Showing papers on "Hydrogen atom abstraction published in 2008"

On the mechanism of low-temperature water gas shift reaction on copper.

Abstract: Periodic, self-consistent density functional theory (DFT-GGA) calculations are used to investigate the water gas shift reaction (WGSR) mechanism on Cu(111). The thermochemistry and activation energy barriers for all the elementary steps of the commonly accepted redox mechanism, involving complete water activation to atomic oxygen, are presented. Through our calculations, we identify carboxyl, a new reactive intermediate, which plays a central role in WGSR on Cu(111). The thermochemistry and activation energy barriers of the elementary steps of a new reaction path, involving carboxyl, are studied. A detailed DFT-based microkinetic model of experimental reaction rates, accounting for both the previous and the new WGSR mechanism show that, under relevant experimental conditions, (1) the carboxyl-mediated route is the dominant path, and (2) the initial hydrogen abstraction from water is the rate-limiting step. Formate is a stable “spectator” species, formed predominantly through CO2 hydrogenation. In addition...

A Valence Bond Modeling of Trends in Hydrogen Abstraction Barriers and Transition States of Hydroxylation Reactions Catalyzed by Cytochrome P450 Enzymes

Abstract: The paper outlines the fundamental factors that govern the mechanisms of alkane hydroxylation by cytochrome P450 and the corresponding barrier heights during the hydrogen abstraction and radical rebound steps of the process. This is done by a combination of density functional theory calculations for 11 alkanes and valence bond (VB) modeling of the results. The energy profiles and transition states for the various steps are reconstructed using VB diagrams (Shaik, S. S. J. Am. Chem. Soc. 1981, 103, 3692–3701. Shaik, S.; Shurki, A. Angew. Chem. Int. Ed. 1999, 38, 586–625.) and the DFT barriers are reproduced by the VB model from raw data based on C−H bond energies. The model explains a variety of other features of P450 hydroxylations: (a) the nature of the polar effect during hydrogen abstraction, (b) the difference between the activation mechanisms leading to the FeIV vs the FeIII electromers, (c) the difference between the gas phase and the enzymatic reaction, and (d) the dependence of the rebound barrier ...

Complexes of Borane and N-Heterocyclic Carbenes: A New Class of Radical Hydrogen Atom Donor

Abstract: Calculations suggest that complexes of borane with N-heterocyclic carbenes (NHC) have B-H bond dissocation energies more then 20 kcal/mol less than free borane, diborane, borane-THF, and related complexes. Values are in the range of popular radical hydrogen atom donors like tin hydrides (70-80 kcal/mol). The resulting prediction that NHC borane complexes could be used as radical hydrogen atom donors was verified by radical deoxygenations of xanthates by using either AIBN or triethylborane as initiator.

Thermal decomposition of methyl butanoate: ab initio study of a biodiesel fuel surrogate.

Abstract: In this paper, we report a detailed analysis of the breakdown kinetic mechanism for methyl butanoate (MB) using theoretical approaches. Electronic structures and structure-related molecular properties of reactants, intermediates, products, and transition states were explored at the BH&HLYP/cc-pVTZ level of theory. Rate constants for the unimolecular and bimolecular reactions in the temperature range of 300−2500 K were calculated using Rice−Ramsperger−Kassel−Marcus and transition state theories, respectively. Thirteen pathways were identified leading to the formation of small compounds such as CH3, C2H3, CO, CO2, and H2CO. For the initial formation of MB radicals, H, CH3, and OH were considered as reactive radicals participating in hydrogen abstraction reactions. Kinetic simulation results for a high temperature pyrolysis environment show that MB radicals are mainly produced through hydrogen abstraction reactions by H atoms. In addition, the C(O)OCH3 = CO + CH3O reaction is found to be the main source of C...

Reaction of phenols with the 2,2-diphenyl-1-picrylhydrazyl radical. Kinetics and DFT calculations applied to determine ArO-H bond dissociation enthalpies and reaction mechanism.

