Vibrations of the phenoxyl radical

Differences in the Reaction Mechanisms of Chlorine Atom and Hydroxyl Radical with Organic Compounds: From Thermodynamics to Kinetics

Hydroxyl radical (HO•) and chlorine atom (Cl•) are common reactive species in aqueous environments. However, the intrinsic difference in their reactions with organic compounds has not been revealed. This study compared the reaction mechanisms of HO• and Cl• with 13 aromatic and 11 aliphatic compounds by quantum chemical calculation and laser flash photolysis. Both HO• and Cl• can spontaneously react with aromatic compounds via radical adduct formation (RAF), hydrogen atom transfer (HAT), and single electron transfer (SET) pathways. The SET reactions of Cl• were more thermodynamically favorable than HO•, but contrary results were obtained for HAT reactions. According to the free energy of activation (ΔGaq‡), the dominant oxidation mechanisms of aromatic compounds were RAF and SET by HO• and SET by Cl•. The important role of SET in the HO• reactions with aromatic compounds was further verified by accurately calculating the solvation free energy of HO•/HO- and experimentally tracking the radical cations, which were generally neglected in previous studies. Meanwhile, the ΔGaq‡ value of each reaction pathway of Cl• was lower than that of HO•, resulting in higher rate constants of Cl• with aromatic compounds than HO•. For saturated aliphatic compounds, HAT was found to be the only mechanism accounting for their transformation by HO• and Cl•. This study proposed general rules for the reaction mechanisms of HO• and Cl• and unraveled their differences in the aspects of thermodynamics and kinetics, providing fundamental information for understanding contaminant transformation in processes involving HO• and Cl•.

Silica Biomineralization with Lignin Involves Si-O-C Bonds That Stabilize Radicals

Plants undergo substantial biomineralization of silicon, which is deposited primarily in cell walls as amorphous silica. The mineral formation could be moderated by the structure and chemistry of lignin, a polyphenol polymer that is a major constituent of the secondary cell wall. However, the reactions between lignin and silica have not yet been well elucidated. Here, we investigate silica deposition onto a lignin model compound. Polyphenyl propanoid was synthesized from coniferyl alcohol by oxidative coupling with peroxidase in the presence of acidic tetramethyl orthosilicate, a silicic acid precursor. Raman, Fourier transform infrared, and X-ray photoelectron spectroscopies detected changes in lignin formation in the presence of silicic acid. Bonds between the Si-O/Si-OH residues and phenoxyl radicals and lignin functional groups formed during the first 3 h of the reaction, while silica continued to form over 3 days. Thermal gravimetric analysis indicated that lignin yields increased in the presence of silicic acid, possibly via the stabilization of phenolic radicals. This, in turn, resulted in shorter stretches of the lignin polymer. Silica deposition initiated within a lignin matrix via the formation of covalent Si-O-C bonds. The silica nucleants grew into 2-5 nm particles, as observed via scanning transmission electron microscopy and energy-dispersive X-ray spectroscopy. Additional silica precipitated into an extended gel. Collectively, our results demonstrate a reciprocal relation by which lignin polymerization catalyzes the formation of silica, and at the same time silicic acid enhances lignin polymerization and yield.

Rotational Spectrum of the Phenoxy Radical

We report the hyperfine-resolved rotational spectrum of the gas-phase phenoxy radical in the 8-25 GHz frequency range using cavity Fourier transform microwave spectroscopy. A complete assignment of its complex but well-resolved fine and hyperfine splittings yielded a precisely determined set of rotational constants, spin-rotation parameters, and nuclear hyperfine coupling constants. These results are interpreted with support from high-level quantum chemical calculations to gain detailed insight into the distribution of the unpaired π electron in this prototypical resonance-stabilized radical. The accurate laboratory rest frequencies enable studies of the chemistry of phenoxy in both the laboratory and space. The prospects of extending the present experimental and theoretical techniques to investigate the rotational spectra of isotopic variants and structural isomers of phenoxy and other important gas-phase radical intermediates that are yet undetected at radio wavelengths are discussed.

