transfer in solution, proteins, and electrochemistry

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.

Structural analysis of the Mn(IV)/Fe(III) cofactor of Chlamydia trachomatis ribonucleotide reductase by extended X-ray absorption fine structure spectroscopy and density functional theory calculations

The class Ic ribonucleotide reductase from Chlamydia trachomatis ( Ct) uses a stable Mn(IV)/Fe(III) cofactor to initiate nucleotide reduction by a free-radical mechanism. Extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) calculations are used to postulate a structure for this cofactor. Fe and Mn K-edge EXAFS data yield an intermetallic distance of approximately 2.92 A. The Mn data also suggest the presence of a short 1.74 A Mn-O bond. These metrics are compared to the results of DFT calculations on 12 cofactor models derived from the crystal structure of the inactive Fe 2(III/III) form of the protein. Models are differentiated by the protonation states of their bridging and terminal OH X ligands as well as the location of the Mn(IV) ion (site 1 or 2). The models that agree best with experimental observation feature a mu-1,3-carboxylate bridge (E120), terminal solvent (H 2O/OH) to site 1, one mu-O bridge, and one mu-OH bridge. The site-placement of the metal ions cannot be discerned from the available data.

Hydrogen atom transfer reactions of a ruthenium imidazole complex: hydrogen tunneling and the applicability of the Marcus cross relation

The reaction of Ru(II)(acac)2(py-imH) (Ru(II)imH) with TEMPO(*) (2,2,6,6-tetramethylpiperidine-1-oxyl radical) in MeCN quantitatively gives Ru(III)(acac)2(py-im) (Ru(III)im) and the hydroxylamine TEMPO-H by transfer of H(*) (H(+) + e(-)) (acac = 2,4-pentanedionato, py-imH = 2-(2'-pyridyl)imidazole). Kinetic measurements of this reaction by UV-vis stopped-flow techniques indicate a bimolecular rate constant k(3H) = 1400 +/- 100 M(-1) s(-1) at 298 K. The reaction proceeds via a concerted hydrogen atom transfer (HAT) mechanism, as shown by ruling out the stepwise pathways of initial proton or electron transfer due to their very unfavorable thermochemistry (Delta G(o)). Deuterium transfer from Ru(II)(acac)2(py-imD) (Ru(II)imD) to TEMPO(*) is surprisingly much slower at k(3D) = 60 +/- 7 M(-1) s(-1), with k(3H)/k(3D) = 23 +/- 3 at 298 K. Temperature-dependent measurements of this deuterium kinetic isotope effect (KIE) show a large difference between the apparent activation energies, E(a3D) - E(a3H) = 1.9 +/- 0.8 kcal mol(-1). The large k(3H)/k(3D) and DeltaE(a) values appear to be greater than the semiclassical limits and thus suggest a tunneling mechanism. The self-exchange HAT reaction between Ru(II)imH and Ru(III)im, measured by (1)H NMR line broadening, occurs with k(4H) = (3.2 +/- 0.3) x 10(5) M(-1) s(-1) at 298 K and k(4H)/k(4D) = 1.5 +/- 0.2. Despite the small KIE, tunneling is suggested by the ratio of Arrhenius pre-exponential factors, log(A(4H)/A(4D)) = -0.5 +/- 0.3. These data provide a test of the applicability of the Marcus cross relation for H and D transfers, over a range of temperatures, for a reaction that involves substantial tunneling. The cross relation calculates rate constants for Ru(II)imH(D) + TEMPO(*) that are greater than those observed: k(3H,calc)/k(3H) = 31 +/- 4 and k(3D,calc)/k(3D) = 140 +/- 20 at 298 K. In these rate constants and in the activation parameters, there is a better agreement with the Marcus cross relation for H than for D transfer, despite the greater prevalence of tunneling for H. The cross relation does not explicitly include tunneling, so close agreement should not be expected. In light of these results, the strengths and weaknesses of applying the cross relation to HAT reactions are discussed.

