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

Hangman salen platforms containing dibenzofuran scaffolds

The synthesis of salen ligands bearing two rigid dibenzofuran spacers functionalized with carboxylic acid and benzoic acid groups completes a series of "Hangman" ligands with the acid functionalities differentially extended across the molecular cleft. Stopped-flow studies show that a high-valent metal oxo intermediate is produced at Hangman platforms when H(2)O(2) is employed as a primary oxidant. The activity of this oxo species in promoting the disproportionation of hydrogen peroxide and olefin epoxidations is discussed in the context of the distance between the acid group and the metal center. The chemistry of the Hangman oxo complexes described here provides a roadmap for water-splitting chemistry.

Photochemical conversion of solar energy

Energy is the most important issue of the 21st century. About 85% of our energy comes from fossil fuels, a finite resource unevenly distributed beneath the Earth's surface. Reserves of fossil fuels are progressively decreasing, and their continued use produces harmful effects such as pollution that threatens human health and greenhouse gases associated with global warming. Prompt global action to solve the energy crisis is therefore needed. To pursue such an action, we are urged to save energy and to use energy in more efficient ways, but we are also forced to find alternative energy sources, the most convenient of which is solar energy for several reasons. The sun continuously provides the Earth with a huge amount of energy, fairly distributed all over the world. Its enormous potential as a clean, abundant, and economical energy source, however, cannot be exploited unless it is converted into useful forms of energy. This Review starts with a brief description of the mechanism at the basis of the natural photosynthesis and, then, reports the results obtained so far in the field of photochemical conversion of solar energy. The "grand challenge" for chemists is to find a convenient means for artificial conversion of solar energy into fuels. If chemists succeed to create an artificial photosynthetic process, "... life and civilization will continue as long as the sun shines!", as the Italian scientist Giacomo Ciamician forecast almost one hundred years ago.

Synthesis and characterization of ruthenium bis(beta-diketonato) pyridine-imidazole complexes for hydrogen atom transfer

Ruthenium bis(beta-diketonato) complexes have been prepared at both the RuII and RuIII oxidation levels and with protonated and deprotonated pyridine-imidazole ligands. RuII(acac)2(py-imH) (1), [RuIII(acac)2(py-imH)]OTf (2), RuIII(acac)2(py-im) (3), RuII(hfac)2(py-imH) (4), and [DBU-H][RuII(hfac)2(py-im)] (5) have been fully characterized, including X-ray crystal structures (acac = 2,4-pentanedionato, hfac = 1,1,1,5,5,5-hexafluoro-2,4-pentanedionato, py-imH = 2-(2'-pyridyl)imidazole, DBU = 1,8-diazabicyclo[5.4.0]undec-7-ene). For the acac-imidazole complexes 1 and 2, cyclic voltammetry in MeCN shows the RuIII/II reduction potential (E1/2) to be -0.64 V versus Cp2Fe+/0. E1/2 for the deprotonated imidazolate complex 3 (-1.00 V) is 0.36 V more negative. The RuII bis-hfac analogues 4 and 5 show the same DeltaE1/2 = 0.36 V but are 0.93 V harder to oxidize than the acac derivatives (0.29 and -0.07 V). The difference in acidity between the acac and hfac derivatives is much smaller, with pKa values of 22.1 and 19.3 in MeCN for 1 and 4, respectively. From the E1/2 and pKa values, the bond dissociation free energies (BDFEs) of the N-H bonds in 1 and 4 are calculated to be 62.0 and 79.6 kcal mol(-1) in MeCN - a remarkable difference of 17.6 kcal mol(-1) for such structurally similar compounds. Consistent with these values, there is a facile net hydrogen atom transfer from 1 to TEMPO* (2,2,6,6-tetramethylpiperidine-1-oxyl radical) to give 3 and TEMPO-H. The DeltaG degrees for this reaction is -4.5 kcal mol(-1). 4 is not oxidized by TEMPO* (DeltaG degrees = +13.1 kcal mol(-1)), but in the reverse direction TEMPO-H readily reduces in situ generated RuIII(hfac)2(py-im) (6). A RuII-imidazoline analogue of 1, RuII(acac)2(py-imnH) (7), reacts with 3 equiv of TEMPO* to give the imidazolate 3 and TEMPO-H, with dehydrogenation of the imidazoline ring.

PELDOR spectroscopy with DOPA-beta2 and NH2Y-alpha2s: distance measurements between residues involved in the radical propagation pathway of E. coli ribonucleotide reductase

Escherichia coli ribonucleotide reductase (RNR) catalyzes the reduction of nucleotides to 2'-deoxynucleotides. The active enzyme is a 1:1 complex of two homodimeric subunits, alpha2 and beta2. The alpha2 is the site of nucleotide reduction, and beta2 harbors a diferric tyrosyl radical (Y122*) cofactor. Turnover requires formation of a cysteinyl radical (C439*) in the active site of alpha2 at the expense of the Y122* in beta2. A docking model for the alpha2beta2 interaction and a pathway for radical transfer from beta2 to alpha2 have been proposed. This pathway contains three Ys: Y356 in beta2 and Y731/Y730 in alpha2. We have previously incorporated 3-hydroxytyrosine and 3-aminotyrosine into these residues and showed that they act as radical traps. In this study, we use these alpha2/beta2 variants and PELDOR spectroscopy to measure the distance between the Y122* in one alphabeta pair and the newly formed radical in the second alphabeta pair. The results yield distances that are similar to those predicted by the docking model for radical transfer. Further, they support a long-range radical initiation process for C439* generation and provide a structural constraint for residue Y356, which is thermally labile in all beta2 structures solved to date.

The first crystal structure of a monomeric phenoxyl radical: 2,4,6-tri-tert-butylphenoxyl radical

Crystals of the 2,4,6-tri-tert-butylphenoxyl radical have been isolated and characterized by X-ray diffraction, and calculations have been performed that give the distribution of spin density in the radical.

