Science.gov

Sample records for radical reactions mechanistic

  1. Free radical scavenging reactions of sulfasalazine, 5-aminosalicylic acid and sulfapyridine: mechanistic aspects and antioxidant activity.

    PubMed

    Joshi, Ravi; Kumar, Sudheer; Unnikrishnan, M; Mukherjee, T

    2005-11-01

    Reactions of sulfasalazine (SAZ) and its metabolites, 5-aminosalicylic acid (5-ASA) and sulfapyridine (SP), with various oxidizing and reducing free radicals (hydroxyl, haloperoxyl, one-electron oxidizing, lipid peroxyl, glutathiyl, superoxide, tryptophanyl, etc.) have been studied to understand the mechanistic aspects of its action against free radicals produced during inflammation. Nanosecond pulse radiolysis technique coupled with transient spectrophotometry has been used for in situ generation of free radicals and to follow their reaction pathways. The transients produced in these reactions have been assigned and radical scavenging rate constants have been measured. In addition to scavenging of various primary and secondary free radicals by SAZ, 5-ASA and SP, 5-ASA has also been observed to efficiently scavenge radicals of biomolecules. 5-ASA has been found to be the active moiety of SAZ involved in the scavenging of oxidizing free radicals whereas reduction of SAZ produced molecular radical anion. The study suggests that free radical scavenging activity of 5-ASA may be a major path of pharmacological action of SAZ against inflammatory bowel diseases (IBD). PMID:16298742

  2. Kinetic and mechanistic studies of free-radical reactions in combustion

    SciTech Connect

    Tully, F.P.

    1993-12-01

    Combustion is driven by energy-releasing chemical reactions. Free radicals that participate in chain reactions carry the combustion process from reactants to products. Research in chemical kinetics enables us to understand the microscopic mechanisms involved in individual chemical reactions as well as to determine the rates at which they proceed. Both types of information are required for an understanding of how flames burn, why engines knock, how to minimize the production of pollutants, and many other important questions in combustion. In this program the authors emphasize accurate measurements over wide temperature ranges of the rates at which ubiquitous free radicals react with stable molecules. The authors investigate a variety of OH, CN, and CH + stable molecule reactions important to fuel conversion, emphasizing application of the extraordinarily precise technique of laser photolysis/continuous-wave laser-induced fluorescence (LP/cwLIF). This precision enables kinetic measurements to serve as mechanistic probes. Since considerable effort is required to study each individual reaction, prudent selection is critical. Two factors encourage selection of a specific reaction: (1) the rates and mechanisms of the subject reaction are required input to a combustion model; and (2) the reaction is a chemical prototype which, upon characterization, will provide fundamental insight into chemical reactivity, facilitate estimation of kinetic parameters for similar reactions, and constrain and test the computational limits of reaction-rate theory. Most studies performed in this project satisfy both conditions.

  3. Mechanistic study of the radical SAM-dependent amine dehydrogenation reactions.

    PubMed

    Ji, Xinjian; Liu, Wan-Qiu; Yuan, Shuguang; Yin, Yue; Ding, Wei; Zhang, Qi

    2016-08-18

    The radical SAM enzyme NosL catalyzes the conversion of l-Trp to 3-methyl-2-indolic acid, and this reaction is initiated by the 5'-deoxyadenosyl (dAdo) radical-mediated hydrogen abstraction from the l-Trp amino group. We demonstrate here that when d-Trp was used in the NosL reaction, hydrogen abstraction occurs promiscuously at both the amino group and Cα of d-Trp. These results inspired us to establish the detailed mechanism of l-Trp amine dehydrogenation catalyzed by a NosL mutant, and to engineer a novel radical SAM-dependent l-Tyr amine dehydrogenase from the thiamine biosynthesis enzyme ThiH. PMID:27492649

  4. Atmospheric chemical reactions of monoethanolamine initiated by OH radical: mechanistic and kinetic study.

    PubMed

    Xie, Hong-Bin; Li, Chao; He, Ning; Wang, Cheng; Zhang, Shaowen; Chen, Jingwen

    2014-01-01

    Monoethanolamine (MEA) is a benchmark and widely utilized solvent in amine-based postcombustion CO2 capture (PCCC), a leading technology for reducing CO2 emission from fossil fuel power plants. The large-scale implementation of PCCC would lead to inevitable discharges of amines to the atmosphere. Therefore, understanding the kinetics and mechanisms of the transformation of representative amine MEA in the atmosphere is of great significance for risk assessment of the amine-based PCCC. In this study, the H-abstraction reaction of MEA with ·OH, and ensuing reactions of produced MEA-radicals, including isomerization, dissociation, and bimolecular reaction MEA-radicals+O2, were investigated by quantum chemical calculation [M06-2X/aug-cc-pVTZ//M06-2X/6-311++G(d,p)] and kinetic modeling. The calculated overall rate constant [(7.27 × 10(-11)) cm(3) molecule(-1) s(-1)] for H-abstraction is in excellent agreement with the experimental value [(7.02 ± 0.46) × 10(-11) cm(3) molecule(-1) s(-1)]. The results show that the product branching ratio of NH2CH2 · CHOH (MEA-β) (43%) is higher than that of NH2 · CHCH2OH (MEA-α) (39%), clarifying that MEA-α is not an exclusive product. On the basis of the unveiled reaction mechanisms of MEA-radicals + O2, the proton transfer reaction mass spectrometry signal (m/z 60.044), not recognized in the experiment, was identified. PMID:24438015

  5. Mechanistic Enzymology of the Radical SAM Enzyme DesII

    PubMed Central

    2016-01-01

    DesII is a member of the radical SAM family of enzymes that catalyzes radical-mediated transformations of TDP-4-amino-4,6-didexoy-D-glucose as well as other sugar nucleotide diphosphates. Like nearly all radical SAM enzymes, the reactions begin with the reductive homolysis of SAM to produce a 5′-deoxyadenosyl radical which is followed by regiospecific hydrogen atom abstraction from the substrate. What happens next, however, depends on the nature of the substrate radical so produced. In the case of the biosynthetically relevant substrate, a radical-mediated deamination ensues; however, when this amino group is replaced with a hydroxyl, one instead observes dehydrogenation. The factors that govern the fate of the initially generated substrate radical as well as the mechanistic details underlying these transformations have been a key focus of research into the chemistry of DesII. This review will discuss recent discoveries pertaining to the enzymology of DesII, how it may relate to understanding other radical-mediated lyases and dehydrogenases and the working hypotheses currently being investigated regarding the mechanism of DesII catalysis.

  6. Catalytic Radical Domino Reactions in Organic Synthesis

    PubMed Central

    Sebren, Leanne J.; Devery, James J.; Stephenson, Corey R.J.

    2014-01-01

    Catalytic radical-based domino reactions represent important advances in synthetic organic chemistry. Their development benefits synthesis by providing atom- and step-economical methods to complex molecules. Intricate combinations of radical, cationic, anionic, oxidative/reductive, and transition metal mechanistic steps result in cyclizations, additions, fragmentations, ring-expansions, and rearrangements. This Perspective summarizes recent developments in the field of catalytic domino processes. PMID:24587964

  7. Free Radical Reactions in Food.

    ERIC Educational Resources Information Center

    Taub, Irwin A.

    1984-01-01

    Discusses reactions of free radicals that determine the chemistry of many fresh, processed, and stored foods. Focuses on reactions involving ascorbic acid, myoglobin, and palmitate radicals as representative radicals derived from a vitamin, metallo-protein, and saturated lipid. Basic concepts related to free radical structure, formation, and…

  8. Spectroscopic, steady-state kinetic, and mechanistic characterization of the radical SAM enzyme QueE, which catalyzes a complex cyclization reaction in the biosynthesis of 7-deazapurines

    PubMed Central

    McCarty, Reid M.; Krebs, Carsten; Bandarian, Vahe

    2013-01-01

    7-Carboxy-7-deazaguanine (CDG) synthase (QueE) catalyzes the complex heterocyclic radical-mediated conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) to CDG in the third step of the biosynthetic pathway to all 7-deazapurines. Here we present a detailed characterization of QueE from Bacillus subtilis to delineate the mechanism of conversion of CPH4 to CDG. QueE is a member of the radical S-adenosyl-L-methionine (SAM) superfamily, all of which use a bound [4Fe-4S]+ cluster to catalyze the reductive cleavage of SAM cofactor to generate methionine and a 5′-deoxyadenosyl radical (5′-dAdo•), which initiates enzymatic transformations requiring H-atom abstraction. The UV-visible, EPR, and Mössbauer spectroscopic features of the homodimeric QueE point to the presence of a single [4Fe-4S] cluster per monomer. Steady-state kinetic experiments indicate a Km of 20 ± 7 μM for CPH4 and kcat of 5.4 ± 1.2 min-1 for the overall transformation. The kinetically determined Kapp for SAM is 45 ± 1 μM. QueE is also magnesium-dependent and exhibits a Kapp for the divalent metal ion of 0.21 ± 0.03 mM. The SAM cofactor supports multiple turnovers, indicating that it is regenerated at the end of each catalytic cycle. The mechanism of rearrangement of QueE was probed with CPH4 isotopologs containing deuterium at C-6 or the two prochiral positions at C-7. These studies implicate 5′-dAdo• as initiating the ring contraction reaction catalyzed by QueE by abstraction of the H-atom from C-6 of CPH4. PMID:23194065

  9. Reaction Coordinates and Mechanistic Hypothesis Tests.

    PubMed

    Peters, Baron

    2016-05-27

    Reaction coordinates are integral to several classic rate theories that can (a) predict kinetic trends across conditions and homologous reactions, (b) extract activation parameters with a clear physical interpretation from experimental rates, and (c) enable efficient calculations of free energy barriers and rates. New trajectory-based rare events methods can provide rates directly from dynamical trajectories without a reaction coordinate. Trajectory-based frameworks can also generate ideal (but abstract) reaction coordinates such as committors and eigenfunctions of the master equation. However, rates and mechanistic insights obtained from trajectory-based methods and abstract coordinates are not readily generalized across simulation conditions or reaction families. We discuss methods for identifying physically meaningful reaction coordinates, including committor analysis, variational transition state theory, Kramers-Langer-Berezhkovskii-Szabo theory, and statistical inference methods that can use path sampling data to screen, mix, and optimize thousands of trial coordinates. Special focus is given to likelihood maximization and inertial likelihood maximization approaches. PMID:27090846

  10. Reaction Coordinates and Mechanistic Hypothesis Tests

    NASA Astrophysics Data System (ADS)

    Peters, Baron

    2016-05-01

    Reaction coordinates are integral to several classic rate theories that can (a) predict kinetic trends across conditions and homologous reactions, (b) extract activation parameters with a clear physical interpretation from experimental rates, and (c) enable efficient calculations of free energy barriers and rates. New trajectory-based rare events methods can provide rates directly from dynamical trajectories without a reaction coordinate. Trajectory-based frameworks can also generate ideal (but abstract) reaction coordinates such as committors and eigenfunctions of the master equation. However, rates and mechanistic insights obtained from trajectory-based methods and abstract coordinates are not readily generalized across simulation conditions or reaction families. We discuss methods for identifying physically meaningful reaction coordinates, including committor analysis, variational transition state theory, Kramers-Langer-Berezhkovskii-Szabo theory, and statistical inference methods that can use path sampling data to screen, mix, and optimize thousands of trial coordinates. Special focus is given to likelihood maximization and inertial likelihood maximization approaches.

  11. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues.

    PubMed

    Ji, Xinjian; Li, Yongzhen; Xie, Liqi; Lu, Haojie; Ding, Wei; Zhang, Qi

    2016-09-19

    Radical S-adenosyl-l-methionine (SAM) enzymes utilize a [4Fe-4S] cluster to bind SAM and reductively cleave its carbon-sulfur bond to produce a highly reactive 5'-deoxyadenosyl (dAdo) radical. In almost all cases, the dAdo radical abstracts a hydrogen atom from the substrates or from enzymes, thereby initiating a highly diverse array of reactions. Herein, we report a change of the dAdo radical-based chemistry from hydrogen abstraction to radical addition in the reaction of the radical SAM enzyme NosL. This change was achieved by using a substrate analogue containing an olefin moiety. We also showed that two SAM analogues containing different nucleoside functionalities initiate the radical-based reactions with high efficiencies. The radical adduct with the olefin produced in the reaction was found to undergo two divergent reactions, and the mechanistic insights into this process were investigated in detail. Our study demonstrates a promising strategy in expanding radical SAM chemistry, providing an effective way to access nucleoside-containing compounds by using radical SAM-dependent reactions. PMID:27573794

  12. The methylthiolation reaction mediated by the Radical-SAM enzymes

    PubMed Central

    Atta, Mohamed; Arragain, Simon; Fontecave, Marc; Mulliez, Etienne; Hunt, John F.; Luff, Jon D.; Forouhar, Farhad

    2014-01-01

    Over the past ten years, considerable progress has been made in our understanding of the mechanistic enzymology of the Radical-SAM enzymes. It is now clear that these enzymes appear to be involved in a remarkably wide range of chemically challenging reactions. This review article highlights mechanistic and structural aspects of the methylthiotransferases (MTTases) sub-class of the Radical-SAM enzymes. The mechanism of methylthio insertion, now observed to be performed by three different enzymes is an exciting unsolved problem. PMID:22178611

  13. Mechanistic studies of the radical SAM enzyme spore photoproduct lyase (SPL).

    PubMed

    Li, Lei

    2012-11-01

    Spore photoproduct lyase (SPL) repairs a special thymine dimer 5-thyminyl-5,6-dihydrothymine, which is commonly called spore photoproduct or SP at the bacterial early germination phase. SP is the exclusive DNA photo-damage product in bacterial endospores; its generation and swift repair by SPL are responsible for the spores' extremely high UV resistance. The early in vivo studies suggested that SPL utilizes a direct reversal strategy to repair the SP in the absence of light. The research in the past decade further established SPL as a radical SAM enzyme, which utilizes a tri-cysteine CXXXCXXC motif to harbor a [4Fe-4S] cluster. At the 1+ oxidation state, the cluster provides an electron to the S-adenosylmethionine (SAM), which binds to the cluster in a bidentate manner as the fourth and fifth ligands, to reductively cleave the CS bond associated with the sulfonium ion in SAM, generating a reactive 5'-deoxyadenosyl (5'-dA) radical. This 5'-dA radical abstracts the proR hydrogen atom from the C6 carbon of SP to initiate the repair process; the resulting SP radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired TpT. SAM is suggested to be regenerated at the end of each catalytic cycle; and only a catalytic amount of SAM is needed in the SPL reaction. The H atom source for the back donation step is suggested to be a cysteine residue (C141 in Bacillus subtilis SPL), and the H-atom transfer reaction leaves a thiyl radical behind on the protein. This thiyl radical thus must participate in the SAM regeneration process; however how the thiyl radical abstracts an H atom from the 5'-dA to regenerate SAM is unknown. This paper reviews and discusses the history and the latest progress in the mechanistic elucidation of SPL. Despite some recent breakthroughs, more questions are raised in the mechanistic understanding of this intriguing DNA repair enzyme. This article is part of a Special Issue

  14. Physiological aspects of free-radical reactions.

    PubMed Central

    Yamazaki, I; Tamura, M; Nakajima, R; Nakamura, M

    1985-01-01

    Enzymes which catalyze the formation of free radicals in vitro will catalyze similar reactions in vivo. We believe that the formation of some kinds of free radicals has definite physiological meanings in metabolism. In this sense, the enzymes forming such free radicals are concluded to be in evolutionally advanced states. Elaborated structure and function of enzymes such as horseradish peroxidase and microsomal flavoproteins support the idea. Deleterious and side reactions caused by free radicals are assumed to be minimized in vivo by localizing the reactions, but this assumption should be verified by future studies. PMID:3007098

  15. Towards mechanistic representations of SOA from BVOC + NO3 reactions

    EPA Science Inventory

    Monoterpene reaction with nitrate radicals is a significant source of organic aerosol in the southeast United States. This source of organic aerosol represents an anthropogenic control on biogenic organic aerosol since nitrate radicals result from NOx emissions and are generally ...

  16. Radical Cyclisation of α-Halo Aluminium Acetals: A Mechanistic Study.

    PubMed

    Bénéteau, Romain; Boussonnière, Anne; Rouaud, Jean-Christophe; Lebreton, Jacques; Graton, Jérôme; Jacquemin, Denis; Sebban, Muriel; Oulyadi, Hassan; Hamdoun, Ghanem; Hancock, Amber N; Schiesser, Carl H; Dénès, Fabrice

    2016-03-24

    α-Bromo aluminium acetals are suitable substrates for Ueno-Stork-like radical cyclisations affording γ-lactols and acid-sensitive methylene-γ-lactols in high yields. The mechanistic study herein sets the scope and limitation of this reaction. The influence of the halide (or chalcogenide) atom X (X=Cl, Br, I, SPh, SePh) in the precursors α-haloesters, as well as influence of the solvent and temperature was studied. The structure of the aluminium acetal intermediates resulting from the reduction of the corresponding α-haloesters has been investigated by low-temperature (13) C-INEPT diffusion-ordered NMR spectroscopy (DOSY) experiments and quantum calculations, providing new insights into the structures of these thermally labile intermediates. Oxygen-bridged dimeric structures with a planar Al2 O2 ring are proposed for the least hindered aluminium acetals, while monomeric structures seem to prevail for the most hindered species. A comparison against the radical cyclisation of aluminium acetals derived from allyl and propargyl alcohols with the parent Ueno-Stork has been made at the BHandHLYP/6-311++G(d,p) level of theory, highlighting mechanistic similarities and differences. PMID:26890896

  17. From formamide to purine: an energetically viable mechanistic reaction pathway.

    PubMed

    Wang, Jing; Gu, Jiande; Nguyen, Minh Tho; Springsteen, Greg; Leszczynski, Jerzy

    2013-02-28

    A step-by-step mechanistic pathway following the transformation of formamide to purine through a five-membered ring intermediate has been explored by density functional theory computations. The highlight of the mechanistic route detailed here is that the proposed pathway represents the simplest reaction pathway. All necessary reactants are generated from a single starting compound, formamide, through energetically viable reactions. Several important reaction steps are involved in this mechanistic route: formylation-dehydration, Leuckart reduction, five- and six-membered ring-closure, and deamination. On the basis of the study of noncatalytic pathways, catalytic water has been found to provide energetically viable step-by-step mechanistic pathways. Among these reaction steps, five-member ring-closure is the rate-determining step. The energy barrier (ca. 42 kcal/mol) of this rate-control step is somewhat lower than the rate-determining step (ca. 44 kcal/mol) for a pyrimidine-based pathway reported previously. The mechanistic pathway reported herein is less energetically demanding than for previously proposed routes to adenine. PMID:23347082

  18. [Mechanistic examination of organometallic electron transfer reactions: Annual report, 1989

    SciTech Connect

    Not Available

    1989-12-31

    Our mechanistic examination of electron transfer reactions between organometallic complexes has required data from our stopped-flow infrared spectrophotometer that was constructed in the first year. Our research on organometallic electron transfer reaction mechanisms was recognized by an invitation to the Symposium on Organometallic Reaction Mechanisms at the National ACS meeting in Miami. We have obtained a reasonable understanding of the electron transfer reactions between metal cations and anions and between metal carbonyl anions and metal carbonyl dimers. In addition we have begun to obtain data on the outer sphere electron transfer between metal carbonyl anions and coordination complexes and on reactions involving cluster anions.

  19. (Mechanistic examination of organometallic electron transfer reactions: Annual report, 1989)

    SciTech Connect

    Not Available

    1989-01-01

    Our mechanistic examination of electron transfer reactions between organometallic complexes has required data from our stopped-flow infrared spectrophotometer that was constructed in the first year. Our research on organometallic electron transfer reaction mechanisms was recognized by an invitation to the Symposium on Organometallic Reaction Mechanisms at the National ACS meeting in Miami. We have obtained a reasonable understanding of the electron transfer reactions between metal cations and anions and between metal carbonyl anions and metal carbonyl dimers. In addition we have begun to obtain data on the outer sphere electron transfer between metal carbonyl anions and coordination complexes and on reactions involving cluster anions.

  20. Unimolecular reaction dynamics of free radicals

    SciTech Connect

    Terry A. Miller

    2006-09-01

    Free radical reactions are of crucial importance in combustion and in atmospheric chemistry. Reliable theoretical models for predicting the rates and products of these reactions are required for modeling combustion and atmospheric chemistry systems. Unimolecular reactions frequently play a crucial role in determining final products. The dissociations of vinyl, CH2= CH, and methoxy, CH3O, have low barriers, about 13,000 cm-1 and 8,000 cm-1, respectively. Since barriers of this magnitude are typical of free radicals these molecules should serve as benchmarks for this important class of reactions. To achieve this goal, a detailed understanding of the vinyl and methoxy radicals is required. Results for dissociation dynamics of vinyl and selectively deuterated vinyl radical are reported. Significantly, H-atom scrambling is shown not to occur in this reaction. A large number of spectroscopic experiments for CH3O and CHD2O have been performed. Spectra recorded include laser induced fluorescence (LIF), laser excited dispersed fluorescence (LEDF), fluorescence dip infrared (FDIR) and stimulated emission pumping (SEP). Such results are critical for implementing dynamics experiments involving the dissociation of methoxy.

  1. Deuterium Substitution used as a Tool for Investigating Mechanisms of Gas-Phase Free-Radical Reactions

    NASA Technical Reports Server (NTRS)

    Wine, P. H.; Hynes, A. J.; Nicovich, J. M.

    1997-01-01

    Results are presented and discussed for a number of gas phase free radical reactions where H/D isotope effects provide valuable mechanistic insights. The cases considered are (1) the reactions of OH, NO3, and Cl with atmospheric reduced sulfur compounds, (2) the reactions of OH and OD with CH3CN and CD3CN, and (3) the reactions of alkyl radicals with HBr and DBr.

  2. Inhibition of hydroxyl radical reaction with aromatics by dissolved natural organic matter

    USGS Publications Warehouse

    Lindsey, M.E.; Tarr, M.A.

    2000-01-01

    Reaction of aromatic compounds with hydroxyl radical is inhibited by dissolved natural organic matter (NOM). The degree of inhibition is significantly greater than that expected based on a simple model in which aromatic compound molecules bound to NOM are considered to be unreactive. In this study, hydroxyl radical was produced at steady-state concentrations using Fenton chemistry (H2O2 + Fe2+ ??? Fe3+ + HO- + HO??). Suwannee River fulvic acid and humic acid were used as NOM. The most likely mechanism for the observed inhibition is that hydroxyl radical formation occurs in microenvironmental sites remote from the aromatic compounds. In addition to changes in kinetics, pyrene hydroxyl radical reaction also exhibited a mechanistic change in the presence of fulvic acid. The mechanism changed from a reaction that was apparently firstorder in pyrene to one that was apparently secondorder in pyrene, indicating that pyrene self-reaction may have become the dominant mechanism in the presence of fulvic acid. Dissolved NOM causes significant changes in the rate and mechanism of hydroxyl radical degradation of aromatic compounds. Consequently, literature rate constants measured in pure water will not be useful for predicting the degradation of pollutants in environmental systems. The kinetic and mechanistic information in this study will be useful for developing improved degradation methods involving Fenton chemistry.Reaction of aromatic compounds with hydroxyl radical is inhibited by dissolved natural organic matter (NOM). The degree of inhibition is significantly greater than that expected based on a simple model in which aromatic compounds molecules bounds to NOM are considered to be unreactive. In this study, hydroxyl radical was produced at steady-state concentrations using Fenton chemistry (H2O2 + Fe2+ ??? Fe3+ + HO- + HO??). Suwannee River fulvic acid and humic acid were used as NOM. The most likely mechanisms for the observed inhibition is that hydroxyl radical

  3. Structural and Mechanistic Aspects of Copper Catalyzed Atom Transfer Radical Polymerization

    NASA Astrophysics Data System (ADS)

    Pintauer, Tomislav; Matyjaszewski, Krzysztof

    During the past decade, atom transfer radical polymerization (ATRP) has had a tremendous impact on the synthesis of macromolecules with well-defined compositions, architectures, and functionalities. Structural features of copper(I) and copper(II) complexes with bidentate, tridentate, tetradentate, and multidentate nitrogen-based ligands commonly utilized in ATRP are reviewed and discussed. Additionally, recent advances in mechanistic understanding of copper-mediated ATRP are outlined.

  4. Mechanistic views on aromatic substitution reactions by gaseous cations.

    PubMed

    Fornarini, S

    1996-01-01

    Recent advances in the understanding of the gas-phase reaction of aromatics with cationic electrophiles in a thermally equilibrated domain are described. The overall substitution reaction is analyzed in terms of its elementary steps. Their contribution to the overall reactivity pattern is dissected by the use of selected systems, which allowed one to highlight the kinetic role of single elementary events. Mechanistic studies have focused on the structure and reactivity of covalent and non-covalent ionic intermediates, which display a rich chemistry and provide benchmark reactivity models. Particular interest has been devoted to proton transfer reactions, which may occur in either an intra- or intermolecular fashion in arenium intermediates. A quantitative study of their rates and associated kinetic isotope effects is reported. © 1997 John Wiley & Sons, Inc. Mass Spectrom Rev 15(6), 365-389, 1997. PMID:27082944

  5. Kinetic and mechanistic investigations of progesterone reaction with ozone.

    PubMed

    Barron, Emmanuelle; Deborde, Marie; Rabouan, Sylvie; Mazellier, Patrick; Legube, Bernard

    2006-06-01

    The removal of progesterone by ozone in aqueous solution was studied in this work. The absolute rate constant was evaluated and first by-products were identified. The reaction was studied in the 2.0-8.0 pH range and was found to be a second-order reaction, first-order relative to each compound concentration. The rate constant, determined by kinetic experiments in presence of an OH radical scavenger (tert-butanol), was independent of pH. The value was evaluated to be equal to 480+/-30 M(-1)s(-1) by two kinetic methods. Mass spectrometry analyses were performed to investigate primary degradation products generated by the reaction of ozone with progesterone. Two by-products were evidenced. According to these results, a degradation pathway of progesterone reacting with ozone was proposed. PMID:16725173

  6. Mechanistic Insight into the Photoredox Catalysis of Anti-Markovnikov Alkene Hydrofunctionalization Reactions

    PubMed Central

    2015-01-01

    We describe our efforts to understand the key mechanistic aspects of the previously reported alkene hydrofunctionalization reactions using 9-mesityl-10-methylacridinium (Mes-Acr+) as a photoredox catalyst. Importantly, we are able to detect alkene cation radical intermediates, and confirm that phenylthiyl radical is capable of oxidizing the persistent acridinyl radical in a fast process that unites the catalytic activity of the photoredox and hydrogen atom transfer (HAT) manifolds. Additionally, we present evidence that diphenyl disulfide ((PhS)2) operates on a common catalytic cycle with thiophenol (PhSH) by way of photolytic cleaveage of the disulfide bond. Transition structure analysis of the HAT step using DFT reveals that the activation barrier for H atom donation from PhSH is significantly lower than 2-phenylmalononitrile (PMN) due to structural reorganization. In the early stages of the reaction, Mes-Acr+ is observed to engage in off-cycle adduct formation, presumably as buildup of PhS− becomes significant. The kinetic differences between PhSH and (PhS)2 as HAT catalysts indicate that the proton transfer step may have significant rate limiting influence. PMID:25390821

  7. Formation of bromate in sulfate radical based oxidation: mechanistic aspects and suppression by dissolved organic matter.