Biology and technology for photochemical fuel production

Sunlight is the ultimate energy source for the vast majority of life on Earth, and organisms have evolved elegant machinery for energy capture and utilization. Solar energy, whether converted to wind, rain, biomass or fossil fuels, is also the primary energy source for human-engineered energy transduction systems. This tutorial review draws parallels between biological and technological energy systems. Aspects of biology that might be advantageously incorporated into emerging technologies are highlighted, as well as ways in which technology might improve upon the principles found in biological systems. Emphasis is placed upon artificial photosynthesis, as well as the use of protonmotive force in biology.

Ultrafast N-H vibrational dynamics of cyclic doubly hydrogen-bonded homo- and heterodimers

Hydrogen-bonded interfaces are essential structural elements in biology. Furthermore, they can mediate electron transport by coupling the electron to proton transfer within the interface. The specific hydrogen-bonding configuration and strength have a large impact on the proton transfer, which exchanges the hydrogen-bonded donor and acceptor species (i.e., NH...O --> N...HO). Modulations of the hydrogen-bonding environment, such as the hydrogen-bond stretch and twist modes, affect the proton-transfer dynamics. Here, we present transient grating and echo peak shift measurements of the NH stretch vibrations of four doubly hydrogen-bonded cyclic dimers in their electronic ground state. The equilibrium vibrational dynamics exhibit strong coherent modulations that we attribute to coupling of the high-frequency NH vibration to the low-frequency interdimer stretch and twist modes and not to interference between multiple Fermi resonances that dominate the substructure of the linear spectra.

Electron transfer in peptides and proteins

Proteins and peptides use their amino acids as medium for electron-transfer reactions that occur either in single-step superexchange or in multistep hopping processes. Whereas the rate of the single-step electron transfer dramatically decreases with the distance, a hopping process is less distance dependent. Electron hopping is possible if amino acids carry oxidizable side chains, like the phenol group in tyrosine. These side chains become intermediate charge carriers. Because of the weak distance dependency of hopping processes, fast electron transfer over very long distances occurs in multistep reactions, as in the enzyme ribonucleotide reductase.

Branched activation- and catalysis-specific pathways for electron relay to the manganese/iron cofactor in ribonucleotide reductase from Chlamydia trachomatis

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 Mn (IV)/Fe (III) cofactor (specifically, the Mn (IV) ion) in place of the Y (*) for radical initiation. Ct R2 is activated when its Mn (II)/Fe (II) form reacts with O 2 to generate a Mn (IV)/Fe (IV) intermediate, which decays by reduction of the Fe (IV) site to the active Mn (IV)/Fe (III) 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 Mn (IV)/Fe (IV) intermediate by approximately 10-fold and diminishes the ability of ascorbate to accelerate the decay by approximately 65-fold but has no detectable effect on the catalytic activity of the Mn (IV)/Fe (III)-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 Mn (IV)/Fe (IV) 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 Mn (IV)/Fe (IV) 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.

A bioinspired construct that mimics the proton coupled electron transfer between P680*+ and the Tyr(Z)-His190 pair of photosystem II

A bioinspired hybrid system, composed of colloidal TiO2 nanoparticles surface modified with a photochemically active mimic of the PSII chlorophyll-Tyr-His complex, undergoes photoinduced stepwise electron transfer coupled to proton motion at the phenolic site. Low temperature electron paramagnetic resonance studies reveal that injected electrons are localized on TiO2 nanoparticles following photoexcitation. At 80 K, 95% of the resulting holes are localized on the phenol moiety and 5% are localized on the porphyrin. At 4.2 K, 52% of the holes remain trapped on the porphyrin. The anisotropic coupling tensors of the phenoxyl radical are resolved in the photoinduced D-band EPR spectra and are in good agreement with previously reported g-tensors of tyrosine radicals in photosystem II. The observed temperature dependence of the charge shift is attributed to restricted nuclear motion at low temperature and is reminiscent of the observation of a trapped high-energy state in the natural system. Electrochemical studies show that the phenoxyl/phenol couple of the model system is chemically reversible and thermodynamically capable of water oxidation.