Insights into the nature of the hydrogen bonding of Tyr272 in apo-galactose oxidase

The synthesis and structure of an o-methylthio-phenol-imidazole, 2-(2'-(4'-tert-butyl-6'-methylsulfanyl)-hydroxyphenyl))-4,5-diphenyl-imidazole ((MeS)LH), is reported; X-ray crystallographic studies have shown that (MeS)LH involves an O-H...N(+) hydrogen bond between the phenol and an imidazole nitrogen. (MeS)LH undergoes a reversible, one-electron, oxidation to form the radical cation [(MeS)LH](*)(+) the EPR spectrum of which is remarkably similar to that of (*)Tyr(272) in Cu-free, oxidized, apo-GO. Density Functional Theory calculations, have shown that the proton-transferred (R-O(*)...H-N(+)) form of [(MeS)LH](*)(+) has a spin density distribution--with a substantial delocalization of the unpaired electron spin density onto the ortho sulfur atom--and EPR properties that are in good agreement with those of (*)Tyr(272) in Cu-free, oxidized, apo-GO whereas the non-proton-transferred (R-O(*)(+)-H...N) form does not. The results reported herein are a further demonstration of the influence of hydrogen bonding on the nature and properties of phenoxyl radicals and strongly suggest that the phenoxyl oxygen of (*)Tyr(272) in Cu-free, oxidized, apo-GO is involved in a O(*)...H-O/N hydrogen bond.

YfaE, a ferredoxin involved in diferric-tyrosyl radical maintenance in Escherichia coli ribonucleotide reductase

Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides in all organisms. The class I RNRs are composed of a 1:1 complex of two homodimeric subunits: alpha and beta. beta contains the diferric-tyrosyl radical (Y*) cofactor essential for the reduction process. In vivo, the mechanism of Y* regeneration from the diferric-beta2 (met-beta2) or apo-beta2 is still unclear. Y* regenerations from met-beta2 and apo-beta2 have been designated the maintenance and biosynthetic pathways, respectively. To understand these two pathways, 181 genomes that contain nrdAnrdB (genes encoding alpha and beta) were examined. In 29% of the cases, an open reading frame annotated 2Fe2S ferredoxin (YfaE in Escherichia coli) is located next to nrdB. Thus, YfaE has been cloned, expressed, resolubilized, reconstituted anaerobically with Fe2+, Fe3+, and S2-, and characterized by Mössbauer, EPR, and visible spectroscopies. Titration of met-beta2 with [2Fe2S]1+-YfaE anaerobically results in the formation of an equilibrium mixture of diferrous-beta2 and [2Fe2S]2+-YfaE with one Fe reduced/YfaE oxidized. At the end point of the titration, O2 is added to the mixture and the diferrous-beta2 rapidly undergoes reaction to form the diferric-Y* with a stoichiometry of 2Fe/Y* and a specific activity correlated to the amount of Y*. The reducing equivalent required for diferric-Y* cofactor biosynthesis is supplied by beta. Under anaerobic conditions, stopped flow kinetics have been used to monitor the disappearance of the diferric cluster and the formation of [2Fe2S]2+-YfaE. The titrations and kinetic studies provide the first evidence for a protein involved in the maintenance pathway and likely the biosynthetic pathway.

AurF from Streptomyces thioluteus and a Possible New Family of Manganese/Iron Oxygenases

We recently reported that the R2 subunit of class Ic ribonucleotide reductase from Chlamydia trachomatis contains a heterodinuclear Mn/Fe redox cofactor [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 N-oxygenase, AurF, from Streptomyces thioluteus catalyzes the six-electron oxidation of p-aminobenzoate to p-nitrobenzoate and contains the EX2HX60-180EX2H sequence motif previously used to identify proteins with non-heme diiron clusters. Two research groups independently obtained evidence for the presence of iron and manganese in preparations of AurF. The electron paramagnetic resonance (EPR) spectrum of purified, resting AurF presented in one of these studies is markedly similar to the spectrum of the MnIII/FeIII form of C. trachomatis R2. We propose that S. thioluteus AurF also may harbor a heterodinuclear Mn/Fe cofactor, which it may use to activate O2 for oxidation of the aryl amine to the nitro compound. Hypothetical proteins encoded in the genomes of several other bacteria have similar sequences and may also be members of this nascent family of oxygen-activating Mn/Fe proteins.

Buffer-Assisted Proton-Coupled Electron Transfer in a Model Rhenium−Tyrosine Complex

The mechanism for tyrosyl radical generation in the [Re(P-Y)(phen)(CO)3]PF6 complex is investigated with a multistate continuum theory for proton-coupled electron transfer (PCET) reactions. Both water and the phosphate buffer are considered as potential proton acceptors. The calculations indicate that the model in which the proton acceptor is the phosphate buffer species HPO(4)2- can successfully reproduce the experimentally observed pH dependence of the overall rate and H/D kinetic isotope effect, whereas the model in which the proton acceptor is water is not physically reasonable for this system. The phosphate buffer species HPO4(2-) is favored over water as the proton acceptor in part because the proton donor-acceptor distance is approximately 0.2 A smaller for the phosphate acceptor due to its negative charge. The physical quantities impacting the overall rate constant, including the reorganization energies, reaction free energies, activation free energies, and vibronic couplings for the various pairs of reactant/product vibronic states, are analyzed for both hydrogen and deuterium transfer. The dominant contribution to the rate arises from nonadiabatic transitions between the ground reactant vibronic state and the third product vibronic state for hydrogen transfer and the fourth product vibronic state for deuterium transfer. These contributions dominate over contributions from lower product states because of the larger vibronic coupling, which arises from the greater overlap between the reactant and product vibrational wave functions. These calculations provide insight into the fundamental mechanism of tyrosyl radical generation, which plays an important role in a wide range of biologically important processes.