    PubMed

    Lutze, Holger V; Bakkour, Rani; Kerlin, Nils; von Sonntag, Clemens; Schmidt, Torsten C

    2014-04-15

    Sulfate radical based oxidation is discussed being a potential alternative to hydroxyl radical based oxidation for pollutant control in water treatment. However, formation of undesired by-products, has hardly been addressed in the current literature, which is an issue in other oxidative processes such as bromate formation in ozonation of bromide containing water (US-EPA and EU drinking water standard of bromate: 10 μg L(-1)). Sulfate radicals react fast with bromide (k = 3.5 × 10(9) M(-1) s(-1)) which could also yield bromate as final product. The mechanism of bromate formation in aqueous solution in presence of sulfate radicals has been investigated in the present paper. Further experiments were performed in presence of humic acids and in surface water for investigating the relevance of bromate formation in context of pollutant control. The formation of bromate by sulfate radicals resembles the well described mechanism of the hydroxyl radical based bromate formation. In both cases hypobromous acid is a requisite intermediate. In presence of organic matter formation of bromate is effectively suppressed. That can be explained by formation of superoxide formed in the reaction of sulfate radicals plus aromatic moieties of organic matter, since superoxide reduces hypobromous acid yielding bromine atoms and bromide. Hence formation of bromate can be neglected in sulfate radical based oxidation at typical conditions of water treatment. PMID:24565691

  8. Revisiting the Radical Initiation Mechanism of the Diamine-Promoted Transition-Metal-Free Cross-Coupling Reaction.

    PubMed

    Zhang, Li; Yang, Huan; Jiao, Lei

    2016-06-01

    Radical chain reactions leading to C-C bond formation are widely used in organic synthesis, and initiation of the radical chain process usually requires thermolabile radical initiators. Recent studies on transition-metal-free cross-coupling reactions between aryl halides and arenes have demonstrated an unprecedented initiation system for radical chain reactions, where the combination of simple organic additives and a base was used in place of conventional radical initiators. Among them, the combination of N,N'-dimethylethylenediamine (DMEDA) and t-BuOK is one of the most efficient and representative reaction systems, and the radical initiation mechanism of this system has attracted considerable research interest. In this study, through the combination of kinetic studies, deuterium labeling experiments, and DFT calculations, the radical initiation mechanism of the diamine-promoted cross-coupling reaction was carefully reinvestigated. In light of the present study, a mechanistic network of radical initiation in the DMEDA/t-BuOK system was revealed, which differs dramatically from the previously realized single radical initiation pathway. In this mechanism, the diamine acts as a hydrogen atom donor and plays a dual role as both "radical amplifier" and "radical regulator" to initiate the radical chain process as well as to control the concentration of reactive radical species. This represents a rare example of a structurally simple molecule playing such a subtle role in the radical chain reaction system. The present study sheds some light on the novel radical initiation mode in transition-metal-free cross-coupling reactions following a base-promoted homolytic aromatic substitution (BHAS) mechanism, and may also help to understand the mechanism of relevant reactions. PMID:27228484

  9. Inactivation efficiencies of radical reactions with biologically active DNA

    NASA Astrophysics Data System (ADS)

    Lafleur, M. V. M.; Retèl, J.; Loman, H.

    Dilute aqueous solutions of biologically active θX174 DNA may serve as a simplified model system of the cell. Damage to the DNA after irradiation with γ-rays, may be ascribed to reactions with .OH, .H and e -aq or secondary radicals, arising from reactions of water radicals with added scavengers. Conversion of primary (water) radicals into secondary (scavenger) radicals leads to a considerable protection of the DNA, which, however, would have been larger if these secondary radicals did not contribute to DNA inactivation. The inactivation yield due to isopropanol or formate (secondary) radicals depends on dose rate as well as DNA concentration. Furthermore the inactivation efficiencies of the reactions of both the primary and the secondary radicals with single-stranded DNA could be established.

  10. Carbonylation reactions of alkyl iodides through the interplay of carbon radicals and Pd catalysts.

    PubMed

    Sumino, Shuhei; Fusano, Akira; Fukuyama, Takahide; Ryu, Ilhyong

    2014-05-20

    Numerous methods for transition metal catalyzed carbonylation reactions have been established. Examples that start from aryl, vinyl, allyl, and benzyl halides to give the corresponding carboxylic acid derivatives have all been well documented. In contrast, the corresponding alkyl halides often encounter difficulty. This is inherent to the relatively slow oxidative addition step onto the metal center and subsequent β-hydride elimination which causes isomerization of the alkyl metal species. Radical carbonylation reactions can override such problems of reactivity; however, carbonylation coupled to iodine atom transfer (atom transfer carbonylation), though useful, often suffers from a slow iodine atom transfer step that affects the outcome of the reaction. We found that atom transfer carbonylation of primary, secondary, and tertiary alkyl iodides was efficiently accelerated by the addition of a palladium catalyst under light irradiation. Stereochemical studies support a mechanistic pathway based on the synergic interplay of radical and Pd-catalyzed reaction steps which ultimately lead to an acylpalladium species. The radical/Pd-combined reaction system has a wide range of applications, including the synthesis of carboxylic acid esters, lactones, amides, lactams, and unsymmetrical ketones such as alkyl alkynyl and alkyl aryl ketones. The design of unique multicomponent carbonylation reactions involving vicinal C-functionalization of alkenes, double and triple carbonylation reactions, in tandem with radical cyclization reactions, has also been achieved. Thus, the radical/Pd-combined strategy provides a solution to a longstanding problem of reactivity involving the carbonylation of alkyl halides. This novel methodology expands the breadth and utility of carbonylation chemistry over either the original radical carbonylation reactions or metal-catalyzed carbonylation reactions. PMID:24712759

  11. Transverse flow reactor studies of the dynamics of radical reactions

    SciTech Connect

    Macdonald, R.G.

    1993-12-01

    Radical reactions are in important in combustion chemistry; however, little state-specific information is available for these reactions. A new apparatus has been constructed to measure the dynamics of radical reactions. The unique feature of this apparatus is a transverse flow reactor in which an atom or radical of known concentration will be produced by pulsed laser photolysis of an appropriate precursor molecule. The time dependence of individual quantum states or products and/or reactants will be followed by rapid infrared laser absorption spectroscopy. The reaction H + O{sub 2} {yields} OH + O will be studied.

  12. Reactions of methyl and ethyl radicals with uranium hexafluoride

    NASA Astrophysics Data System (ADS)

    Lyman, John L.; Laguna, Glenn

    1985-01-01

    We have measured the rates of reaction of both methyl and ethyl radicals with uranium hexafluoride (UF6) in the gas phase. The method we used was to photolyze samples of UF6 in the presence of either methane or ethane. The radicals produced by reaction of fluorine atoms with these species then react with either themselves or with UF6. We inferred the rate constants from ratios of the reaction products and the published rate constants for radical recombination. The diagnostic technique was gas chromatography. The resulting rate constants for reaction with UF6 were (1.6±0.8)×10-14 cm3 molecule-1 s-1 for methyl radicals and (4±2)×10-11 cm3 molecule-1 s-1 for ethyl radicals.

  13. Mechanistic Studies of the Radical SAM Enzyme DesII with TDP-d-Fucose**

    PubMed Central

    Ko, Yeonjin; Ruszczycky, Mark W.; Choi, Sei-Hyun

    2014-01-01

    DesII is a radical SAM enzyme that catalyzes the C4-deamination of TDP-4-amino-4,6-dideoxyglucose via a C3 radical intermediate. However, if the C4 amino group is replaced with a hydroxyl (TDP-quinovose), the hydroxyl at C3 is oxidized to a ketone with no C4-dehydration. It is hypothesized that hyperconjugation between the C4 C–N/O bond and the partially filled p-orbital at C3 of the radical intermediate modulates the degree to which elimination competes with dehydrogenation. To investigate this hypothesis, the reaction of DesII with the C4-epimer of TDP-quinovose (TDP-fucose) was examined. The majority of the reaction results in the formation of TDP-6-deoxygulose and likely regeneration of TDP-fucose. The remainder of the substrate radical partitions roughly equally between C3-dehydrogenation and C4-dehydration. Thus, changing the stereochemistry at C4 permits a more balanced competition between elimination and dehydrogenation. PMID:25418063

  14. Hydrogen transfer in SAM-mediated enzymatic radical reactions.

    PubMed

    Hioe, Johnny; Zipse, Hendrik

    2012-12-14

    S-adenosylmethionine (SAM) plays an essential role in a variety of enzyme-mediated radical reactions. One-electron reduction of SAM is currently believed to generate the C5'-desoxyadenosyl radical, which subsequently abstracts a hydrogen atom from the actual substrate in a catalytic or a non-catalytic fashion. Using a combination of theoretical and experimental bond dissociation energy (BDE) data, the energetics of these radical processes have now been quantified. SAM-derived radicals are found to react with their respective substrates in an exothermic fashion in enzymes using SAM in a stoichiometric (non-catalytic) way. In contrast, the catalytic use of SAM appears to be linked to a sequence of moderately endothermic and exothermic reaction steps. The use of SAM in spore photoproduct lyase (SPL) appears to fit neither of these general categories and appears to constitute the first example of a SAM-initiated radical reaction propagated independently of the cofactor. PMID:23139189

  15. Radical-initiated reaction of methyl linoleate with dialkyl phosphites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The addition of dialkyl phosphite (methyl, ethyl and n-butyl) to methyl linoleate (MeLin) double bonds was investigated. The reaction proved to be more challenging than the analogous reaction with methyl oleate (MeOl), due to inhibition of the radical reaction by the bis-allylic hydrogens of MeLin a...

  16. Characteristics of Radical Reactions, Spin Rules, and a Suggestion for the Consistent Use of a Dot on Radical Species

    ERIC Educational Resources Information Center

    Wojnarovits, Laszlo

    2011-01-01

    In many chemical reactions, reactive radicals have been shown to be transient intermediates. The free radical character of a chemical species is often, but not always, indicated by adding a superscript dot to the chemical formula. A consistent use of this radical symbol on all species that have radical character is suggested. Free radicals have a…

  17. Kinetic and mechanistic studies of reactive intermediates in photochemical and transition metal-assisted oxidation, decarboxylation and alkyl transfer reactions

    SciTech Connect

    Carraher, Jack McCaslin

    2014-01-01

    Reactive species like high-valent metal-oxo complexes and carbon and oxygen centered radicals are important intermediates in enzymatic systems, atmospheric chemistry, and industrial processes. Understanding the pathways by which these intermediates form, their relative reactivity, and their fate after reactions is of the utmost importance. Herein are described the mechanistic detail for the generation of several reactive intermediates, synthesis of precursors, characterization of precursors, and methods to direct the chemistry to more desirable outcomes yielding ‘greener’ sources of commodity chemicals and fuels.

  18. Mechanistic Diversity of Radical S-Adenosylmethionine (SAM)-dependent Methylation*

    PubMed Central

    Bauerle, Matthew R.; Schwalm, Erica L.; Booker, Squire J.

    2015-01-01

    Radical S-adenosylmethionine (SAM) enzymes use the oxidizing power of a 5′-deoxyadenosyl 5′-radical to initiate an amazing array of transformations, usually through the abstraction of a target substrate hydrogen atom. A common reaction of radical SAM (RS) enzymes is the methylation of unactivated carbon or phosphorous atoms found in numerous primary and secondary metabolites, as well as in proteins, sugars, lipids, and RNA. However, neither the chemical mechanisms by which these unactivated atoms obtain methyl groups nor the actual methyl donors are conserved. In fact, RS methylases have been grouped into three classes based on protein architecture, cofactor requirement, and predicted mechanism of catalysis. Class A methylases use two cysteine residues to methylate sp2-hybridized carbon centers. Class B methylases require a cobalamin cofactor to methylate both sp2-hybridized and sp3-hybridized carbon centers as well as phosphinate phosphorous atoms. Class C methylases share significant sequence homology with the RS enzyme, HemN, and may bind two SAM molecules simultaneously to methylate sp2-hybridized carbon centers. Lastly, we describe a new class of recently discovered RS methylases. These Class D methylases, unlike Class A, B, and C enzymes, which use SAM as the source of the donated methyl carbon, are proposed to methylate sp2-hybridized carbon centers using methylenetetrahydrofolate as the source of the appended methyl carbon. PMID:25477520

  19. Mechanistic diversity of radical S-adenosylmethionine (SAM)-dependent methylation.

    PubMed

    Bauerle, Matthew R; Schwalm, Erica L; Booker, Squire J

    2015-02-13

    Radical S-adenosylmethionine (SAM) enzymes use the oxidizing power of a 5'-deoxyadenosyl 5'-radical to initiate an amazing array of transformations, usually through the abstraction of a target substrate hydrogen atom. A common reaction of radical SAM (RS) enzymes is the methylation of unactivated carbon or phosphorous atoms found in numerous primary and secondary metabolites, as well as in proteins, sugars, lipids, and RNA. However, neither the chemical mechanisms by which these unactivated atoms obtain methyl groups nor the actual methyl donors are conserved. In fact, RS methylases have been grouped into three classes based on protein architecture, cofactor requirement, and predicted mechanism of catalysis. Class A methylases use two cysteine residues to methylate sp(2)-hybridized carbon centers. Class B methylases require a cobalamin cofactor to methylate both sp(2)-hybridized and sp(3)-hybridized carbon centers as well as phosphinate phosphorous atoms. Class C methylases share significant sequence homology with the RS enzyme, HemN, and may bind two SAM molecules simultaneously to methylate sp(2)-hybridized carbon centers. Lastly, we describe a new class of recently discovered RS methylases. These Class D methylases, unlike Class A, B, and C enzymes, which use SAM as the source of the donated methyl carbon, are proposed to methylate sp(2)-hybridized carbon centers using methylenetetrahydrofolate as the source of the appended methyl carbon. PMID:25477520

  20. Competitive reactions of organophosphorus radicals on coke surfaces.

    PubMed

    Catak, Saron; Hemelsoet, Karen; Hermosilla, Laura; Waroquier, Michel; Van Speybroeck, Veronique

    2011-10-17

    The efficacy of organophosphorus radicals as anticoking agents was subjected to a computational study in which a representative set of radicals derived from industrially relevant organophosphorus additives was used to explore competitive reaction pathways on the graphene-like coke surface formed during thermal cracking. The aim was to investigate the nature of the competing reactions of different organophosphorus radicals on coke surfaces, and elucidate their mode of attack and inhibiting effect on the forming coke layer by use of contemporary computational methods. Density functional calculations on benzene and a larger polyaromatic hydrocarbon, namely, ovalene, showed that organophosphorus radicals have a high propensity to add to the periphery of the coke surface, inhibiting methyl radical induced hydrogen abstraction, which is known to be a key step in coke growth. Low addition barriers reported for a phosphatidyl radical suggest competitive aptitude against coke formation. Moreover, organophosphorus additives bearing aromatic substituents, which were shown to interact with the coke surface through dispersive π-π stacking interactions, are suggested to play a nontrivial role in hindering further stacking among coke surfaces. This may be the underlying rationale behind experimental observation of softer coke in the presence of organophosphorus radicals. The ultimate goal is to provide information that will be useful in building single-event microkinetic models. This study presents pertinent information on potential reactions that could be taken up in these models. PMID:21956815

  1. Kinetics and mechanistic study of the gas-phase reaction of ozone with methylbutenol

    NASA Astrophysics Data System (ADS)

    Klawatsch-Carrasco, N.; Doussin, J. F.; Rea, G.; Wenger, J.; Carlier, P.

    2003-04-01

    Biogenic volatile organic compounds (BVOCs) account for around 90% of hydrocarbon emissions into the Earth's atmosphere ([1], [2]). Several thousand different BVOCs have been identified, the most well known being unsaturated hydrocarbons. However, over the last ten years an increasing number of oxygenated BVOCs, such as methylbutenol (MBO), have also been detected in field measurement campaigns and plant emission studies ([3], [4]). In order to determine the environmental impact of BVOCs, a thorough knowledge of the rates and mechanisms for their atmospheric degradation is required. The major atmospheric degradation processes for BVOCs are gas-phase reaction with hydroxyl radicals (OH), nitrate radicals (NO_3) and ozone (O_3). These reactions produce oxidised hydrocarbons, ozone and secondary organic aerosol and, as a result, exert a strong influence on the chemical composition of the atmosphere. Very few studies are available concerning the reactivity of MBO. To extend the available database on the atmospheric chemistry of biogenic compounds, the reaction of O_3 with MBO at 296(±2) K has been investigated in atmospheric simulation chambers at LISA in Créteil (France) and CRAC in Cork (Ireland), using complementary techniques such as FTIR spectroscopy, PFBHA derivatization with GC-MS detection and a particle sizer and counter. The rate constant for the reaction was determined using an absolute rate technique, yielding a value of (8.3±0.9)× 10-18 cm^3 molecule-1s-1. Mechanistic studies of the reaction lead to the following observations: a primary formation of only three carbonyl compounds, formaldehyde (yield=0.40±0.03), acetone (yield=0.27±0.02) and 2-methyl-2-hydroxy-propanal. In addition, there is a noticeable formation of aerosols at the very beginning of the reaction that seemed to depend on the relative humidity. References: [1] Wayne, R. P. (2000). 3rd edition. Oxford university press inc. Edition. [2] Finlayson-Pitts, B. and Pitts Jr, J. N. ( 2000

  2. Tropospheric reactions of the haloalkyl radicals formed from hydroxyl radical reaction with a series of alternative fluorocarbons

    NASA Technical Reports Server (NTRS)

    Atkinson, Roger

    1990-01-01

    In the present assessment, the hydrogen containing halocarbons being considered as alternatives to the the presently used chlorofluorocarbons are the hydrochlorofluorocarbons (HCFCs) 123 (CF3CHCl2), 141b (CFCl2CH3), 142b (CF2ClCH3), 22 (CHF2Cl) and 124 (CF3CHFCl) and the hydrofluorocarbons (HFCs) 134a (CF3CH2F), 152a (CHF2CH3) and 125 (CF3CHF2). All of these HCFCs and HFCs will react with the hydroxyl (OH) radical in the troposphere, giving rise to haloalkyl radicals which then undergo a complex series of reactions in the troposphere. These reactions of the haloalkyl radicals formed from the initial OH radical reactions with the HCFCs and HFCs under tropospheric conditions are the focus here.

  3. Crossed-beam studies of the dynamics of radical reactions

    SciTech Connect

    Liu, K.

    1993-12-01

    The objective of this program is to characterize the detailed dynamics of elementary radical reactions and to provide a better understanding of radical reactivity in general. The radical beam is typically generated by a laser photolysis method. After colliding with the reacting molecule in a crossed-beam apparatus, the reaction product state distribution is interrogated by laser spectroscopic techniques. Several radicals of combustion significance, such as O, CH, OH, CN and NCO have been successfully generated and their collisional behavior at the state-to-state integral cross section level of detail has been studied in this manner. During the past year, the detection system has been converted from LIF to REMPI schemes, and the emphasis of this program shifted to investigate the product angular distributions. Both inelastic and reactive processes have been studied.

  4. Pressure effects on the radical-radical recombination reaction of photochromic bridged imidazole dimers.

    PubMed

    Mutoh, Katsuya; Abe, Jiro

    2014-09-01

    The bridged imidazole dimers are some of the attractive fast photochromic compounds which have potential applications to the ophthalmic lenses, real-time hologram and molecular machines. The strategy for expanding their photochromic properties such as the colour variation and tuning the decolouration rates has been vigorously investigated, but the insight into the structural changes along the photochromic reactions has not been demonstrated in detail. Here, we demonstrated the pressure dependence of the radical-radical recombination reaction of the bridged imidazole dimers. The radical-radical interaction can be controlled by applying high pressure. Our results give fundamental information about the molecular dynamics of the bridged imidazole dimers, leading to the development of new functional photochromic machines and pressure-sensitive photochromic materials. PMID:25025786

  5. Reaction kinetics of resveratrol with tert-butoxyl radicals

    NASA Astrophysics Data System (ADS)

    Džeba, Iva; Pedzinski, Tomasz; Mihaljević, Branka

    2012-09-01

    The rate constant for the reaction of t-butoxyl radicals with resveratrol was studied under pseudo-first order conditions. The rate constant was determined by measuring the phenoxyl radical formation rate at 390 nm as function of resveratrol concentration in acetonitrile. The rate constant was determined to be 6.5×108 M-1s-1. This high value indicates the high reactivity consistent with the strong antioxidant activity of resveratrol.

  6. Roaming dynamics in radical addition-elimination reactions

    NASA Astrophysics Data System (ADS)

    Joalland, Baptiste; Shi, Yuanyuan; Kamasah, Alexander; Suits, Arthur G.; Mebel, Alexander M.

    2014-06-01

    Radical addition-elimination reactions are a major pathway for transformation of unsaturated hydrocarbons. In the gas phase, these reactions involve formation of a transient strongly bound intermediate. However, the detailed mechanism and dynamics for these reactions remain unclear. Here we show, for reaction of chlorine atoms with butenes, that the Cl addition-HCl elimination pathway occurs from an abstraction-like Cl-H-C geometry rather than a conventional three-centre or four-centre transition state. Furthermore, access to this geometry is attained by roaming excursions of the Cl atom from the initially formed adduct. In effect, the alkene π cloud serves to capture the Cl atom and hold it, allowing many subsequent opportunities for the energized intermediate to find a suitable approach to the abstraction geometry. These bimolecular roaming reactions are closely related to the roaming radical dynamics recently discovered to play an important role in unimolecular reactions.

  7. Detection of hydroxyl radical in plasma reaction on toluene removal.

    PubMed

    Guo, Yufang; Liao, Xiaobin; Ye, Daiqi

    2008-01-01

    A new method was introduced to detect the concentration of OH radical in dielectric barrier discharge (DBD) reaction. A film, which was impregnated with salicylic acid, was used to detect OH radical in plasma reaction at room temperature and atmospheric pressure. Salicylic acid reacts with OH radical and produces 2,5-dihydroxybenzoic acid (2,5-DHBA). Then, a high performance liquid chromatography (HPLC) was carried out to detect the concentration of 2,5-DHBA. Therefore, OH radical in nonthermal plasma reaction could be calculated. In this plasma reaction, the applied voltage was controlled at 10 kV, the initial concentration of toluene was 400 mg/m3, and the gas flow rate was 300 ml/min. It was observed that when the film was placed away from the plasma area, 2,5-DHBA could not be detected by HPLC, although the sampling time lasted for 48 h. On the other hand, when the film was placed in the plasma area and the sampling time being too long (> 4 h), the concentration of 2,5-DHBA was also below detection limit, and it could not be detected by HPLC. However, when the film was placed in the plasma reaction field with the sampling time being 3 h, the concentration of OH radical was calculated to be 10.54 x 10(12) cm(-3). In addition, concentration of OH radical was investigated under different humidity, such as 0.2%, 0.4%, 0.6%, 0.8%, and 1.0%. The results showed that the amount of OH radical stayed at order of magnitude of 10(12) cm(-3) and increased with the increase of humidity. PMID:19209627

  8. REACTIONS OF OXY RADICALS IN THE ATMOSPHERE

    EPA Science Inventory

    Results are presented of a research program concerned with the study of selected reactions of importance in atmospheric chemistry. The decomposition of peroxyacetyl nitrate (PAN) was studied over the temperature range 25-39C. The rate constant was determined to be log k = 16.29 -...

  9. Insights into gas-phase reaction mechanisms of small carbon radicals using isomer-resolved product detection.

    PubMed

    Trevitt, Adam J; Goulay, Fabien

    2016-02-17

    For reactive gas-phase environments, including combustion, extraterrestrials atmospheres and our Earth's atmosphere, the availability of quality chemical data is essential for predictive chemical models. These data include reaction rate coefficients and product branching fractions. This perspective overviews recent isomer-resolved production detection experiments for reactions of two of the most reactive gas phase radicals, the CN and CH radicals, with a suite of small hydrocarbons. A particular focus is given to flow-tube experiments using synchrotron photoionization mass spectrometry. Coupled with computational studies and other experiment techniques, flow tube isomer-resolved product detection have provided significant mechanistic details of these radical + neutral reactions with some general patterns emerging. PMID:26841339

  10. Vibrationally Driven Hydrogen Abstraction Reaction by Bromine Radical in Solution

    NASA Astrophysics Data System (ADS)

    Shin, Jae Yoon; Shalowski, Michael A.; Crim, F. Fleming

    2013-06-01

    Previously, we have shown that preparing reactants in specific vibrational states can affect the product state distribution and branching ratios in gas phase reactions. In the solution phase, however, no vibrational mediation study has been reported to date. In this work, we present our first attempt of vibrationally mediated bimolecular reaction in solution. Hydrogen abstraction from a solvent by a bromine radical can be a good candidate to test the effect of vibrational excitation on reaction dynamics because this reaction is highly endothermic and thus we can suppress any thermally initiated reaction in our experiment. Br radical quickly forms CT (charge transfer) complex with solvent molecule once it is generated from photolysis of a bromine source. The CT complex strongly absorbs visible light, which allows us to use electronic transient absorption for tracking Br radical population. For this experiment, we photolyze bromoform solution in dimethyl sulfoxide (DMSO) solvent with 267 nm to generate Br radical and excite the C-H stretch overtone of DMSO with 1700 nm a few hundred femtoseconds after the photolysis. Then, we monitor the population of Br-DMSO complex with 400 nm as a function of delay time between two pump beams and probe beam. As a preliminary result, we observed the enhancement of loss of Br-DMSO complex population due to the vibrational excitation. We think that increased loss of Br-DMSO complex is attributed to more loss of Br radical that abstracts hydrogen from DMSO and it is the vibrational excitation that promotes the reaction. To make a clear conclusion, we will next utilize infrared probing to directly detect HBr product formation.

  11. How Well Can New-Generation Density Functionals Describe the Energetics of Bond-Dissociation Reactions Producing Radicals?

    SciTech Connect

    Zhao, Yan; Truhlar, Donald G.

    2008-02-14

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The performance of various density functionals has been tested for three sets of reaction energies involving radicals. It is shown that two recently designed functionals, M05-2X and M06-2X, provide the best performance. These functionals provide useful and affordable methods for future mechanistic studies involving organic radicals.

  12. Mechanistic insights into light-driven graphene-induced peroxide decomposition: radical generation and disproportionation.

    PubMed

    Chu, Ya-Lan; Chen, Yen-An; Li, Wei-Chin; Chu, Jean-Ho; Chen, Chun-Hu; Chiang, Chao-Ming

    2016-07-28

    Interaction between adsorbed t-butyl peroxybenzoate and photoexcited graphene rendered trapped phenyl and t-butoxy radicals. Post-irradiation thermal desorption showed benzene, t-butanol, and isobutylene oxide as the end products. The required hydrogen atoms were obtained via the radical disproportionation. Graphene enabled radical species to be captured and their on-surface chemistry to be revealed. PMID:27366795

  13. Modeling of the Reaction Mechanism of Enzymatic Radical C-C Coupling by Benzylsuccinate Synthase.

    PubMed

    Szaleniec, Maciej; Heider, Johann

    2016-01-01

    Molecular modeling techniques and density functional theory calculations were performed to study the mechanism of enzymatic radical C-C coupling catalyzed by benzylsuccinate synthase (BSS). BSS has been identified as a glycyl radical enzyme that catalyzes the enantiospecific fumarate addition to toluene initiating its anaerobic metabolism in the denitrifying bacterium Thauera aromatica, and this reaction represents the general mechanism of toluene degradation in all known anaerobic degraders. In this work docking calculations, classical molecular dynamics (MD) simulations, and DFT+D2 cluster modeling was employed to address the following questions: (i) What mechanistic details of the BSS reaction yield the most probable molecular model? (ii) What is the molecular basis of enantiospecificity of BSS? (iii) Is the proposed mechanism consistent with experimental observations, such as an inversion of the stereochemistry of the benzylic protons, syn addition of toluene to fumarate, exclusive production of (R)-benzylsuccinate as a product and a kinetic isotope effect (KIE) ranging between 2 and 4? The quantum mechanics (QM) modeling confirms that the previously proposed hypothetical mechanism is the most probable among several variants considered, although C-H activation and not C-C coupling turns out to be the rate limiting step. The enantiospecificity of the enzyme seems to be enforced by a thermodynamic preference for binding of fumarate in the pro(R) orientation and reverse preference of benzyl radical attack on fumarate in pro(S) pathway which results with prohibitively high energy barrier of the radical quenching. Finally, the proposed mechanism agrees with most of the experimental observations, although the calculated intrinsic KIE from the model (6.5) is still higher than the experimentally observed values (4.0) which suggests that both C-H activation and radical quenching may jointly be involved in the kinetic control of the reaction. PMID:27070573

  14. Modeling of the Reaction Mechanism of Enzymatic Radical C–C Coupling by Benzylsuccinate Synthase

    PubMed Central

    Szaleniec, Maciej; Heider, Johann

    2016-01-01

    Molecular modeling techniques and density functional theory calculations were performed to study the mechanism of enzymatic radical C–C coupling catalyzed by benzylsuccinate synthase (BSS). BSS has been identified as a glycyl radical enzyme that catalyzes the enantiospecific fumarate addition to toluene initiating its anaerobic metabolism in the denitrifying bacterium Thauera aromatica, and this reaction represents the general mechanism of toluene degradation in all known anaerobic degraders. In this work docking calculations, classical molecular dynamics (MD) simulations, and DFT+D2 cluster modeling was employed to address the following questions: (i) What mechanistic details of the BSS reaction yield the most probable molecular model? (ii) What is the molecular basis of enantiospecificity of BSS? (iii) Is the proposed mechanism consistent with experimental observations, such as an inversion of the stereochemistry of the benzylic protons, syn addition of toluene to fumarate, exclusive production of (R)-benzylsuccinate as a product and a kinetic isotope effect (KIE) ranging between 2 and 4? The quantum mechanics (QM) modeling confirms that the previously proposed hypothetical mechanism is the most probable among several variants considered, although C–H activation and not C–C coupling turns out to be the rate limiting step. The enantiospecificity of the enzyme seems to be enforced by a thermodynamic preference for binding of fumarate in the pro(R) orientation and reverse preference of benzyl radical attack on fumarate in pro(S) pathway which results with prohibitively high energy barrier of the radical quenching. Finally, the proposed mechanism agrees with most of the experimental observations, although the calculated intrinsic KIE from the model (6.5) is still higher than the experimentally observed values (4.0) which suggests that both C–H activation and radical quenching may jointly be involved in the kinetic control of the reaction. PMID:27070573

  15. Phosphite radicals and their reactions. Examples of redox, substitution, and addition reactions. [Gamma rays and electrons

    SciTech Connect

    Schaefer, K.; Asmus, K.D.

