Vibrations of the phenoxyl radical

Femtosecond IR spectroscopy of peroxycarbonate photodecomposition: S1-lifetime determines decarboxylation rate

The ultrafast photofragmentation of arylperoxycarbonates R-O-C(O)O-O-tert-butyl (R = naphthyl, phenyl) is studied using femtosecond UV excitation at 266 nm and mid-infrared broadband probe pulses to elucidate the dissociation mechanism. Our experiments show that the rate of fragmentation is determined by the S1-lifetime of the peroxide, i.e., the time constants of S1 decay and of CO2 and R-O* formation are identical. The fragmentation times are solvent dependent and for tert-butyl-2-naphthylperoxycarbonate (TBNC) vary from 25 ps in CH2Cl2 to 52 ps in n-heptane. In the case of the tert-butylphenylperoxycarbonate (TBPC) the decomposition takes 5.5 ps in CD2Cl2 and 12 ps in n-heptane. The CO2 fragment is formed vibrationally hot with an excess energy of about 5000 cm(-1). The hot CO2 spectra at high energy can be modeled assuming Boltzmann distributions with initial vibrational temperatures of ca. 2500 K which relax to ambient temperature with time constants of 280 ps in CCl4 and 130 ps in n-heptane. In CCl4 the relaxed spectra at 1.5 ns show 3.5% residual excitation in the n = 1 level of the asymmetric stretch vibration.

Normal modes of redox-active tyrosine: conformation dependence and comparison to experiment

Redox-active tyrosine residues play important roles in long-distance electron reactions in enzymes such as prostaglandin H synthase, ribonucleotide reductase, and photosystem II (PSII). Spectroscopic characterization of tyrosyl radicals in these systems provides a powerful experimental probe into the role of the enzyme in mediation of long-range electron transfer processes. Interpretation of such data, however, relies critically on first establishing a spectroscopic fingerprint of isotopically labeled tyrosinate and tyrosyl radicals in nonenzymatic environments. In this report, FT-IR results obtained from tyrosinate, tyrosyl radical (produced by ultraviolet photolysis of polycrystalline tyrosinate), and their isotopologues at 77 K are presented. Assignment of peaks and isotope shifts is aided by density-functional B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) calculations of tyrosine and tyrosyl radical in several different charge and protonation states. In addition, characterization of the potential energy surfaces of tyrosinate and tyrosyl radical as a function of the backbone and ring torsion angles provides detailed insight into the sensitivity of the vibrational frequencies to conformational changes. These results provide a detailed spectroscopic interpretation, which will elucidate the structures of redox-active tyrosine residues in complex protein environments. Specific application of these data is made to enzymatic systems.

Ultrafast Electron Diffraction: Structural Dynamics of Molecular Rearrangement in the NO Release from Nitrobenzene

Nitro compounds release NO, NO2, and other species, but neither the structures during the reactions nor the time scales are known. Ultrafast electron diffraction (UED) allowed the study of the NO release from nitrobenzene, and the molecular pathways and the structures of the transient species were identified. It was observed, in contrast to previous inferences, that nitric oxide and phenoxyl radicals are formed dominantly and that the time scale of formation is 8.8+/-2.2 ps. The structure of the phenoxyl radical was determined for the first time, and found to be quinoid-like. The mechanism proposed involves a repulsive triplet state, following intramolecular rearrangement. This efficient generation of NO may have important implications for the control of by-products in drug delivery and other applications.

Lignin radicals in the plant cell wall probed by Kerr-gated resonance Raman spectroscopy

Lignin radicals are crucial intermediates for lignin biosynthesis in the cell wall of vascular plants. In this work they were for the first time, to our knowledge, selectively observed in wood cell walls by laser-based Kerr-gated resonance Raman spectroscopy, and the observations were supported by density functional theory prediction of their vibrational properties. For dry wood cells a lignin radical Raman band is observed at 1,570 cm(-1) irrespective of species. For wet beech cells they were generated in situ and observed at 1,606 cm(-1). DFT/B3LYP/6-31+G(d) modeling results support that in beech they are formed from syringyl (S) phenolic moieties and in spruce from guaiacyl (G) phenolic moieties. The observed lignin radical band is predicted as G is approximately 1,597 cm(-1) and S is approximately 1,599 cm(-1), respectively, and is assigned the (Wilson notation) nu(8a) phenyl ring mode. The RR band probes lignin radical properties, e.g., spin density distribution, and these respond to charge polarization or hydrogen bonding to proximate water molecules. These observations can be crucial for an understanding of the factors that control cell wall structure during biosynthesis of vascular plants and demonstrate the unique potential of RR spectroscopy of lignin radicals.