Abstract: The formal H-atom abstraction by the 2,2-diphenyl-1-picrylhydrazyl (dpph(*)) radical from 27 phenols and two unsaturated hydrocarbons has been investigated by a combination of kinetic measurements in apolar solvents and density functional theory (DFT). The computed minimum energy structure of dpph(*) shows that the access to its divalent N is strongly hindered by an ortho H atom on each of the phenyl rings and by the o-NO(2) groups of the picryl ring. Remarkably small Arrhenius pre-exponential factors for the phenols [range (1.3-19) x 10(5) M(-1) s(-1)] are attributed to steric effects. Indeed, the entropy barrier accounts for up to ca. 70% of the free-energy barrier to reaction. Nevertheless, rate differences for different phenols are largely due to differences in the activation energy, E(a,1) (range 2 to 10 kcal/mol). In phenols, electronic effects of the substituents and intramolecular H-bonds have a large influence on the activation energies and on the ArO-H BDEs. There is a linear Evans-Polanyi relationship between E(a,1) and the ArO-H BDEs: E(a,1)/kcal x mol(-1) = 0.918 BDE(ArO-H)/kcal x mol(-1) - 70.273. The proportionality constant, 0.918, is large and implies a "late" or "product-like" transition state (TS), a conclusion that is congruent with the small deuterium kinetic isotope effects (range 1.3-3.3). This Evans-Polanyi relationship, though questionable on theoretical grounds, has profitably been used to estimate several ArO-H BDEs. Experimental ArO-H BDEs are generally in good agreement with the DFT calculations. Significant deviations between experimental and DFT calculated ArO-H BDEs were found, however, when an intramolecular H-bond to the O(*) center was present in the phenoxyl radical, e.g., in ortho semiquinone radicals. In these cases, the coupled cluster with single and double excitations correlated wave function technique with complete basis set extrapolation gave excellent results. The TSs for the reactions of dpph(*) with phenol, 3- and 4-methoxyphenol, and 1,4-cyclohexadiene were also computed. Surprisingly, these TS structures for the phenols show that the reactions cannot be described as occurring exclusively by either a HAT or a PCET mechanism, while with 1,4-cyclohexadiene the PCET character in the reaction coordinate is much better defined and shows a strong pi-pi stacking interaction between the incipient cyclohexadienyl radical and a phenyl ring of the dpph(*) radical.

The unusual reaction of semiquinone radicals with molecular oxygen

Abstract: Hydroquinones (benzene-1,4-diols) are naturally occurring chain-breaking antioxidants, whose reactions with peroxyl radicals yield 1,4-semiquinone radicals. Unlike the 1,2-semiquinone radicals derived from catechols (benzene-1,2-diols), the 1,4-semiquinone radicals do not always trap another peroxyl radical, and instead the stoichiometric factor of hydroquinones varies widely between 0 and 2 as a function of ring-substitution and reaction conditions. This variable antioxidant behavior has been attributed to the competing reaction of the 1,4-semiquinone radical with molecular oxygen. Herein we report the results of experiments and theoretical calculations focused on understanding this key reaction. Our experiments, which include detailed kinetic and mechanistic investigations by laser flash photolysis and inhibited autoxidation studies, and our theoretical calculations, which include detailed studies of the reactions of both 1,4-semiquinones and 1,2-semiquinones with O2, provide many important insights. They show that the reaction of O2 with 2,5-di-tert-butyl-1,4-semiquinone radical (used as model compound) has a rate constant of 2.4 +/- 0.9 x 10(5) M-1 s-1 in acetonitrile and as high as 2.0 +/- 0.9 x 10(6) M-1 s-1 in chlorobenzene, i.e., similar to that previously reported in water at pH approximately 7. These results, considered alongside our theoretical calculations, suggest that the reaction occurs by an unusual hydrogen atom abstraction mechanism, taking place in a two-step process consisting first of addition of O2 to the semiquinone radical and second an intramolecular H-atom transfer concerted with elimination of hydroperoxyl to yield the quinone. This reaction appears to be much more facile for 1,4-semiquinones than for their 1,2-isomers.