Comparison of intra- vs intermolecular long-range electron transfer in crystals of ruthenium-modified azurin

Selective metal-ion incorporation and ligand substitution are employed to control whether electrons tunnel over intra- or intermolecular separations in crystals of P. aeruginosa azurin modified with Ru-polypyridine complexes. Cu(1+)-to-Ru3+ electron transfer (ET) across a specific protein-protein interface in the crystal lattice has a time constant 5-10 times longer than ET between the same donor and acceptor within a single protein (tauET = 5 vs 0.5-1.0 micros). Slower intermolecular ET agrees well with a longer distance between redox centers across the inter-protein (18.9 A) compared to the intra-protein separation (17.0 A) and indicates that the closest donor/acceptor pair dominates crystal ET. Lowering the crystal pH accelerates inter-protein ET (tauET = 1.0 micros) but not intra-protein ET. Faster inter-protein ET likely results from a pH-induced peptide bond flip that perturbs hydrogen bonding in the path between Ru and Cu centers on adjacent molecules.

A manganese(IV)/iron(IV) intermediate in assembly of the manganese(IV)/iron(III) cofactor of Chlamydia trachomatis ribonucleotide reductase

We recently showed that the class Ic ribonucleotide reductase from the human pathogen Chlamydia trachomatis uses a Mn(IV)/Fe(III) cofactor to generate protein and substrate radicals in its catalytic mechanism [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]. Here, we have dissected the mechanism of formation of this novel heterobinuclear redox cofactor from the Mn(II)/Fe(II) cluster and O2. An intermediate with a g = 2 EPR signal that shows hyperfine coupling to both 55Mn and 57Fe accumulates almost quantitatively in a second-order reaction between O2 and the reduced R2 complex. The otherwise slow decay of the intermediate to the active Mn(IV)/Fe(III)-R2 complex is accelerated by the presence of the one-electron reductant, ascorbate, implying that the intermediate is more oxidized than Mn(IV)/Fe(III). Mössbauer spectra show that the intermediate contains a high-spin Fe(IV) center. Its chemical and spectroscopic properties establish that the intermediate is a Mn(IV)/Fe(IV)-R2 complex with an S = 1/2 electronic ground state arising from antiferromagnetic coupling between the Mn(IV) (S(Mn) = 3/2) and high-spin Fe(IV) (S(Fe) = 2) sites.

Spectroscopic and electronic structure studies of intermediate X in ribonucleotide reductase R2 and two variants: a description of the FeIV-oxo bond in the FeIII-O-FeIV dimer

Spectroscopic and electronic structure studies of the class I Escherichia coli ribonucleotide reductase (RNR) intermediate X and three computationally derived model complexes are presented, compared, and evaluated to determine the electronic and geometric structure of the FeIII-FeIV active site of intermediate X. Rapid freeze-quench (RFQ) EPR, absorption, and MCD were used to trap intermediate X in R2 wild-type (WT) and two variants, W48A and Y122F/Y356F. RFQ-EPR spin quantitation was used to determine the relative contributions of intermediate X and radicals present, while RFQ-MCD was used to specifically probe the FeIII/FeIV active site, which displayed three FeIV d-d transitions between 16,700 and 22,600 cm(-1), two FeIV d-d spin-flip transitions between 23,500 and 24,300 cm(-1), and five oxo to FeIV and FeIII charge transfer (CT) transitions between 25,000 and 32,000 cm(-1). The FeIV d-d transitions were perturbed in the two variants, confirming that all three d-d transitions derive from the d-pi manifold. Furthermore, the FeIV d-pi splittings in the WT are too large to correlate with a bis-mu-oxo structure. The assignment of the FeIV d-d transitions in WT intermediate X best correlates with a bridged mu-oxo/mu-hydroxo [FeIII(mu-O)(mu-OH)FeIV] structure. The mu-oxo/mu-hydroxo core structure provides an important sigma/pi superexchange pathway, which is not present in the bis-mu-oxo structure, to promote facile electron transfer from Y122 to the remote FeIV through the bent oxo bridge, thereby generating the tyrosyl radical for catalysis.

Adiabatic and Non-adiabatic Concerted Proton−Electron Transfers. Temperature Effects in the Oxidation of Intramolecularly Hydrogen-Bonded Phenols

The one-electron electrochemical and homogeneous oxidations of two closely similar aminophenols that undergo a concerted proton-electron transfer reaction, in which the phenolic proton is transferred to the nitrogen atom in concert with electron transfer, are taken as examples to test procedures that allow the separate determination of the degree of adiabaticity and the reorganization energy of the reaction. The Marcus (or Marcus-Hush-Levich) formalism is applicable in both cases, but not necessarily in its adiabatic version. Linearization of the activation-driving force laws simplifies the treatment of the kinetic data, notably allowing the use of Arrhenius plots to treat the temperature dependence of the rate constant. A correct estimation of the adiabaticity and reorganization energy requires the determination of the variation of the driving force with temperature. Application of these procedures led to the conclusion that, unlike previous reports, the homogeneous reaction is non-adiabatic, with a transmission coefficient of the order of 0.005, and that the self-exchange reorganization energy is about 1 eV lower than previously estimated. With such systems, the intramolecular reorganization energy, although sizable, is in fact rather modest, being only slightly larger than that for the outer-sphere electron transfer that produced the cation radical. The electrochemical reaction is, in contrast, adiabatic, as revealed by the temperature dependence of its standard rate constant obtained from cyclic voltammetric experiments. This difference in behavior is deemed to derive from the effect of the strong electric field within which the electrochemical reaction takes place, stabilizing a zwitterionic form of the reactant (in which the proton has been transferred from oxygen to nitrogen). Taking this difference in adiabaticity into account, the magnitudes of the reorganization energies of the two reactions appear to be quite compatible with one another, as revealed by an analysis of the solvent and intramolecular contributions in both cases.