    1980-08-21

    Phosphite radicals HPO/sub 3/- and PO/sub 3//sup 2/-, which exist in an acid-base equilibrium with pK = 5.75, are shown to take part in various types of reactions. In the absence of scavengers, they disappear mainly by second-order disproportionation and combination; a first-order contribution to the decay is also indicated. HPO/sub 3/- and PO/sub 3//sup 2/- are good reductants toward electron acceptors such as tetranitromethane. In this reaction phosphate and C(NO/sub 2/)/sub 3/- are formed. Phosphite radicals can, however, also act as good oxidants, e.g., toward thiols and thiolate ions. These reactions lead to the formation of RS. radicals which were identified either directly, as in the case of penicillamine, through the optical absorption of PenS. or more indirectly through equilibration of RS. with RS- to the optically absorbing RSSR-. disulfide radical anion. A homolytic substitution reaction (S/sub H/2) occurs in the reaction of the phosphite radicals with aliphatic disulfides, yielding RS. radicals and phosphate thioester RSPO/sub 3//sup 2/-. Lipoic acid, as an example of a cyclic disulfide, is reduced to the corresponding RSSR-. radical anion and also undergoes the S/sub H/2 reaction with about equal probability. An addition reaction is observed between phosphite radicals and molecular oxygen. The resulting peroxo phosphate radicals establish an acid-base equilibrium HPO/sub 5//sup -/. reversible PO/sub 5//sup 2 -/. + H+ with a pK = 3.4. Absolute rate constants were determined for all reactions discussed.

  16. Reaction of hydroxyl radical with B- and Z-DNA

    SciTech Connect

    Michalik, V.; Tartier, L.; Spotheim-Maurizot, M.; Charlier, M.

    1995-12-31

    Up to now the mechanisms of formation of DNA damages by the {center_dot}OH radical attack are only poorly understood. For example, it is not clear if {center_dot}OH radical attack depends on the DNA polymeric structure, if it is sequence specific and to what extent the {center_dot}OH induced base radicals contribute to the formation of frank strand breaks (FSB), mainly due to attack of sugars. It is accepted now that depending on sequence, topological constraints and environmental factors DNA can adopt different forms such as A, B, C, Z double helices, triple and quadruple helices. Since there are large structural differences between the DNA in B- and Z-forms one may expect differences in the {center_dot}OH radical reaction with the two forms as well as differences in the processes subsequent to {center_dot}OH radical attack which lead to strand breakage. The authors have performed a modeling of {center_dot}OH radical attack on DNA in the B- and Z-form and compared the theoretical results with the experimental patterns of strand breakage in B- and Z-DNA. The calculated probabilities of {center_dot}OH radical attack on sugars and bases in DNA of a given sequence and form were compared to the experimental yields of FSB, i.e. revealed in a neutral pH, and alkali revealed breaks (ARB) in B- and Z-DNA irradiated in dilute aqueous solution. The possible mechanism underlying the pathways from {center_dot}OH radical attack to strand breakage are discussed.

  17. In Situ Catalyst Modification in Atom Transfer Radical Reactions with Ruthenium Benzylidene Complexes.

    PubMed

    Lee, Juneyoung; Grandner, Jessica M; Engle, Keary M; Houk, K N; Grubbs, Robert H

    2016-06-01

    Ruthenium benzylidene complexes are well-known as olefin metathesis catalysts. Several reports have demonstrated the ability of these catalysts to also facilitate atom transfer radical (ATR) reactions, such as atom transfer radical addition (ATRA) and atom transfer radical polymerization (ATRP). However, while the mechanism of olefin metathesis with ruthenium benzylidenes has been well-studied, the mechanism by which ruthenium benzylidenes promote ATR reactions remains unknown. To probe this question, we have analyzed seven different ruthenium benzylidene complexes for ATR reactivity. Kinetic studies by (1)H NMR revealed that ruthenium benzylidene complexes are rapidly converted into new ATRA-active, metathesis-inactive species under typical ATRA conditions. When ruthenium benzylidene complexes were activated prior to substrate addition, the resulting activated species exhibited enhanced kinetic reactivity in ATRA with no significant difference in overall product yield compared to the original complexes. Even at low temperature, where the original intact complexes did not catalyze the reaction, preactivated catalysts successfully reacted. Only the ruthenium benzylidene complexes that could be rapidly transformed into ATRA-active species could successfully catalyze ATRP, whereas other complexes preferred redox-initiated free radical polymerization. Kinetic measurements along with additional mechanistic and computational studies show that a metathesis-inactive ruthenium species, generated in situ from the ruthenium benzylidene complexes, is the active catalyst in ATR reactions. Based on data from (1) H, (13)C, and (31)P NMR spectroscopy and X-ray crystallography, we suspect that this ATRA-active species is a RuxCly(PCy3)z complex. PMID:27186790

  18. Reactive radical facilitated reaction-diffusion modeling for holographic photopolymerization

    SciTech Connect

    Liu Jianhua; Pu Haihui; Gao Bin; Gao Hongyue; Yin Dejin; Dai Haitao

    2010-02-08

    A phenomenological concentration of reactive radical is proposed to take the role of curing light intensity in explicit proportion to the reaction rate for the conventional reaction-diffusion model. This revision rationally eliminates the theoretical defect of null reaction rate in modeling of the postcuring process, and facilitates the applicability of the model in the whole process of holographic photopolymerizations in photocurable monomer and nematic liquid crystal blend system. Excellent consistencies are obtained in both curing and postcuring processes between simulated and experimentally measured evolutions of the first order diffraction efficiency of the formed composite Bragg gratings.

  19. Heterogeneous oxidation of folpet and dimethomorph by OH radicals: A kinetic and mechanistic study

    NASA Astrophysics Data System (ADS)

    Al Rashidi, M.; Chakir, A.; Roth, E.

    2014-01-01

    This study investigates the heterogeneous OH oxidation of folpet and dimethomorph, two fungicides identified in the atmosphere of the Champagne-Ardenne region. Kinetic experiments were conducted in the relative mode, using terbuthylazine as a reference compound. The experimental method employed makes use of a simulation chamber coupled to a GC/MS analytical system. Meanwhile, the identification of (4-chlorophenyl)(3,4-dimethoxyphenyl)methanone (CPMPM), a degradation product of the OH oxidation of dimethomorph, is achieved using SPME/GC/MS. Moreover, a degradation mechanism of dimethomorph is proposed, and the heterogeneous OH reactivity of CPMPM is evaluated. The obtained OH reaction rate constants (cm3 molecule-1 s-1) are: kZ-dimethomorph = (2.0 ± 1.2) 10-14, kE-dimethomorph = (1.7 ± 1.2) 10-14, kFolpet = (1.6 ± 0.9) 10-13 and kCPMPM = (1.9 ± 1.0) 10-12. The implicated tropospheric life-times are up to 2 months, which shows that the investigated pesticides are relatively persistent towards oxidation removal processes. CPMPM, the identified product of OH oxidation of dimethomorph, is less persistent with a life time of only 6 days relative to heterogeneous oxidation by OH radicals.

  20. MICROWAVE EFFECTS IN ORGANIC SYNTHESIS: MECHANISTIC AND REACTION MEDIUM CONSIDERATIONS

    EPA Science Inventory

    The scope of applications of microwave irradiation relates to a wide spectrum of organic syntheses with numerous benefits (reduction in reaction times, improved purity of products and better yields) encompassing advantages of both thermal and (or) specific non-purely thermal effe...

  1. An improved semiclassical theory of radical pair recombination reactions.

    PubMed

    Manolopoulos, D E; Hore, P J

    2013-09-28

    We present a practical semiclassical method for computing the electron spin dynamics of a radical in which the electron spin is hyperfine coupled to a large number of nuclear spins. This can be used to calculate the singlet and triplet survival probabilities and quantum yields of radical recombination reactions in the presence of magnetic fields. Our method differs from the early semiclassical theory of Schulten and Wolynes [J. Chem. Phys. 68, 3292 (1978)] in allowing each individual nuclear spin to precess around the electron spin, rather than assuming that the hyperfine coupling-weighted sum of nuclear spin vectors is fixed in space. The downside of removing this assumption is that one can no longer obtain a simple closed-form expression for the electron spin correlation tensor: our method requires a numerical calculation. However, the computational effort increases only linearly with the number of nuclear spins, rather than exponentially as in an exact quantum mechanical calculation. The method is therefore applicable to arbitrarily large radicals. Moreover, it approaches quantitative agreement with quantum mechanics as the number of nuclear spins increases and the environment of the electron spin becomes more complex, owing to the rapid quantum decoherence in complex systems. Unlike the Schulten-Wolynes theory, the present semiclassical theory predicts the correct long-time behaviour of the electron spin correlation tensor, and it therefore correctly captures the low magnetic field effect in the singlet yield of a radical recombination reaction with a slow recombination rate. PMID:24089749

  2. Binuclear metallohydrolases: complex mechanistic strategies for a simple chemical reaction.

    PubMed

    Schenk, Gerhard; Mitić, Nataša; Gahan, Lawrence R; Ollis, David L; McGeary, Ross P; Guddat, Luke W

    2012-09-18

    Binuclear metallohydrolases are a large family of enzymes that require two closely spaced transition metal ions to carry out a plethora of hydrolytic reactions. Representatives include purple acid phosphatases (PAPs), enzymes that play a role in bone metabolism and are the only member of this family with a heterovalent binuclear center in the active form (Fe(3+)-M(2+), M = Fe, Zn, Mn). Other members of this family are urease, which contains a di-Ni(2+) center and catalyzes the breakdown of urea, arginase, which contains a di-Mn(2+) center and catalyzes the final step in the urea cycle, and the metallo-β-lactamases, which contain a di-Zn(2+) center and are virulence factors contributing to the spread of antibiotic-resistant pathogens. Binuclear metallohydrolases catalyze numerous vital reactions and are potential targets of drugs against a wide variety of human disorders including osteoporosis, various cancers, antibiotic resistance, and erectile dysfunctions. These enzymes also tend to catalyze more than one reaction. An example is an organophosphate (OP)-degrading enzyme from Enterobacter aerogenes (GpdQ). Although GpdQ is part of a pathway that is used by bacteria to degrade glycerolphosphoesters, it hydrolyzes a variety of other phosphodiesters and displays low levels of activity against phosphomono- and triesters. Such a promiscuous nature may have assisted the apparent recent evolution of some binuclear metallohydrolases to deal with situations created by human intervention such as OP pesticides in the environment. OP pesticides were first used approximately 70 years ago, and therefore the enzymes that bacteria use to degrade them must have evolved very quickly on the evolutionary time scale. The promiscuous nature of enzymes such as GpdQ makes them ideal candidates for the application of directed evolution to produce new enzymes that can be used in bioremediation and against chemical warfare. In this Account, we review the mechanisms employed by binuclear

  3. Kinetics of the Self Reaction of Cyclopentadienyl Radicals.

    PubMed

    Knyazev, Vadim D; Popov, Konstantin V

    2015-07-16

    The kinetics of the self-reaction of cyclopentadienyl radicals (c-C5H5) was studied by laser photolysis/photoionization mass spectroscopy. Overall rate constants were obtained in direct real-time experiments in the temperature region 304-600 K and at bath gas densities of (3.00-12.0) × 10(16) molecules cm(-3). The room-temperature value of the rate constant, (3.98 ± 0.41) × 10(-10) cm(3) molecule(-1) s(-1), is significantly higher than the rate constants for most hydrocarbon radical-radical reactions and coincides with the estimated collision rate. The observed overall c-C5H5 + c-C5H5 rate constant demonstrates an unprecedented strong negative temperature dependence: k1 = 2.9 × 10(-12) exp(+1489 K/T) cm(3) molecule(-1) s(-1), with estimated uncertainty increasing with temperature, from 13% at 304 to 32% at 600 K. Formation of C10H10 as the primary product of cyclopentadienyl self-reaction was observed. In additional experiments performed at the temperature of 800 K, formation of C10H10, C10H9, and C10H8 was observed. Final product analysis by gas chromatography/mass spectrometry detected two isomers of C10H8 at 800 K: naphthalene (major) and azulene (minor). PMID:25760686

  4. Kinetics of hydroperoxy radical reactions with acetone/HO2 adduct and with acetonylperoxy radical

    NASA Astrophysics Data System (ADS)

    Grieman, F. J.; VanDerGeest, K.; Newenhouse, E.; Watkins, K.; Noell, A. C.; Hui, A.; Sander, S. P.; Okumura, M.

    2013-12-01

    Reactions of hydroperoxy radical, HO2, with acetone and with acetonylperoxy radical, CH3C(O)CH2OO, may play an important role in the oxidation chemistry of the troposphere. Using a temperature-controlled slow-flow tube cell and laser flash photolysis of Cl2 to produce HO2 and CH3C(O)CH2OO from methanol and acetone, respectively, we studied the chemical kinetics involved over the temperature range of 215 to 298 K at 100 Torr. Rates of chemical reactions were determined by monitoring the HO2 concentration as a function of time by near-IR diode laser wavelength modulation spectroscopy. (See Fig.1.) The primary reactions are rapid (<100 μsec) reactions to form the adducts HO2-CH3OH and HO2-CH3C(O)CH3 followed by HO2 reactions with itself, the adducts (chaperone mechanisms), and acetonylperoxy radical. The equilibrium constants for adduct formation were determined in previous work.1,2 In this work, rate coefficients were determined for the acetone chaperone mechanism over the entire temperature range. (E.g., see Fig. 2.) The rate coefficients and energies obtained are very similar to those found for the methanol case.1 Rate coefficients for the CH3C(O)CH2OO/HO2 reaction were also determined over a smaller temperature range, extending the measured value beyond room temperature, and yielding an activation energy. 1. Christensen et al. J. Phys. Chem. A 2006, 110, 6948-6959. 2. Grieman et al. J. Phys. Chem. A 2011, 115, 10527-10538. Fig.1. HO2 decay for HO2/Acetone chemistry at T = 298 K. Fig.2. Determining rate coefficient (k") for HO2/acetone chaperone effect at T = 222.5 K.

  5. Kinetic and mechanistic study of the reaction of OH radicals with methylated benzenes: 1,4-dimethyl-, 1,3,5-trimethyl-, 1,2,4,5-, 1,2,3,5- and 1,2,3,4-tetramethyl-, pentamethyl-, and hexamethylbenzene.

    PubMed

    Alarcón, P; Bohn, B; Zetzsch, C

    2015-05-21

    The reaction of OH radicals with a series of methylated benzenes was studied in a temperature range 300-350 K using a flash-photolysis resonance fluorescence technique. Reversible OH additions led to complex OH decays dependent on the number of distinguishable adducts. Except for hexamethylbenzene, triexponential OH decay curves were obtained, consistent with formation of at least two adduct species. For three compounds that can strictly form two adduct isomers for symmetry reasons (1,4-dimethyl-, 1,3,5-trimethyl-, and 1,2,4,5-tetramethylbenzene) with OH bound ortho or ipso with respect to the methyl groups, OH decay curves were analysed in terms of a reaction mechanism in which the two adducts can be formed directly by OH addition or indirectly by isomerization. In all cases one adduct (add1) is dominating the decomposition back to OH. The other (add2) is more elusive and only detectable at elevated temperatures, similar to the single OH adduct of hexamethylbenzene. Two limiting cases of the general reaction mechanism could be examined quantitatively: reversible formation of add2 exclusively in the OH reaction or by isomerization of add1. Total OH rate constants, adduct loss rate constants and products of forward and reverse rate constants of reversible reactions were determined. From these quantities, adduct yields, equilibrium constants, as well as reaction enthalpies and entropies were derived for the three aromatics. Adduct yields strongly depend on the selected reaction model but generally formation of add1 predominates. For both models equilibrium constants of OH reactions lie between those of OH + benzene from the literature and those obtained for OH + hexamethylbenzene. The corresponding reaction enthalpies of add1 and add2 formations are in a range -87 ± 20 kJ mol(-1), less exothermic than for hexamethylbenzene (-101 kJ mol(-1)). Reaction enthalpies of possible add1 → add2 isomerizations are comparatively small. Because results for 1

  6. Parameterization of phosphine ligands reveals mechanistic pathways and predicts reaction outcomes

    NASA Astrophysics Data System (ADS)

    Niemeyer, Zachary L.; Milo, Anat; Hickey, David P.; Sigman, Matthew S.

    2016-06-01

    The mechanistic foundation behind the identity of a phosphine ligand that best promotes a desired reaction outcome is often non-intuitive, and thus has been addressed in numerous experimental and theoretical studies. In this work, multivariate correlations of reaction outcomes using 38 different phosphine ligands were combined with classic potentiometric analyses to study a Suzuki reaction, for which the site selectivity of oxidative addition is highly dependent on the nature of the phosphine. These studies shed light on the generality of hypotheses regarding the structural influence of different classes of phosphine ligands on the reaction mechanism(s), and deliver a methodology that should prove useful in future studies of phosphine ligands.

  7. Mechanistic examination of aerobic Pt oxidation: insertion of molecular oxygen into Pt-H bonds through a radical chain mechanism.

    PubMed

    Keith, Jason M; Ye, Yixin; Wei, Haochuan; Buck, Matthew R

    2016-07-19

    DFT calculations were performed in an effort to evaluate the mechanism of O2 insertion into the Pt-H bond of Tp(Me2)Pt(IV)Me2H catalyzed by AIBN or light. Results are consistent with a radical chain mechanism involving H˙ loss to form a Pt(III)˙ species followed by addition of O2 to form Pt(III)OO˙. Subsequent radical propagation involving this Pt(III)OO˙ species and an additional equivalent of the Pt(IV) starting material result in the formation of the observed Pt(IV)OOH and regeneration of the Pt(III)˙. In addition examination of the reaction between AIBN and the Pt(IV) hydroperoxo product demonstrates that radical initiation reactions involving the product occur with a lower barrier than with the initial starting material supporting the idea of autoacceleration in this reaction. Other possible mechanisms were examined in an effort to understand the limited reactivity reported in the absence of light or radical initiators. TDDFT calculations were performed in an effort to understand the reported parallel photo-induced reaction. These calculations found the reactant to be transparent in the relevant light range. An experimental UV-Vis spectrum was obtained and is in agreement with the calculations. PMID:27364984

  8. Formation of Chlorotriophenoxy Radicals from Complete Series Reactions of Chlorotriophenols with H and OH Radicals

    PubMed Central

    Xu, Fei; Shi, Xiangli; Zhang, Qingzhu; Wang, Wenxing

    2015-01-01

    The chlorothiophenoxy radicals (CTPRs) are key intermediate species in the formation of polychlorinated dibenzothiophenes/thianthrenes (PCDT/TAs). In this work, the formation of CTPRs from the complete series reactions of 19 chlorothiophenol (CTP) congeners with H and OH radicals were investigated theoretically by using the density functional theory (DFT) method. The profiles of the potential energy surface were constructed at the MPWB1K/6-311+G(3df,2p)//MPWB1K/6-31+G(d,p) level. The rate constants were evaluated by the canonical variational transition-state (CVT) theory with the small curvature tunneling (SCT) contribution at 600–1200 K. The present study indicates that the structural parameters, thermal data, and rate constants as well as the formation potential of CTPRs from CTPs are strongly dominated by the chlorine substitution at the ortho-position of CTPs. Comparison with the study of formation of chlorophenoxy radicals (CPRs) from chlorophenols (CPs) clearly shows that the thiophenoxyl-hydrogen abstraction from CTPs by H is more efficient than the phenoxyl-hydrogen abstraction from CPs by H, whereas the thiophenoxyl-hydrogen abstraction from CTPs by OH is less impactful than the phenoxyl-hydrogen abstraction from CPs by OH. Reactions of CTPs with H can occur more readily than that of CTPs with OH, which is opposite to the reactivity comparison of CPs with H and OH. PMID:26270566

  9. Formation of Chlorotriophenoxy Radicals from Complete Series Reactions of Chlorotriophenols with H and OH Radicals.

    PubMed

    Xu, Fei; Shi, Xiangli; Zhang, Qingzhu; Wang, Wenxing

    2015-01-01

    The chlorothiophenoxy radicals (CTPRs) are key intermediate species in the formation of polychlorinated dibenzothiophenes/thianthrenes (PCDT/TAs). In this work, the formation of CTPRs from the complete series reactions of 19 chlorothiophenol (CTP) congeners with H and OH radicals were investigated theoretically by using the density functional theory (DFT) method. The profiles of the potential energy surface were constructed at the MPWB1K/6-311+G(3df,2p)//MPWB1K/6-31+G(d,p) level. The rate constants were evaluated by the canonical variational transition-state (CVT) theory with the small curvature tunneling (SCT) contribution at 600-1200 K. The present study indicates that the structural parameters, thermal data, and rate constants as well as the formation potential of CTPRs from CTPs are strongly dominated by the chlorine substitution at the ortho-position of CTPs. Comparison with the study of formation of chlorophenoxy radicals (CPRs) from chlorophenols (CPs) clearly shows that the thiophenoxyl-hydrogen abstraction from CTPs by H is more efficient than the phenoxyl-hydrogen abstraction from CPs by H, whereas the thiophenoxyl-hydrogen abstraction from CTPs by OH is less impactful than the phenoxyl-hydrogen abstraction from CPs by OH. Reactions of CTPs with H can occur more readily than that of CTPs with OH, which is opposite to the reactivity comparison of CPs with H and OH. PMID:26270566

  10. Ion-molecule reactions with CF3 radical

    NASA Astrophysics Data System (ADS)

    Miller, Thomas M.; Shuman, Nicholas S.; Wiens, Justin P.; Sawyer, Jordan C.; Martinez, Oscar, Jr.; Ard, Shaun G.; Viggiano, Albert A.

    2015-09-01

    The first measurements of reaction rate coefficients and products are reported for reactions of the radical CF3 with Ar+, Xe+, O2+,NO+, CO2+,and C2F5+,at 300 K. The work was carried out in a fast flow of typically 1.5 Torr helium buffer gas (4% argon) using the variable electron and neutral density attachment mass spectrometry (VENDAMS) technique. CF3 was produced via dissociative electron attachment to CF3I, resulting in CF3 concentrations that were well-quantified because the plasma diffusion rate, the electron concentration, and the rate coefficient for attachment to CF3I were separately measured in the experiment. The Ar+ + CF3 reaction was found to proceed at nearly the calculated collisional rate coefficient, yielding 90% CF2+along with CF3+.Reaction of CF3 with C2F5+is slower and yields 75% C2F4+along with CF3+.CF3 undergoes charge transfer reaction with Xe+, O2+,NO+, and CO2+,yielding CF3+.Arguments will be made regarding reaction mechanisms, including the role of spin conservation. Comparisons with Ar+ and O2+reaction with CH3 will be made. Supported by Air Force Office of Scientific Research, AFOSR-2303EP.

  11. Influence of restricted diffusion on retrogressive free-radical reactions

    SciTech Connect

    Buchanan, A.C.; Britt, P.F. III; Thomas, K.B.

    1993-07-01

    The effects of restricted mass transport on retrogressive reaction pathways can be probed through the study of model compounds immobilized on silica surfaces. Silica-immobilized bibenzyl undergoes a free radical chain rearrangement reaction that converts the thermally labile bibenzylic linkage into a more refractory diphenylmethane-type linkage. The efficiency of this process was found to be quite sensitive to the structure of neighboring molecules on the surface. Co-immobilized naphthalene was more effective that co-immobilized tetralin (a hydrogen donor) in inhibiting the process, apparently by retarding the key hydrogen atom transfer step. The effect of the co-attached molecules on the retrogressive cyclization-dehydrogenation path as well as other reaction pathways for this complex system remain under investigation.

  12. Surface Modification of Polymers by Reaction of Alkyl Radicals.

    PubMed

    Hetemi, Dardan; Médard, Jérôme; Kanoufi, Frédéric; Combellas, Catherine; Pinson, Jean; Podvorica, Fetah I

    2016-01-19

    The surfaces of poly(methyl methacrylate) and polyethylene are modified either (i) by a two-step process including the thermal reaction of alkyl radicals derived from bromohexanoic acid in a mixture of 2,6-dimethylbenzene diazonium salt and neat isopentyl nitrite at 60 °C, followed by reaction with p-nitroaniline, anthraquinone, neutral red, and polyethylene glycol moieties, or (ii) by reaction of a previously anthraquinone-modified bromohexanoic acid. The modified surfaces are characterized by IR, XPS, UV, and water contact angles. A mechanism is proposed to rationalize the results. This approach is an efficient way to modify and pattern polymer surfaces with different organic groups and chemical functionalities under mild conditions. PMID:26653398

  13. Oxygen-18 tracer studies of enzyme reactions with radical/cation diagnostic probes

    SciTech Connect

    Moe, Luke A.; Fox, Brian G. . E-mail: bgfox@biochem.wisc.edu

    2005-12-09

    This review considers reactions of enzymes with the cyclopropanoid radical/cation diagnostic probes norcarane, 1,1-dimethylcyclopropane, and 1,1-diethylcyclopropane as elaborated by the use of {sup 18}O{sub 2} and {sup 18}OH{sub 2} to trace the origin of O-atoms incorporated during catalysis. The reactions of soluble and integral membrane diiron enzymes are summarized and compared to results obtained from cytochrome P450 studies. Norcarane proved to be an excellent substrate for the diiron enzyme toluene 4-monooxygenase and its engineered isoforms, with k {sub cat} and coupling between NADH utilization and total hydroxylated products comparable to that determined for toluene, the natural substrate. Results obtained with toluene 4-monooxygenase show that the un-rearranged and radical-rearranged alcohol products have a high percentage of O-atom incorporation (>80-95%) from O{sub 2}, while the cation-derived ring-expansion products have O-atom incorporation primarily derived from solvent water. Mechanistic possibilities accounting for this difference are discussed.

  14. New mechanistic insights in the NH3-SCR reactions at low temperature

    DOE PAGESBeta

    Ruggeri, Maria Pia; Selleri, Tomasso; Nova, Isabella; Tronconi, Enrico; Pihl, Josh A.; Toops, Todd J.; Partridge, Jr., William P.

    2016-05-06

    The present study is focused on the investigation of the low temperature Standard SCR reaction mechanism over Fe- and Cu-promoted zeolites. Different techniques are employed, including in situ DRIFTS, transient reaction analysis and chemical trapping techniques. The results present strong evidence of nitrite formation in the oxidative activation of NO and of their role in SCR reactions. These elements lead to a deeper understanding of the standard SCR chemistry at low temperature and can potentially improve the consistency of mechanistic mathematical models. Furthermore, comprehension of the mechanism on a fundamental level can contribute to the development of improved SCR catalysts.