Rate and Selectivity Enhancements Mediated by OH Radicals in the Oxidative Coupling of Methane Catalyzed by Mn/Na2WO4/SiO2†

Abstract: ion increases the {(k1 + k 0 2)/(k 0 3 +k 0 4)} ratios markedly, from 0.03 for surface-mediated pathways to 0.14 for OHmediated pathways (Table 1). H2O also leads to lower k 0 5/k 0 1 ratios (4.3 without H2O; 0.63 for OH-mediated pathways; Table 1), which is consistent with the preferential enhancement of CH4 over C2H4 activation rates by OH-mediated routes. Surfaces oxidize C2H4 (k 0 5) more effectively than CH4 (k 0 2) or C2H6 (k 0 4), in spite of the strong C H bonds in C2H4 (463 kJmol ), apparently because C2H4 is strongly adsorbed. [23] OH-mediated pathways do not involve adsorption and lead to k5/k 0 1 values below unity (0.63). These ratios faithfully reflect the stronger C H bonds in C2H4, without compensation by adsorption energies. In fact, these previously unrecognized OH-mediated pathways are essential to achieving the maximumC2 yields reported (up to 26%), which could not be reached with contributions from surface-mediated pathways only. We have achieved C2+ yields of 26% by replenishing O2 after it is depleted in order to avoid explosive reactant mixtures (Figure 4). These yields match the highest values Figure 2. Plot of incremental differential CH4 conversion rate (obtained from measured differences in rates with and without H2O) vs. P 1=4 O2 P H2O. *: steady state reaction; &: H2O added. The arrows indicate the increase in contact time (0.02 g, 1073 K, unit volume: 550–650 mL, 10.7 kPa CH4, CH4/O2 6:1, 0.4 kPa H2O (when added), 101 kPa total pressure, balance He). Table 1: First-order rate constants (mmolg 1 s 1 kPa ) for the steps shown in Scheme 1 (0.02 g, 1073 K, 10.7 kPa CH4, 1.7 kPa O2, 0.4 kPa C2H6/ C2H4, 0 or 0.4 kPa H2O). Rate constant Surface-mediated OH-mediated k1 0.05 0.16 k2 (k 0 2/k 0 1) 0.01 (0.25) 0.02 (0.11) k3 [b] (k3/k 0 1) 1.7 (33) 1.1 (6.8) k4 [b] (k4/k 0 1) 0.14 (2.7) 0.12 (0.73) k5 [c] (k5/k 0 1) 0.22 (4.3) 0.10 (0.63) (k1+ k 0 2)/(k 0 3+ k 0 4) 0.03 0.14 [a] Calculated from rate differences with and without H2O; [b] calculated from CH4/O2/C2H6(/H2O) mixtures; [c] calculated from CH4/O2/ C2H4(/H2O) mixtures. Figure 3. Ratios of rate constants kRCH4/k R C2H6 for H-abstraction from CH4 relative to C2H6 for various abstracting entities (R) vs. DH for the recombination reaction R + H ! R H at 1073 K. Angewandte Chemie 7691 Angew. Chem. Int. Ed. 2008, 47, 7689 –7693 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim www.angewandte.org reported previously. A kinetic model based on Scheme 1 and rate constants for surfaceand OH-mediated pathways (Table 1; see the Supporting Information for further details) accurately describes the measured yields and predicts a maximum possible C2 yield of 29%. Figure 4 shows that the rate constants for surface-mediated pathways, which prevail in the absence of H2O, cannot account for observed C2 yields and predict maximum values of only 15%. In summary, this study provides mechanistic evidence that OH-mediated C H bond activation pathways are essential