Suppression of the phenolic SOA formation in the presence of electrolytic inorganic seed

Phenolic compounds are largely attributed to wildfire gases and rapidly react with atmospheric oxidants to form persistent phenoxy free radicals, which influence atmospheric chemistry and secondary organic aerosol (SOA) formation. In this study, phenol or o-cresol was photochemically oxidized under various conditions (NO_x levels, humidity, and seed conditions) in an outdoor photochemical reactor. Unexpectedly, SOA growth of both phenols was suppressed in the presence of salted aqueous aerosol compared to non-seed SOA. This discovery is different from the typical SOA formation of aromatic or biogenic hydrocarbons, which show noticeably higher SOA yields via organic aqueous reactions. Phenol, o-cresol, and their phenolic products (e.g., catechols) are absorbed in aqueous aerosol and form phenoxy radicals via heterogeneous reactions under sunlight. The resulting phenoxy radicals are redistributed between the gas and particle phases. Gaseous phenoxy radicals quickly react with ozone to form phenyl peroxide radicals and regenerated through a NO_x cycle to retard phenol oxidation and SOA formation. The explicit oxidation mechanisms of phenol or o-cresol in the absence of aqueous phase were derived including the Master Chemical Mechanism (MCM v3.3.1) and the path for peroxy radical adducts originating from the addition of an OH radical to phenols to form low volatility products (e.g., multi-hydroxy aromatics). The resulting gas mechanisms of phenol or o-cresol were, then, applied to the Unified Partitioning Aerosol Phase Reaction (UNIPAR) model to predict SOA formation via multiphase partitioning of organics and aerosol-phase oligomerization. The model well simulated chamber-generated phenolic SOA in absence of wet-inorganic seed, but significantly overestimated SOA mass in presence of wet seed. This study suggests that heterogeneous chemistry to form phenoxy radicals needs to be included to improve SOA prediction from phenols. The suppression of atmospheric oxidation due to phenoxy radicals in wet inorganic aerosol can explain the low SOA formation during wildfire episodes.

Alkoxy Radicals See the Light: New Paradigms of Photochemical Synthesis

Alkoxy radicals are highly reactive species that have long been recognized as versatile intermediates in organic synthesis. However, their development has long been impeded due to a lack of convenient methods for their generation. Thanks to advances in photoredox catalysis, enabling facile access to alkoxy radicals from bench-stable precursors and free alcohols under mild conditions, research interest in this field has been renewed. This review comprehensively summarizes the recent progress in alkoxy radical-mediated transformations under visible light irradiation. Elementary steps for alkoxy radical generation from either radical precursors or free alcohols are central to reaction development; thus, each section is categorized and discussed accordingly. Throughout this review, we have focused on the different mechanisms of alkoxy radical generation as well as their impact on synthetic utilizations. Notably, the catalytic generation of alkoxy radicals from abundant alcohols is still in the early stage, providing intriguing opportunities to exploit alkoxy radicals for diverse synthetic paradigms.

UV-Induced Photochemistry of 1,3-Benzoxazole, 2-Isocyanophenol, and 2-Cyanophenol Isolated in Low-Temperature Ar Matrixes

The monomers of 1,3-benzoxazole isolated in a cryogenic argon matrix were characterized by infrared spectroscopy. The photochemistry of matrix-isolated 1,3-benzoxazole, induced by excitation with a frequency-tunable narrowband UV light, was investigated. Irradiation at 233 nm resulted in a nearly quantitative conversion of 1,3-benzoxazole into 2-isocyanophenol. The individual photochemical behavior of the in situ produced 2-isocyanophenol was studied upon excitations at 290 nm, where 1,3-benzoxazole does not react. The photochemistry of isomeric matrix-isolated 2-cyanophenol was also studied. The photoreactions of 2-substituted (cyano- or isocyano-) phenols were found to have many similarities: (i) OH bond cleavage, yielding a 2-substituted (cyano- or isocyano-) phenoxyl radical and an H-atom, (ii) recombination of the detached H-atom, resulting in an oxo tautomer, and (iii) decomposition leading to fulvenone, together with HCN and HNC. In another photoprocess, 2-cyanophenol undergoes a [1,5] H-shift from the hydroxyl group to the cyano group yielding isomeric ketenimine. The analogous [1,5] H-shift from the hydroxyl group to the isocyano group must have also occurred in 2-isocyanophenol; however, the resulting nitrile ylide isomer is kinetically unstable and collapses to benzoxazole. All photoproducts were characterized by comparing their observed infrared spectra with those computed at the B3LYP/6-311++G(d,p) level. The mechanistic analysis of the photochemistry occurring in the family of the title compounds is presented.