  15. Peroxyl radical reactions with carotenoids in microemulsions: Influence of microemulsion composition and the nature of peroxyl radical precursor.

    PubMed

    El-Agamey, Ali; McGarvey, David J

    2016-01-01

    The reactions of acetylperoxyl radicals with different carotenoids (7,7'-dihydro-β-carotene and ζ-carotene) in SDS and CTAC microemulsions of different compositions were investigated using laser flash photolysis (LFP) coupled with kinetic absorption spectroscopy. The primary objective of this study was to explore the influence of microemulsion composition and the type of surfactant used on the yields and kinetics of various transients formed from the reaction of acetylperoxyl radicals with carotenoids. Also, the influence of the site (hydrocarbon phases or aqueous phase) of generation of the peroxyl radical precursor was examined by using 4-acetyl-4-phenylpiperidine hydrochloride (APPHCl) and 1,1-diphenylacetone (11DPA) as water-soluble and lipid-soluble peroxyl radical precursors, respectively. LFP of peroxyl radical precursors with 7,7'-dihydro-β-carotene (77DH) in different microemulsions gives rise to the formation of three distinct transients namely addition radical (λmax=460 nm), near infrared transient1 (NIR, λmax=700 nm) and 7,7'-dihydro-β-carotene radical cation (77DH(•+), λmax=770 nm). In addition, for ζ-carotene (ZETA) two transients (near infrared transient1 (NIR1, λmax=660 nm) and ζ-carotene radical cation (ZETA(•+), λmax=730-740 nm)) are generated following LFP of peroxyl radical precursors in the presence of ζ-carotene (ZETA) in different microemulsions. The results show that the composition of the microemulsion strongly influences the observed yield and kinetics of the transients formed from the reactions of peroxyl radicals (acetylperoxyl radicals) with carotenoids (77DH and ZETA). Also, the type of surfactant used in the microemulsions influences the yield of the transients formed. The dependence of the transient yields and kinetics on microemulsion composition (or the type of surfactant used in the microemulsion) can be attributed to the change of the polarity of the microenvironment of the carotenoid. Furthermore, the nature of

  16. Spin-selective recombination reactions of radical pairs: Experimental test of validity of reaction operators

    SciTech Connect

    Maeda, Kiminori; Liddell, Paul; Gust, Devens; Hore, P. J.

    2013-12-21

    Spin-selective reactions of radical pairs are conventionally modelled using an approach that dates back to the 1970s [R. Haberkorn, Mol. Phys. 32, 1491 (1976)]. An alternative approach based on the theory of quantum measurements has recently been suggested [J. A. Jones and P. J. Hore, Chem. Phys. Lett. 488, 90 (2010)]. We present here the first experimental attempt to discriminate between the two models. Pulsed electron paramagnetic resonance spectroscopy has been used to investigate intramolecular electron transfer in the radical pair form of a carotenoid-porphyrin-fullerene molecular triad. The rate of spin-spin relaxation of the fullerene radical in the triad was found to be inconsistent with the quantum measurement description of the spin-selective kinetics, and in accord with the conventional model when combined with spin-dephasing caused by rotational modulation of the anisotropic g-tensor of the fullerene radical.

  17. Mechanistic Insights from Reaction of α-Oxiranyl-Aldehydes with Cyanobacterial Aldehyde Deformylating Oxygenase

    PubMed Central

    Das, Debasis; Ellington, Benjamin; Paul, Bishwajit; Marsh, E. Neil G.

    2014-01-01

    The biosynthesis of long-chain aliphatic hydrocarbons, which are derived from fatty acids, is widespread in Nature. The last step in this pathway involves the decarbonylation of fatty aldehydes to the corresponding alkanes or alkenes. In cyanobacteria this is catalyzed by an aldehyde deformylating oxygenase. We have investigated the mechanism of this enzyme using substrates bearing an oxirane ring adjacent to the aldehyde carbon. The enzyme catalyzed the deformylation of these substrates to produce the corresponding oxiranes. Performing the reaction in D2O allowed the facial selectivity of proton addition to be examined by 1H-NMR spectroscopy. The proton is delivered with equal probability to either face of the oxirane ring, indicating the formation of an oxiranyl radical intermediate that is free to rotate during the reaction. Unexpectedly, the enzyme also catalyzes a side reaction in which oxiranyl-aldehydes undergo tandem deformylation to furnish alkanes two carbons shorter. We present evidence that this involves the rearrangement of the intermediate oxiranyl radical formed in the first step, resulting an aldehyde that is further deformylated in a second step. These observations provide support for a radical mechanism for deformylation and, furthermore, allow the lifetime of the radical intermediate to be estimated based on prior measurements of rate constants for the rearrangement of oxiranyl radicals. PMID:24313866

  18. Pressure Effects on Product Channels of Hydrocarbon Radical-Radical Reactions; Implications for Modelling of Planetary Atmospheres

    NASA Astrophysics Data System (ADS)

    Fahr, A.; Halpern, J.; N'doumi, M.

    2011-10-01

    Previously we had studied the kinetics and product channels of small unsaturated hydrocarbon radical (C2 and C3s) reactions relevant to planetary atmospheric modelling. Reactions of C2 radicals (such as vinyl, H2CCH and ethynyl C2H) and C3 radicals (such as propargyl, HCCCH2 and allyl, H2CCCH3) can affect the abundances of a large number of stable observable C3, C4, C5, C6 and larger molecules, including linear, aromatic and even poly aromatic molecules. We have experimentally determined pressuredependent product yields for self- and cross-radical reactions performed at 298 K and at selected pressures between ~4 Torr (0.5 kPa) and 760 Torr (101 kPa). Final products were determined by gas chromatograph with mass spectrometry/flame ionization detection (GC/MS/FID). In some cases complementary computational studies extended the pressure and temperature range of the observations and provided valuable information on complex reaction mechanisms. These studies provide a systematic framework so that important energetic and structural parameters for radical-radical reactions can be assessed. Here we report a compilation of our earlier results relevant to planetary atmospheres in addition to recent ones for allyl radical (H2CCCH3) reactions.

  19. Studies on the interaction of isocyanides with imines: reaction scope and mechanistic variations

    PubMed Central

    Ghashghaei, Ouldouz; Manna, Consiglia Annamaria; Vicente-García, Esther; Revés, Marc

    2014-01-01

    Summary The interaction of imines with isocyanides has been studied. The main product results from a sequential process involving the attack of two units of isocyanide, under Lewis acid catalysis, upon the carbon–nitrogen double bond of the imine to form the 4-membered ring system. The scope of the reaction regarding the imine and isocyanide ranges has been determined, and also some mechanistic variations and structural features have been described. PMID:24454559

  20. Studies on the interaction of isocyanides with imines: reaction scope and mechanistic variations.

    PubMed

    Ghashghaei, Ouldouz; Manna, Consiglia Annamaria; Vicente-García, Esther; Revés, Marc; Lavilla, Rodolfo

    2014-01-01

    The interaction of imines with isocyanides has been studied. The main product results from a sequential process involving the attack of two units of isocyanide, under Lewis acid catalysis, upon the carbon-nitrogen double bond of the imine to form the 4-membered ring system. The scope of the reaction regarding the imine and isocyanide ranges has been determined, and also some mechanistic variations and structural features have been described. PMID:24454559

  1. Kinetics of the reaction of hydroxyl radicals with nitric acid

    NASA Technical Reports Server (NTRS)

    Margitan, J. J.; Watson, R. T.

    1982-01-01

    An extensive study was made of the reaction of hydroxyl radicals with nitric acid in a laser photolysis-resonance fluorescence system. A 266 nm laser was used to photolyze HNO3 in the temperature range 225-415 K at pressures of 20-300 torr. A temperature dependence was detected below room temperature, with a leveling off at 298 K and a wide spread in the rate constants. A pressure dependence was observed over the entire range and was more pronounced at lower temperatures. The results are noted to be in agreement with those of previous investigations. However, the wide range of rate constants are suggested to be a problem for stratospheric HO(x) modeling for anthropogenic effects. No explanation could be given of the varying results obtained by other investigators regarding the kinetics of the reactions.

  2. Mechanistic Investigation of Phosphate Ester Bond Cleavages of Glycylphosphoserinyltryptophan Radical Cations under Low-Energy Collision-Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Quan, Quan; Hao, Qiang; Song, Tao; Siu, Chi-Kit; Chu, Ivan K.

    2013-04-01

    Under the conditions of low-energy collision-induced dissociation (CID), the canonical glycylphosphoserinyltryptophan radical cation having its radical located on the side chain of the tryptophan residue ([G p SW]•+) fragments differently from its tautomer with the radical initially generated on the α-carbon atom of the glycine residue ([G• p SW]+). The dissociation of [G• p SW]+ is dominated by the neutral loss of H3PO4 (98 Da), with backbone cleavage forming the [b2 - H]•+/y1 + pair as the minor products. In contrast, for [G p SW]•+, competitive cleavages along the peptide backbone, such as the formation of [G p SW - CO2]•+ and the [c2 + 2H]+/[z1 - H]•+ pair, significantly suppress the loss of neutral H3PO4. In this study, we used density functional theory (DFT) to examine the mechanisms for the tautomerizations of [G• p SW]+ and [G p SW]•+ and their dissociation pathways. Our results suggest that the dissociation reactions of these two peptide radical cations are more efficient than their tautomerizations, as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. We also propose that the loss of H3PO4 from both of these two radical cationic tautomers is preferentially charge-driven, similar to the analogous dissociations of even-electron protonated peptides. The distonic radical cationic character of [G• p SW]+ results in its charge being more mobile, thereby favoring charge-driven loss of H3PO4; in contrast, radical-driven pathways are more competitive during the CID of [G p SW]•+.

  3. Kinetics of the self reaction of cyclohexyl radicals.

    PubMed

    Loginova, Ksenia A; Knyazev, Vadim D

    2011-08-11

    The kinetics of the self-reaction of cyclohexyl radicals was studied by laser photolysis/photoionization mass spectroscopy. Overall rate constants were obtained in direct real-time experiments in the temperature region 303-520 K and at bath gas (helium with up to 5% of radical precursors) densities (3.00-12.0) × 10(16) molecules cm(-3). Cyclohexyl radicals were produced by a combination of the 193 nm photolysis of oxalyl chloride ((CClO)(2)) with the subsequent fast reaction of Cl atoms with cyclohexane, and their initial concentrations were determined from real-time profiles of HCl. The observed overall c-C(6)H(11) + c-C(6)H(11) rate constants demonstrate negative temperature dependence, which can be described by the following expressions: k(1) = 4.8 × 10(-12) exp(+542 K/T) cm(3) molecule(-1) s(-1), with estimated uncertainty of 16% over the 303-520 K temperature range. The fraction of disproportionation equal to 41 ± 7% was determined at 305 K; analysis of earlier experimental determinations of the disproportionation-to-recombination branching ratio leads to recommending this room-temperature value for other temperatures. The corresponding temperature dependences of the recombination (1a, bicyclohexyl product) and the disproportionation (1b, cyclohexene and cyclohexane products) channels are k(1a) = 2.8 × 10(-12) exp(+542 K/T) and k(1b) = 2.0 × 10(-12) exp(+542 K/T) cm(3) molecule(-1) s(-1), with estimated uncertainties of 20% and 29%, respectively. PMID:21702489

  4. Steric Effects in the Reaction of Aryl Radicals on Surfaces

    SciTech Connect

    Combellas, Catherine; Jiang, Deen; Kanoufi, Frederic; Pinson, Jean; Podvorica, Fetah

    2009-01-01

    Steric effects are investigated in the reaction of aryl radicals with surfaces. The electrochemical reduction of 2-, 3-, 4-methyl, 2-methoxy, 2-ethyl, 2,6-, 2,4-, and 3,5-dimethyl, 4-tert-butyl, 3,5-bis-tert-butyl benzenediazonium, 3,5-bis(trifluoromethyl), and pentafluoro benzenediazonium tetrafluoroborates is examined in acetonitrile solutions. It leads to the formation of grafted layers only if the steric hindrance at the 2- or 2,6-position(s) is small. When the 3,5-positions are crowded with tert-butyl groups, the growth of the organic layer is limited by steric effects and a monolayer is formed. The efficiency of the grafting process is assessed by cyclic voltammetry, X-ray photoelectron spectroscopy, infrared, and ellipsometry. These experiments, together with density functional computations of bonding energies of substituted phenyl groups on a copper surface, are discussed in terms of the reactivity of aryl radicals in the electrografting reaction and in the growth of the polyaryl layer.

  5. Mechanistic studies of the radical S-adenosylmethionine enzyme DesII with TDP-D-fucose.

    PubMed

    Ko, Yeonjin; Ruszczycky, Mark W; Choi, Sei-Hyun; Liu, Hung-wen

    2015-01-12

    DesII is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the C4-deamination of TDP-4-amino-4,6-dideoxyglucose through a C3 radical intermediate. However, if the C4 amino group is replaced with a hydroxy group (to give TDP-quinovose), the hydroxy group at C3 is oxidized to a ketone with no C4-dehydration. It is hypothesized that hyperconjugation between the C4 C-N/O bond and the partially filled p orbital at C3 of the radical intermediate modulates the degree to which elimination competes with dehydrogenation. To investigate this hypothesis, the reaction of DesII with the C4-epimer of TDP-quinovose (TDP-fucose) was examined. The reaction primarily results in the formation of TDP-6-deoxygulose and likely regeneration of TDP-fucose. The remainder of the substrate radical partitions roughly equally between C3-dehydrogenation and C4-dehydration. Thus, changing the stereochemistry at C4 permits a more balanced competition between elimination and dehydrogenation. PMID:25418063

  6. Reaction of Phenyl Radical with O2: Thermodynamic Properties, Important Reaction Paths and Kinetics

    SciTech Connect

    Bozzelli, J; Sebbar, N; Pitz, W; Bockhorn, H

    2001-04-12

    The Phenyl + O{sub 2} association results in a chemically activated phenyl-peroxy radical which can dissociate to phenoxy radical + O, undergo intramolecular addition of the peroxy radical to several unsaturated carbon sites or react back to phenyl + O{sub 2}. The intramolecular addition channels further react through several paths to ring opening (unsaturated + carbonyl moieties) as well as cyclopentadieny radical + CO{sub 2}. Enthalpy ({Delta}H{sub f(298)}{sup o}), Entropy (S{sub 298}), and heat capacities Cp(T) for species in the decomposition of the ring are evaluated using density functional and ab initio calculations and by comparisons to vinyl + O{sub 2} data of Mebel et al, and phenyl + O{sub 2} data of Hadad et al. Isodesmic reaction analysis is used to estimate enthalpy values of the intermediates and well depths of the adducts. High Pressure limit kinetic parameters are obtained from the calculation results using canonical Transition State Theory. Quantum RRK analysis is utilized to obtain k(E) and modified strong collision or master equation analysis is used for evaluation of pressure fall-off in this complex bimolecular, chemical activation, reaction system. Uncertainty in key barriers is discussed, resulting variations in important reaction product ratios are illustrated, and changes in these branching ratios are evaluated with a detailed reaction mechanism.

  7. Mechanisms of free-radical reactions. XX. Reactivity in the free-radical halogenation reactions of arylfluoroalkanes

    SciTech Connect

    Dneprovskii, A.S.; Eliseenkov, E.V.

    1987-09-20

    The free-radical chlorination and bromination of meta- and para-substituted benzyl fluorides and 1,1-difluoro-2-phenylethane and also the chlorination of 1-fluoro-2-arylethanes by phenylchloroiodonium chloride and the bromination of meta- and para-substituted benzyl bromides were studied by the method of competing reactions. In all cases a good correlation is observed between log k/sub rel/ and the Brown sigma/sup +/ constants. In cases where change in the reactivity in the transition from one reaction series to another is due mainly to the polar effect of the substituent while the selectivity is measured in relation to the polar effect direct relationships are observed between the reactivity and the selectivity.

  8. New aspects in the reaction mechanism of phenol with peroxynitrite: the role of phenoxy radicals.

    PubMed

    Daiber, A; Mehl, M; Ullrich, V

    1998-01-01

    The decomposition of peroxynitrite (PON) in aqueous solutions was investigated by monitoring the release of dioxygen as a function of pH together with the various reaction products generated from phenol. This substrate was used as a mechanistic model for tyrosine nitration in prostacyclin synthase for which we have reported a highly efficient nitration and inhibition by PON (Zou, M., Martin, C., and Ullrich, V. (1997) Biol Chem. 378, 707-713). Nitrite as a contaminant and product of PON generated 4-nitrosophenol and some nitrophenols in the acidic pH range. In the alkaline range high amounts of 4-nitrosophenol originated from the disproportionation of PON yielding dioxygen and NOx species. The hydroxylation of phenol occurred between pH 3 and 8 with a maximum at 4.5. The nitration by PON also required a pH between 4 and 8 but had a second maximum between 10 and 12, suggesting that in this pH range phenolate was the reacting species. All isomeric biphenols were found as dimerization products as well as 4-phenoxyphenol (4-hydroxydiphenyl ether), indicating phenoxy radicals as intermediates. Since anisol when incubated under the same conditions yielded only hydroxylation but virtually no nitration products, it was concluded that nitration of phenolic compounds requires a one-electron oxidation as a primary step, followed by addition of the nitrogen dioxide radical. PMID:9851367

  9. Structural and Mechanistic Analysis through Electronic Spectra: Aqueous Hyponitrite Radical (N2O2-) and Nitrosyl Hyponitrite Anion (N3O3-)

    SciTech Connect

    Valiev, Marat; Lymar, Sergei V.

    2011-11-03

    Aqueous hyponitrite radical (N{sub 2}O{sub 2}{sup -}) and nitrosyl hyponitrite anion (N{sub 3}O{sub 3}{sup -}) species are important intermediates in the reductive chemistry of NO. The structures and absorption spectra of various hydrated isomers of these compounds were investigated in this work using high-level quantum mechanical calculations combined with the explicit classical description of the aqueous environment. For N{sub 2}O{sub 2}{sup -}, comparison of the calculated spectra and energetics with the experimental data reveals that: (1) upon the one-electron oxidation of trans-hyponitrite (ON=NO{sub 2}{sup -}), the trans configuration of the resulting ON=NO{sup -} radical is preserved; (2) although cis- and trans-ON=NO{sup -} are energetically nearly equivalent, the barrier for the trans-cis isomerization is prohibitively high due to the partial double character of the NN bond; (3) the UV spectrum of ON=NO{sup -} was misinterpreted in the earlier pulse radiolysis work and its more recent revision has been justified. For the N{sub 3}O{sub 3}{sup -} ion, the symmetric isomer is the dominant observable species, and the asymmetric isomer contributes little to the experimental spectrum. Coherent analysis of the calculated and experimental data suggests a re-interpretation of the N{sub 2}O{sub 2}{sup -} + NO reaction mechanism, according to which the reaction evenly bifurcates to yield both the symmetric and asymmetric isomers of N{sub 3}O{sub 3}{sup -}. While the latter isomer rapidly decomposes to the final NO{sub 2}{sup -} + N{sub 2}O products, the former isomer is stable toward this decomposition but its formation is reversible with the homolysis equilibrium constant Khom = 2.2 - 10{sup -7} M. Collectively, these results demonstrate that advanced theoretical modeling can be of significant benefit in structural and mechanistic analysis of UV spectra.

  10. Parameterization of phosphine ligands reveals mechanistic pathways and predicts reaction outcomes.

    PubMed

    Niemeyer, Zachary L; Milo, Anat; Hickey, David P; Sigman, Matthew S

    2016-06-01

    The mechanistic foundation behind the identity of a phosphine ligand that best promotes a desired reaction outcome is often non-intuitive, and thus has been addressed in numerous experimental and theoretical studies. In this work, multivariate correlations of reaction outcomes using 38 different phosphine ligands were combined with classic potentiometric analyses to study a Suzuki reaction, for which the site selectivity of oxidative addition is highly dependent on the nature of the phosphine. These studies shed light on the generality of hypotheses regarding the structural influence of different classes of phosphine ligands on the reaction mechanism(s), and deliver a methodology that should prove useful in future studies of phosphine ligands. PMID:27219707

  11. The kinetics and mechanism of an aqueous phase isoprene reaction with hydroxy radical

    NASA Astrophysics Data System (ADS)

    Huang, D.; Zhang, X.; Chen, Z. M.; Zhao, Y.; Shen, X. L.

    2011-03-01

    Aqueous phase chemical processes of organic compounds in the atmosphere have received increasing attention, partly due to their potential contribution to the formation of secondary organic aerosol (SOA). Here, we analyzed the aqueous oxidation of isoprene in clouds and its reaction products, including carbonyl compounds and organic acids. We also performed a laboratory simulation to improve our understanding of the kinetics and mechanisms for the products of aqueous isoprene oxidation that are significant precursors of SOA; these included methacrolein (MACR), methyl vinyl ketone (MVK), methyl glyoxal (MG), and glyoxal (GL). We used a novel chemical titration method to monitor the concentration of isoprene in the aqueous phase. We used a box model to interpret the mechanistic differences between aqueous- and gas-phase OH radical-initiated isoprene oxidations. Our results were the first demonstration of the rate constant for the reaction between isoprene and OH radical in water, 3.50 (± 0.98) × 109 M-1 s-1 at 283 K. Molar yields were determined based on consumed isoprene. Of note, the ratio of the yields of MVK (18.9 ± 0.8%) to MACR (9.0 ± 1.1%) in the aqueous phase isoprene oxidation was approximately double that observed for the corresponding gas phase reaction. We hypothesized that this might be explained by a water-induced enhancement in the self-reaction of a hydroxy isoprene peroxyl radical (HOCH2C(CH3)(O2)CH = CH2) produced in the aqueous reaction. The observed yields for MG and GL were 11.4 ± 0.3% and 3.8 ± 0.1%, respectively. Model simulations indicated that several potential pathways may contribute to the formation of MG and GL. Finally, oxalic acid increased steadily throughout the course of the study, even after isoprene was consumed completely. The observed yield of oxalic acid was 26.2 ± 0.8% at 6 h. The observed carbon balance accounted for ~50% of the consumed isoprene. The presence of high-molecular-weight compounds may have accounted for a

  12. The kinetics and mechanism of an aqueous phase isoprene reaction with hydroxyl radical

    NASA Astrophysics Data System (ADS)

    Huang, D.; Zhang, X.; Chen, Z. M.; Zhao, Y.; Shen, X. L.

    2011-08-01

    Aqueous phase chemical processes of organic compounds in the atmosphere have received increasing attention, partly due to their potential contribution to the formation of secondary organic aerosol (SOA). Here, we analyzed the aqueous OH-initiated oxidation of isoprene and its reaction products including carbonyl compounds and organic acids, regarding the acidity and temperature as in-cloudy conditions. We also performed a laboratory simulation to improve our understanding of the kinetics and mechanisms for the products of aqueous isoprene oxidation that are significant precursors of SOA; these included methacrolein (MACR), methyl vinyl ketone (MVK), methyl glyoxal (MG), and glyoxal (GL). We used a novel chemical titration method to monitor the concentration of isoprene in the aqueous phase. We used a box model to interpret the mechanistic differences between aqueous and gas phase OH radical-initiated isoprene oxidations. Our results were the first demonstration of the rate constant for the reaction between isoprene and OH radical in water, 1.2 ± 0.4) × 1010 M-1 s-1 at 283 K. Molar yields were determined based on consumed isoprene. Of note, the ratio of the yields of MVK (24.1 ± 0.8 %) to MACR (10.9 ± 1.1%) in the aqueous phase isoprene oxidation was approximately double that observed for the corresponding gas phase reaction. We hypothesized that this might be explained by a water-induced enhancement in the self-reaction of a hydroxy isoprene peroxyl radical (HOCH2C(CH3)(O2)CH = CH2) produced in the aqueous reaction. The observed yields for MG and GL were 11.4 ± 0.3 % and 3.8 ± 0.1 %, respectively. Model simulations indicated that several potential pathways may contribute to the formation of MG and GL. Finally, oxalic acid increased steadily throughout the course of the study, even after isoprene was consumed completely. The observed yield of oxalic acid was 26.2 ± 0.8 % at 6 h. The observed carbon balance accounted for ~50 % of the consumed isoprene. The

  13. OH Production from Reactions of Organic Peroxy Radicals with HO2 : Recent Studies on Ether-Derived Peroxy Radicals

    NASA Astrophysics Data System (ADS)

    Orlando, J. J.; Tyndall, G. S.; Kegley Owen, C. S.; Reynoldson, N.

    2013-12-01

    There is now ample evidence supporting significant formation of OH radicals in the reaction of HO2 with certain organic peroxy radicals (RO2). These reaction channels serve to promote radical propagation, and thus have the potential to alter HOx budgets and partitioning and hence tropospheric oxidative capacity. While much focus has been placed on OH production from reactions involving carbonyl-containing RO2 species, it is also the case that other oxygen- substituted peroxy species (e.g., CH3OCH2OO, HOCH2OO) likely generate OH in their reactions with HO2 (see ref. 1 and refs therein). In this work, the Cl-atom-initiated oxidation of two ethers, diethyl and diisopropyl ether, is investigated over ranges of conditions in an environmental chamber, using both FTIR and GC-FID methods for product quantification. Preliminary analysis suggests that significant OH production is occurring in the reaction of HO2 with CH3CH2OCH(OO)CH3, and also provides evidence for a rapid unimolecular reaction of diisopropyl ether-derived peroxy radicals. Details of these and other results will be described. 1. Orlando, J. J., and G. S. Tyndall, 2012: Laboratory studies of organic peroxy radical chemistry: an overview with emphasis on recent issues of atmospheric significance, Chemical Society Reviews, 41, 6294-6317, doi: 10.1039/C2CS35166H.

  14. Synthetic and Mechanistic Studies of Strained Heterocycle Opening Reactions Mediated by Zirconium(IV) Imido Complexes

    PubMed Central

    Blum, Suzanne A.; Rivera, Vicki A.; Ruck, Rebecca T.; Michael, Forrest E.; Bergman, Robert G.

    2005-01-01

    The reactions of the bis(cyclopentadienyl)(tert-butylimido)zirconium complex (Cp2Zr=N-t-Bu)(THF) (1) with epoxides, aziridines, and episulfides were investigated. Heterocycles without accessible β-hydrogens undergo insertion/protonation of the C–X bond to produce 1,2-amino alcohols (X = O) and 1,2-diamines (X = NR), whereas heterocycles with accessible β-hydrogens undergo elimination/protonation to produce allylic alcohols (X = O) and allylic sulfides (X = S). Mechanistic investigations support a stepwise pathway with zwitterionic intermediates for the first reaction class and a concerted pathway for the second reaction class. Additionally, the feasibility of chirality transfer from the planar-chiral ebthi (ebthi = ethylenebis(tetrahydroindenyl)) ligand was demonstrated with a chiral analogue, (ebthi)-Zr=NAr(THF) (Ar = 2,6-dimethylphenyl), 2, through the diastereoselective ring opening of meso epoxides. PMID:16508693

  15. Kinetic studies of the hydroxyl radical reaction with PAHs

    NASA Astrophysics Data System (ADS)

    Ananthula, Rajeshwar

    An existing quartz optical reactor heating system was designed to permit higher temperature kinetic measurements more closely associated with post-combuston conditions (up to 1200 K). A pulsed laser photolysis/pulsed laser-induced fluorescence (PLP/PLIF) technique was then applied with this modified reactor to study the OH radical kinetics with polycyclic aromatic hydrocarbons (PAHs). The kinetics of the reaction of a surrogate three-ring PAH, anthracene (and its deuterated form) with hydroxyl (OH) radicals was investigated over the temperature range of 373 to 1200 K. This study represents the first examination of the OH kinetics for this class of reactions at elevated temperatures (>470 K). The results indicate a complex temperature dependence similar to that observed for simpler aromatic compounds, e.g., benzene. At low temperatures (373-498 K), the rate measurements exhibited Arrhenius behavior (1.82 x 10-11 exp(542.35/T) in units of cm3 molecule -1 s-1) and kinetic isotope effect (KIE) measurements were consistent with an OH addition mechanism. The low temperature results are extrapolated to atmospheric temperatures and compared with previous measurements. Rate measurements between 673 and 923 K exhibited a sharp decrease in the magnitude of the rate coefficients (a factor of 9). KIE measurements under these conditions were still consistent with an OH addition mechanism. The following modified Arrhenius equation is the best fit to our anthracene measurements between 373 and 923 K, 8.17 x 1014 T-8.3 exp(-3171.71/T) (in units of cm3 molecule-1 s-1). For a limited temperature range between 1000 and 1200 K, the rate measurements exhibited an apparent positive temperature dependence with the following Arrhenius equation the best fit to the data, 2.18 x 10-11*exp(-1734.11/T) (in units of cm3molecule-1s -1). KIE measurements above 999 K were slightly larger than unity, but inclusive regarding the mechanism of the reaction. Theoretical calculations of the KIE indicate

  16. Reactions of flavosemiquinone radicals in the presence of metal ions

    NASA Astrophysics Data System (ADS)

    Porkhun, V. I.; Sivko, A. N.; Porkhun, E. V.; Rakhimov, A. I.