Photoelectron Spectra and Ion Chemistry of Imidazolide†

The 351.1 nm photoelectron spectrum of imidazolide anion has been measured. The electron affinity (EA) of the imidazolyl radical is determined to be 2.613 +/- 0.006 eV. Vibrational frequencies of 955 +/- 15 and 1365 +/- 20 cm(-1) are observed in the spectrum of the (2)B1 ground state of the imidazolyl radical. The main features in the spectrum are well-reproduced by Franck-Condon simulation based on the optimized geometries and the normal modes obtained at the B3LYP/6-311++G(d,p) level of density functional theory. The two vibrational frequencies are assigned to totally symmetric modes with C-C and N-C stretching motions. Overtone peaks of an in-plane nontotally symmetric mode are observed in the spectrum and attributed to Fermi resonance. Also observed is the photoelectron spectrum of the anion formed by deprotonation of imidazole at the C5 position. The EA of the corresponding radical, 5-imidazolyl, is 1.992 +/- 0.010 eV. The gas phase acidity of imidazole has been determined using a flowing afterglow-selected ion tube; delta(acid)G298 = 342.6 +/- 0.4 and delta(acid)H298 = 349.7 +/- 0.5 kcal mol(-1). From the EA of imidazolyl radical and gas phase acidity of imidazole, the bond dissociation energy for the N-H bond in imidazole is determined to be 95.1 +/- 0.5 kcal mol(-1). These thermodynamic parameters for imidazole and imidazolyl radical are compared with those for pyrrole and pyrrolyl radical, and the effects of the additional N atom in the five-membered ring are discussed.

Infrared spectra of phenyl nitrite and phenoxyl radical-nitric oxide complex in solid argon

Infrared spectra and frequency assignment of two isomers of nitrobenzene, namely the phenyl nitrite C6H(5-)ONO molecule and the phenoxyl radical-nitric oxide complex C6H5O-NO, in solid argon are presented. The phenoxyl radical-nitric oxide complex was produced through UV light irradiation of nitrobenzene in low-temperature solid argon matrix. The complex rearranged to the more stable phenyl nitrite molecule on sample annealing. The aforementioned species were identified on the basis of isotopic IR studies with C6H(5-)(15)NO2 and C6D5NO2, as well as density functional theory calculations.

Vibrational spectroscopy to study the properties of redox-active tyrosines in photosystem II and other proteins

Tyrosine radicals play catalytic roles in essential metalloenzymes. Their properties--midpoint potential, stability...--or environment varies considerably from one enzyme to the other. To understand the origin of these properties, the redox tyrosines are studied by a number of spectroscopic techniques, including Fourier transform infrared (FTIR) and resonance Raman (RR) spectroscopy. An increasing number of vibrational data are reported for the (modified-) redox active tyrosines in ribonucleotide reductases, photosystem II, heme catalase and peroxidases, galactose and glyoxal oxidases, and cytochrome oxidase. The spectral markers for the tyrosinyl radicals have been recorded on models of (substituted) phenoxyl radicals, free or coordinated to metals. We review these vibrational data and present the correlations existing between the vibrational modes of the radicals and their properties and interactions formed with their environment: we present that the nu7a(C-O) mode of the radical, observed both by RR and FTIR spectroscopy at 1480-1515 cm(-1), is a sensitive marker of the hydrogen bonding status of (substituted)-phenoxyl and Tyr*, while the nu8a(C-C) mode may probe coordination of the Tyr* to a metal. For photosystem II, the information obtained by light-induced FTIR difference spectroscopy for the two redox tyrosines TyrD and TyrZ and their hydrogen bonding partners is discussed in comparison with those obtained by other spectroscopic methods.

Inactivation of Horseradish Peroxidase by Phenoxyl Radical Attack

To test the hypothesis that horseradish peroxidase (HRP) can be inactivated by phenoxyl radicals upon reaction with H(2)O(2)/phenol, we probed HRP-catalyzed phenol oxidation at various phenol/H(2)O(2) concentrations. To this end the total protein, phenolic product, active protein, and iron concentrations in the aqueous phase were determined by protein assay, phenol-(14)C isotopic labeling, resonance Raman and atomic absorption spectroscopy, respectively. Additionally, resonance Raman and FTIR measurements were carried out to probe possible structural changes of the enzyme during the reaction. The data obtained provide the first experimental support for the hypothesis that HRP can be inactivated by a phenoxyl radical attack. The heme macrocycle destruction involving deprivation of the heme iron occurs as a result of the reaction. An intermediate type of the active protein was observed by Raman difference spectra at low concentrations which features a stabilization of the quantum mixed state of the heme iron and a significant amount of phenoxylphenol-type oligomers in solution and probably also in the heme pocket. This work provides a basis for evaluating the relative contributions of different HRP inactivation mechanisms and is thus critical for optimizing engineering applications involving HRP reactions.