for attaining practical yields and describing the evolution of C2 yields during catalytic reactions. The ability of oxide catalysts to generate equilibrium OH-radical concentrations provides opportunities to exploit pathways mediated by such radicals in related chemistries. Our data provide compelling evidence for the benefits of using more reactive species (or higher temperatures) to weaken the sensitivity of H-abstraction reactions to C H bond energies, a challenge and hurdle that limits the maximum attainable yields of the desired products in most practical applications of oxidation catalysis. Experimental Section SiO2 (Davison chemical, Silica Gel Grade 57) was impregnated with aqueous Mn(NO3)2 (50 wt.%, STREM Chemicals; 2 mLg 1 of SiO2) and the mixture dried in ambient air at 403 K for 5 h. This sample was then impregnated with an aqueous solution of Na2WO4·2H2O (99%, Sigma–Aldrich, 2 mLg 1 of SiO2) to give a sample containing 2 wt.% Mn and 5 wt.% Na2WO4. This sample was dried at 403 K for 5 h and then heated in flowing dry air (Praxair, UHP, 0.167 mLs ) at 1173 K (temperature increase: 0.033 Ks ) for 8 h. The samples were sieved to retain 0.25–0.35-mm aggregates. OCM rates and selectivities were measured in flow or recirculating batch reactors using a U-shaped quartz cell (4 mm I.D.). Samples (0.02 g) were mixed with quartz powder (0.5 g; Fluka, SiO2, 0.25–0.35 mm) and held onto quartz wool. The temperature was maintained with a Watlow controller (Series 982) coupled to a resistively heated furnace and measured with a type K thermocouple set outside the catalyst bed. CH4 (Praxair, 99.999%) and O2 (Praxair, 99.999%) were introduced with He (Praxair, 99.999%) as diluent. In batch experiments, the recirculation loop (275–650 mL) was evacuated to < 0.1 Pa before introducing the reactants, which were circulated with a graphite gear micropump (> 2.5 mLs ). H2O was removed from the reactor loop using a dry ice/acetone trap, which does not condense other products. Reactant and product concentrations were measured with an HP5890 gas chromatograph using a Carbosieve SII packed column (Supelco, 3.2 mmJ2 m) with thermal conductivity detection and a HP-PLOT Q capillary column (Agilent, 0.32 mmJ30 m) with flame ionization detection. Differential rates were obtained from time-derivatives of CH4 concentration profiles vs. time measured in batch reactors after regression to a polynomial fit. Selectivities are reported on a carbon basis as cumulative (integral) values. CD4 (Isotec, 99 atom%-D) and D2O (Cambridge Isotope Laboratories, Inc., 99.9%) were used to measure kinetic isotope effects. Tracer studies used labeled CH4 (Isotec, 99 atom%C) in the presence of C2H6 (Praxair, 99.999%) or C2H4 (Praxair, 99.999%). These isotopic measurements were carried out in a batch recirculating reactor equipped with two HP5890 gas chromatographs, with combined thermal conductivity, flame ionization and mass selective detectors. The latter was connected to an HP-PLOT Q capillary column used for isotopic detection. Received: June 4, 2008 Published online: September 2, 2008 .