Facile concerted proton-electron transfers in a ruthenium terpyridine-4'-carboxylate complex with a long distance between the redox and basic sites

We have designed and prepared ruthenium complexes with terpyridine-4'-carboxylate (tpyCOO) ligands, in which there are six bonds between the redox-active Ru and the basic carboxylate. The protonated Ru(II) complex, RuII(dipic)(tpyCOOH) (Ru(II)COOH), is prepared in one-pot from [(p-cymene)RuCl2]2, tpyCOONa, and then sodium pyridine-2,6-dicarboxylate [Na(dipic)]. A crystal structure of the deprotonated Ru(II) complex, Ru(II)COO-, shows a distance of 6.9 A between the metal and basic sites. The Ru(III) complex (Ru(III)COO) has been isolated by one-electron oxidation of Ru(II)COO- with triarylaminium radical cations (NAr3*+). Ru(III)COO has a bond dissociation free energy (BDFE) of 81 +/- 1 kcal mol(-1), from pKa and E1/2 measurements. It oxidizes 2,4,6-tri-tert-butylphenol (BDFE = 77 +/- 1 kcal mol(-1)) by removal of e- and H+ (triple bond H*) to form 2,4,6-tri-tert-butylphenoxyl radical and Ru(II)COOH, with a second-order rate constant of (2.3 0.2) x 10(4) M(-1) s(-1) and a kH/kD of 7.7 1.2. Thermochemical analysis suggests a concerted proton-electron transfer (CPET) mechanism for this reaction, despite the 6.9 A distance between the redox-active Ru and the H+-accepting oxygen. Ru(III)COO also oxidizes the hydroxylamine TEMPOH to the stable free radical TEMPO and xanthene to bixanthyl. These reactions appear to be similar to processes that have been previously termed hydrogen atom transfer.

Electronic design criteria for O-O bond formation via metal-oxo complexes

Metal-oxos are critical intermediates for the management of oxygen and its activation. The reactivity of the metal-oxo is central to the formation of O-O bonds, which is the essential step for oxygen generation. Two basic strategies for the formation of O-O bonds at metal-oxo active sites are presented. The acid-base (AB) strategy involves the attack of a nucleophilic oxygen species (e.g., hydroxide) on an electrophilic metal-oxo. Here, active-site designs must incorporate the assembly of a hydroxide (or water) proximate to a high-valent metal-oxo of even d electron count. For the radical coupling (RC) strategy, two high-valent metal-oxos of an odd d electron count are needed to drive O-O coupling. This Forum Article focuses on the different electronic structures of terminal metal-oxos that support AB and RC strategies and the design of ligand scaffolds that engender these electronic structures.

One-step versus stepwise mechanism in protonated amino acid-promoted electron-transfer reduction of a quinone by electron donors and two-electron reduction by a dihydronicotinamide adenine dinucleotide analogue. Interplay between electron transfer and hydrogen bonding