Copper Inhibition of Triplet-Sensitized Phototransformation of Phenolic and Amine Contaminants

Excited triplet states of natural organic matter (³NOM*) are important reactive intermediates in phototransformation of organic contaminants in sunlit waters. The main goal of this study was to explore the influence of Cu on triplet-sensitized transformation rates of 20 selected phenolic and amine contaminants. Fourteen of the compounds examined exhibited a marked decrease in their 4-carboxybenzophenone (CBBP)-mediated phototransformation rate in the presence of trace amounts of Cu(II) (25-500 nM). Both mathematical modeling of these rate data and transient absorption spectroscopy measurements support the hypothesis that the decrease in the rate and extent of phototransformation of organic contaminants is due to the reduction of radical intermediates of the contaminants by photochemically formed Cu(I). The Cu-induced inhibition of oxidation of organic contaminants photosensitized by Suwannee River NOM (SRNOM) could also take place in the presence of nanomolar concentrations of Cu. The inhibitory effect of Cu on the oxidation rates of amine contaminants in SRNOM solutions was found to be significantly weaker compared to that in CBBP solutions, but little difference was observed on depletion of phenols. This behavior was attributed to the intrinsic inhibitory effect of the antioxidant moieties present in NOM on phototransformation of amine compounds, partially neutralizing the potential for further Cu inhibition.

Insights into the Mechanism of Nonadiabatic Photodissociation from Product Vibrational Distributions. The Remarkable Case of Phenol

The fate of a photoexcited molecule is often strongly influenced by electronic degeneracies, such as conical intersections, which break the Born-Oppenheimer separation of electronic and nuclear motion. Detailed information concerning internal energy redistribution in a nonadiabatic process can be extracted from the product state distribution of a photofragment in photodissociation. Here, we focus on the nonadiabatic photodissociation of phenol and discuss the internal excitation of the phenoxyl fragment using both symmetry analysis and wave packet dynamics. It is shown that unique and general selection rules exist, which can be attributed to the geometric phase in the adiabatic representation. Further, our results provide a reinterpretation of the experimental data, shedding light on the impact of conical intersections on the product state distribution.

SERS activity and spectroscopic properties of Zn and ZnO nanostructures obtained by electrochemical and green chemistry methods for applications in biology and medicine

This work evaluates the ability of homogeneous, stable, and pure zinc oxide nanoparticles (ZnONPs-GS) synthesized by “green chemistry” for the selective detection of four neurotransmitters present in body fluids and promotion of the SERS effect.

Pivotal role of the redox-active tyrosine in driving the water splitting catalyzed by photosystem II

TyrZ oxidation state triggers hydrogen bond modification in the water oxidation catalysis.

Rate Constants and Mechanisms of the Reactions of Cl• and Cl2•- with Trace Organic Contaminants

Cl^• and Cl₂^•- radicals contribute to the degradation of trace organic contaminants (TrOCs) such as pharmaceutical and personal care products and endocrine-disrupting chemicals. However, little is known about their reaction rate constants and mechanisms. In this study, the reaction rate constants of Cl^• and Cl₂^•- with 88 target compounds were determined using laser flash photolysis. Decay kinetics, product buildup kinetics, and competition kinetics were applied to track the changes in their transient spectra. Cl^• exhibited quite high reactivity toward TrOCs with reaction rate constants ranging from 3.10 × 10⁹ to 4.08 × 10¹⁰ M^-1 s^-1. Cl₂^•- was less reactive but more selective, with reaction rate constants varying from <1 × 10⁶ to 2.78 × 10⁹ M^-1 s^-1. Three QSAR models were developed, which were capable of predicting the reaction rate constants of Cl₂^•- with TrOCs bearing phenol, alkoxy benzene, and aniline groups. The detection of Cl^•-adducts of many TrOCs suggested that Cl^• addition was an important reaction mechanism. Single electron transfer (SET) predominated in reactions of Cl^• with TrOCs bearing electron-rich moieties (e.g., sulfonamides), and their cation radicals were observed. Cl^• might also abstract hydrogen atoms from phenolic compounds to generate phenoxyl radicals. Moreover, Cl^• could react with TrOCs through multiple pathways since more than one transient intermediate was detected simultaneously. SET was the major reaction mechanism of Cl₂^•- reactions with TrOCs bearing phenols, alkoxy benzenes, and anilines groups. Cl₂^•- was found to play an important role in TrOC degradation, though it has been often neglected in previous studies. The results improve the understanding of halogen radical-involved chemistry in TrOC degradation.