Structure of the high-valent FeIIIFeIV state in ribonucleotide reductase (RNR) of Chlamydia trachomatis--combined EPR, 57Fe-, 1H-ENDOR and X-ray studies

A recently discovered subgroup of class I ribonucleotide reductase (RNR) found in the infectious bacterium Chlamydia trachomatis (C. trachomatis) was shown to exhibit a high-valent Fe(III)Fe(IV) center instead of the tyrosyl radical observed normally in all class I RNRs. The X-ray structure showed that C. trachomatis WT RNR has a phenylalanine at the position of the active tyrosine in Escherichia coli RNR. In this paper the X-ray structure of variant F127Y is presented, where the tyrosine is restored. Using (1)H- and (57)Fe-ENDOR spectroscopy it is shown, that in WT and variants F127Y and Y129F of C. trachomatis RNR, the Fe(III)Fe(IV) center is virtually identical with the short-lived intermediate X observed during the iron oxygen reconstitution reaction in class I RNR from E. coli. The experimental data are consistent with a recent theoretical model for X, proposing two bridging oxo ligands and one terminal water ligand. A surprising extension of the lifetime of the Fe(III)Fe(IV) state in C. trachomatis from a few seconds to several hours at room temperature was observed under catalytic conditions in the presence of substrate. These findings suggest a possible new role for the Fe(III)Fe(IV) state also in other class I RNR, during the catalytic radical transfer reaction, by which the substrate turnover is started.

Comparison of thermodynamic and kinetic aspects of oxidative addition of PhE-EPh (E = S, Se, Te) to Mo(CO)3(PR3)2, W(CO)3(PR3)2, and Mo(N[tBu]Ar)3 complexes. The role of oxidation state and ancillary ligands in metal complex induced chalcogenyl radical generation

Enthalpies of oxidative addition of PhE-EPh (E = S, Se, Te) to the M(0) complexes M(PiPr3)2(CO)3 (M = Mo, W) to form stable complexes M(*EPh)(PiPr3)2(CO)3 are reported and compared to analogous data for addition to the Mo(III) complexes Mo(N[tBu]Ar)3 (Ar = 3,5-C6H3Me2) to form diamagnetic Mo(IV) phenyl chalcogenide complexes Mo(N[tBu]Ar)3(EPh). Reactions are increasingly exothermic based on metal complex, Mo(PiPr3)2(CO)3 < W(PiPr3)2(CO)3 < Mo(N[tBu]Ar)3, and in terms of chalcogenide, PhTe-TePh < PhSe-SePh < PhS-SPh. These data are used to calculate LnM-EPh bond strengths, which are used to estimate the energetics of production of a free *EPh radical when a dichalcogenide interacts with a specific metal complex. To test these data, reactions of Mo(N[tBu]Ar)3 and Mo(PiPr3)2(CO)3 with PhSe-SePh were studied by stopped-flow kinetics. First- and second-order dependence on metal ion concentration was determined for these two complexes, respectively, in keeping with predictions based on thermochemical data. ESR data are reported for the full set of bound chalcogenyl radical complexes (PhE*)M(PiPr3)2(CO)3; g values increase on going from S to Se, to Te, and from Mo to W. Calculations of electron densities of the SOMO show increasing electron density on the chalcogen atom on going from S to Se to Te. The crystal structure of W(*TePh)(PiPr3)2(CO)3 is reported.

Direct Preparation of Nucleoside Vinyl Disulfides from 2-(Trimethylsilyl)ethyl Sulfides, an Access to Vinylthiols

We report here a straightforward preparation of various nucleoside vinyl disulfides in high yields under mild conditions using the new reaction of vinyl 2-(trimethylsilyl)ethyl (TMSE) sulfides with sulfenyl chlorides. This reaction allows the preparation of various mixed disulfides from stable silyl sulfides without formation of oxidizable and/or unstable thiols. The easy preparation of vinyl disulfides through this reaction should offer new perspectives in vinylthiol chemistry.

High catalytic activity achieved with a mixed manganese-iron site in protein R2 ofChlamydiaribonucleotide reductase

Ribonucleotide reductase (class I) contains two components: protein R1 binds the substrate, and protein R2 normally has a diferric site and a tyrosyl free radical needed for catalysis. In Chlamydia trachomatis RNR, protein R2 functions without radical. Enzyme activity studies show that in addition to a diiron cluster, a mixed manganese-iron cluster provides the oxidation equivalent needed to initiate catalysis. An EPR signal was observed from an antiferromagnetically coupled high-spin Mn(III)-Fe(III) cluster in a catalytic reaction mixture with added inhibitor hydroxyurea. The manganese-iron cluster in protein R2 confers much higher specific activity than the diiron cluster does to the enzyme.

The active form of Chlamydia trachomatis ribonucleotide reductase R2 protein contains a heterodinuclear Mn(IV)/Fe(III) cluster with S = 1 ground state

The class I ribonucleotide reductase from Chlamydia trachomatis uses a stable MnIV/FeIII cofactor to initiate nucleotide reduction by a free-radical mechanism. The enzyme provides the first example both of a Mn-dependent ribonucleotide reductase and of a Mn/Fe redox cofactor. In this work, we have used variable-field Mössbauer spectroscopy to demonstrate that the active cofactor has an S = 1 ground state due to antiferromagnetic coupling between the MnIV (S Mn = 3/2) and high-spin FeIII (S Fe = 5/2) sites.

A manganese(IV)/iron(III) cofactor in Chlamydia trachomatis ribonucleotide reductase

In a conventional class I ribonucleotide reductase (RNR), a diiron(II/II) cofactor in the R2 subunit reacts with oxygen to produce a diiron(III/IV) intermediate, which generates a stable tyrosyl radical (Y*). The Y* reversibly oxidizes a cysteine residue in the R1 subunit to a cysteinyl radical (C*), which abstracts the 3'-hydrogen of the substrate to initiate its reduction. The RNR from Chlamydia trachomatis lacks the Y*, and it had been proposed that the diiron(III/IV) complex in R2 directly generates the C* in R1. By enzyme activity measurements and spectroscopic methods, we show that this RNR actually uses a previously unknown stable manganese(IV)/iron(III) cofactor for radical initiation.