Oxidative reactivity difference among the metal oxo and metal hydroxo moieties: pH dependent hydrogen abstraction by a manganese(IV) complex having two hydroxide ligands.

Abstract: Clarifying the difference in redox reactivity between the metal oxo and metal hydroxo moieties for the same redox active metal ion in identical structures and oxidation states, that is, Mn+═O and Mn+−OH, contributes to the understanding of nature’s choice between them (Mn+═O or Mn+−OH) as key active intermediates in redox enzymes and electron transfer enzymes, and provides a basis for the design of synthetic oxidation catalysts. The newly synthesized manganese(IV) complex having two hydroxide ligands, [Mn(Me2EBC)2(OH)2](PF6)2, serves as the prototypic example to address this issue, by investigating the difference in the hydrogen abstracting abilities of the MnIV═O and MnIV−OH functional groups. Independent thermodynamic evaluations of the O−H bond dissociation energies (BDEOH) for the corresponding reduction products, MnIII−OH and MnIII−OH2, reveal very similar oxidizing power for MnIV═O and MnIV−OH (83 vs 84.3 kcal/mol). Experimental tests showed that hydrogen abstraction proceeds at reasonable rates for...

Accurate Benchmark Calculation of the Reaction Barrier Height for Hydrogen Abstraction by the Hydroperoxyl Radical from Methane. Implications for CnH2n+2 where n = 2 → 4

Abstract: The CH4 + HO2(*) reaction is studied by using explicitly correlated coupled-cluster theory with singles and doubles (CCSD-R12) in a large 19s14p8d6f4g3h basis (9s6p4d3f for H) to approach the basis-set limit at the coupled-cluster singles-doubles level. A correction for connected triple excitations is obtained from the conventional CCSD(T) coupled-cluster approach in the correlation-consistent quintuple-zeta basis (cc-pV5Z). The highly accurate results for the methane reaction are used to calibrate the calculations of the hydroperoxyl-radical hydrogen abstraction from other alkanes. For the alkanes C(n)H(2n+2) with n = 2 --> 4, the reactions are investigated at the CCSD(T) level in the correlation-consistent triple-zeta (cc-pVTZ) basis. The results are adjusted to the benchmark methane reaction and compared with those from other approaches that are commonly used in the field such as CBS-QB3, CBS-APNO, and density functional theory. Rate constants are computed in the framework of transition state theory, and the results are compared with previous values available.

Effect of external electric fields on the C-H bond activation reactivity of nonheme iron-oxo reagents.

Abstract: The effect of external electric fields (EFs) on the reactivity of nonheme iron(IV)−oxo species toward alkanes is investigated computationally using density functional theory. It is shown that an external EF changes the energy landscape of the process and thereby impacts the mechanisms, rates, and selectivities of the reactions, in a manner dependent on the nature of the iron(IV)−oxo/alkane pair. When the iron−oxo species is a good electron acceptor, like N4PyFeO2+, and the alkane is a good electron donor, like toluene, the application of the EF changes the mechanism from hydrogen abstraction to electron transfer. With cyclohexane, which is a poorer electron donor than toluene, the EF promotes hydride transfer and generates a carbocation. However, in the reaction between a poorer electron acceptor TMC(SR)FeO+ and cyclohexane, the EF preserves the hydrogen abstraction/rebound mechanism but improves its features by lowering the barriers for both the C−H activation and rebound steps; larger effects were obser...

Copper-Catalyzed Oxidative Coupling of Benzylic C−H Bonds with 1,3-Dicarbonyl Compounds

Abstract: A copper-catalyzed oxidative coupling of benzylic C-H bonds with 1,3-dicarbonyl compounds is described. The reaction utilizes an inexpensive copper catalyst-oxidant system that is suitable for the coupling of a range of benzylic C-H bonds with various 1,3-dicarbonyl compounds. Kinetic isotope studies support a mechanism involving a benzylic hydrogen abstraction.

Sustainable radical reduction through catalytic hydrogen atom transfer.

Abstract: A system with coupled catalytic cycles is described that allows radical reduction by hydrogen atom abstraction from rhodium hydrides. These intermediates are generated from H2 activation by Wilkinson’s catalyst. Radical generation is carried out by titanocene-catalyzed electron transfer to epoxides.

The photochemistry of human retinal lipofuscin as studied by EPR.