    2014-06-01

    The rate constants of disproportionation of flavosemiquinone radicals were obtained by pulsed spectroscopy. The yield of the flavosemiquinone radical increased when Mohr's salt was introduced in the aqueous solutions of riboflavin. The spectral kinetic characteristics of complexes of flavosemiquinone radical anions with Zn2+ and Cd2+ ions were determined.

  17. Medium effects on reactions of the carbonate radical with thiocyanate, iodide, and ferrocyanide ions

    NASA Astrophysics Data System (ADS)

    Lymar, Sergei V.; Schwarz, Harold A.; Czapski, Gidon

    2000-10-01

    Results are presented which show that there is no pH dependence of the carbonate radical reactivity toward SCN -, I -, and Fe(CN) 64- above pH 8.5. It is demonstrated that observations in the literature on these reactions which have been interpreted to show a p Ka of 9.5 for the carbonate radical, in disagreement with other reports that the radical is not protonated in this pH region, can be explained by the medium effects. It is also shown that previous studies of the reaction between carbonate radical and thiocyanate are in error, and the mechanism of this reaction is elucidated.

  18. Electron Spin Resonance Spectroscopic Studies of Radical Cation Reactions.

    NASA Astrophysics Data System (ADS)

    Dai, Sheng

    1990-01-01

    A spin Hamiltonian suitable for theoretical analyses of ESR spectra in this work is derived by using the general effective Hamiltonian theory in the usual Schrodinger representation. The Permutation Indices method is extended to obtain the dynamic exchange equations used in ESR lineshape simulation. The correlation between beta-hydrogen coupling constants and their geometric orientations is derived through the use of a perturbation method. The three electron bond model is extended to rationalize unimolecular rearrangements of radical cations. The ring-closed radical cations of 9,10-octalin oxide and syn-sesquinorbornene oxide have been characterized by ESR spectroscopy in the CFCl_3 matrix at low temperature. The ESR spectra of the former radical cation exhibit a novel alternating linewidth effect arising from an internal relation between the coupling constants for the four equivalent pairs of hydrogens. The self-electron-transfer rate constants between the methyl viologen dication and cation have been determined by dynamic ESR lineshape simulations at room temperature in allyl alcohol, water, methanol and propargyl alcohol solvents. The radical cation formed by the radiolytic oxidation of allylamine in Freon matrices at 77 K is shown to be the 3-iminiopropyl distonic species(3-iminium-1-propyl radical) resulting from a symmetry-allowed 1,2-hydrogen shift in the parent radical cation. The nucleophilic endocyclization of the but-3-en-1-ol radical cation to the protonated tetrahydrofuran -3-yl radical was observed in the radiolytic oxidation of but-3-en-1-ol in Freon matrices. ESR studies of the radiolytic oxidation of 1,5-hexadiyne have resulted in the first spectroscopic characterization of the radical cation Cope rearrangement, the 1,5-hexadiyne radical cation isomerizing to the 1,2,4,5 -hexatetraene radical cation. ESR studies show that the symmetric(C_{rm 2v}) bicyclo (3.3.0) -octa-2,6-diene-4,8-diyl(a bridged 1,4 -bishomobenzene species) radical cation is

  19. Reaction of oleic acid particles with NO3 radicals: Products, mechanism, and implications for radical-initiated organic aerosol oxidation.

    PubMed

    Docherty, Kenneth S; Ziemann, Paul J

    2006-03-16

    The heterogeneous reaction of liquid oleic acid aerosol particles with NO3 radicals in the presence of NO2, N2O5, and O2 was investigated in an environmental chamber using a combination of on-line and off-line mass spectrometric techniques. The results indicate that the major reaction products, which are all carboxylic acids, consist of hydroxy nitrates, carbonyl nitrates, dinitrates, hydroxydinitrates, and possibly more highly nitrated products. The key intermediate in the reaction is the nitrooxyalkylperoxy radical, which is formed by the addition of NO3 to the carbon-carbon double bond and subsequent addition of O2. The nitrooxyalkylperoxy radicals undergo self-reactions to form hydroxy nitrates and carbonyl nitrates, and may also react with NO2 to form nitrooxy peroxynitrates. The latter compounds are unstable and decompose to carbonyl nitrates and dinitrates. It is noteworthy that in this reaction nitrooxyalkoxy radicals appear not to be formed, as indicated by the absence of the expected products of decomposition or isomerization of these species. This is different from gas-phase alkene-NO3 reactions, in which a large fraction of the products are formed through these pathways. The results may indicate that, for liquid organic aerosol particles in low NOx environments, the major products of the radical-initiated oxidation (including by OH radicals) of unsaturated and saturated organic compounds will be substituted forms of the parent compound rather than smaller decomposition products. These compounds will remain in the particle and can potentially enhance particle hygroscopicity and the ability of particles to act as cloud condensation nuclei. PMID:16526637

  20. Mechanistic studies of an unprecedented enzyme-catalyzed 1,2-phosphono migration reaction

    PubMed Central

    Chang, Wei-chen; Dey, Mishtu; Liu, Pinghua; Mansoorabadi, Steven O.; Moon, Sung-Ju; Zhao, Zongbao K.; Drennan, Catherine L.; Liu, Hung-wen

    2013-01-01

    (S)-2-Hydroxypropylphosphonate ((S)-2-HPP) epoxidase (HppE) is a mononuclear non-heme iron-dependent enzyme1,2,3 responsible for the last step in the biosynthesis of the clinically useful antibiotic fosfomycin4. Enzymes of this class typically catalyze oxygenation reactions that proceed via the formation of substrate radical intermediates. In contrast, HppE catalyzes an unusual dehydrogenation reaction while converting the secondary alcohol of (S)-2-HPP to the epoxide ring of fosfomycin1,5. HppE is shown here to also catalyze a biologically unprecedented 1,2-phosphono migration with the alternative substrate (R)-1-HPP. This transformation likely involves an intermediary carbocation based on observations with additional substrate analogues, such as (1R)-1-hydroxy-2-aminopropylphosphonate, and model reactions for both radical- and carbocation-mediated migration. The ability of HppE to catalyze distinct reactions depending on the regio- and stereochemical properties of the substrate is given a structural basis using X-ray crystallography. These results provide compelling evidence for the formation of a substrate-derived cation intermediate in the catalytic cycle of a mononuclear non-heme iron-dependent enzyme. The underlying chemistry of this unusual phosphono migration may represent a new paradigm for the in vivo construction of phosphonate-containing natural products that can be exploited for the preparation of novel phosphonate derivatives. PMID:23552950

  1. Selective Radical-Radical Cross-Couplings: Design of a Formal β-Mannich Reaction.

    PubMed

    Jeffrey, Jenna L; Petronijević, Filip R; MacMillan, David W C

    2015-07-01

    A direct β-coupling of cyclic ketones with imines has been accomplished via the synergistic combination of photoredox catalysis and organocatalysis. Transient β-enaminyl radicals derived from ketones via enamine and oxidative photoredox catalysis readily combine with persistent α-amino radicals in a highly selective hetero radical-radical coupling. This novel pathway to γ-aminoketones is predicated upon the use of DABCO as both a base and an electron transfer agent. This protocol also formally allows for the direct synthesis of β-Mannich products via a chemoselective three-component coupling of aryl aldehydes, amines, and ketones. PMID:26075347

  2. Isomerization and decomposition reactions in the pyrolysis of branched hydrocarbons: 4-methyl-1-pentyl radical.

    PubMed

    McGivern, W Sean; Awan, Iftikhar A; Tsang, Wing; Manion, Jeffrey A

    2008-07-31

    The kinetics of the decomposition of 4-methyl-1-pentyl radicals have been studied from 927-1068 K at pressures of 1.78-2.44 bar using a single pulse shock tube with product analysis. The reactant radicals were formed from the thermal C-I bond fission of 1-iodo-4-methylpentane, and a radical inhibitor was used to prevent interference from bimolecular reactions. 4-Methyl-1-pentyl radicals undergo competing decomposition and isomerization reactions via beta-bond scission and 1, x-hydrogen migrations (x = 4, 5), respectively, to form short-chain radicals and alkenes. Major alkene products, in decreasing order of concentration, were propene, ethene, isobutene, and 1-pentene. The observed products are used to validate a RRKM/master equation (ME) chemical kinetics model of the pyrolysis. The presence of the branched methyl moiety has a significant impact on the observed reaction rates relative to analogous reaction rates in straight-chain radical systems. Systems that result in the formation of substituted radical or alkene products are found to be faster than reactions that form primary radical and alkene species. Pressure-dependent reaction rate constants from the RRKM/ME analysis are provided for all four H-transfer isomers at 500-1900 K and 0.1-1000 bar pressure for all of the decomposition and isomerization reactions in this system. PMID:18613654

  3. Detection of free radicals produced from the reaction of cytochrome P-450 with linoleic acid hydroperoxide.

    PubMed Central

    Rota, C; Barr, D P; Martin, M V; Guengerich, F P; Tomasi, A; Mason, R P

    1997-01-01

    The ESR spin-trapping technique was employed to investigate the reaction of rabbit cytochrome P-450 1A2 (P450) with linoleic acid hydroperoxide. This system was compared with chemical systems where FeSO4 or FeCl3 was used in place of P450. The spin trap 5, 5'-dimethyl-1-pyrroline N-oxide (DMPO) was employed to detect and identify radical species. The DMPO adducts of hydroxyl, O2-., peroxyl, methyl and acyl radicals were detected in the P450 system. The reaction did not require NADPH-cytochrome P-450 reductase or NADPH. The same DMPO-radical adducts were detected in the FeSO4 system. Only DMPO-.OH radical adduct and carbon-centred radical adducts were detected in the FeCl3 system. Peroxyl radical production was completely O2-dependent. We propose that polyunsaturated fatty acids are initially reduced to form alkoxyl radicals, which then undergo intramolecular rearrangement to form epoxyalkyl radicals. Each epoxyalkyl radical reacts with O2, forming a peroxyl radical. Subsequent unimolecular decomposition of this peroxyl radical eliminates O2-. radical. PMID:9371716

  4. Reactions of Hydroxyalkyl Radicals with Cysteinyl Peptides in a NanoESI Plume

    NASA Astrophysics Data System (ADS)

    Stinson, Craig A.; Xia, Yu

    2014-07-01

    In biological systems, carbon-centered small molecule radicals are primarily formed via external radiation or internal radical reactions. These radical species can react with a variety of biomolecules, most notably nucleic acids, the consequence of which has possible links to gene mutation and cancer. Sulfur-containing peptides and proteins are reactive toward a variety of radical species and many of them behave as radical scavengers. In this study, the reactions between alkyl alcohol carbon-centered radicals (e.g., •CH2OH for methanol) and cysteinyl peptides within a nanoelectrospray ionization (nanoESI) plume were explored. The reaction system involved ultraviolet (UV) irradiation of a nanoESI plume using a low pressure mercury lamp consisting of 185 and 254 nm emission bands. The alkyl alcohol was added as solvent into the nanoESI solution and served as the precursor of hydroxyalkyl radicals upon UV irradiation. The hydroxyalkyl radicals subsequently reacted with cysteinyl peptides either containing a disulfide linkage or free thiol, which led to the formation of peptide- S-hydroxyalkyl product. This radical reaction coupled with subsequent MS/MS was shown to have analytical potential by cleaving intrachain disulfide linked peptides prior to CID to enhance sequence information. Tandem mass spectrometry via collision-induced dissociation (CID), stable isotope labeling, and accurate mass measurement were employed to verify the identities of the reaction products.

  5. Palladium(0)/NHC-Catalyzed Reductive Heck Reaction of Enones: A Detailed Mechanistic Study.

    PubMed

    Raoufmoghaddam, Saeed; Mannathan, Subramaniyan; Minnaard, Adriaan J; de Vries, Johannes G; Reek, Joost N H

    2015-12-14

    We have studied the mechanism of the palladium-catalyzed reductive Heck reaction of para-substituted enones with 4-iodoanisole by using N,N-diisopropylethylamine (DIPEA) as the reductant. Kinetic studies and in situ spectroscopic analysis have provided a detailed insight into the reaction. Progress kinetic analysis demonstrated that neither catalyst decomposition nor product inhibition occurred during the catalysis. The reaction is first order in the palladium and aryl iodide, and zero order in the activated alkene, N-heterocyclic carbene (NHC) ligand, and DIPEA. The experiments with deuterated solvent ([D7]DMF) and deuterated base ([D15]Et3N) supported the role of the amine as a reductant in the reaction. The palladium complex [Pd(0)(NHC)(1)] has been identified as the resting state. The kinetic experiments by stopped-flow UV/Vis also revealed that the presence of the second substrate, benzylideneacetone 1, slows down the oxidative addition of 4-iodoanisole through its competing coordination to the palladium center. The kinetic and mechanistic studies indicated that the oxidative addition of the aryl iodide is the rate-determining step. Various scenarios for the oxidative addition step have been analyzed by using DFT calculations (bp86/def2-TZVP) that supported the inhibiting effect of substrate 1 by formation of resting state [Pd(0)(NHC)(1)] species at the cost of further increase in the energy barrier of the oxidative addition step. PMID:26561034

  6. Structural and Mechanistic Analysis through Electronic Spectra: Aqueous Hyponitrite Radical (N(2)O(2)(-)) and Nitrosyl Hyponitrite Anion (N(3)O(3)(-))

    SciTech Connect

    Lymar S. V.; Valiev M.

    2011-11-03

    Aqueous hyponitrite radical (N{sub 2}O{sub 2}{sup -}) and nitrosyl hyponitrite anion (N{sub 3}O{sub 3}{sup -}) are important intermediates in the reductive chemistry of NO. The structures and absorption spectra of various hydrated isomers of these compounds were investigated in this work using high-level quantum mechanical calculations combined with the explicit classical description of the aqueous environment. For N{sub 2}O{sub 2}{sup -}, comparison of the calculated spectra and energetics with the experimental data reveals that (1) upon the one-electron oxidation of trans-hyponitrite (ON{double_bond}NO{sup 2-}), the trans configuration of the resulting ON{double_bond}NO{sup -} radical is preserved; (2) although cis- and trans-ON{double_bond}NO{sup -} are energetically nearly equivalent, the barrier for the trans-cis isomerization is prohibitively high because of the partial double character of the NN bond; (3) the calculations confirm that the UV spectrum of ONNO{sup -} was misinterpreted in the earlier pulse radiolysis work, and its more recent revision has been justified. For the N{sub 3}O{sub 3}{sup -} ion, the symmetric isomer the dominant observable species, and the asymmetric isomer contributes insignificantly to the experimental spectrum. Coherent analysis of the calculated and experimental data suggests a reinterpretation of the N{sub 2}O{sub 2}{sup -} + NO reaction mechanism according to which the reaction evenly bifurcates to yield both the symmetric and asymmetric isomers of N{sub 3}O{sub 3}{sup -}. While the latter isomer rapidly decomposes to the final NO{sub 2}{sup -} + N{sub 2}O products, the former isomer is stable toward this decomposition, but its formation is reversible with the homolysis equilibrium constant K{sub hom} = 2.2 x 10{sup -7} M. Collectively, these results demonstrate that advanced theoretical modeling can be of significant benefit in structural and mechanistic analysis on the basis of the electronic spectra of aqueous transients.

  7. Laboratory studies of the kinetics of tropospheric and stratospheric atom and radical reactions

    NASA Technical Reports Server (NTRS)

    Golde, Michael F.

    1987-01-01

    Direct measurements of reaction rate constants and branching fractions for elementary reactions necessary in the modeling of the troposphere or stratosphere are provided. Details of reaction mechanisms are elucidated by studying pressure and temperature dependences of reactions, as well as by use of isotopic labels. Measurement techniques are improved for radical species in the laboratory. Progress and results in each area are given.

  8. Quantum trajectory tests of radical-pair quantum dynamics in CIDNP measurements of photosynthetic reaction centers

    NASA Astrophysics Data System (ADS)

    Tsampourakis, K.; Kominis, I. K.

    2015-11-01

    Chemically induced dynamic nuclear polarization is a ubiquitous phenomenon in photosynthetic reaction centers. The relevant nuclear spin observables are a direct manifestation of the radical-pair mechanism. We here use quantum trajectories to describe the time evolution of radical-pairs, and compare their prediction of nuclear spin observables to the one derived from the radical-pair master equation. While our approach provides a consistent description, we unravel a major inconsistency within the conventional theory, thus challenging the theoretical interpretation of numerous CIDNP experiments sensitive to radical-pair reaction kinetics.

  9. Radical-based destruction of nitramines in water: kinetics and efficiencies of hydroxyl radical and hydrated electron reactions.

    PubMed

    Mezyk, Stephen P; Razavi, Behnaz; Swancutt, Katy L; Cox, Casandra R; Kiddle, James J

    2012-08-01

    In support of the potential use of advanced oxidation and reduction process technologies for the removal of carcinogenic nitro-containing compounds in water reaction rate constants for the hydroxyl radical and hydrated electron with a series of low molecular weight nitramines (R(1)R(2)-NNO(2)) have been determined using a combination of electron pulse radiolysis and transient absorption spectroscopy. The hydroxyl radical reaction rate constant was fast, ranging from 0.54-4.35 × 10(9) M(-1) s(-1), and seen to increase with increasing complexity of the nitramine alkyl substituents suggesting that oxidation primarily occurs by hydrogen atom abstraction from the alkyl chains. In contrast, the rate constant for hydrated electron reaction was effectively independent of compound structure, (k(av) = (1.87 ± 0.25) × 10(10) M(-1) s(-1)) indicating that the reduction predominately occurred at the common nitramine moiety. Concomitant steady-state irradiation and product measurements under aerated conditions also showed a radical reaction efficiency dependence on compound structure, with the overall radical-based degradation becoming constant for nitramines containing more than four methylene groups. The quantitative evaluation of these efficiency data suggest that some (~40%) hydrated electron reduction also results in quantitative nitramine destruction, in contrast to previously reported electron paramagnetic measurements on these compounds that proposed that this reduction only produced a transient anion adduct that would transfer its excess electron to regenerate the parent molecule. PMID:22788844

  10. Helical-Peptide-Catalyzed Enantioselective Michael Addition Reactions and Their Mechanistic Insights.

    PubMed

    Ueda, Atsushi; Umeno, Tomohiro; Doi, Mitsunobu; Akagawa, Kengo; Kudo, Kazuaki; Tanaka, Masakazu

    2016-08-01

    Helical peptide foldamer catalyzed Michael addition reactions of nitroalkane or dialkyl malonate to α,β-unsaturated ketones are reported along with the mechanistic considerations of the enantio-induction. A wide variety of α,β-unsaturated ketones, including β-aryl, β-alkyl enones, and cyclic enones, were found to be catalyzed by the helical peptide to give Michael adducts with high enantioselectivities (up to 99%). On the basis of X-ray crystallographic analysis and depsipeptide study, the amide protons, N(2)-H and N(3)-H, at the N terminus in the α-helical peptide catalyst were crucial for activating Michael donors, while the N-terminal primary amine activated Michael acceptors through the formation of iminium ion intermediates. PMID:27384597

  11. Reactions of Co(III)-nitrosyl complexes with superoxide and their mechanistic insights.

    PubMed

    Kumar, Pankaj; Lee, Yong-Min; Park, Young Jun; Siegler, Maxime A; Karlin, Kenneth D; Nam, Wonwoo

    2015-04-01

    New Co(III)-nitrosyl complexes bearing N-tetramethylated cyclam (TMC) ligands, [(12-TMC)Co(III)(NO)](2+) (1) and [(13-TMC)Co(III)(NO)](2+) (2), were synthesized via [(TMC)Co(II)(CH3CN)](2+) + NO(g) reactions. Spectroscopic and structural characterization showed that these compounds bind the nitrosyl moiety in a bent end-on fashion. Complexes 1 and 2 reacted with KO2/2.2.2-cryptand to produce [(12-TMC)Co(II)(NO2)](+) (3) and [(13-TMC)Co(II)(NO2)](+) (4), respectively; these possess O,O'-chelated nitrito ligands. Mechanistic studies using (18)O-labeled superoxide ((18)O2(•-)) showed that one O atom in the nitrito ligand is derived from superoxide and the O2 produced comes from the other superoxide O atom. Evidence supporting the formation of a Co-peroxynitrite intermediate is also presented. PMID:25793706

  12. Free radicals. XXIII. Reaction of triphenylimidazolyl with CH acids

    SciTech Connect

    Tanaseichuk, B.S.; Belozerov, A.I.; Sanaeva, E.P.; Butin, K.P.

    1986-01-10

    The triphenylimidazolyl radical is capable of dehydrogenating ..beta..-dicarbonyl compounds which are characterized by a high content of the enolic form. The dehydrogenation rate increases with increase in the pK/sub a/ value of the enol. The formation of short-lived radicals during the dehydrogenation of CH acids by triphenylimidazolyl was confirmed by their capture by a spin trap (2,4,6-tribromo-nitrosobenzene). The diphenylaminyl radical also dehydrogenates nonenolizing CH acids with a sufficiently acid CH bond.

  13. An electron spin resonance study of the reactions of lipid peroxyl radicals with antioxidants

    SciTech Connect

    Zhu, J.; Johnson, W.J.; Sevilla, C.L.; Herrington, J.W.; Sevilla, M.D. )

    1990-09-06

    The reactions of lipid carbon-centered radicals and their corresponding peroxyl radicals (RO{sub 2}{sup {sm bullet}}, LO{sub 2}{sup {sm bullet}}) with five phenolic antioxidants (BHT, BHA, PG, TBHQ, and vitamin E) in frozen saturated and unsaturated lipids at low temperatures have been elucidated through electron spin resonance spectroscopy. The lipid radicals are formed after the {gamma} or UV irradiation of the lipid matrices in the absence or presence of oxygen at 77 K. Upon warming oxygenated samples to 135 K, molecular oxygen adds to the carbon radicals forming peroxyl radicals. At 170 K peroxyl radicals in tributyrin react with added antioxidants (AH) to form antioxidant radicals (A{sup {sm bullet}}). The relative rates of reactions of these five antioxidants with the peroxyl radical of tributyrin decrease in the order BHT > TBHQ > E {>=} PG > BHA. For the reactions with triolein and trilinolein peroxyl radicals, the order of reactivity is BHT > E > BHA > TBHQ. This difference in reaction order of antioxidants in tributyrin and unsaturated lipids is explained by a dispersion model of antioxidants in lipid matrices.

  14. Dynamic Kinetic Resolution Enabled by Intramolecular Benzoin Reaction: Synthetic Applications and Mechanistic Insights.

    PubMed

    Zhang, Guoxiang; Yang, Shuang; Zhang, Xiaoyan; Lin, Qiqiao; Das, Deb K; Liu, Jian; Fang, Xinqiang

    2016-06-29

    The highly enantio-, diastereo-, and regioselective dynamic kinetic resolution of β-ketoesters and 1,3-diketones was achieved via a chiral N-heterocyclic carbene catalyzed intramolecular cross-benzoin reaction. A variety of tetralone derivatives bearing two contiguous stereocenters and multiple functionalities were liberated in moderate to excellent yields and with high levels of stereoselectivity (>95% ee and >20:1 dr in most cases). In addition, the excellent regioselectivity control for aryl/alkyl 1,3-diketones, and the superior electronic differentiation of 1,3-diarylketones were highlighted. Moreover, a set of new mechanistic rationale that differs with the currently widely accepted understanding of intramolecular benzoin reactions was established to demonstrate the superior preference of benzoin over aldol transformation: (1) A coexistence of competitive aldol and benzoin reactions was detected, but a retro-aldol-irreversible benzoin process performs a vital role in the generation of predominant benzoin products. (2) The most essential role of an N-electron-withdrawing substituent in triazolium catalysts was revealed to be accelerating the rate of the benzoin transformation, rather than suppressing the aldol process through reducing the inherent basicity of the catalyst. PMID:27270409

  15. Vibrational Excitation of Both Products of the Reaction of CN Radicals with Acetone in Solution

    PubMed Central

    2015-01-01

    Transient electronic and vibrational absorption spectroscopy unravel the mechanisms and dynamics of bimolecular reactions of CN radicals with acetone in deuterated chloroform solutions. The CN radicals are produced by ultrafast ultraviolet photolysis of dissolved ICN. Two reactive forms of CN radicals are distinguished by their electronic absorption bands: “free” (uncomplexed) CN radicals, and “solvated” CN radicals that are complexed with solvent molecules. The lifetimes of the free CN radicals are limited to a few picoseconds following their photolytic production because of geminate recombination to ICN and INC, complexation with CDCl3 molecules, and reaction with acetone. The acetone reaction occurs with a rate coefficient of (8.0 ± 0.5) × 1010 M–1 s–1 and transient vibrational spectra in the C=N and C=O stretching regions reveal that both the nascent HCN and 2-oxopropyl (CH3C(O)CH2) radical products are vibrationally excited. The rate coefficient for the reaction of solvated CN with acetone is 40 times slower than for free CN, with a rate coefficient of (2.0 ± 0.9) × 109 M–1 s–1 obtained from the rise in the HCN product v1(C=N stretch) IR absorption band. Evidence is also presented for CN complexes with acetone that are more strongly bound than the CN–CDCl3 complexes because of CN interactions with the carbonyl group. The rates of reactions of these more strongly associated radicals are slower still. PMID:26192334

  16. Vibrational Excitation of Both Products of the Reaction of CN Radicals with Acetone in Solution.

    PubMed

    Dunning, Greg T; Preston, Thomas J; Greaves, Stuart J; Greetham, Gregory M; Clark, Ian P; Orr-Ewing, Andrew J

    2015-12-17

    Transient electronic and vibrational absorption spectroscopy unravel the mechanisms and dynamics of bimolecular reactions of CN radicals with acetone in deuterated chloroform solutions. The CN radicals are produced by ultrafast ultraviolet photolysis of dissolved ICN. Two reactive forms of CN radicals are distinguished by their electronic absorption bands: "free" (uncomplexed) CN radicals, and "solvated" CN radicals that are complexed with solvent molecules. The lifetimes of the free CN radicals are limited to a few picoseconds following their photolytic production because of geminate recombination to ICN and INC, complexation with CDCl3 molecules, and reaction with acetone. The acetone reaction occurs with a rate coefficient of (8.0 ± 0.5) × 10(10) M(-1) s(-1) and transient vibrational spectra in the C═N and C═O stretching regions reveal that both the nascent HCN and 2-oxopropyl (CH3C(O)CH2) radical products are vibrationally excited. The rate coefficient for the reaction of solvated CN with acetone is 40 times slower than for free CN, with a rate coefficient of (2.0 ± 0.9) × 10(9) M(-1) s(-1) obtained from the rise in the HCN product v1(C═N stretch) IR absorption band. Evidence is also presented for CN complexes with acetone that are more strongly bound than the CN-CDCl3 complexes because of CN interactions with the carbonyl group. The rates of reactions of these more strongly associated radicals are slower still. PMID:26192334

  17. Time-resolved FTIR emission studies of laser photofragmentation and radical reactions

    SciTech Connect

    Leone, S.R.

    1993-12-01

    Recent studies have focused specifically on collision processes, such as single collision energy transfer, reaction dynamics, and radical reactions. The authors employ novel FTIR techniques in the study of single collision energy transfer processes using translationally fast H atom, as well as radical-radical reactions, e.g. CH{sub 3} + O, CF{sub 3} + H(D), and Cl + C{sub 2}H{sub 5}. The fast atoms permit unique high energy regions of certain transition states of combustion species to be probed for the first time.