Semiquinone radical anion of 1-(p-tolylsulfinyl)-2,5-benzoquinone (TolSQ(*-)) forms a strong hydrogen bond with protonated histidine (TolSQ(*-)/His x 2 H(+)), which was successfully detected by electron spin resonance. Strong hydrogen bonding between TolSQ(*-) and His x 2 H(+) results in acceleration of electron transfer (ET) from ferrocenes [R2Fc, R = C5H5, C5H4(n-Bu), C5H4Me] to TolSQ, when the one-electron reduction potential of TolSQ is largely shifted to the positive direction in the presence of His x 2 H(+). The rates of His x 2 H(+)-promoted ET from R2Fc to TolSQ exhibit deuterium kinetic isotope effects due to partial dissociation of the N-H bond in His x 2 H(+) at the transition state, when His x 2 H(+) is replaced by the deuterated compound (His x 2 D(+)-d6). The observed deuterium kinetic isotope effect (kH/kD) decreases continuously with increasing the driving force of ET to approach kH/kD = 1.0. On the other hand, His x 2 H(+) also promotes a hydride reduction of TolSQ by an NADH analogue, 9,10-dihydro-10-methylacridine (AcrH2). The hydride reduction proceeds via the one-step hydride-transfer pathway. In such a case, a large deuterium kinetic isotope effect is observed in the rate of the hydride transfer, when AcrH2 is replaced by the dideuterated compound (AcrD2). In sharp contrast to this, no deuterium kinetic isotope effect is observed, when His x 2 H(+) is replaced by His x 2 D(+)-d6. On the other hand, direct protonation of TolSQ and 9,10-phenanthrenequinone (PQ) also results in efficient reductions of TolSQH(+) and PQH(+) by AcrH2, respectively. In this case, however, the hydride-transfer reactions occur via the ET pathway, that is, ET from AcrH2 to TolSQH(+) and PQH(+) occurs in preference to direct hydride transfer from AcrH2 to TolSQH(+) and PQH(+), respectively. The AcrH2(*+) produced by the ET oxidation of AcrH2 by TolSQH(+) and PQH(+) was directly detected by using a stopped-flow technique.

Biological contexts for DNA charge transport chemistry

Many experiments have now shown that double helical DNA can serve as a conduit for efficient charge transport (CT) reactions over long distances in vitro. These results prompt the consideration of biological roles for DNA-mediated CT. DNA CT has been demonstrated to occur in biologically relevant environments such as within the mitochondria and nuclei of HeLa cells as well as in isolated nucleosomes. In mitochondria, DNA damage that results from CT is funneled to a crucial regulatory element. Thus, DNA CT provides a strategy to funnel damage to particular sites in the genome. DNA CT might also be important in long-range signaling to DNA-bound proteins. Both DNA repair proteins, containing Fe-S clusters, and the transcription factor, p53, which is regulated through thiol-disulfide switches, can be oxidized from a distance through DNA-mediated CT. These observations highlight a means through which oxidative stress may be chemically signaled in the genome over long distances through CT from guanine radicals to DNA-bound proteins. Moreover, DNA-mediated CT may also play a role in signaling among DNA-binding proteins, as has been proposed as a mechanism for how DNA repair glycosylases more efficiently detect lesions inside the cell.

The multiple functions of the thiol-based electron flow pathways of Escherichia coli: Eternal concepts revisited

Electron flow via thiols is a theme with many variations in all kingdoms of life. The favourable physichochemical properties of the redox active couple of two cysteines placed in the optimised environment of the thioredoxin fold allow for two electron transfers in between top biological reductants and ultimate oxidants. The reduction of ribonucleotide reductases by thioredoxin and thioredoxin reductase of Escherichia coli (E. coli) was one of the first pathways to be elucidated. Diverse functions such as protein folding in the periplasm, maturation of respiratory enzymes, detoxification of hydrogen peroxide and prevention of oxidative damage may be based on two electron transfers via thiols. A growing field is the relation of thiol reducing pathways and the interaction of E. coli with different organisms. This concept combined with the sequencing of the genomes of different bacteria may allow for the identification of fine differences in the systems employing thiols for electron flow between pathogens and their corresponding mammalian hosts. The emerging possibility is the development of novel antibiotics.