Abstract: Fluorescent material generated in the human retina accumulates within lipofuscin (HLF) granules of the retinal pigment epithelium (RPE) during aging. We have been investigating the possible light-induced contribution of these fluorophores to various diseases including age-related macular degeneration. Our studies have shown that some of the fluorescent components of HLF are products of the reaction of retinaldehyde with ethanolamine and that synthetic mixtures of this reaction can serve as a useful model for photophysical studies. Previous research by us has demonstrated that irradiation of either natural or synthetic lipofuscin resulted in the formation of a triplet state and possibly a free radical. Here EPR studies were performed to verify the formation of that radical. The UV irradiation of either synthetic or natural human retinal lipofuscin extracts in oxygen-free methanol led to the formation of a 5,5-dimethylpyrroline-N-oxide (DMPO) spin-trapped carbon-centered radical resulting from either hydrogen atom or electron abstraction from solvent molecules. In the presence of oxygen superoxide was formed, which was observed as a DMPO adduct. It is concluded that certain components of the chloroform-soluble fluorophores of human RPE lipofuscin granules and the fluorescent reaction products of retinaldehyde and ethanolamine are photophysically similar but not the same. Electron or hydrogen abstraction from a substrate by these fluorophores in vivo and the resulting radical products may contribute to the age-related decline of RPE function and blue light damage in the retina.

Oxidative conversion of C1–C3 alkanes by vanadium oxide catalysts. DFT results and their accuracy†

Abstract: Elementary steps in the oxidative conversion of methane, ethane, and propane by supported vanadium oxide species are studied by density functional theory, specifically B3LYP. Two models are adopted, namely OV(OH)3 and OVSi7O12H7, which yield similar energy profiles. The initial and rate-determining step is hydrogen abstraction. Within the C1–C3 series, energy barriers and reaction energies follow the same trend as the CH bond strength in the different alkanes. For methane, only methanol formation is possible whereas for ethane and propane, oxidative dehydrogenation yields the corresponding alkenes. Single point CCSD(T)/TZVP calculations are used to assess the B3LYP error. For the barrier of the initial hydrogen abstraction the B3LYP error is larger than usual, −40 to −60 kJ/mol. With the non-hybrid BP86 and PBE functionals even larger errors occur and the potential energy surface is qualitatively different. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Electronic description of four flavonoids revisited by DFT method

Abstract: Structural and electronic characteristics of four flavonoids, namely quercetin, luteolin, catechin and taxifolin, have been revisited by means of B3LYP density functional. Rotation energy of the catechol moieties together with HOMO–LUMO, dipole moments analyses are reported for each flavonoid. Deprotonation and hydrogen abstraction energies of the O3H and O4′H hydroxyl groups are compared and analyzed with the help of an electronic description for each structure. Our results put forward the significant role of π-delocalization upon stabilization but have also shown that inductive effects play a major role in the stabilization of deprotonated forms. Inspection of the charge transfer together with analysis of a simple model of catechol has also demonstrated the relative independence of each structural motif when hydrogen abstraction processes are considered.

Theoretical Explanation of Nonexponential OH Decay in Reactions with Benzene and Toluene under Pseudo-First-Order Conditions

Abstract: OH radical reactions with benzene and toluene have been studied in the 200−600 K temperature range via the CBS-QB3 quantum chemistry method and conventional transition-state theory. Our study takes into account all possible hydrogen abstraction and OH-addition channels, including ipso addition. Reaction rates have been obtained under pseudo-first-order conditions, with aromatic concentrations in large excess compared to OH concentrations, which is the case in the reported experiments as well as in the atmosphere. The reported results are in excellent agreement with the experimental data and reproduce the discontinuity in the Arrhenius plots in the 300 K < T < 400 K temperature range. They support the suggestion that the observed nonexponential OH decay is caused by the existence of competing addition and abstraction channels and by the decomposition of thermalized OH−aromatic adducts back to reactants. We also find that the low-temperature onset of the nonexponential decay depends on the concentration of ...

Branching Ratios of Aliphatic Amines + OH Gas-Phase Reactions: A Variational Transition-State Theory Study.