Photoactive Peptides for Light-Initiated Tyrosyl Radical Generation and Transport into Ribonucleotide Reductase

The mechanism of radical transport in the alpha2 (R1) subunit of class I E. coli ribonucleotide reductase (RNR) has been investigated by the phototriggered generation of a tyrosyl radical, *Y356, on a 20-mer peptide bound to alpha2. This peptide, Y-R2C19, is identical to the C-terminal peptide tail of the beta2 (R2) subunit and is a known competitive inhibitor of binding of the native beta2 protein to alpha2. *Y356 radical initiation is prompted by excitation (lambda >or= 300 nm) of a proximal anthraquinone, Anq, or benzophenone, BPA, chromophore on the peptide. Transient absorption spectroscopy has been employed to kinetically characterize the radical-producing step by time resolving the semiquinone anion (Anq*-), ketyl radical (*-BPA), and Y* photoproducts on (i) BPA-Y and Anq-Y dipeptides and (ii) BPA/Anq-Y-R2C19 peptides. Light-initiated, single-turnover assays have been carried out with the peptide/alpha2 complex in the presence of [14C]-labeled cytidine 5'-diphosphate substrate and ATP allosteric effector. We show that both the Anq- and BPA-containing peptides are competent in deoxycytidine diphosphate formation and turnover occurs via Y731 to Y730 to C439 pathway-dependent radical transport in alpha2. Experiments with the Y730F mutant exclude a direct superexchange mechanism between C439 and Y731 and are consistent with a PCET model for radical transport in which there is a unidirectional transport of the electron and proton transport among residues of alpha2.

Long-range distance determinations in biomacromolecules by EPR spectroscopy

Electron paramagnetic resonance (EPR) spectroscopy provides a variety of tools to study structures and structural changes of large biomolecules or complexes thereof. In order to unravel secondary structure elements, domain arrangements or complex formation, continuous wave and pulsed EPR methods capable of measuring the magnetic dipole coupling between two unpaired electrons can be used to obtain long-range distance constraints on the nanometer scale. Such methods yield reliably and precisely distances of up to 80 A, can be applied to biomolecules in aqueous buffer solutions or membranes, and are not size limited. They can be applied either at cryogenic or physiological temperatures and down to amounts of a few nanomoles. Spin centers may be metal ions, metal clusters, cofactor radicals, amino acid radicals, or spin labels. In this review, we discuss the advantages and limitations of the different EPR spectroscopic methods, briefly describe their theoretical background, and summarize important biological applications. The main focus of this article will be on pulsed EPR methods like pulsed electron-electron double resonance (PELDOR) and their applications to spin-labeled biosystems.

Photophysical Properties of Ruthenium Bipyridine (4-Carboxylic acid-4‘-methyl-2,2‘-bipyridine) Complexes and Their Acid−Base Chemistry

Photophysical properties such as absorption and emission spectra, lifetimes, and redox potentials of eight ruthenium complexes, Ru(LL)2(MebpyCOOH)2+, where LL represents bpy, phen, Me2bpy, Me4bpy, (MeO)2bpy, (EtO)2bpy, Cl2bpy, and NO2phen, have been measured. The acid dissociation constants of ground and excited states have been determined. The ground-state pKa values were obtained from the pH dependence of the complex absorbance changes. The excited-state pKa* values were extracted from the emission titration curve and corrected for the excited-state lifetime of both protonated and deprotonated species. The largest DeltapKa, pKa*-pKa, found for Ru(Me2bpy)2(MebpyCOOH)2+ and Ru(Me4bpy)2(MebpyCOOH)2+ of 1.7 indicate that MebpyCOOH gains most of the MLCT excited-state electron. The big negative DeltapKa found for Ru(Cl2bpy)2(MebpyCOOH)2+, -4.2, clearly indicates the metal-to-ligand charge transfer to the Cl2bpy ligands.

Site-specific incorporation of fluorotyrosines into the R2 subunit of E. coli ribonucleotide reductase by expressed protein ligation

Expressed protein ligation (EPL) allows semisynthesis of a target protein with site-specific incorporation of probes or unnatural amino acids at its N or C termini. Here, we describe the protocol that our lab has developed for incorporating fluorotyrosines (F(n)Ys) at residue 356 of the small subunit of Escherichia coli ribonucleotide reductase using EPL. In this procedure, the majority of the protein (residues 1-353 out of 375) is fused to an intein domain and prepared by recombinant expression, yielding the protein in a thioester-activated, truncated form. The remainder of the protein, a 22-mer peptide, is prepared by solid-phase peptide synthesis and contains the F(n)Y at the desired position. Ligation of the 22-mer peptide to the thioester-activated R2 and subsequent purification yield full-length R2 with the F(n)Y at residue 356. The procedure to generate 100 mg quantities of Y356F(n)Y-R2 takes 3-4 months.

Large ground-state entropy changes for hydrogen atom transfer reactions of iron complexes