A ligand field chemistry of oxygen generation by the oxygen-evolving complex and synthetic active sites

Oxygen-oxygen bond formation and O2 generation occur from the S4 state of the oxygen-evolving complex (OEC). Several mechanistic possibilities have been proposed for water oxidation, depending on the formal oxidation state of the Mn atoms. All fall under two general classifications: the AB mechanism in which nucleophilic oxygen (base, B) attacks electrophilic oxygen (acid, A) of the Mn4Ca cluster or the RC mechanism in which radical-like oxygen species couple within OEC. The critical intermediate in either mechanism involves a metal oxo, though the nature of this oxo for AB and RC mechanisms is disparate. In the case of the AB mechanism, assembly of an even-electron count, high-valent metal-oxo proximate to a hydroxide is needed whereas, in an RC mechanism, two odd-electron count, high-valent metal oxos are required. Thus the two mechanisms give rise to very different design criteria for functional models of the OEC active site. This discussion presents the electron counts and ligand geometries that support metal oxos for AB and RC O-O bond-forming reactions. The construction of architectures that bring two oxygen functionalities together under the purview of the AB and RC scenarios are described.

Rapid and quantitative activation of Chlamydia trachomatis ribonucleotide reductase by hydrogen peroxide

We recently showed that the class Ic ribonucleotide reductase (RNR) from the human pathogen Chlamydia trachomatis ( Ct) uses a Mn (IV)/Fe (III) cofactor in its R2 subunit to initiate catalysis [Jiang, W., Yun, D., Saleh, L., Barr, E. W., Xing, G., Hoffart, L. M., Maslak, M.-A., Krebs, C., and Bollinger, J. M., Jr. (2007) Science 316, 1188-1191]. The Mn (IV) site of the novel cofactor functionally replaces the tyrosyl radical used by conventional class I RNRs to initiate substrate radical production. As a first step in evaluating the hypothesis that the use of the alternative cofactor could make the RNR more robust to reactive oxygen and nitrogen species [RO(N)S] produced by the host's immune system [Högbom, M., Stenmark, P., Voevodskaya, N., McClarty, G., Gräslund, A., and Nordlund, P. (2004) Science 305, 245-248], we have examined the reactivities of three stable redox states of the Mn/Fe cluster (Mn (II)/Fe (II), Mn (III)/Fe (III), and Mn (IV)/Fe (III)) toward hydrogen peroxide. Not only is the activity of the Mn (IV)/Fe (III)-R2 intermediate stable to prolonged (>1 h) incubations with as much as 5 mM H 2O 2, but both the fully reduced (Mn (II)/Fe (II)) and one-electron-reduced (Mn (III)/Fe (III)) forms of the protein are also efficiently activated by H 2O 2. The Mn (III)/Fe (III)-R2 species reacts with a second-order rate constant of 8 +/- 1 M (-1) s (-1) to yield the Mn (IV)/Fe (IV)-R2 intermediate previously observed in the reaction of Mn (II)/Fe (II)-R2 with O 2 [Jiang, W., Hoffart, L. M., Krebs, C., and Bollinger, J. M., Jr. (2007) Biochemistry 46, 8709-8716]. As previously observed, the intermediate decays by reduction of the Fe site to the active Mn (IV)/Fe (III)-R2 complex. The reaction of the Mn (II)/Fe (II)-R2 species with H 2O 2 proceeds in three resolved steps: sequential oxidation to Mn (III)/Fe (III)-R2 ( k = 1.7 +/- 0.3 mM (-1) s (-1)) and Mn (IV)/Fe (IV)-R2, followed by decay of the intermediate to the active Mn (IV)/Fe (III)-R2 product. The efficient reaction of both reduced forms with H 2O 2 contrasts with previous observations on the conventional class I RNR from Escherichia coli, which is efficiently converted from the fully reduced (Fe 2 (II/II)) to the "met" (Fe 2 (III/III)) form [Gerez, C., and Fontecave, M. (1992) Biochemistry 31, 780-786] but is then only very inefficiently converted from the met to the active (Fe 2 (III/III)-Y (*)) form [Sahlin, M., Sjöberg, B.-M., Backes, G., Loehr, T., and Sanders-Loehr, J. (1990) Biochem. Biophys. Res. Commun. 167, 813-818].