  18. Exploiting time-resolved magnetic field effects for determining radical ion reaction rates

    NASA Astrophysics Data System (ADS)

    Bessmertnykh, A. O.; Borovkov, V. I.; Bagryansky, V. A.; Molin, Yu N.

    2016-07-01

    The capabilities of the method of time-resolved magnetic field effect in determining the rates of charge transfer reactions between radical ions and molecules on a nanosecond time scale have been investigated. The approach relies on the electron spin coherence in radical pair's partners generated by ionizing radiation. The spin evolution of the pair is sensitive to the reaction since the latter results in changing magnetic interactions of the unpaired electron. This process can be monitored by magnetic-field-sensitive fluorescence from an irradiated sample that is illustrated using reactions involving alkane radical cations. The accuracy and limitations of the approach are discussed.

  19. Comparing the gas-phase fragmentation reactions of protonated and radical cations of the tripeptides GXR

    NASA Astrophysics Data System (ADS)

    Wee, Sheena; O'Hair, Richard A. J.; McFadyen, W. David

    2004-05-01

    Electrospray ionization (ESI) mass spectrometry of methanolic solutions of mixtures of the copper salt (2,2':6',2''-terpyridine)copper(II) nitrate monohydrate ([Cu(II)(tpy)(NO3)2].H2O) and a tripeptide GXR (where X = 1 of the 20 naturally occurring amino acids) yielded [Cu(II)(tpy)(GXR)][radical sign]2+ ions, which were then subjected to collision induced dissociation (CID). In all but one case (GRR), these [Cu(II)(tpy)(GXR)][radical sign]2+ ions fragment to form odd electron GXR[radical sign]+ radical cations with sufficient abundance to examine their gas-phase fragmentation reactions. The GXR[radical sign]+ radical cations undergo a diverse range of fragmentation reactions which depend on the nature of the side chain of X. Many of these reactions can be rationalized as arising from the intermediacy of isomeric distonic ions in which the charge (i.e. proton) is sequestered by the highly basic arginine side chain and the radical site is located at various positions on the tripeptide including the peptide back bone and side chains. The radical sites in these distonic ions often direct the fragmentation reactions via the expulsion of small radicals (to yield even electron ions) or small neutrals (to form radical cations). Both classes of reaction can yield useful structural information, allowing for example, distinction between leucine and isoleucine residues. The gas-phase fragmentation reactions of the GXR[radical sign]+ radical cations are also compared to their even electron [GXR+H]+ and [GXR+2H]2+ counterparts. The [GXR+H]+ ions give fewer sequence ions and more small molecule losses while the [GXR+2H]2+ ions yield more sequence information, consistent with the [`]mobile proton model' described in previous studies. In general, all three classes of ions give complementary structural information, but the GXR[radical sign]+ radical cations exhibit a more diverse loss of small species (radicals and neutrals). Finally, links between these gas-phase results and key

  20. Kinetic analysis of free-radical reactions in the low-temperature autoxidation of triglycerides

    SciTech Connect

    Zhu, Jingmin; Sevilla, M.D. )

    1990-02-22

    The kinetics of the low-temperature autoxidation of triglycerides has been investigated by electron spin resonance spectroscopy. After initial radical production, four reaction stages are found in the overall autoxidation of unsaturated lipids: (1) formation of peroxyl radicals by addition of molecular oxygen to the initial carbon radicals, (2) consumption of oxygen in the autoxidation cycle, (3) decay of the lipid peroxyl radical into allylic and pentadienyl radicals, and (4) recombination of the carbon-centered radicals. Peroxyl radical decay in saturated lipids follows second-order kinetics with an apparent activation energy of ca. 50 kJ/mol. The authors find that, for polyunsaturated lipids, even at quite low temperatures (120 K), the autoxidation process occurs readily and must be considered in the storage of biological samples.

  1. Reactions of methyl radicals with silica supported silver nanoparticles in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Zidki, Tomer; Hänel, Andreas; Bar-Ziv, Ronen

    2016-07-01

    Silica supported silver nanoparticles (Ag°-SiO2-NCs, NCs=nanocomposites) suspended in aqueous solutions are efficient catalysts for the dimerization of methyl radicals to produce ethane, while bare silica is quite inert towards the interaction with methyl radicals. In the presence of small amounts of ethanol adsorbed on the SiO2 surface, the reaction path with methyl radicals is changed and methane is formed as the major product.

  2. Radical cascade reaction of alkynes with N-fluoroarylsulfonimides and alcohols.

    PubMed

    Zheng, Guangfan; Li, Yan; Han, Jingjie; Xiong, Tao; Zhang, Qian

    2015-01-01

    Cascade reactions initiated by radical addition to alkynes are synthetically very attractive because they enable access to highly complex molecular skeletons in only few synthetic steps under usually mild conditions. Here we report a general radical cascade reaction of alkynes, N-fluoroarylsulfonimides and alcohols, enabling the efficient synthesis of important α-amino-α-aryl ketones from readily available starting materials via a single operation. During this process, the highly regioselective nitrogen-centred radical addition to internal and terminal alkynes generating vinyl radicals and the next explicit migration of aryl group from the nitrogen source lead the following efficient desulfonylation, oxygenation, and semi-pinacol rearrangement. In addition, the semi-pinacol rearrangement precursors, α-alkyloxyl-α,α-diaryl imines, could also be efficiently obtained under milder conditions. This methodology might open a new entry for designing intermolecular radical cascade reaction of alkynes. PMID:25901840

  3. Coherent chemical kinetics as quantum walks. I. Reaction operators for radical pairs

    NASA Astrophysics Data System (ADS)

    Chia, A.; Tan, K. C.; Pawela, Ł.; Kurzyński, P.; Paterek, T.; Kaszlikowski, D.

    2016-03-01

    Classical chemical kinetics uses rate-equation models to describe how a reaction proceeds in time. Such models are sufficient for describing state transitions in a reaction where coherences between different states do not arise, in other words, a reaction that contains only incoherent transitions. A prominent example of a reaction containing coherent transitions is the radical-pair model. The kinetics of such reactions is defined by the so-called reaction operator that determines the radical-pair state as a function of intermediate transition rates. We argue that the well-known concept of quantum walks from quantum information theory is a natural and apt framework for describing multisite chemical reactions. By composing Kraus maps that act only on two sites at a time, we show how the quantum-walk formalism can be applied to derive a reaction operator for the standard avian radical-pair reaction. Our reaction operator predicts the same recombination dephasing rate as the conventional Haberkorn model, which is consistent with recent experiments [K. Maeda et al., J. Chem. Phys. 139, 234309 (2013), 10.1063/1.4844355], in contrast to previous work by Jones and Hore [J. A. Jones and P. J. Hore, Chem. Phys. Lett. 488, 90 (2010), 10.1016/j.cplett.2010.01.063]. The standard radical-pair reaction has conventionally been described by either a normalized density operator incorporating both the radical pair and reaction products or a trace-decreasing density operator that considers only the radical pair. We demonstrate a density operator that is both normalized and refers only to radical-pair states. Generalizations to include additional dephasing processes and an arbitrary number of sites are also discussed.

  4. EFFECTS OF RING STRAIN ON GAS-PHASE RATE CONSTANTS. 2. OH RADICAL REACTIONS WITH CYCLOALKENES

    EPA Science Inventory

    Relative rate constants for the gas phase reactions of OH radicals with a series of cycloalkenes have been determined at 298 + or - 2 K, using methyl nitrite photolysis in air as a source of OH radicals. The data show that the rate constants for the nonconjugated cycloalkenes stu...

  5. Mn-, Fe-, and Co-Catalyzed Radical Hydrofunctionalizations of Olefins.

    PubMed

    Crossley, Steven W M; Obradors, Carla; Martinez, Ruben M; Shenvi, Ryan A

    2016-08-10

    Cofactor-mimetic aerobic oxidation has conceptually merged with catalysis of syngas reactions to form a wide range of Markovnikov-selective olefin radical hydrofunctionalizations. We cover the development of the field and review contributions to reaction invention, mechanism, and application to complex molecule synthesis. We also provide a mechanistic framework for understanding this compendium of radical reactions. PMID:27461578

  6. Restricted mass transport effects on free radical reactions

    NASA Astrophysics Data System (ADS)

    Buchanan, A. C., III; Britt, P. F.; Thomas, K. B.

    Coal possesses a complex chemical and physical structure. The cross-linked, network structure can lead to alterations in normal thermally-induced, free-radical decay pathways as a consequence of restrictions on mass transport. Moreover, in coal liquefaction, access of an external hydrogen donor to a reactive radical site can be hindered by the substantial domains of microporosity present in coals. However, previous work indicates that diffusion effects do not appear to be playing an important role in this coal conversion chemistry. Several possible explanations for this phenomenon were advanced including the potential involvement of a hydrogen hopping/radical relay mechanism recently discovered model systems in the authors' laboratories. The authors have employed silica-anchored compounds to explore the effects of restricted mass transport on the pyrolysis mechanisms of coal model compounds. In studies of two-component systems, cases have been discovered where radical centers can be rapidly relocated in the diffusionally constrained environment as a consequence of rapid serial hydrogen atom transfers. This chemistry can have substantial effects on thermal decomposition rates and on product selectivities. In this study, the authors examine additional surfaces to systematically investigate the impact of molecular structure on the hydrogen atom transfer promoted radical relay mechanism. Silica-attached 1,3-diphenylpropane (approximately Ph(CH2)3Ph, or approximately DPP) was chosen as the thermally reactive component, since it can be considered prototypical of linkages in coal that do not contain weak bonds easily cleaved at coal liquefaction temperatures (ca. 4000 C), but which crack at reasonable rates if benzylic radicals can be generated by hydrogen abstraction. The rate of such hydrogen transfers under restricted diffusion will be highly dependent on the structure and proximity of neighboring molecules.

  7. Radical Coupling Reactions in Lignin Synthesis: A Density Functional Theory Study

    SciTech Connect

    Sangha, A. K.; Parks, J. M.; Standaert, R. F.; Ziebell, A.; Davis, M.; Smith, J. C.

    2012-04-26

    Lignin is a complex, heterogeneous polymer in plant cell walls that provides mechanical strength to the plant stem and confers resistance to degrading microbes, enzymes, and chemicals. Lignin synthesis initiates through oxidative radical-radical coupling of monolignols, the most common of which are p-coumaryl, coniferyl, and sinapyl alcohols. Here, we use density functional theory to characterize radical-radical coupling reactions involved in monolignol dimerization. We compute reaction enthalpies for the initial self- and cross-coupling reactions of these monolignol radicals to form dimeric intermediates via six major linkages observed in natural lignin. The 8-O-4, 8-8, and 8-5 coupling are computed to be the most favorable, whereas the 5-O-4, 5-5, and 8-1 linkages are less favorable. Overall, p-coumaryl self- and cross-coupling reactions are calculated to be the most favorable. For cross-coupling reactions, in which each radical can couple via either of the two sites involved in dimer formation, the more reactive of the two radicals is found to undergo coupling at its site with the highest spin density.

  8. Reaction mechanisms of secondary and tertiary amines with OH and NO3 radicals

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Emissions of aliphatic amines are common near agricultural facilities such as animal feed lots. Determining the reactions of these amines with common atmospheric radicals is important to understanding both daytime and nighttime atmospheric chemistry. Several smog chamber experiments were conducted ...

  9. Free radical reactions and antioxidant activities of sesamol: pulse radiolytic and biochemical studies.

    PubMed

    Joshi, Ravi; Kumar, M Sudheer; Satyamoorthy, K; Unnikrisnan, M K; Mukherjee, Tulsi

    2005-04-01

    Sesamol (from Sesamum indicum) is a dietary compound, which is soluble in aqueous as well as lipid phases. Free radical scavenging reactions of sesamol, 5-hydroxy-1,3-benzodioxole, have been studied using a nanosecond pulse radiolysis technique. Sesamol efficiently scavenges hydroxyl, one-electron oxidizing, organo-haloperoxyl, lipid peroxyl, and tryptophanyl radicals. Its antioxidant activity has also been evaluated with cyclic voltammetry. In biochemical studies, it has been found to inhibit lipid peroxidation, hydroxyl radical-induced deoxyribose degradation, and DNA cleavage. These antioxidant and free radical scavenging activities of sesamol have been reported in the paper. PMID:15796613

  10. Structure and reactions of cation-radicals of esters in freon matrices

    SciTech Connect

    Belevskii, V.N.; Belopushkin, S.I.; Fel'dman, V.I.

    1987-11-01

    In CFCl/sub 3/ matrices the cation-radicals of methyl and ethyl formates, formed in ..gamma..-irradiated solutions, at 77 K efficiently undergo intramolecular H atom transfer to form the secondary cation-radicals HC(OH)OCH/sub 2/CH/sub 2/ and DC(OH)OCD/sub 2/CH/sub 2/. This process does not occur in the deuteroformate cation-radical DCOOCH/sub 2/CD/sub 3//sup +./, which is observed in the ESR spectra in different conformations, depending on the temperature. Ion-molecule reactions involving cation-radicals are indicated

  11. Organic radicals for the enhancement of oxygen reduction reaction in Li-O2 batteries.

    PubMed

    Tesio, A Y; Blasi, D; Olivares-Marín, M; Ratera, I; Tonti, D; Veciana, J

    2015-12-25

    We examine for the first time the ability of inert carbon free-radicals as soluble redox mediators to catalyze and enhance the oxygen reduction reaction in a (TEGDME)-based electrolyte. We demonstrate that the tris(2,4,6-trichlorophenyl)methyl (TTM) radical is capable of chemically favoring the oxygen reduction reaction improving significantly the Li-O2 battery performance. PMID:26488114

  12. Cascade Reaction of Donor-Acceptor Cyclopropanes: Mechanistic Studies on Cycloadditions with Nitrosoarenes and cis-Diazenes.

    PubMed

    Chidley, Tristan; Vemula, Naresh; Carson, Cheryl A; Kerr, Michael A; Pagenkopf, Brian L

    2016-06-17

    Tandem ring opening, elimination, and cycloaddition of donor-acceptor cyclopropanes were observed in Yb(OTf)3-catalyzed cycloaddition with nitrosoarenes. The reaction results in formation of tetrahydro-1,2-oxazine instead of the normal cycloadduct isoxazolidine via in situ nitrone formation. A similar cascade sequence was observed with cis-diazines. Mechanistic studies on this unique transformation offer an entirely new approach for reaction design with donor-acceptor cyclopropanes. PMID:27267360

  13. PRODUCTS OF THE GAS-PHASE REACTIONS OF THE OH RADICAL WITH N-BUTYL METHYL ETHER AND 2-ISOPROPOXYETHANOL: REACTIONS OF ROC(O)< RADICALS. (R825252)

    EPA Science Inventory

    The products of the gas-phase reactions of the OH radical with n-butyl methyl ether and 2-isopropoxyethanol in the presence of NO have been investigated at 298 ? 2 K and 740 Torr total pressure of air by gas chromatography and in situ atmospheric pressure ionization...

  14. Reaction of diethyl maleate and diethyl fumarate with hydrated electrons and hydroxyl radicals

    NASA Astrophysics Data System (ADS)

    Bíró, Á.; Wojnárovits, L.

    1996-03-01

    In dilute aqueous solution diethyl maleate (DEM) and diethyl fumarate (DEF) scavenge hydrated electrons with a rate constant of 2.2·10 10 mol -1 dm 3 s -1. DEM - reversibly protonates with pK a = 5.2. The pK a of DEF - is below 4. The electron adducts decay in second order reactions. The OH radicals add to the double bonds with 5.9·10 9 mol -1 dm 3 s -1. In the reaction α-carboxyalkyl radicals are produced. In disproportionation of radicals oxalacetic acid ethylester forms that in alkaline solution leads to strong permanent absorbency in the UV.

  15. Effects of electron acceptors and radical scavengers on nonchain radical nucleophilic substitution reactions

    SciTech Connect

    Xianman Zhang; Dilun Yang; Youcheng Liu )

    1993-01-01

    The yields of reaction products from thermal nucleophilic substitution reactions in dimethyl sulfoxide (DMSO) of six o- and p-nitrohalobenzenes with the sodium salt of ethyl [alpha]-cyanoacetate carbanion [Na[sup +][sup [minus

  16. Thermochemistry and reaction paths in the oxidation reaction of benzoyl radical: C6H5C•(═O).

    PubMed

    Sebbar, Nadia; Bozzelli, Joseph W; Bockhorn, Henning

    2011-10-27

    Alkyl substituted aromatics are present in fuels and in the environment because they are major intermediates in the oxidation or combustion of gasoline, jet, and other engine fuels. The major reaction pathways for oxidation of this class of molecules is through loss of a benzyl hydrogen atom on the alkyl group via abstraction reactions. One of the major intermediates in the combustion and atmospheric oxidation of the benzyl radicals is benzaldehyde, which rapidly loses the weakly bound aldehydic hydrogen to form a resonance stabilized benzoyl radical (C6H5C(•)═O). A detailed study of the thermochemistry of intermediates and the oxidation reaction paths of the benzoyl radical with dioxygen is presented in this study. Structures and enthalpies of formation for important stable species, intermediate radicals, and transition state structures resulting from the benzoyl radical +O2 association reaction are reported along with reaction paths and barriers. Enthalpies, ΔfH298(0), are calculated using ab initio (G3MP2B3) and density functional (DFT at B3LYP/6-311G(d,p)) calculations, group additivity (GA), and literature data. Bond energies on the benzoyl and benzoyl-peroxy systems are also reported and compared to hydrocarbon systems. The reaction of benzoyl with O2 has a number of low energy reaction channels that are not currently considered in either atmospheric chemistry or combustion models. The reaction paths include exothermic, chain branching reactions to a number of unsaturated oxygenated hydrocarbon intermediates along with formation of CO2. The initial reaction of the C6H5C(•)═O radical with O2 forms a chemically activated benzoyl peroxy radical with 37 kcal mol(-1) internal energy; this is significantly more energy than the 21 kcal mol(-1) involved in the benzyl or allyl + O2 systems. This deeper well results in a number of chemical activation reaction paths, leading to highly exothermic reactions to phenoxy radical + CO2 products. PMID:21942384

  17. Time-resolved infrared absorption studies of the dynamics of radical reactions.

    SciTech Connect

    Macdonald, R. G.

    2008-01-01

    There is very little information available about the dynamics of radical+radical interactions. These processes are important in combustion being chain termination steps as well as generating new molecular species. To study these processes, a new experimental apparatus has been constructed to investigate radical-radical dynamics. The first radical or atomic species is produced with a known concentration in a microwave discharge flow system. The second is produced by pulsed laser photolysis of a suitable photolyte. The time dependence of individual rovibrational states of the product is followed by absorption of a continuous infrared laser. This approach will allow the reaction of interest to be differentiated from other radical reactions occurring simultaneously. The experimental approach is highly versatile, being able to detect a number of molecular species of particular interest to combustion processes such as water, methane, acetylene etc. at the state specific level. State specific infrared absorption coefficients of radicals can be measured in situ allowing for the determination of the absolute concentrations and hence branching ratios for reactions having multiple reaction pathways.

  18. Thermochemistry and Kinetic Analysis of the Unimolecular Oxiranyl Radical Dissociation Reaction: A Theoretical Study.

    PubMed

    Wang, Heng; Bozzelli, Joseph W

    2016-07-01

    Oxirane structures are important in organic synthesis, and they are important initial products in the oxidation reactions of alkyl radicals. The thermochemical properties (enthalpy of formation, entropy, and heat capacity) for the reaction steps of the unimolecular oxiranyl radical dissociation reaction are determined and compared with the available literature. The overall ring opening and subsequent steps involve four types of reactions: β-scission ring opening, intramolecular hydrogen transfer, β-scission hydrogen elimination, and β-scission methyl radical elimination. The enthalpies of formation of the transition states are determined and evaluated using six popular Density Functional Theory (DFT) calculation methods (B3LYP, B2PLYP, M06, M06-2X, ωB97X, ωB97XD), each combined with three different basis sets. The DFT enthalpy values are compared with five composite calculation methods (G3, G4, CBS-QB3, CBS-APNO, W1U), and by CCSD(T)/aug-cc-pVTZ. Kinetic parameters are determined versus pressure and temperature for the unimolecular dissociation pathways of an oxiranyl radical, which include the chemical activation reactions of the ring-opened oxiranyl radical relative to the ring-opening barrier. Multifrequency quantum Rice Ramsperger Kassel (QRRK) analysis is used to determine k(E) with master equation analysis for falloff. The major overall reaction pathway at lower combustion temperatures is oxiranyl radical dissociation to a methyl radical and carbon monoxide. Oxiranyl radical dissociation to a ketene and hydrogen atom is the key reaction path above 700 K. PMID:26990491

  19. Mechanistic study of copper-catalyzed aerobic oxidative coupling of arylboronic esters and methanol: insights into an organometallic oxidase reaction.

    PubMed

    King, Amanda E; Brunold, Thomas C; Stahl, Shannon S

    2009-04-15

    Copper-catalyzed aerobic oxidative coupling of arylboronic acid derivatives and heteroatom nucleophiles is a highly useful method for the formation of aryl-heteroatom bonds. Mechanistic studies reveal that this reaction proceeds via an "oxidase"-style mechanism. Kinetic and spectroscopic studies establish that transmetalation of the aryl group from boron to Cu(II) is the turnover-limiting step and reoxidation of the reduced catalyst by O(2) is rapid. Further mechanistic analysis implicates the involvement of an aryl-copper(III) intermediate that undergoes facile C-O bond formation. PMID:19309072

  20. Free Radical Reactions in Aqueous Solutions: Examples from Advanced Oxidation Processes for Wastewater from the Chemistry in Airborne Water Droplets

    NASA Astrophysics Data System (ADS)

    Baird, N. Colin

    1997-07-01

    Inorganic chemistry involving free radicals in aqueous solutions can be important in environmental processes. A common free radical reaction in aqueous solution is electron transfer, especially to the hydroxyl radical and to ozone. Hydrogen peroxide and free radicals related to it act as weak acids, so both their neutral and deprotonated forms must be considered in reactions. In Advanced Oxidation Processes, the hydroxyl radical concentration in water is greatly increased by reactions involving ozone and/or ultraviolet light. Irradiation of solid titanium dioxide can also be used to generate the radicals. The hydroxyl radicals are used in the Processes to initiate the oxidation of dissolved organic pollutants. Free radical reactions also play an important role in the chemistry of water droplets suspended in air in clouds and fogs. The radicals arise indirectly from the photoionization of dissolved organic compounds such as aldehydes and from the iron-catalyzed decomposition of dissolved hydrogen peroxide. They oxidize dissolved sulfur dioxide and certain organic compounds.

  1. Desaturase reactions complicate the use of norcarane as a mechanistic probe. Unraveling the mixture of twenty-plus products formed in enzyme-catalyzed oxidations of norcarane.

    PubMed

    Newcomb, Martin; Chandrasena, R Esala P; Lansakara-P, Dharmika S P; Kim, Hye-Yeong; Lippard, Stephen J; Beauvais, Laurance G; Murray, Leslie J; Izzo, Viviana; Hollenberg, Paul F; Coon, Minor J

    2007-02-16

    Norcarane, bicyclo[4.1.0]heptane, has been widely used as a mechanistic probe in studies of oxidations catalyzed by several iron-containing enzymes. We report here that, in addition to oxygenated products, norcarane is also oxidized by iron-containing enzymes in desaturase reactions that give 2-norcarene and 3-norcarene. Furthermore, secondary products from further oxidation reactions of the norcarenes are produced in yields that are comparable to those of the minor products from oxidation of the norcarane. We studied oxidations catalyzed by a representative spectrum of iron-containing enzymes including four cytochrome P450 enzymes, CYP2B1, CYPDelta2B4, CYPDelta2E1, and CYPDelta2E1 T303A, and three diiron enzymes, soluble methane monooxygenase (sMMO) from Methylococcus capsulatus (Bath), toluene monooxygenase (ToMO) from Pseudomonas stutzeri OX1, and phenol hydroxylase (PH) from Pseudomonas stutzeri OX1. 2-Norcarene and 3-norcarene and their oxidation products were found in all reaction mixtures, accounting for up to half of the oxidation products in some cases. In total, more than 20 oxidation products were identified from the enzyme-catalyzed reactions of norcarane. The putative radical-derived product from the oxidation of norcarane, 3-hydroxymethylcyclohexene (21), and the putative cation-derived product from the oxidation of norcarane, cyclohept-3-enol (22), coelute with other oxidation products on low-polarity GC columns. The yields of product 21 found in this study are smaller than those previously reported for the same or similar enzymes in studies where the products from norcarene oxidations were ignored, and therefore, the limiting values for lifetimes of radical intermediates produced in the enzyme-catalyzed oxidation reactions are shorter than those previously reported. PMID:17288366

  2. Radical-neutral chemical reactions studied at low temperature with VUV synchrotron photoionization mass spectrometry

    NASA Astrophysics Data System (ADS)

    Soorkia, Satchin; Leone, Stephen R.; Wilson, Kevin R.

    2012-11-01

    A pulsed Laval nozzle apparatus employing tunable VUV synchrotron photoionization and quadrupole mass spectrometry for the study of radical-neutral chemical reactions of importance for modeling the atmosphere of Titan and the outer planets is described. The apparatus enables the study of low-temperature kinetics and isomer-resolved product branching of highly reactive radicals with unsaturated hydrocarbons reactions. The low-temperature branching ratio for the reaction of the ethynyl radical (C2H) with allene (C3H4) has been measured for the first time at 79 K. This reaction is found to yield 1,4-pentadiyne as the major reaction product (50+10%), followed by ethynylallene (28+10%) and methyldiacetylene (22+10%) via H-atom elimination from the initially formed C5H5 adduct. The derived branching ratios can be directly used to predict the chemical evolution of Titan's atmosphere.

  3. Reactions of a persistent phosphinyl radical/diphosphine with heteroallenes.

    PubMed

    Giffin, Nick A; Hendsbee, Arthur D; Masuda, Jason D

    2016-08-01

    The persistent phosphinyl radical, (H2C)2(NDipp)2P˙, formed upon dissolution from the homolytic cleavage of the P-P bond in the diphosphane [(H2C)2(NDipp)2P]2, was reacted with carbon disulfide, phenyl isocyanate, and phenyl isothiocyanate. The phosphinyl fragments add across the C[double bond, length as m-dash]S or C[double bond, length as m-dash]O double bond to give neutral, diamagnetic species. PMID:27443569

  4. Kinetic and Mechanistic Studies of Carbon-to-Metal Hydrogen Atom Transfer Involving Os-Centered Radicals: Evidence for Tunneling

    SciTech Connect

    Lewandowska-Androlojc, Anna; Grills, David C.; Zhang, Jie; Bullock, R. Morris; Miyazawa, Akira; Kawanishi, Yuji; Fujita, Etsuko

    2014-03-05

    We have investigated the kinetics of novel carbon-to-metal hydrogen atom transfer reactions, in which homolytic cleavage of a C-H bond is accomplished by a single metal-centered radical. Studies by means of time-resolved IR spectroscopic measurements revealed efficient hydrogen atom transfer from xanthene, 9,10-dihydroanthracene and 1,4-cyclohexadiene to Cp(CO)2Os• and (n5-iPr4C5H)(CO)2Os• radicals, formed by photoinduced homolysis of the corresponding osmium dimers. The rate constants for hydrogen abstraction from these hydrocarbons were found to be in the range 1.54 × 105 M 1 s 1 -1.73 × 107 M 1 s-1 at 25 °C. For the first time, kinetic isotope effects for carbon-to-metal hydrogen atom transfer were determined. Large primary kinetic isotope effects of 13.4 ± 1.0 and 16.6 ± 1.4 were observed for the hydrogen abstraction from xanthene to form Cp(CO)2OsH and (n5-iPr4C5H)(CO)2OsH, respectively, at 25 °C. Temperature-dependent measurements of the kinetic isotope effects over a 60 -C temperature range were carried out to obtain the difference in activation energies and the pre-exponential factor ratio. For hydrogen atom transfer from xanthene to (n5-iPr4C5H)(CO)2Os•, the (ED - EH) = 3.25 ± 0.20 kcal/mol and AH/AD = 0.056 ± 0.018 values are greater than the semi-classical limits and thus suggest a quantum mechanical tunneling mechanism. The work at BNL was carried out under contract DE-AC02-98CH10886 with the U.S. Department of Energy and supported by its Division of Chemical Sciences, Geosciences & Biosciences, Office of Basic Energy Sciences. RMB also thanks the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences for support. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  5. Electron transfer reactions within zeolites: Radical cation from benzonorbornadiene

    SciTech Connect

    Pitchumani, K.; Ramamurthy, V.; Corbin, D.R.