Reported herein are the hydrogen atom transfer (HAT) reactions of two closely related dicationic iron tris(alpha-diimine) complexes. FeII(H2bip) (iron(II) tris[2,2'-bi-1,4,5,6-tetrahydropyrimidine]diperchlorate) and FeII(H2bim) (iron(II) tris[2,2'-bi-2-imidazoline]diperchlorate) both transfer H* to TEMPO (2,2,6,6-tetramethyl-1-piperidinoxyl) to yield the hydroxylamine, TEMPO-H, and the respective deprotonated iron(III) species, FeIII(Hbip) or FeIII(Hbim). The ground-state thermodynamic parameters in MeCN were determined for both systems using both static and kinetic measurements. For FeII(H2bip) + TEMPO, DeltaG degrees = -0.3 +/- 0.2 kcal mol-1, DeltaH degrees = -9.4 +/- 0.6 kcal mol-1, and DeltaS degrees = -30 +/- 2 cal mol-1 K-1. For FeII(H2bim) + TEMPO, DeltaG degrees = 5.0 +/- 0.2 kcal mol-1, DeltaH degrees = -4.1 +/- 0.9 kcal mol-1, and DeltaS degrees = -30 +/- 3 cal mol-1 K-1. The large entropy changes for these reactions, |TDeltaS degrees | = 9 kcal mol-1 at 298 K, are exceptions to the traditional assumption that DeltaS degrees approximately 0 for simple HAT reactions. Various studies indicate that hydrogen bonding, solvent effects, ion pairing, and iron spin equilibria do not make major contributions to the observed DeltaS degrees HAT. Instead, this effect arises primarily from changes in vibrational entropy upon oxidation of the iron center. Measurement of the electron-transfer half-reaction entropy, |DeltaS degrees Fe(H2bim)/ET| = 29 +/- 3 cal mol-1 K-1, is consistent with a vibrational origin. This conclusion is supported by UHF/6-31G* calculations on the simplified reaction [FeII(H2N=CHCH=NH2)2(H2bim)]2+...ONH2 left arrow over right arrow [FeII(H2N=CHCH=NH2)2(Hbim)]2+...HONH2. The discovery that DeltaS degrees HAT can deviate significantly from zero has important implications on the study of HAT and proton-coupled electron-transfer (PCET) reactions. For instance, these results indicate that free energies, rather than enthalpies, should be used to estimate the driving force for HAT when transition-metal centers are involved.

Lone pair-pi and pi-pi interactions play an important role in proton-coupled electron transfer reactions

Proton-coupled electron transfer (PCET), a class of formal hydrogen atom transfer (HAT) reactions, is of widespread interest because it is implicated in a broad range of chemical and biochemical processes. PCET is typically differentiated from HAT by the fact that it occurs when a proton and electron are transferred between different sets of molecular orbitals. Previous theoretical work predicted that hydrogen bonding between reactants is a necessary but not sufficient condition for H exchanges to take place by PCET. This implies that HAT is the only mechanism for H exchange between two carbon atoms. In this work, we present computational results that show that the H exchange in the tert-butylperoxyl/phenol couple, a prototypical antioxidant exchange reaction, occurs by PCET and that the transfer of the electron can occur via an oxygen lone pair-ring pi overlap. We then show that the H exchange in a model for the tyrosyl/tyrosine couple, which is implicated in ribonucleotide reductase chemistry, occurs via PCET and that one path for the electron transfer is provided by a strong pi-stacking interaction. Finally, we show that a pi-stacking interaction in the benzyl/toluene couple, a system in which there is no H-bonding, can result in this exchange occurring via PCET to some extent. Collectively, these results indicate that PCET reactions are not unique to systems that can engage in H-bonding and that lone pair-pi and pi-pi interactions in these systems may be more important than previously understood.

The stacking tryptophan of galactose oxidase: a second-coordination sphere residue that has profound effects on tyrosyl radical behavior and enzyme catalysis

The function of the stacking tryptophan, W290, a second-coordination sphere residue in galactose oxidase, has been investigated via steady-state kinetics measurements, absorption, CD and EPR spectroscopy, and X-ray crystallography of the W290F, W290G, and W290H variants. Enzymatic turnover is significantly slower in the W290 variants. The Km for D-galactose for W290H is similar to that of the wild type, whereas the Km is greatly elevated in W290G and W290F, suggesting a role for W290 in substrate binding and/or positioning via the NH group of the indole ring. Hydrogen bonding between W290 and azide in the wild type-azide crystal structure are consistent with this function. W290 modulates the properties and reactivity of the redox-active tyrosine radical; the Y272 tyrosyl radicals in both the W290G and W290H variants have elevated redox potentials and are highly unstable compared to the radical in W290F, which has properties similar to those of the wild-type tyrosyl radical. W290 restricts the accessibility of the Y272 radical site to solvent. Crystal structures show that Y272 is significantly more solvent exposed in the W290G variant but that W290F limits solvent access comparable to the wild-type indole side chain. Spectroscopic studies indicate that the Cu(II) ground states in the semireduced W290 variants are very similar to that of the wild-type protein. In addition, the electronic structures of W290X-azide complexes are also closely similar to the wild-type electronic structure. Azide binding and azide-mediated proton uptake by Y495 are perturbed in the variants, indicating that tryptophan also modulates the function of the catalytic base (Y495) in the wild-type enzyme. Thus, W290 plays multiple critical roles in enzyme catalysis, affecting substrate binding, the tyrosyl radical redox potential and stability, and the axial tyrosine function.

Concerted Proton−Electron Transfer Reactions in Water. Are the Driving Force and Rate Constant Depending on pH When Water Acts as Proton Donor or Acceptor?

The competition between stepwise and concerted (CPET) pathways in proton-coupled electron-transfer reactions in water is discussed on thermodynamic and kinetic bases. In the case where water is the proton acceptor, the CPET pathway may compete favorably with the stepwise pathway. The main parameter of the competition is pK of the oxidized form of the substrate being smaller or larger than 0. The driving force of the forward reaction is however independent of pH, despite the equilibrium redox potential of the proton-electron system being a function of pH. At high pH values, CPET reactions involving OH- as proton acceptor may likewise compete favorably with stepwise pathways. The overall reaction rate constant is an increasing function of pH, not because the driving force depends on pH but because OH- is a reactant. In buffered media, association of the substrate with the basic components of the buffer offers an alternative CPET route; the driving force comes closer to that offered by the pH-dependent equilibrium redox potential.

What's new in stable radical chemistry?

Many kinds of radicals are stable enough to isolate, handle, and store without any special precautions. The diversity in molecular architectures of these stable radicals is sufficiently large that the common factors governing radical stability/persistence, geometric and electronic structure, association/dimerization preferences, and reactivity have generally not been well articulated or appreciated. This review provides a survey of the major classes of stable or persistent organic/organomain group radicals with a view to presenting a unified description of the interdependencies between radical molecular structure and properties.