Ultrafast structural rearrangement dynamics induced by the photodetachment of phenoxide in aqueous solution

The elementary processes that accompany the interaction of ionizing radiation with biologically relevant molecules are of fundamental importance. However, the ultrafast structural rearrangement dynamics induced by the ionization of biomolecules in aqueous solution remain hitherto unknown. Here, we employ femtosecond optical pump-probe spectroscopy to elucidate the vibrational wave packet dynamics that follow the photodetachment of phenoxide, a structural mimic of tyrosine, in aqueous solution. Photodetachment of phenoxide leads to wave packet dynamics of the phenoxyl radical along 12 different vibrational modes. Eight of the modes are totally symmetric and support structural rearrangement upon electron ejection. Comparison to a previous photodetachment study of phenoxide in the gas phase reveals the important role played by the solvent environment in driving ultrafast structural reorganization induced by ionizing radiation. This work provides insight into the ultrafast molecular dynamics that follow the interaction of ionizing radiation with molecules in aqueous solution.

The interaction of biomolecules with ionizing radiation induces structural changes which are still largely unknown. The authors use femtosecond wave packet spectroscopy to observe ultrafast structural dynamics that follow the photodetachment of phenoxide in aqueous solution.

Fast beam photofragment translational spectroscopy of the phenoxy radical at 225 nm, 290 nm, and 533 nm

Photodissociation of the phenoxy radical (C6H5O) is investigated using fast beam photofragment translational spectroscopy. Phenoxy radicals are generated through photodetachment of phenoxide anions (C6H5O-) at 532 nm. Following photoexcitation of the radicals at 225 nm (5.51 eV), 290 nm (4.27 eV), or 533 nm (2.33 eV), photofragments are collected in coincidence to determine their masses, translational energy, and scattering angle for each dissociation event. Two-body dissociation yields exclusively CO + C5H5, and three-body dissociation to CO + C2H2 + C3H3 and CO + C5H4 + H is also seen at the two higher energies. The translational energy distributions for two-body dissociation suggest that dissociation occurs via internal conversion to the ground electronic state followed by statistical dissociation. The absorption of an additional 532 nm photon in the photodetachment region provides some C6H5O radicals with an additional 2.33 eV of energy, leading to much of the two-body dissociation observed at 533 nm and the three-body dissociation at the two higher excitation energies.

Structural Characterization of Phenoxy Radical with Mass-Correlated Broadband Microwave Spectroscopy

A combination of broadband microwave spectroscopy and VUV photoionization time-of-flight mass spectra has been used to record rotational spectra of the prototypical phenoxy radical, its per-deuterated isotopomers, and the full set of singly 13C-substituted analogues. Rotational parameters associated with the fits to the full set of isotopomers produce a highly accurate r0 structure for the phenoxy radical. High-level ab initio calculations accurately reproduce the rotational constants and spin-rotation parameters. The structure of the phenoxy radical is distinctly quinoidal, with delocalization of the unpaired electron spin density on the oxygen and phenyl ring. The fitted Fermi contact terms for the 13C atoms reflect a weighting of resonance structures that is 27% on the O atom, 21.5% on each of the two ortho C's, and 30% on the para C, providing a quantitative measure of its sites for subsequent reactions that will control its abundances in combustion and atmospheric environments.