Abstract: A theoretical study on the mechanism of the OH + aliphatic amines reactions is presented. Geometry optimization and frequencies calculations have been performed at the BHandHLYP/6-311++G(2d,2p) level of theory for all stationary points. Energy values have been improved by single-point calculations at the above geometries using CCSD(T) and the same basis set. All the possible hydrogen abstraction channels have been modeled, involving the rupture of C-H and N-H bonds. It was found that as the temperature decreases the contributions of the channels involving NH sites to the overall reaction also decrease, suggesting that for upper layers in the troposphere these channels become less important. Their percentage contributions to the overall reaction, at 298 K, were found to be about 20%, 2%, and 48% for methylamine, ethlylamine, and dimethylamine, respectively.

Kinetic Monte Carlo Studies of Hydrogen Abstraction from Graphite

Abstract: We present Monte Carlo simulations on Eley-Rideal abstraction reactions of atomic hydrogen chemisorbed on graphite. The results are obtained via a hybrid approach where energy barriers derived from density functional theory calculations are used as input to Monte Carlo simulations. By comparing with experimental data, we discriminate between contributions from different Eley-Rideal mechanisms. A combination of two different mechanisms yields good quantitative and qualitative agreement between the experimentally derived and the simulated Eley-Rideal abstraction cross sections and surface configurations. These two mechanisms include a direct Eley-Rideal reaction with fast diffusing H atoms and a dimer mediated Eley-Rideal mechanism with increased cross section at low coverage. Such a dimer mediated Eley-Rideal mechanism has not previously been proposed and serves as an alternative explanation to the steering behavior often given as the cause of the coverage dependence observed in Eley-Rideal reaction cross sections.

Theoretical Prediction of a Perepoxide Intermediate for the Reaction of Singlet Oxygen with trans-Cyclooctene Contrasts with the Two-Step No-Intermediate Ene Reaction for Acyclic Alkenes

Abstract: B3LYP/6-31G* and CASMP2 calculations have been employed to study the ene reaction of singlet oxygen with trans-cyclooctene. These methods predict that the reaction involves a perepoxide intermediate, whereas alkenes such as tetramethylethylene are predicted by the same methods to occur by a two-step no-intermediate mechanism, with no perepoxide intermediate. The change in mechanism arises because the trans-cyclooctene imposes a substantial strain in the transition state for hydrogen abstraction. The perepoxide is formed through a polarized diradical intermediate that can lead to the observation of alkene isomerization. The polarized diradical also becomes a minimum because of the barrier to abstraction.

Mechanistic study on the reaction of a radical SAM dehydrogenase BtrN by electron paramagnetic resonance spectroscopy.

Abstract: BtrN is a radical SAM (S-adenosyl-l-methionine) enzyme that catalyzes the oxidation of 2-deoxy-scyllo-inosamine (DOIA) into 3-amino-2,3-dideoxy-scyllo-inosose (amino-DOI) during the biosynthesis of 2-deoxystreptamine (DOS) in the butirosin producer Bacillus circulans. Recently, we have shown that BtrN catalyzes the transfer of a hydrogen atom at C-3 of DOIA to 5′-deoxyadenosine, and thus, the reaction was proposed to proceed through the hydrogen atom abstraction by the 5′-deoxyadenosyl radical. In this work, the BtrN reaction was analyzed by EPR spectroscopy. A sharp double triplet EPR signal was observed when the EPR spectrum of the enzyme reaction mixture was recorded at 50 K. The spin coupling with protons partially disappeared by reaction with [2,2-2H2]DOIA, which unambiguously proved the observed signal to be a radical on C-3 of DOIA. On the other hand, the EPR spectrum of the [4Fe-4S] cluster of BtrN during the reaction showed a complex signal due to the presence of several species. Comparison of si...

Full dimensional time-dependent quantum dynamics study of the H + NH3 --> H2 + NH2 reaction.