    1996-08-28

    Zeolites are being used as solid acid catalysts in a number of commercial processes. Occasionally zeolites are also reported to perform as electron transfer agents. Recently, we observed that radical cations of certain olefins and thiophene oligomers can be generated spontaneously within ZSM-5 zeolites. We noticed that these radical cations generated from diphenyl polyenes and thiophene oligomers were remarkably stable (at room temperature) within ZSM-5 and can be characterized spectroscopically at leisure. We have initiated a program on electron transfer processes within large pore zeolites. The basis of this approach is that once a cation radical is generated within a large pore zeolite, it will have sufficient room to undergo a molecular transformation. Our aim is to identify a condition under which electron transfer can be routinely and reliably carried out within large pore zeolites such as faujasites. To our great surprise, when benzonorbornadiene A and a number of olefins were included in divalent cation exchanged faujasites. they were transformed into products very quickly (<15 min). This observation allowed us to explore the use of zeolites as oxidants. Results of our studies on benzonorbornadiene are presented in this communication. 16 refs., 1 fig.

  6. Novel reactions of one-electron oxidized radicals of selenomethionine in comparison with methionine.

    PubMed

    Mishra, B; Sharma, A; Naumov, S; Priyadarsini, K I

    2009-05-28

    Pulse radiolysis studies on hydroxyl (*OH) radical reactions of selenomethionine (SeM), a selenium analogue of methionine, were carried out, and the resultant transient radical cations and their subsequent reactions have been reported. At pH<3, the >Se*-OH radical adducts produced on reaction of SeM with *OH radical were converted to selenium centered radical cations (Se*+M), which react with another molecule of SeM to form dimer radical cation M(Se therefore Se)M+. At pH 7, the >Se*-OH radical adducts were converted to a monomer radical of the type (Se therefore N)M+ that acquires intramolecular stability through interaction with the lone pair of the N atom and this radical is denoted as SeM*+. SeM*+ decayed by first order kinetics, and the reduction potential of the couple SeM*+/SeM was determined to be 1.21+/-0.05 V vs NHE at pH 7. SeM*+ oxidized ABTS2- and TMPD with rate constants of (2.5+/-0.1)x10(8) and (6.1+/-0.2)x10(8) M(-1) s(-1), respectively, and reacted with hydroxide ion with a rate constant of (3.8+/-0.9)x10(5) M(-1) s(-1). SeM*+ reacts with molecular oxygen, and the rate constant for this reaction was determined to be (4.3+/-0.2)x10(8) M(-1) s(-1); similar reaction with methionine could not be observed experimentally. Like methionine radical cations, SeM*+ undergoes decarboxylation, although with lesser yield, to produce reducing 3-methyl-selenopropyl amino radicals (referred as alpha-amino radicals). The formation of these radicals was confirmed both by the estimation of the liberated CO2 and by one-electron reduction of MV2+, thionine, and PNAP. These results have been supported by quantum chemical calculations. Implications of these results in the biological role of SeM have also been briefly discussed. PMID:19408939

  7. Carbon–sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE

    NASA Astrophysics Data System (ADS)

    Rohac, Roman; Amara, Patricia; Benjdia, Alhosna; Martin, Lydie; Ruffié, Pauline; Favier, Adrien; Berteau, Olivier; Mouesca, Jean-Marie; Fontecilla-Camps, Juan C.; Nicolet, Yvain

    2016-05-01

    Carbon–sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a radical-based reaction mechanism that is best described as the formation of a C-centred radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5‧-deoxyadenosyl radical species that triggers the reaction in radical SAM enzymes is not an isolable intermediate.

  8. Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE.

    PubMed

    Rohac, Roman; Amara, Patricia; Benjdia, Alhosna; Martin, Lydie; Ruffié, Pauline; Favier, Adrien; Berteau, Olivier; Mouesca, Jean-Marie; Fontecilla-Camps, Juan C; Nicolet, Yvain

    2016-05-01

    Carbon-sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a radical-based reaction mechanism that is best described as the formation of a C-centred radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5'-deoxyadenosyl radical species that triggers the reaction in radical SAM enzymes is not an isolable intermediate. PMID:27102684

  9. Formation of radical-anions and radicals in the reaction of sodium sulfide with aromatic halogen compounds

    SciTech Connect

    Annenkova, V.Z.; Antonik, L.M.; Vakul'skaya, T.I.; Voronkov, M.G.

    1986-03-20

    The ESR and UV spectroscopic methods were used to establish the mechanism of the substitution of a chlorine atom by sulfide sulfur in the reactions of 2,5-dichloro-nitrobenzene (i) and p-dichlorobenzene (II) with sodium sulfide in N-methyl-2-pyrrolidone. The S/sub 2//sup -./ and S/sub 3//sup -./ radical-anions were detected and identified. The former corresponds to a narrow singlet with a g factor of 2.005 (lambdamax 440 nm), while the latter corresponds to a broad ESR signal with a g value of 2.028 (lambdamax 618 nm) (1-3). The formation of the radical-anion of the reagent gave grounds for supposing that the reaction of (I) and (II) with sodium sulfide takes place through a one-electron transfer stage. Thus, a stable radical-anion characterized by hyperfine structure (hfs) (3/sub N/ x 2/sub H/ x 3/sub H/ x 3/sub H/ with constants of 11.6, 3.7, 3.5, and 0.7 Oe respectively) is formed in the nitrobenzene-sodium sulfide system.

  10. Reaction of chlorine radical with tetrahydrofuran: a theoretical investigation on mechanism and reactivity in gas phase.

    PubMed

    Begum, Samiyara; Subramanian, Ranga

    2014-06-01

    Reaction of chlorine (Cl) radical with heterocyclic saturated ether, tetrahydrofuran has been studied. The detailed reactivity and mechanism of this reaction is analyzed using hybrid density functional theory (DFT), B3LYP and BB1K methods, and aug-cc-pVTZ basis set. To explore the mechanism of the reaction of tetrahydrofuran with Cl radical, four possible sites of hydrogen atom (H) abstraction pathways in tetrahydrofuran were analyzed. The barrier height and rate constants are calculated for the four H-abstraction channels. The BB1K calculated rate constant for α-axial H-abstraction is comparable with the experimentally determined rate constant. It reflects that α-axial H-abstraction is the main degradation pathway of tetrahydrofuran with Cl radical. DFT-based reactivity descriptors are also calculated and these values describe α-axial H-abstraction as the main reaction channel. PMID:24867438

  11. Theoretical study on the mechanism and kinetics of acetaldehyde and hydroperoxyl radical: An important atmospheric reaction

    NASA Astrophysics Data System (ADS)

    Farnia, Solaleh; Vahedpour, Morteza; Abedi, Mostafa; Farrokhpour, Hossein

    2013-09-01

    A systematic theoretical study was performed on the mechanism and kinetics of the atmospheric reaction of acetaldehyde (CH3CHO) and hydroperoxyl radical (HO2) in the gas phase. The DFT-B3LYP/6-311++G(3df,3pd) and CCSD(T)/6-311++G(d,p) methods were employed for calculations. Based on the calculations, this reaction leads to four different products through radical addition and hydrogen abstraction mechanisms which are very important in atmospheric and combustion chemistry. The favorable reaction paths begin with α-hydroxyethylperoxy radical, CH3CH(OO)OH, in a exothermic process and finally leads to the product P1 (CH3COOH + OH). The overall rate constants for favorite reaction paths have been calculated at different temperatures (200-2500 K).

  12. Formation of environmentally persistent free radicals from the heterogeneous reaction of ozone and polycyclic aromatic compounds.

    PubMed

    Borrowman, Cuyler K; Zhou, Shouming; Burrow, Timothy E; Abbatt, Jonathan P D

    2016-01-01

    In the 1980s long-lived radical species were identified in cigarette tar. Since then, environmentally persistent free radicals (EPFRs) have been observed in ambient particulate matter, and have been generated in particulate matter generated from internal combustion engines. For the first time, we measure in situ the formation and decay of EPFRs through the heterogeneous reaction of ozone and several polycyclic aromatic compounds (PAC). Solid anthracene (ANT), pyrene (PY), benzo[a]pyrene (BAP), benzo[ghi]perylene (BGHIP), 1,4-naphthoquinone (1,4NQ), and 9,10-anthraquinone (AQ) were reacted with gas-phase ozone in a flow system placed in the active cavity of an electron paramagnetic resonance (EPR) spectrometer, and the formation of radicals was measured on the timescale of tens of minutes at ambient levels of ozone down to 30 ppb. For most substrates the net radical production is initially rapid, slows at intermediate times, and is followed by a slow decay. For oxidized solid BAP, radical signal persists for many days in the absence of ozone. To evaluate the effect of substrate phase, the solid PAHs were also dissolved in squalane, an organic oil inert to ozone, which yielded a much higher maximum radical concentration and faster radical decay when exposed to ozone. With higher mobility, reactants were apparently able to more easily diffuse and react with each other, yielding the higher radical concentrations. The EPR spectra exhibit three radicals types, two of which have been assigned to semiquinone species and one to a PAH-derived, carbon-centered radical. Although our system uses levels of PAC not typically found in the environment it is worth noting that the amounts of radical formed, on the order of 10(18) radicals per g, are comparable to those observed in ambient particulate matter. PMID:26603953

  13. Direct Observation of Sulfur Radicals as Reaction Media in lithium Sulfur Batteries

    SciTech Connect

    Wang, Qiang; Zheng, Jianming; Walter, Eric D.; Pan, Huilin; Lu, Dongping; Zuo, Pengjian; Chen, Honghao; Deng, Zhiqun; Liaw, Bor Yann; Yu, Xiqian; Yang, Xiaoning; Zhang, Jiguang; Liu, Jun; Xiao, Jie

    2014-12-09

    Lithium sulfur (Li-S) battery has been regaining tremendous interest in recent years because of its attractive attributes such as high gravimetric energy, low cost and environmental benignity. However, it is still not conclusively known how polysulfide ring/chain participates in the whole cycling and whether the discharge and charge process follow the same pathway. Herein, we demonstrate the direct observation of sulfur radicals by using in situ electron paramagnetic resonance (EPR) technique. Based on the concentration changes of sulfur radicals at different potentials, it is revealed that the chemical and electrochemical reactions in Li-S cell are driven each other to proceed through sulfur radicals, leading to two completely different reaction pathways during discharge and charge. The proposed radical mechanism may provide new insights to investigate the interactions between sulfur species and the electrolyte, inspiring novel strategies to develop Li-S battery technology.

  14. Direct Observation of Sulfur Radicals as Reaction Media in Lithium Sulfur Batteries

    DOE PAGESBeta

    Wang, Qiang; Zheng, Jianming; Walter, Eric; Pan, Huilin; Lv, Dongping; Zuo, Pengjian; Chen, Honghao; Deng, Z. D.; Liaw, Bor Y.; Yu, Xiqian; et al

    2015-01-09

    Lithium sulfur (Li-S) battery has been regaining tremendous interest in recent years because of its attractive attributes such as high gravimetric energy, low cost and environmental benignity. However, it is still not conclusively known how polysulfide ring/chain participates in the whole cycling and whether the discharge and charge processes follow the same pathway. Herein, we demonstrate the direct observation of sulfur radicals by using in situ electron paramagnetic resonance (EPR) technique. Based on the concentration changes of sulfur radicals at different potentials and the electrochemical characteristics of the cell, it is revealed that the chemical and electrochemical reactions in Li-Smore » cell are driving each other to proceed through sulfur radicals, leading to two completely different reaction pathways during discharge and charge. The proposed radical mechanism may provide new perspectives to investigate the interactions between sulfur species and the electrolyte, inspiring novel strategies to develop Li-S battery technology.« less

  15. Direct Observation of Sulfur Radicals as Reaction Media in Lithium Sulfur Batteries

    SciTech Connect

    Wang, Qiang; Zheng, Jianming; Walter, Eric; Pan, Huilin; Lv, Dongping; Zuo, Pengjian; Chen, Honghao; Deng, Z. D.; Liaw, Bor Y.; Yu, Xiqian; Yang, Xiao-Qing; Zhang, Ji-Guang; Liu, Jun; Xiao, Jie

    2015-01-09

    Lithium sulfur (Li-S) battery has been regaining tremendous interest in recent years because of its attractive attributes such as high gravimetric energy, low cost and environmental benignity. However, it is still not conclusively known how polysulfide ring/chain participates in the whole cycling and whether the discharge and charge processes follow the same pathway. Herein, we demonstrate the direct observation of sulfur radicals by using in situ electron paramagnetic resonance (EPR) technique. Based on the concentration changes of sulfur radicals at different potentials and the electrochemical characteristics of the cell, it is revealed that the chemical and electrochemical reactions in Li-S cell are driving each other to proceed through sulfur radicals, leading to two completely different reaction pathways during discharge and charge. The proposed radical mechanism may provide new perspectives to investigate the interactions between sulfur species and the electrolyte, inspiring novel strategies to develop Li-S battery technology.

  16. Rate constants for the reactions of free radicals with oxygen in solution

    SciTech Connect

    Maillard, B.; Ingold, K.U.; Scaiano, J.C.

    1983-07-27

    The kinetics of the rections of several free radicals with oxygen have been examined in solution at 300 K using laser flash photolysis techniques. The reactions of resonance-stabilized radicals are only slightly slower than those of nonstabilized radicals: for example, for tert-butyl (in cyclohexane), 4.93 x 10/sup 9/; benzyl, 2.36 x 10/sup 9/ (in cyclohexane); cyclohexadienyl (in benzene), 1.64 x 10/sup 9/ M/sup -1/ s/sup -1/. The reaction of butyl-tin (n-Bu/sub 3/Sn.) radicals is unusually fast (7.5 x 10/sup 9/ M/sup -1/ s/sup -1/), a fact that has been tentatively attributed to a relaxation of spin selection rules due to heavy atom effects. 1 table.

  17. Branching ratios between the abstraction and addition channels in the reactions of OH radicals with monoterpenes

    NASA Astrophysics Data System (ADS)

    Rio, C.; Loison, J. C.; Caralp, F.; Flaud, P. M.; Villenave, E.

    2009-04-01

    Secondary Organic Aerosol (SOA) formation in the atmosphere is described as a mass transfer of volatile organic compound oxidation products with low vapour pressures in particular phases. Among the different aerosol components, the SOA represent an important fraction, but, the fundamental processes governing their physics and chemistry in the atmosphere are poorly understood. So it is important to characterize and understand the mechanisms of their formation. It is well-known that atmospheric oxidation of monoterpenes is an important process in tropospheric SOA formation. Consequently, the identification and quantification of reaction products from the oxidation of monoterpenes in the gas phase have been receiving great attention over the past years. However, the atmospheric degradation leads to the formation of a plethora of reaction products and proceeds through a very complex mechanism that is still not fully characterised. In our study, we have focused on SOA formation from OH + monoterpene reactions and more precisely on the primary oxidation steps of γ-terpinene and d-limonene by OH radicals. Indeed, the primary reaction of monoterpenes with hydroxyl radicals can in principle occur by two reaction pathways: OH-addition and H-abstraction. In this work, we have determined branching ratios of these reactions. Although there seems to be a consensus in the literature that OH-monoterpene reactions proceed almost exclusively by addition, several measurements have shown that in some case H-abstraction can represent up to 30% of the total reaction rate constant. Therefore it is necessary to determine this branching ratio in order to know, in particular, the main peroxy radicals formed and propose a mechanism for the gas phase oxidation of terpene by hydroxyl radicals. (γ-terpinene + OH) and (d-limonene + OH) reactions have been studied i) at atmospheric pressure, using laser photolysis coupled with UV absorption radical detection, and ii) at low pressure, using

  18. Metal-Catalyzed β-Functionalization of Michael Acceptors through Reductive Radical Addition Reactions.

    PubMed

    Streuff, Jan; Gansäuer, Andreas

    2015-11-23

    Transition-metal-catalyzed radical reactions are becoming increasingly important in modern organic chemistry. They offer fascinating and unconventional ways for connecting molecular fragments that are often complementary to traditional methods. In particular, reductive radical additions to α,β-unsaturated compounds have recently gained substantial attention as a result of their broad applicability in organic synthesis. This Minireview critically discusses the recent landmark achievements in this field in context with earlier reports that laid the foundation for today's developments. PMID:26471460

  19. Spectroscopy and reaction dynamics of collision complexes containing hydroxyl radicals

    SciTech Connect

    Lester, M.I.

    1993-12-01

    The DOE supported work in this laboratory has focused on the spectroscopic characterization of the interaction potential between an argon atom and a hydroxyl radical in the ground X{sup 2}II and excited A {sup 2}{summation}{sup +} electronic states. The OH-Ar system has proven to be a test case for examining the interaction potential in an open-shell system since it is amenable to experimental investigation and theoretically tractable from first principles. Experimental identification of the bound states supported by the Ar + OH (X {sup 2}II) and Ar + OH(A {sup 2}{summation}{sup +}) potentials makes it feasible to derive realistic potential energy surfaces for these systems. The experimentally derived intermolecular potentials provide a rigorous test of ab initio theory and a basis for understanding the dramatically different collision dynamics taking place on the ground and excited electronic state surfaces.

  20. Reactions and structural investigation of chlorpromazine radical cation

    NASA Astrophysics Data System (ADS)

    Joshi, Ravi; Ghanty, Tapan K.; Mukherjee, T.

    2008-10-01

    Experimental and theoretical studies have been carried out to understand pro-oxidant behaviour of chlorpromazine radical cation (CPZ rad + ). Pulse radiolysis studies have shown that CPZ rad + oxidizes physiological antioxidants (uric acid and bilirubin), and biomolecules like, tyrosine and proteins (bovine serum albumin and casein), thereby acting as a pro-oxidant. Ab-initio quantum chemical calculations suggest structural and electronic changes on oxidation of CPZ. The calculations with Hartree-Fock and density functional methods show that ring nitrogen atom is the site of electron removal from CPZ and sulfur atom is the site of maximum spin in CPZ rad + . The calculations also suggest that oxidation of CPZ leads to increase in planarity of the tricyclic ring as well as tilting of alkyl side chain towards chlorine containing ring. The structural changes on oxidation of CPZ and spin delocalization in CPZ rad + fairly explain the pro-oxidant activity of CPZ.

  1. Mapping Nanomagnetic Fields Using a Radical Pair Reaction

    NASA Astrophysics Data System (ADS)

    Lee, Hohjai; Yang, Nan; Cohen, Adam

    2012-02-01

    We visualized the magnetic field around ferromagnetic nanostructures using a combination of a standard epifluorescence microscope and a fluorescence chemical indicator of magnetic field (H. Lee et al., Nano Lett. DOI: 10.1021/nl202950h). The indicator was a chain-linked electron donor-acceptor molecule, phenanthrene-(CH2)12-O-(CH2)2-dimethylaniline, that forms spin-correlated radical pairs upon photoexcitation. The magnetic field altered the coherence spin dynamics, yielding an 80% increase in exciplex fluorescence in a 0.1 T magnetic field. The magnetic field distributions were quantified to precision of 1.8 x 10-4 T by image analysis and agreed with finite-element nonmagnetic simulations.

  2. Determination of the upper and lower limits of the mechanistic stoichiometry of incompletely coupled fluxes. Stoichiometry of incompletely coupled reactions.

    PubMed

    Beavis, A D; Lehninger, A L

    1986-07-15

    A rationale is formulated for the design of experiments to determine the upper and lower limits of the mechanistic stoichiometry of any two incompletely coupled fluxes J1 and J2. Incomplete coupling results when there is a branch at some point in the sequence of reactions or processes coupling the two fluxes. The upper limit of the mechanistic stoichiometry is given by the minimum value of dJ2/dJ1 obtained when the fluxes are systematically varied by changes in steps after the branch point. The lower limit is given by the maximum value of dJ2/dJ1 obtained when the fluxes are varied by changes in steps prior to the branch point. The rationale for determining these limits is developed from both a simple kinetic model and from a linear nonequilibrium thermodynamic treatment of coupled fluxes, using the mechanistic approach [Westerhoff, H. V. & van Dam, K. (1979) Curr. Top. Bioenerg. 9, 1-62]. The phenomenological stoichiometry, the flux ratio at level flow and the affinity ratio at static head of incompletely coupled fluxes are defined in terms of mechanistic conductances and their relationship to the mechanistic stoichiometry is discussed. From the rationale developed, experimental approaches to determine the mechanistic stoichiometry of mitochondrial oxidative phosphorylation are outlined. The principles employed do not require knowledge of the pathway or the rate of transmembrane leaks or slippage and may also be applied to analysis of the stoichiometry of other incompletely coupled systems, including vectorial H+/O and K+/O translocation coupled to mitochondrial electron transport. PMID:3015612

  3. Catalytic N-radical cascade reaction of hydrazones by oxidative deprotonation electron transfer and TEMPO mediation

    PubMed Central

    Hu, Xiao-Qiang; Qi, Xiaotian; Chen, Jia-Rong; Zhao, Quan-Qing; Wei, Qiang; Lan, Yu; Xiao, Wen-Jing

    2016-01-01

    Compared with the popularity of various C-centred radicals, the N-centred radicals remain largely unexplored in catalytic radical cascade reactions because of a lack of convenient methods for their generation. Known methods for their generation typically require the use of N-functionalized precursors or various toxic, potentially explosive or unstable radical initiators. Recently, visible-light photocatalysis has emerged as an attractive tool for the catalytic formation of N-centred radicals, but the pre-incorporation of a photolabile groups at the nitrogen atom largely limited the reaction scope. Here, we present a visible-light photocatalytic oxidative deprotonation electron transfer/2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO)-mediation strategy for catalytic N-radical cascade reaction of unsaturated hydrazones. This mild protocol provides a broadly applicable synthesis of 1,6-dihydropyradazines with complete regioselectivity and good yields. The 1,6-dihydropyradazines can be easily transformed into diazinium salts that showed promising in vitro antifungal activities against fungal pathogens. DFT calculations are conducted to explain the mechanism. PMID:27048886

  4. Structure reactivity relationship in the reaction of DNA guanyl radicals with hydroxybenzoates

    NASA Astrophysics Data System (ADS)

    Do, Trinh T.; Tang, Vicky J.; Aguilera, Joseph A.; Milligan, Jamie R.

    2010-11-01

    In DNA, guanine bases are the sites from which electrons are most easily removed. As a result of hole migration to this stable location on guanine, guanyl radicals are major intermediates in DNA damage produced by the direct effect of ionizing radiation (ionization of the DNA itself and not through the intermediacy of water radicals). We have modeled this process by employing gamma irradiation in the presence of thiocyanate ions, a method which also produces single electron oxidized guanyl radicals in plasmid DNA in aqueous solution. The stable products formed in DNA from these radicals are detected as strand breaks after incubation with the FPG protein. When a phenolic compound is present in the solution during gamma irradiation, the formation of guanyl radical species is decreased by electron donation from the phenol to the guanyl radical. We have quantified the rate of this reaction for four different phenolic compounds bearing carboxylate substituents as proton acceptors. A comparison of the rates of these reactions with the redox strengths of the phenolic compounds reveals that salicylate reacts ca. 10-fold faster than its structural analogs. This observation is consistent with a reaction mechanism involving a proton coupled electron transfer, because intra-molecular transfer of a proton from the phenolic hydroxyl group to the carboxylate group is possible only in salicylate, and is favored by the strong 6-membered ring intra-molecular hydrogen bond in this compound.

  5. Catalytic N-radical cascade reaction of hydrazones by oxidative deprotonation electron transfer and TEMPO mediation.

    PubMed

    Hu, Xiao-Qiang; Qi, Xiaotian; Chen, Jia-Rong; Zhao, Quan-Qing; Wei, Qiang; Lan, Yu; Xiao, Wen-Jing

    2016-01-01

    Compared with the popularity of various C-centred radicals, the N-centred radicals remain largely unexplored in catalytic radical cascade reactions because of a lack of convenient methods for their generation. Known methods for their generation typically require the use of N-functionalized precursors or various toxic, potentially explosive or unstable radical initiators. Recently, visible-light photocatalysis has emerged as an attractive tool for the catalytic formation of N-centred radicals, but the pre-incorporation of a photolabile groups at the nitrogen atom largely limited the reaction scope. Here, we present a visible-light photocatalytic oxidative deprotonation electron transfer/2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO)-mediation strategy for catalytic N-radical cascade reaction of unsaturated hydrazones. This mild protocol provides a broadly applicable synthesis of 1,6-dihydropyradazines with complete regioselectivity and good yields. The 1,6-dihydropyradazines can be easily transformed into diazinium salts that showed promising in vitro antifungal activities against fungal pathogens. DFT calculations are conducted to explain the mechanism. PMID:27048886

  6. Reaction kinetics of the CN radical with methyl bromide

    NASA Astrophysics Data System (ADS)

    Hodny, Michael; Hershberger, John F.

    2016-02-01

    The kinetics of the CN + CH3Br reaction were studied using transient infrared laser absorption spectroscopy to detect CN reactants and HCN products. This reaction has a rate constant of k = (2.20 ± 0.6) × 10-12 exp (453 ± 98/T) cm3 molecule-1 s-1 over the range 298-523 K. Hydrogen abstraction to produce HCN + CH2Br is only a minor reaction product, with a branching fraction of 0.12 ± 0.02. Other product channels, including BrCN + CH3, CH2CN + HBr, CH3CN + Br are likely. An upper limit of 0.01 was established for the HBr yield. These results are in qualitative agreement with recent ab initio calculations.

  7. Reaction dynamics of phenyl radicals in extreme environments: a crossed molecular beam study.

    PubMed

    Gu, Xibin; Kaiser, Ralf I

    2009-02-17

    Polycyclic aromatic hydrocarbons (PAHs)organic compounds that consist of fused benzene ringsand their hydrogen-deficient precursors have attracted extensive interest from combustion scientists, organic chemists, astronomers, and planetary scientists. On Earth, PAHs are toxic combustion products and a source of air pollution. In the interstellar medium, research suggests that PAHs play a role in unidentified infrared emission bands, diffuse interstellar bands, and the synthesis of precursor molecules to life. To build clean combustion devices and to understand the astrochemical evolution of the interstellar medium, it will be critical to understand the elementary reaction mechanisms under single collision conditions by which these molecules form in the gas phase. Until recently, this work had been hampered by the difficulty in preparing a large concentration of phenyl radicals, but the phenyl radical represents one of the most important radical species to trigger PAH formation in high-temperature environments. However, we have developed a method for producing these radical species and have undertaken a systematic experimental investigation. In this Account, we report on the chemical dynamics of the phenyl radical (C(6)H(5)) reactions with the unsaturated hydrocarbons acetylene (C(2)H(2)), ethylene (C(2)H(4)), methylacetylene (CH(3)CCH), allene (H(2)CCCH(2)), propylene (CH(3)CHCH(2)), and benzene (C(6)H(6)) utilizing the crossed molecular beams approach. For nonsymmetric reactants such as methylacetylene and propylene, steric effects and the larger cones of acceptance drive the addition of the phenyl radical to the nonsubstituted carbon atom of the hydrocarbon reactant. Reaction intermediates decomposed via atomic hydrogen loss pathways. In the phenyl-propylene system, the longer lifetime of the reaction intermediate yielded a more efficient energy randomization compared with the phenyl-methylacetylene system. Therefore, two reaction channels were open: hydrogen

  8. [Riboflavin-radical formation by mechanochemical solid-state reaction using stainless steel vessel].