First multi-tool exploration of a gas-condensate-pyrolysate system from the environment of burning coal mine heaps: An in situ FTIR and laboratory GC and PXRD study based on Upper Silesian materials

A methodological approach to the complex geochemical analysis of the coal fire in burning coal mine heaps (BCMH) of Upper Silesian Coal Basin has been developed. The other approach used is gas chromatography and indicatory tubes. Powder X-Ray Diffraction is applied for phase analysis to determine the species composition of mineral condensates present within and around gas flues. The gas compositions are proved to be extremely variable, when comparing both different BCMH and flues or flue zones of the same heaps. One outstanding determination concerns GeCl₄, found in most samples often in large quantities. No evident dependence between the gas and mineral condensate compositions is found: N-rich condensates may but do not have to be associated with NH₃-, pyridine-, or NO_x-rich gases. This is also true for S-rich and Cl-rich mineralization in connection with gases of SO₂, H₂S, OCS, CS₂, thiophene, dimethyl sulfide, dimethyl disulfide, HCl, and various halogenated hydrocarbons. Fluorine is rarely present as HF, whereas SiF₄ occurs more frequently and in much larger quantities. AsH₃ is mainly a trace gas but may locally be enriched. Besides the common gases, a number of trace gases is also determined based on residual FTIR spectra. Those with the highest presence chance include cyanogen isocyanate, cyanogen N-oxide, (iso)cyanic acid, c-cyanomethanimine (ethylenediimine), isocyanatomethane, iodocyanoacetylene, acetonitrile, acetaldehyde, m-hydroxybenzonitrile (m-cyanophenol), isonitrosyl chloride, nitrosyl isocyanide, difluorosilane, pentacene, triphenylene, thiazolidine, cyclohexane, and a trinitrenetriazine. The occurrence of some metals and semimetals (e.g., Al, Mg, Ga) as neutral hydroxides, suggested by other authors to occur in natural gases, is possibly confirmed. The presence of trace metal carbonyls, nitrosyls and hydrides is also possible.

Calcium, conformational selection, and redox-active tyrosine YZ in the photosynthetic oxygen-evolving cluster

In Photosystem II (PSII), YZ (Tyr161D1) participates in radical transfer between the chlorophyll donor and the Mn₄CaO₅ cluster. Under flashing illumination, the metal cluster cycles among five S_n states, and oxygen is evolved from water. The essential YZ is transiently oxidized and reduced on each flash in a proton-coupled electron transfer (PCET) reaction. Calcium is required for function. Of reconstituted divalent ions, only strontium restores oxygen evolution. YZ is predicted to hydrogen bond to calcium-bound water and to His190D1 in PSII structures. Here, we report a vibrational spectroscopic study of YZ radical and singlet in the presence of the metal cluster. The S₂ state is trapped by illumination at 190 K; flash illumination then generates the S₂YZ radical. Using reaction-induced FTIR spectroscopy and divalent ion depletion/substitution, we identify calcium-sensitive tyrosyl radical and tyrosine singlet bands in the S₂ state. In calcium-containing PSII, two CO stretching bands are detected at 1,503 and 1,478 cm^-1 These bands are assigned to two different radical conformers in calcium-containing PSII. At pH 6.0, the 1,503-cm^-1 band shifts to 1,507 cm^-1 in strontium-containing PSII, and the band is reduced in intensity in calcium-depleted PSII. These effects are consistent with a hydrogen-bonding interaction between the calcium site and one conformer of radical YZ. Analysis of the amide I region indicates that calcium selects for a PCET reaction in a subset of the YZ conformers, which are trapped in the S₂ state. These results support the interpretation that YZ undergoes a redox-coupled conformational change, which is calcium dependent.