Compatible Injection and Detection Systems for Studying the Kinetics of Excess Electron Transfer

[reaction: see text] A design for fast kinetic studies of electron transfer in radical anions is reported. alpha-Hydroxy radicals formed by 355 nm laser flash photolysis of alpha-phenacyl alcohols are deprotonated under basic conditions to give ketyl radical anions that serve as electron injectors in inter- and intramolecular electron-transfer reactions. The 2,2-diphenylcyclopropyl group serves as a reporter. When an electron is injected and transferred such that spin character is adjacent to the reporter, cyclopropyl ring opening gives a readily detected diphenylalkyl radical.

Side-chain losses in electron capture dissociation to improve peptide identification

Analysis of a database of some 20 000 conventional electron-capture dissociation (ECD) mass spectra of doubly charged ions belonging to tryptic peptides revealed widespread appearance of w ions and related u ions that are due to partial side chain losses from radical z* ions. Half of all z* ions that begin with Leu or Ile produce w ions in conventional one-scan ECD mass spectra, which differentiates these isomeric residues with >97% reliability. Other residues exhibiting equally frequent side chain losses are Gln, Glu, Asp, and Met (cysteine was not included in this work). Unexpectedly, Asp lost not a radical group like other amino acids but a molecule CO2, thus giving rise to a radical w* ion with the possibility of a radical cascade. Losses from amino acids as distant as seven residues away from the cleavage site were detected. The mechanism of such losses seems to be related to radical migration from the original site at the alphaCn atom in a zn* ion to other alphaC and betaC atoms. The side chain losses confirm sequence assignment, improve the database matching score, and can be useful in de novo sequencing.

Coupling coherence distinguishes structure sensitivity in protein electron transfer

Quantum mechanical analysis of electron tunneling in nine thermally fluctuating cytochrome b562 derivatives reveals two distinct protein-mediated coupling limits. A structure-insensitive regime arises for redox partners coupled through dynamically averaged multiple-coupling pathways (in seven of the nine derivatives) where heme-edge coupling leads to the multiple-pathway regime. A structure-dependent limit governs redox partners coupled through a dominant pathway (in two of the nine derivatives) where axial-ligand coupling generates the single-pathway limit and slower rates. This two-regime paradigm provides a unified description of electron transfer rates in 26 ruthenium-modified heme and blue-copper proteins, as well as in numerous photosynthetic proteins.

Fe–S complexes containing five-membered heterocycles: novel models for the active site of hydrogenases with unusual low reduction potential

Three biomimetic 2Fe2S complexes [{(micro-SCH2)2NCH2(2-C4H3O)}](Fe2(CO)6), [{(micro-SCH2)2 NCH2(2-C4H3S)}](Fe2(CO)6) and [{(micro-SCH2)2NCH2(5-Br-2-C4H2S)}Fe2(CO)6] were prepared as models for the active site of Fe-only hydrogenase by the convergent process from [(micro-S2)Fe2(CO)6] and N,N-bis(hydromethyl)-2-furan and thiophene. The structures of these complexes were identified spectroscopically and crystallographically. The electrochemical behavior of the complexes and was unique as they showed catalytic proton reduction with a low reduction potential at -1.13 and -1.09 V vs Fc/Fc+, respectively, in the presence of HClO4.

Circular dichroism and magnetic circular dichroism studies of the active site of p53R2 from human and mouse: iron binding and nature of the biferrous site relative to other ribonucleotide reductases

Ribonucleotide reductases (RNR) catalyze the rate-limiting step in the synthesis of deoxyribonucleotides from the corresponding ribonucleotides in the synthesis of DNA. Class I RNR has two subunits: R1 with the substrate binding and active site and R2 with a stable tyrosyl radical and diiron cluster. Biferrous R2 reacts with oxygen to form the tyrosyl radical needed for enzymatic activity. A novel R2 form, p53R2, is a 351-amino acid protein induced by the "tumor suppressor gene" p53. p53R2 has been studied using a combination of circular dichroism, magnetic circular dichroism, variable-temperature variable-field MCD, and EPR spectroscopies. The active site of biferrous p53R2 in both the human (hp53R2) and mouse (mp53R2) forms is found to have one five-coordinate and one four-coordinate iron, which are weakly antiferromagnetically coupled through mu-1,3-carboxylate bridges. These spectroscopic data are very similar to those of Escherichia coli R2, and mouse R2, with a stronger resemblance to data of the former. Titrations of apo-hp53R2 and apo-mp53R2 with Fe(II) were pursued for the purpose of comparing their metal binding affinities to those of other R2s. Both p53R2s were found to have a high affinity for Fe(II), which is different from that of mouse R2 and may reflect differences in the regulation of enzymatic activity, as p53R2 is mainly triggered during DNA repair. The difference in ferrous affinity between mammalian R2 and p53R2 suggests the possibility of specific inhibition of DNA precursor synthesis during cell division.

X-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, Pseudomonas sp. OX1 phenol hydroxylase

Phenol hydroxylase (PH) belongs to a family of bacterial multicomponent monooxygenases (BMMs) with carboxylate-bridged diiron active sites. Included are toluene/o-xylene (ToMO) and soluble methane (sMMO) monooxygenase. PH hydroxylates aromatic compounds, but unlike sMMO, it cannot oxidize alkanes despite having a similar dinuclear iron active site. Important for activity is formation of a complex between the hydroxylase and a regulatory protein component. To address how structural features of BMM hydroxylases and their component complexes may facilitate the catalytic mechanism and choice of substrate, we determined X-ray structures of native and SeMet forms of the PH hydroxylase (PHH) in complex with its regulatory protein (PHM) to 2.3 A resolution. PHM binds in a canyon on one side of the (alphabetagamma)2 PHH dimer, contacting alpha-subunit helices A, E, and F approximately 12 A above the diiron core. The structure of the dinuclear iron center in PHH resembles that of mixed-valent MMOH, suggesting an Fe(II)Fe(III) oxidation state. Helix E, which comprises part of the iron-coordinating four-helix bundle, has more pi-helical character than analogous E helices in MMOH and ToMOH lacking a bound regulatory protein. Consequently, conserved active site Thr and Asn residues translocate to the protein surface, and an approximately 6 A pore opens through the four-helix bundle. Of likely functional significance is a specific hydrogen bond formed between this Asn residue and a conserved Ser side chain on PHM. The PHM protein covers a putative docking site on PHH for the PH reductase, which transfers electrons to the PHH diiron center prior to O2 activation, suggesting that the regulatory component may function to block undesired reduction of oxygenated intermediates during the catalytic cycle. A series of hydrophobic cavities through the PHH alpha-subunit, analogous to those in MMOH, may facilitate movement of the substrate to and/or product from the active site pocket. Comparisons between the ToMOH and PHH structures provide insights into their substrate regiospecificities.