Abstract: A rigorous full dimensional time-dependent wave packet method has been developed for the reactive scattering between an atom and a tetra-atomic molecule. The method has been applied to the hydrogen abstraction reaction H+NH(3)-> H(2)+NH(2). Initial state-selected total reaction probabilities are investigated for the reactions from the ground vibrational state and from four excited vibrational states of ammonia. The total reaction probabilities from two lowest "tunneling doublets" due to the inversion barrier for the umbrella bending motion of NH(3) and from two pairs of doubly degenerate vibrational states of NH(3) are also inspected. Integral cross sections and rate constants are calculated for the reaction from the ground state with the centrifugal-sudden approximation. The calculated results are compared with those from the previous seven dimensional calculations [M. Yang and J. C. Corchado, J. Chem. Phys. 126, 214312 (2007)]. This work shows that the full dimensional rate constants are a factor of 3 larger than the corresponding seven dimensional calculated values at T=200 K and are overall smaller than those obtained from the variational transition state theory in the whole temperature region. The work also reveals that nonreactive NH bonds of NH(3) cannot be treated as spectators due to the fact that three NH bonds are coupled with each other during the reaction process.

Modeling the photochemistry of the reference phototoxic drug lomefloxacin by steady-state and time-resolved experiments, and DFT and post-HF calculations.

Abstract: The irradiation in water of 1-ethyl-6,8-difluoro-7(3-methylpiperazino)3-quinolone-2-carboxylic acid (lomefloxacin), a bactericidal agent whose use is limited by its serious phototoxicity (and photomutagenicity in the mouse), leads to formation of the aryl cation in position eight that inserts into the 1-ethyl chain. Trapping of the cation was examined and it was found that chloride and bromide straightforwardly add in position eight, but with iodide and with pyrrole the 1-(2-iodoethyl) and the 1-[2-(2-pyrrolyl)ethyl] derivatives are formed. Flash photolysis reveals the triplet of lomefloxacin, a short-lived species (lambda max=370 nm, tau=40 ns) that generates the triplet cation (lambda max=480 nm, tau approximately 120 ns). The last intermediate is quenched both by halides and by pyrrole. DFT and post-HF methods have shown that the triplet is the lowest state of the cation (Delta G(ST)=13.3 kcal mol(-1)) and intersystem crossing (ISC) to the singlet has no role because a less endothermic process occurs, that is, intramolecular hydrogen abstraction from the N-ethyl chain (9.2 kcal mol(-1)) that finally leads to cyclization. The halides form weak complexes with the triplet cation (kq from 4.9 x 10(8) for Cl(-) to 7.0 x 10(9) m(-1) s(-1) for I-). With Cl(-) and Br(-) ISC occurs in the complex along with C8--X bond formation. However, this latter process is slow with bulky iodide and with neutral pyrrole, and in these cases moderately endothermic electron transfer (ca. 7 kcal mol(-1)) yielding the 8-quinolinyl radical occurs. Hydrogen exchange leads to a new radical on the 1-ethyl chain and to the observed products. These findings suggest that the mutagenic activity of the DNA-intercalated drug involves attack of the photogenerated cation to the heterocyclic bases.

Correlation of hydrogen-atom abstraction reaction efficiencies for aryl radicals with their vertical electron affinities and the vertical ionization energies of the hydrogen-atom donors.

Abstract: The factors that control the reactivities of aryl radicals toward hydrogen-atom donors were studied by using a dual-cell Fourier-transform ion cyclotron resonance mass spectrometer. Hydrogen-atom abstraction reaction efficiencies for two substrates, cyclohexane and isopropyl alcohol, were measured for 23 structurally different, positively charged aryl radicals, which included dehydrobenzenes, dehydronaphthalenes, dehydropyridines, and dehydro(iso)quinolines. A logarithmic correlation was found between the hydrogen-atom abstraction reaction efficiencies and the (calculated) vertical electron affinities (EA) of the aryl radicals. Transition state energies calculated for the reaction of three of the aryl radicals with isopropyl alcohol were found to correlate linearly with their (calculated) EAs. No correlation was found between the hydrogen-atom abstraction reaction efficiencies and the (calculated) enthalpy changes for the reactions. Measurement of the reaction efficiencies for the reactions of 15 differen...