A tyrosine-tryptophan dyad and radical-based charge transfer in a ribonucleotide reductase-inspired maquette

In class 1a ribonucleotide reductase (RNR), a substrate-based radical is generated in the α2 subunit by long-distance electron transfer involving an essential tyrosyl radical (Y122O·) in the β2 subunit. The conserved W48 β2 is ∼10 Å from Y122OH; mutations at W48 inactivate RNR. Here, we design a beta hairpin peptide, which contains such an interacting tyrosine–tryptophan dyad. The NMR structure of the peptide establishes that there is no direct hydrogen bond between the phenol and the indole rings. However, electronic coupling between the tyrosine and tryptophan occurs in the peptide. In addition, downshifted ultraviolet resonance Raman (UVRR) frequencies are observed for the radical state, reproducing spectral downshifts observed for β2. The frequency downshifts of the ring and CO bands are consistent with charge transfer from YO· to W or another residue. Such a charge transfer mechanism implies a role for the β2 Y-W dyad in electron transfer.

Tyrosine-tryptophan dyads are known to mediate electron transfer reactions in a range of different proteins. Here, the authors study a beta hairpin peptide, probing the tyrosine-tryptophan interaction and showing no hydrogen bonding but rather charge transfer between the tyrosyl radical and tryptophan'.

Are the three hydroxyphenyl radical isomers created equal?--The role of the phenoxy radical

We have investigated the thermal decomposition of the three hydroxyphenyl radicals (˙C6H4OH) in a heated microtubular reactor. Intermediates and products were identified isomer-selectively applying photoion mass-selected threshold photoelectron spectroscopy with vacuum ultraviolet synchrotron radiation. Similarly to the phenoxy radical (C6H5-O˙), hydroxyphenyl decomposition yields cyclopentadienyl (c-C5H5) radicals in a decarbonylation reaction at elevated temperatures. This finding suggests that all hydroxyphenyl isomers first rearrange to form phenoxy species, which subsequently decarbonylate, a mechanism which we also investigate computationally. Meta- and para-radicals were selectively produced and spectroscopically detectable, whereas the ortho isomer could not be traced due to its fast rethermalization and rapid decomposition in the reactor. A smaller barrier to isomerization to phenoxy was found to be the reason for this observation. Since hydroxyphenyl species may be present under typical sooting conditions in flames, the resonantly stabilized cyclopentadienyl radical adds to the hydrocarbon pool and can contribute to the formation of polycyclic aromatic hydrocarbons, which are precursors in soot formation.

Hydrogen atom transfer reactions in thiophenol: photogeneration of two new thione isomers

The photochemistry of thiophenol monomers confined in cryogenic argon matrices is dominated by hydrogen atom transfer reactions and leads to the formation of two new thione isomers, which were characterized in this work by infrared spectroscopy and theoretical calculations.

Reaction dynamics and proton coupled electron transfer: studies of tyrosine-based charge transfer in natural and biomimetic systems

In bioenergetic reactions, electrons are transferred long distances via a hopping mechanism. In photosynthesis and DNA synthesis, the aromatic amino acid residue, tyrosine, functions as an intermediate that is transiently oxidized and reduced during long distance electron transfer. At physiological pH values, oxidation of tyrosine is associated with a deprotonation of the phenolic oxygen, giving rise to a proton coupled electron transfer (PCET) reaction. Tyrosine-based PCET reactions are important in photosystem II, which carries out the light-induced oxidation of water, and in ribonucleotide reductase, which reduces ribonucleotides to form deoxynucleotides. Photosystem II contains two redox-active tyrosines, YD (Y160 in the D2 polypeptide) and YZ (Y161 in the D1 polypeptide). YD forms a light-induced stable radical, while YZ functions as an essential charge relay, oxidizing the catalytic Mn₄CaO₅ cluster on each of four photo-oxidation reactions. In Escherichia coli class 1a RNR, the β2 subunit contains the radical initiator, Y122O•, which is reversibly reduced and oxidized in long range electron transfer with the α2 subunit. In the isolated E. coli β2 subunit, Y122O• is a stable radical, but Y122O• is activated for rapid PCET in an α2β2 substrate/effector complex. Recent results concerning the structure and function of YD, YZ, and Y122 are reviewed here. Comparison is made to recent results derived from bioengineered proteins and biomimetic compounds, in which tyrosine-based charge transfer mechanisms have been investigated. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

Full-dimensional potentials and state couplings and multidimensional tunneling calculations for the photodissociation of phenol

Full-dimensional potentials and state couplings were developed for the photodissociation of phenol. We also present multidimensional tunneling calculations at the transition state on the shoulder of the first conical intersection.