On the identity and reactivity patterns of the “second oxidant” of the T252A mutant of cytochrome P450cam in the oxidation of 5-methylenenylcamphor

Density functional calculations show that in the absence of Compound I, the primary oxidant species of P450, the precursor species, Compound 0 (FeOOH), can effect double bond activation of 5-methylenylcamphor (1). The mechanism is initiated by homolytic cleavage of the O-O bond and formation of an OH radical bound to the Compound II species by hydrogen bonding interactions. Subsequently, the so-formed OH radical can either activate the double bond of 1 or attack the meso position of the heme en route to heme degradation. The calculations show that double bond activation is preferred over attack on the heme. Past the double bond activation, the intermediate can either lead to epoxidation or to a glycol formation. The glycol formation is predicted to be preferred, although in the P450(cam) pocket the competition may be closer. Therefore, in the absence of Compound I, Compound 0 will be capable of epoxidizing double bonds. Previous studies [E. Derat, D. Kumar, H. Hirao, S. Shaik, J. Am. Chem. Soc. 128 (2006) 473-484] showed that in the case of a substrate that can undergo only C-H activation, the bound OH prefers heme degradation over hydrogen abstraction. Since the epoxidation barrier for Compound I is much smaller than that of Compound 0 (12.8 vs. 18.9kcal/mol), when Compound I is present in the cycle, Compound 0 will be silent. As such, our mechanism explains lucidly why T252A P450(cam) can epoxidize olefins like 5-methylenylcamphor but is ineffective in camphor hydroxylation [S. Jin, T.M. Makris, T. A. Bryson, S.G. Sligar, J.H. Dawson, J. Am. Chem. Soc. 125 (2003) 3406-3407]. Our calculations show that the glycol formation is a marker reaction of Compound 0 with 5-methylenylcamphor. If this product can be found in T252A P450(cam) or in similar mutants of other P450 isozymes, this will constitute a more definitive proof for the action of Cpd 0 in P450 enzymes.

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 35A away via an amino acid radical-hopping pathway spanning two protein subunits.

Hangman Salen Platforms Containing Two Xanthene Scaffolds

A synthetic strategy for the construction of chiral salen ligands bearing two rigid xanthene spacers functionalized with carboxylic acid and ester groups is presented. Suzuki cross-coupling methodology is used to furnish the appropriately functionalized xanthene spacers to a salicylaldehyde, which is subsequently condensed with (1R,2R)-(-)-1,2-diaminocyclohexane to produce salen ligands featuring an expandable molecular cleft capable of multiple hydrogen-bonding interactions in addition to metallosalen oxidation chemistry. The ability of these "Hangman" platforms to support multielectron chemistry mediated by proton-coupled electron transfer (PCET) is established by their proclivity to promote the catalytic disproportionation of hydrogen peroxide to oxygen and water via a high-valent metal oxo. Within this functionalized Hangman framework, the stereochemistry of the cyclohexyl backbone of the salen platform is revealed in the epoxidation of 1,2-dihydronaphthalene by the metal oxo.

Anomalous temperature-isotope dependence in proton-coupled electron transfer

Motivated by the experiments of Hodgkiss et al. [J. Phys. Chem. (submitted)] on electron transfer (ET) through a H-bonding interface, we present a new theoretical model for proton-coupled electron transfer (PCET) in the condensed phase, that does not involve real proton transfer. These experiments, which directly probe the joint T-isotope effects in coupled charge transfer reactions, show anomalous T dependence in k(H)k(D), where k(H) and k(D) are the ET rates through the H-bonding interface with H-bonded protons and deuterons, respectively. We address the anomalous T dependence of the k(H)k(D) in our model by attributing the modulation of the electron tunneling dynamics to bath-induced fluctuations in the proton coordinate, so that the mechanism for coupled charge transfer might be better termed vibrationally assisted ET rather than PCET. We argue that such a mechanism may be relevant to understanding traditional PCET processes, i.e., those in which protons undergo a transfer from donor to acceptor during the course of ET, provided there is an appropriate time scale separating both coupled charge transfers. Likewise, it may also be useful in understanding long-range ET in proteins, where tunneling pathways between redox cofactors often pass through H-bonded amino acid residues, or other systems with sufficiently decoupled proton and electron donating functionalities.

Electron Transfer Reactions of Fluorotyrosyl Radicals

The complex Re(bpy)(CO)3CN is an excited state oxidant of tyrosine upon deprotonation of the tyrosyl phenol. A series of Re(bpy-FnY)(CO)3CN complexes ([Re]-FnY: [Re]-Y, [Re]-3-FY, [Re]-3,5-F2Y, [Re]-2,3-F2Y, [Re]-2,3,5-F3Y, [Re]-2,3,6-F3Y, and [Re]-F4Y) have been prepared so as to vary the FnY*/FnY- reduction potential and thus the driving force for electron transfer in this system. Time-resolved emission and nanosecond absorption spectroscopies have been used to measure the rates for charge separation, CS, and charge recombination, CR, for each complex. A driving force analysis reveals that CS is well described by Marcus' theory for ET, is strongly driving force dependent (activated), and occurs in the normal region for ET. CR, on the other hand, is weakly driving force dependent (near activationless) and occurs in the inverted region for ET. These data demonstrate that fluorotyrosines will be powerful probes for unraveling charge transport mechanisms in enzymes that utilize tyrosyl radicals.