Redox-linked conformational control of proton-coupled electron transfer: Y122 in the ribonucleotide reductase β2 subunit

Tyrosyl radicals play essential roles in biological proton-coupled electron transfer (PCET) reactions. Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides and is vital in DNA replication in all organisms. Class Ia RNRs consist of α2 and β2 homodimeric subunits. In class Ia RNR, such as the E. coli enzyme, an essential tyrosyl radical (Y122O(•))-diferric cofactor is located in β2. Although Y122O(•) is extremely stable in free β2, Y122O(•) is highly reactive in the quaternary substrate-α2β2 complex and serves as a radical initiator in catalytic PCET between β2 and α2. In this report, we investigate the structural interactions that control the reactivity of Y122O(•) in a model system, isolated E. coli β2. Y122O(•) was reduced with hydroxyurea (HU), a radical scavenger that quenches the radical in a clinically relevant reaction. In the difference FT-IR spectrum, associated with this PCET reaction, amide I (CO) and amide II (CN/NH) bands were observed. Specific (13)C-labeling of the tyrosine C1 carbon assigned a component of these bands to the Y122-T123 amide bond. Comparison to density functional calculations on a model dipeptide, tyrosine-threonine, and structural modeling demonstrated that PCET is associated with a Y122 rotation and a 7.2 Å translation of the Y122 phenolic oxygen. To test for the functional consequences of this structural change, a proton inventory defined the origin of the large solvent isotope effect (SIE = 16.7 ± 1.0 at 25 °C) on this reaction. These data suggest that the one-electron, HU-mediated reduction of Y122O(•) is associated with two, rate-limiting (full or partial) proton transfer reactions. One is attributable to HU oxidation (SIE = 11.9, net H atom transfer), and the other is attributable to coupled, hydrogen-bonding changes in the Y122O(•)-diferric cofactor (SIE = 1.4). These results illustrate the importance of redox-linked changes to backbone and ring dihedral angles in high potential PCET and provide evidence for rate-limiting, redox-linked hydrogen-bonding interactions between Y122O(•) and the iron cluster.

Substituent effects in the absorption spectra of phenol radical species: origin of the redshift caused by 3,5-dimethoxyl substitution

The ground-state equilibrium geometries, electronic structures and vertical excitation energies of methyl- and methoxyl-substituted phenol radical cations and phenoxyl radicals have been investigated using time-dependent density-functional theory (namely TD-B3LYP) and complete-active-space second-order perturbation theory (CASPT2). The "anomalous" large redshifts of the absorption maxima of the phenol radical species observed in the ultraviolet-visible spectral region upon di-meta-methoxyl substitution are reproduced by the calculations. Furthermore, these "anomalous" shifts which were unexplained to date can be rationalized on the basis of a qualitative molecular orbital perturbation analysis.

Proton Coupled Electron Transfer and Redox Active Tyrosines: Structure and Function of the Tyrosyl Radicals in Ribonucleotide Reductase and Photosystem II

Proton coupled electron transfer (PCET) reactions are important in many biological processes. Tyrosine oxidation/reduction can play a critical role in facilitating these reactions. Two examples are photosystem II (PSII) and ribonucleotide reductase (RNR). RNR is essential in DNA synthesis in all organisms. In E. coli RNR, a tyrosyl radical, Y122(•), is required as a radical initiator. Photosystem II (PSII) generates molecular oxygen from water. In PSII, an essential tyrosyl radical, YZ(•), oxidizes the oxygen evolving center. However, the mechanisms, by which the extraordinary oxidizing power of the tyrosyl radical is controlled, are not well understood. This is due to the difficulty in acquiring high-resolution structural information about the radical state. Spectroscopic approaches, such as EPR and UV resonance Raman (UVRR), can give new information. Here, we discuss EPR studies of PCET and the PSII YZ radical. We also present UVRR results, which support the conclusion that Y122 undergoes an alteration in ring and backbone dihedral angle when it is oxidized. This conformational change results in a loss of hydrogen bonding to the phenolic oxygen. Our analysis suggests that access of water is an important factor in determining tyrosyl radical lifetime and function. TOC graphic.