    PubMed

    Kondo, Shin-ichi; Furuta, Youji; Okita, Shintarou; Sasai, Yasushi; Aramaki, Hideki; Kuzuya, Masayuki

    2004-03-01

    The mechanochemical reaction of free riboflavin (FR) due to vibratory ball milling was carried out in a stainless steel vessel at room temperature under anaerobic conditions. The ESR of the fractured sample showed a broad single-line spectrum. It is suggested that the solid-state single-electron transfer (SSET) reaction from the surface of the stainless steel vessel to FR proceeded during the vibratory milling, resulting in the formation of the corresponding anion radicals. When the mechanochemical reaction of FR in the presence of calcium pantothenate (PC) was carried out, the radical concentration increased with the increasing PC content. It was shown that the anion radical in the metal complex was stable for a lengthy period of time even in highly humid air. PMID:15049132

  9. Gas Phase Degradation of Polybrominated Diphenylethers: Photolysis vs. Reaction with OH Radical

    NASA Astrophysics Data System (ADS)

    Raff, J. D.; Hites, R. A.

    2005-12-01

    Polybrominated diphenylethers (PBDEs) are a class of flame-retardants produced in large quantities (70,000 metric tons in 2003) and added to polymers used to fabricate materials for electronics, textiles, construction, and other applications. Their volatility and persistence make them susceptible to atmospheric transport and their structural resemblance to polychlorinated diphenyls (PCBs) and dibenzo-p-dioxins (PCDDs) has raised concern about their possible toxicity. The dominant atmospheric loss processes for PBDEs are by direct photolysis and reaction with OH radical. Data on OH radical rate constants of selected PBDE congeners determined by a relative rate technique utilizing a small volume reaction chamber and mass spectrometric detection will be presented. Estimated photolysis rate constants have also been derived for PBDEs and will be discussed in terms of the relative importance of photolysis vs. reaction with OH radical as loss processes for PBDEs in the troposphere.

  10. Study on the NO{sub 3} radical reactivity: Reactions with cyclic alkenes

    SciTech Connect

    Martinez, E.; Cabanas, B.; Aranda, A.; Martin, P.; Notario, A.; Salgado, S.

    1999-07-08

    Much effort has been expended in studies of NO{sub 3} radical chemistry. The emphasis has been placed on investigating reaction rates and products of various organic and inorganic compounds to understand the behavior of this reactive radical in the atmosphere. The rate constants of the reactions of NO{sub 3} with cyclopentene, cyclohexene, cycloheptene, 1-methylcyclohexene, and methylenecyclohexane have been measured as a function of temperature at low pressure in a fast flow system with LiF detection of NO{sub 3}. The measured room temperature (298 K) rate constants for these reactions are given. The proposed Arrhenius expressions for the studied reactions are also given. The influence of substitution in the double bond and the ring size effect in unsubstituted cyclic monoalkenes has been investigated for the reactivity of the NO{sub 3} radical reactions. The rate coefficients and the activation energies for the reaction of the nitrate radical with methylenecyclohexane and 1-methylcyclohexene have also been compared with the corresponding values of some selected terpenes with similar structure to these compounds.

  11. Photoinduced reactions of 1-(dimethylethyl)-2,2-dimethylpropyl and cyclohexyl radicals in low-temperature solids

    NASA Astrophysics Data System (ADS)

    Koizumi, Hitoshi; Takada, Tomoya; Ichikawa, Tsuneki; Lund, Anders

    2001-06-01

    Photoinduced reactions of 1-(dimethylethyl)-2,2-dimethylpropyl and cyclohexyl radicals in 77 K solids were studied by the ESR method. 1-(Dimethylethyl)-2,2-dimethylpropyl is converted to 2,2,4,4-tetramethylpentyl radical with photoirradiation of 254 nm light. A hydrogen atom of methyl groups can hence directly transfer to the radical site at a carbon atom other than an adjacent one in the photoinduced reactions of alkyl radicals. Cyclohexyl radical is converted to cyclopentylmethyl radical with irradiation of 254 nm light. The photolysis of cyclohexyl radical causes C-C bond scission, and results in the formation of 5-hexenyl radical. It is then converted to cyclopentylmethyl radical through intramolecular rearrangement.

  12. Growth of polyaromatic molecules via ion-molecule reactions: An experimental and theoretical mechanistic study

    SciTech Connect

    Ascenzi, Daniela; Aysina, Julia; Tosi, Paolo; Maranzana, Andrea; Tonachini, Glauco

    2010-11-14

    The reactivity of naphthyl cations with benzene is investigated in a joint experimental and theoretical approach. Experiments are performed by using guided ion beam tandem mass spectrometers equipped with electron impact or atmospheric pressure chemical ion sources to generate C{sub 10}H{sub 7}{sup +} with different amounts of internal excitation. Under single collision conditions, C-C coupling reactions leading to hydrocarbon growth are observed. The most abundant ionic products are C{sub 16}H{sub 13}{sup +}, C{sub 16}H{sub n}{sup +} (with n=10-12), and C{sub 15}H{sub 10}{sup +}. From pressure-dependent measurements, absolute cross sections of 1.0{+-}0.3 and 2{+-}0.6 A{sup 2} (at a collision energy of about 0.2 eV in the center of mass frame) are derived for channels leading to the formation of C{sub 16}H{sub 12}{sup +} and C{sub 15}H{sub 10}{sup +} ions, respectively. From cross section values a phenomenological total rate constant k=(5.8{+-}1.9)x10{sup -11} cm{sup 3} s{sup -1} at an average collision energy of about 0.27 eV can be estimated for the process C{sub 10}H{sub 7}{sup +}+C{sub 6}H{sub 6}{yields} all products. The energy behavior of the reactive cross sections, as well as further experiments performed using partial isotopic labeling of reagents, support the idea that the reaction proceeds via a long lived association product, presumably the covalently bound protonated phenylnaphthalene, from which lighter species are generated by elimination of neutral fragments (H, H{sub 2}, CH{sub 3}). A major signal relevant to the fragmentation of the initial adduct C{sub 16}H{sub 13}{sup +} belongs to C{sub 15}H{sub 10}{sup +}. Since it is not obvious how CH{sub 3} loss from C{sub 16}H{sub 13}{sup +} can take place to form the C{sub 15}H{sub 10}{sup +} radical cation, a theoretical investigation focuses on possible unimolecular transformations apt to produce it. Naphthylium can act as an electrophile and add to the {pi} system of benzene, leading to a barrierless

  13. Characterization of the peroxidase mechanism upon reaction of prostacyclin synthase with peracetic acid. Identification of a tyrosyl radical intermediate.

    PubMed

    Yeh, Hui-Chun; Gerfen, Gary J; Wang, Jinn-Shyan; Tsai, Ah-Lim; Wang, Lee-Ho

    2009-02-10

    Prostacyclin synthase (PGIS) is a membrane-bound class III cytochrome P450 that catalyzes an isomerization of prostaglandin H(2), an endoperoxide, to prostacyclin. We report here the characterization of the PGIS intermediates in reactions with other peroxides, peracetic acid (PA), and iodosylbenzene. Rapid-scan stopped-flow experiments revealed an intermediate with an absorption spectrum similar to that of compound ES (Cpd ES), which is an oxo-ferryl (Fe(IV)O) plus a protein-derived radical. Cpd ES, formed upon reaction with PA, has an X-band (9 GHz) EPR signal of g = 2.0047 and a half-saturation power, P(1/2), of 0.73 mW. High-field (130 GHz) EPR reveals the presence of two species of tyrosyl radicals in Cpd ES with their g-tensor components (g(x), g(y), g(z)) of 2.00970, 2.00433, 2.00211 and 2.00700, 2.00433, 2.00211 at a 1:2 ratio, indicating that one is involved in hydrogen bonding and the other is not. The line width of the g = 2 signal becomes narrower, while its P(1/2) value becomes smaller as the reaction proceeds, indicating migration of the unpaired electron to an alternative site. The rate of electron migration ( approximately 0.2 s(-1)) is similar to that of heme bleaching, suggesting the migration is associated with the enzymatic inactivation. Moreover, a g = 6 signal that is presumably a high-spin ferric species emerges after the appearance of the amino acid radical and subsequently decays at a rate comparable to that of enzymatic inactivation. This loss of the g = 6 species thus likely indicates another pathway leading to enzymatic inactivation. The inactivation, however, was prevented by the exogenous reductant guaiacol. The studies of PGIS with PA described herein provide a mechanistic model of a peroxidase reaction catalyzed by the class III cytochromes P450. PMID:19187034

  14. Trajectory calculations of OH radical- and Cl atom-initiated reaction of glyoxal: atmospheric chemistry of the HC(O)CO radical.

    PubMed

    Setokuchi, Osamu

    2011-04-01

    On-the-fly quasi-classical trajectory calculations using the density functional method were carried out to investigate the dynamics of the HC(O)CO radical, formed by OH radical- and Cl atom-initiated reactions of glyoxal at 298 K. The energy difference between the A' HC(O)CO radical, formed immediately after H atom abstraction, and the most stable A″ HC(O)CO radical is estimated to be 6.0 kcal mol(-1). The surplus energy followed by relaxation from A' HC(O)CO to A″ HC(O)CO goes to internal energy of the nascent HC(O)CO radicals and causes prompt decomposition into HCO + CO. The average internal energy partitioned into the HC(O)CO radical is higher in the OH reaction than in the Cl reaction, in accordance with exothermicity of the reactions. A fraction of the nascent HC(O)CO radicals (91% for the OH reaction and 47% for the Cl reaction) promptly decomposes into HCO and CO within 2.5 ps. The remaining HC(O)CO radicals, which do not undergo prompt decomposition, decompose thermally or add with O(2) in the presence of O(2). I re-evaluated the previous two experiment results of the product yield ratio [CO]/[CO(2)] vs. [O(2)](-1) in the Cl atom-initiated reaction, in light of the reaction mechanism involving prompt decomposition. The two results give 9.5 × 10(6) s(-1) and 1.08 × 10(7) s(-1) for the thermal decomposition rate and 47% and 41% for the fraction of prompt decomposition in the Cl atom-initiated reaction, in good agreement with the present trajectory calculation. PMID:21359367

  15. EPR Spin Trapping of an Oxalate-Derived Free Radical in the Oxalate Decarboxylase Reaction

    PubMed Central

    Imaram, Witcha; Saylor, Benjamin T.; Centonze, Christopher P.; Richards, Nigel G. J.; Angerhofer, Alexander

    2011-01-01

    EPR spin trapping experiments on bacterial oxalate decarboxylase from Bacillus subtilis under turn-over conditions are described. The use of doubly 13C-labeled oxalate leads to a characteristic splitting of the observed radical adducts using the spin trap N-tert-butyl-α-phenylnitrone linking them directly to the substrate. The radical was identified as the carbon dioxide radical anion which is a key intermediate in the hypothetical reaction mechanism of both decarboxylase and oxidase activities. X-ray crystallography had identified a flexible loop, SENS161-4, which acts as a lid to the putative active site. Site directed mutagenesis of the hinge amino acids, S161 and T165 was explored and showed increased radical trapping yields compared to the wild type. In particular, T165V shows approximately ten times higher radical yields while at the same time its decarboxylase activity was reduced by about a factor of ten. This mutant lacks a critical H-bond between T165 and R92 resulting in compromised control over its radical chemistry allowing the radical intermediate to leak into the surrounding solution. PMID:21277974

  16. Gas-phase reactions of aryl radicals with 2-butyne: experimental and theoretical investigation employing the N-methyl-pyridinium-4-yl radical cation.

    PubMed

    Lam, A K Y; Li, C; Khairallah, G; Kirk, B B; Blanksby, S J; Trevitt, A J; Wille, U; O'Hair, R A J; da Silva, G

    2012-02-21

    Aromatic radicals form in a variety of reacting gas-phase systems, where their molecular weight growth reactions with unsaturated hydrocarbons are of considerable importance. We have investigated the ion-molecule reaction of the aromatic distonic N-methyl-pyridinium-4-yl (NMP) radical cation with 2-butyne (CH(3)C≡CCH(3)) using ion trap mass spectrometry. Comparison is made to high-level ab initio energy surfaces for the reaction of NMP and for the neutral phenyl radical system. The NMP radical cation reacts rapidly with 2-butyne at ambient temperature, due to the apparent absence of any barrier. The activated vinyl radical adduct predominantly dissociates via loss of a H atom, with lesser amounts of CH(3) loss. High-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry allows us to identify small quantities of the collisionally deactivated reaction adduct. Statistical reaction rate theory calculations (master equation/RRKM theory) on the NMP+2-butyne system support our experimental findings, and indicate a mechanism that predominantly involves an allylic resonance-stabilized radical formed via H atom shuttling between the aromatic ring and the C(4) side-chain, followed by cyclization and/or low-energy H atom β-scission reactions. A similar mechanism is demonstrated for the neutral phenyl radical (Ph˙)+2-butyne reaction, forming products that include 3-methylindene. The collisionally deactivated reaction adduct is predicted to be quenched in the form of a resonance-stabilized methylphenylallyl radical. Experiments using a 2,5-dichloro substituted methyl-pyridiniumyl radical cation revealed that in this case CH(3) loss from the 2-butyne adduct is favoured over H atom loss, verifying the key role of ortho H atoms, and the shuttling mechanism, in the reactions of aromatic radicals with alkynes. As well as being useful phenyl radical analogues, pyridiniumyl radical cations may form in the ionosphere of Titan, where they could undergo rapid

  17. Formation of TEMPOL-hydroxylamine during reaction between TEMPOL and hydroxyl radical: HPLC/ECD study.

    PubMed

    Kudo, Wataru; Yamato, Mayumi; Yamada, Ken-Ichi; Kinoshita, Yuichi; Shiba, Takeshi; Watanabe, Toshiaki; Utsumi, Hideo

    2008-05-01

    Nitroxyl radicals are important antioxidants that have been used to protect animal tissues from oxidative damage. Their reaction with hydroxyl radical ((*)OH) is generally accepted to be the mechanism of antioxidant function. However, the direct interaction of nitroxyl radicals with (*)OH does not always provide a satisfactory explanation in various pH, because the concentration of hydrogen ion may affect the generation of secondary (*)OH-derived radicals. In the present study, it was confirmed that the reaction between 4-hydroxy-2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPOL) and (*)OH generated TEMPOL-hydroxylamine, 4-oxo-2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPON) and TEMPON-hydroxylamine using HPLC coupled with electrochemical detection. In the absence of NADH, TEMPOL-H may be generated by the reaction with secondary (*)OH-derived radicals in acidic condition. In the presence of NADH, a large proportion of the non-paramagnetic products was TEMPOL-H. Finally, it was clarified that TEMPOL-H was generated during dopamine metabolism, which is believed to be one of the (*)OH sources in pathological processes such as Parkinson's disease. PMID:18484414

  18. Polycyclic aromatic hydrocarbon (PAH) formation from benzyl radicals: a reaction kinetics study.

    PubMed

    Sinha, Sourab; Raj, Abhijeet

    2016-03-01

    The role of resonantly stabilized radicals such as propargyl, cyclopentadienyl and benzyl in the formation of aromatic hydrocarbons such as benzene and naphthalene in the high temperature environments has been long known. In this work, the possibility of benzyl recombination to form three-ring aromatics, phenanthrene and anthracene, is explored. A reaction mechanism for it is developed, where reaction energetics are calculated using density functional theory (B3LYP functional with 6-311++G(d,p) basis set) and CBS-QB3, while temperature-dependent reaction kinetics are evaluated using transition state theory. The mechanism begins with barrierless formation of bibenzyl from two benzyl radicals with the release of 283.2 kJ mol(-1) of reaction energy. The further reactions involve H-abstraction by a H atom, H-desorption, H-migration, and ring closure to gain aromaticity. Through mechanism and rate of production analyses, the important reactions leading to phenanthrene and anthracene formation are determined. Phenanthrene is found to be the major product at high temperatures. Premixed laminar flame simulations are carried out by including the proposed reactions for phenanthrene formation from benzyl radicals and compared to experimentally observed species profiles to understand their effects on species concentrations. PMID:26923612

  19. Kinetic and mechanistic studies of reactive intermediates in photochemical and transition metal-assisted oxidation, decarboxylation and alkyl transfer reactions

    NASA Astrophysics Data System (ADS)

    Carraher, Jack McCaslin

    Reactive species like high-valent metal-oxo complexes and carbon and oxygen centered radicals are important intermediates in enzymatic systems, atmospheric chemistry, and industrial processes. Understanding the pathways by which these intermediates form, their relative reactivity, and their fate after reactions is of the utmost importance. Herein are described the mechanistic detail for the generation of several reactive intermediates, synthesis of precursors, characterization of precursors, and methods to direct the chemistry to more desirable outcomes yielding 'greener' sources of commodity chemicals and fuels. High-valent Chromium from Hydroperoxido-Chromium(III). The decomposition of pentaaquahydroperoxido chromium(III) ion (hereafter Cr aqOOH2+) in acidic aqueous solutions is kinetically complex and generates mixtures of products (Craq3+, HCrO 4-, H2O2, and O2). The yield of high-valent chromium products (known carcinogens) increased from a few percent at pH 1 to 70 % at pH 5.5 (near biological pH). Yields of H 2O2 increased with acid concentration. The reproducibility of the kinetic data was poor, but became simplified in the presence of H2O2 or 2,2‧-azinobis(3-ethylbenzothiazoline-6-sulfonate) dianion (ABTS2-). Both are capable of scavenging strongly oxidizing intermediates). The observed rate constants (pH 1, [O2] ≤ 0.03 mM) in the presence of these scavengers are independent of [scavenger] and within the error are the same (k,ABTS2- = (4.9 +/- 0.2) x 10-4 s-1 and kH2O2 = (5.3 +/- 0.7) x 10-4 s-1); indicating involvement of the scavengers in post-rate determining steps. In the presence of either scavenger, decomposition of CrOOH2+ obeyed a two-term rate law, k obs / s-1 = (6.7 +/- 0.7) x 10-4 + (7.6 +/- 1.1) x 10-4 [H+]. Effect of [H+] on the kinetics and the product distribution, cleaner kinetics in the presence of scavengers, and independence of kobs on [scavenger] suggest a dual-pathway mechanism for the decay of Craq OOH2+. The H+-catalyzed path

  20. Atmospheric Reactions of a Series of Hexenols with OH Radical and Ozone

    NASA Astrophysics Data System (ADS)

    Gai, Yanbo; Lin, Xiaoxiao; Ma, Qiao; Yang, Chengqiang; Zhao, Weixiong; Zhang, Weijun

    2016-04-01

    C6 hexenols are one of the most significant groups of biogenic volatile organic compounds (BVOCs). Because of their antibacterial properties, C6 hexenols can be emitted by a wide number of plants in response to changes in the ambient environment. The oxidation of these compounds in the atmosphere is involved in the formation of tropospheric ozone and secondary organic aerosols (SOA), thus causing significant effects on atmospheric chemistry and the climate. The lack of corresponding kinetic parameters and product information of their oxidation reactions will result in incomplete atmospheric chemical mechanisms and models. In this paper, we will overview our recent research progress on the study of the atmospheric reactions of a series of C6 hexenols with OH radicals and ozone. A series of studies were conducted using both experimental and theoretical methods. Corresponding rate constants were obtained, and reaction mechanisms were also analyzed. It could be concluded that both the nature of the substituent and its position play a fundamental role in the reactivity of the C6 hexenols toward OH radicals and O3. An activating effect of the -OH group in OH radical reactions was found, thus making the H-abstraction channel non-negligible in reactions of these unsaturated alcohols with OH radicals. The removal of these C6 hexenols by ozone also showed great importance and could be competitive with the major recognized sinks by OH radicals. These studies are of great significance for understanding the mechanism of atmospheric chemical reactions of hexenols and improving the atmospheric chemistry model. Experimental detail and corresponding results will be presented. Acknowledgements. This work was supported by the National Natural Science Foundation of China (21307137, 41575125 and 91544228), and the Natural Science Foundation of Anhui Province (1508085J03).

  1. Synthesis of Tetrahydronaphthyridines from Aldehydes and HARP Reagents via Radical Pictet-Spengler Reactions.

    PubMed

    Jackl, Moritz K; Kreituss, Imants; Bode, Jeffrey W

    2016-04-15

    The combination of aldehydes with newly designed HARP (halogen amine radical protocol) reagents gives access to α-substituted tetrahydronaphthyridines. By using different HARP reagents, various regioisomeric structures can be prepared in a single operation. These products, which are of high value in medicinal chemistry, are formed in a predictable manner via a formal Pictet-Spengler reaction of electron-poor pyridines that would not participate in the corresponding polar reactions. PMID:27026179

  2. Unusual spin-trap chemistry for the reaction of hydroxyl radical with the carcinogen N-nitrosodimethylamine

    NASA Astrophysics Data System (ADS)

    Wink, David A.; Desrosiers, Marc F.

    The reaction of the potent carcinogen N-nitrosodimethylamine (NDMA) with hydroxyl radical generated via radiolysis was studied using EPR techniques. Attempts to spin trap NDMA radical intermediates with 3,5-dibromo-4-nitrosobenzene sulfonate (DBNBS) produced only unusual DBNBS radicals. One of these radicals was shown to be generated by both reaction of DBNBS with nitric oxide, and direct oxidation of DBNBS with an inorganic oxidant ( .Br -2). Another DBNBS radical was identified as a sulfite spin adduct resulting from the degradation of DBNBS by a NDMA reactive intermediate. In the absence of DBNBS, hydroxyl radical reaction with NDMA gave the dimethylnitroxide radical. Unexpectedly, addition of DBNBS to a solution containing dimethylnitroxide produced an EPR spectrum nearly identical to that of NDMA solutions with DBNBS added before radiolysis. A proposed mechanism accounting for these observations is presented.

  3. A theoretical and experimental study of unimolecular and biomolecular radical hydrogen transfer reactions

    SciTech Connect

    Franz, J.A.; Autrey, T.; Gleicher, G.J.; Camaioni, D.M; Ferris, K.F.

    1991-04-01

    We have examined the intramolecular radical hydrogen transfer (RHT) reaction of the 2-(2-phenylethyl)cyclohexadienyl radical. Intramolecular hydrogen shift from the cyclohexadienyl ring to the ipso position of the phenyl ring, followed by {beta}-scission would have given benzene and ethylbenzene as products. Competing with this reaction is {beta}-scission to give benzyl radical and isotoluene, or hydrogen loss to give bibenzyl. Studies to date suggest a barrier for thermoneutral hydrogen transfer in the RHT reaction between aromatic systems of ca. 18 kcal/mole. None of the studies of RHT or equivalent mechanisms have attempted to directly observe H{sub 2}, and direct determination of Arrhenius parameters and a detailed examination of the pathway of the hydrogen transfer process remains to be carried out. To better understand the structural and energetic aspects of RHT, we have carried out a semiempirical molecular orbital study of bimolecular and intramolecular RHT reactions for a variety of aromatic systems. We also examined in detail the energetics of hydrogen transfer between ethyl radical and ethylene via RHT, an addition/metathesis/scission pathway, and a hybrid concerted'' pathway. 11 refs., 1 fig., 4 tabs.

  4. Temperature-dependent kinetics of the vinyl radical (C2H3) self-reaction.

    SciTech Connect

    Jusinski, Leonard E.; Zador, Judit; Taatjes, Craig A.; Selby, Talitha M.; Meloni, Giovanni; Knepp, Adam M.; Ismail, Huzeifa; Green, William H.; Abel, Paul R.; Fahr, Askar; Osborn, David L

    2008-10-01

    The rate coefficient for the self-reaction of vinyl radicals has been measured by two independent methods. The rate constant as a function of temperature at 20 Torr has been determined by a laser-photolysis/laser absorption technique. Vinyl iodide is photolyzed at 266 nm, and both the vinyl radical and the iodine atom photolysis products are monitored by laser absorption. The vinyl radical concentration is derived from the initial iodine atom concentration, which is determined by using the known absorption cross section of the iodine atomic transition to relate the observed absorption to concentration. The measured rate constant for the self-reaction at room temperature is approximately a factor of 2 lower than literature recommendations. The reaction displays a slightly negative temperature dependence, which can be represented by a negative activation energy, (E{sub a}/R) = -400 K. The laser absorption results are supported by independent experiments at 298 K and 4 Torr using time-resolved synchrotron-photoionization mass-spectrometric detection of the products of divinyl ketone and methyl vinyl ketone photolysis. The photoionization mass spectrometry experiments additionally show that methyl + propargyl are formed in the vinyl radical self-reaction, with an estimated branching fraction of 0.5 at 298 K and 4 Torr.

  5. Rate of reaction of superoxide radical with chloride-containing species

    SciTech Connect

    Long, C.A.; Bielski, B.H.J.

    1980-01-01

    This paper evaluates the rate constants for the reaction of superoxide radical with five common chloride-containing species (Cl/sup -/, ClO/sup -/, ClO/sub 2//sup -/, ClO/sub 3//sup -/, and ClO/sub 4//sup -/ and proposes a mechanism for those which react.

  6. KINETICS AND PRODUCTS OF THE REACTIONS OF SELECTED DIOLS WITH THE OH RADICAL. (R825252)

    EPA Science Inventory

    Using a relative rate method, rate constants have been measured at 296 ? 2 K for the gas-phase reactions of OH radicals with 1,2-butanediol, 2,3-butanediol, 1,3-butanediol, and 2-methyl-2,4-pentanediol, with rate constants (in units of 10-12 cm3 molecule

  7. On the Outcome of the Reactions Between Hydrocarbon Radicals and O2 in Helium Nanodroplets

    NASA Astrophysics Data System (ADS)

    Morrison, A. M.; Douberly, G. E.

    2012-06-01

    Helium nanodroplet isolation and infrared laser spectroscopy are used to investigate the CH3 + O2 and C3H3 (propargyl) + O2 reactions. The hydrocarbon radicals are generated in an effusive pyrolysis source located upstream from a differentially pumped O2 gas pick-up cell. In this experimental configuration, the reaction occurs between sequentially picked-up and presumably cold fragments. The CH3 + O2 reaction leads barrierlessly to the methyl-peroxy radical, and despite having to dissipate an energy of approximately 30 kcal/mol, the infrared spectra reveal a large abundance of droplets containing the cold CH3O2 radical. Theoretical studies have predicted an approximately 2-4 kcal/mol barrier in the entrance channel of the C3H3 + O2 reaction. Therefore, we initially expected to see a weakly bound “entrance channel” C3H3--O2 van-der-Waals complex, given the rapid cooling provided by the dissipative helium environment. However, only the trans-acetylenic isomer of the propargyl-peroxy radical is observed. The dipole moment of this species is measured with infrared laser Stark spectroscopy.

  8. Markovnikov free radical addition reactions, a sleeping beauty kissed to life.

    PubMed

    Hoffmann, Reinhard W

    2016-02-01

    This review covers free radical additions, which are initiated by the formal addition of a hydrogen atom to a C[double bond, length as m-dash]C double bond. These reactions originated in the realms of inorganic chemistry, polymer chemistry, and organic chemistry, whereby barriers between these disciplines impeded the rapid implementation of the findings. PMID:26753913

  9. Energies and kinetics of radical pairs involving bacteriochlorophyll and bacteriopheophytin in bacterial reaction centers

    PubMed Central

    Shuvalov, Vladimir A.; Parson, William W.

    1981-01-01

    Absorbance changes reflecting the formation of a transient radical-pair state, PF, were measured in reaction centers from Rhodopseudomonas sphaeroides under conditions that blocked electron transfer to a later carrier (a quinone, Q). The temperature dependence of the absorbance changes suggests that PF is an equilibrium mixture of two states, which appear to be mainly 1[P[unk]B[unk

  10. Radical formation in the [MeReO3]-catalyzed aqueous peroxidative oxidation of alkanes: a theoretical mechanistic study.

    PubMed

    Kuznetsov, Maxim L; Pombeiro, Armando J L

    2009-01-01

    Plausible mechanisms of radical formation in the catalytic system [MeReO(3)]/H(2)O(2)/H(2)O-CH(3)CN for the oxidation of alkanes to alcohols and ketones, via radical pathways, are investigated extensively at the density functional theory level. The most favorable route is based on the monoperoxo complex [MeReO(2)(O(2))(H(2)O)] and includes the formation of an H(2)O(2) adduct, water-assisted H-transfer from H(2)O(2) to the peroxo ligand, and generation of HOO(*). The thus formed reduced Re(VI) complex [MeReO(2)(OOH)(H(2)O)] reacts with H(2)O(2), resulting, upon water-assisted H-transfer and O-OH bond homolysis, in the regeneration of the oxo-Re(VII) catalyst and formation of the HO(*) radical that reacts further with the alkane. Water plays a crucial role by (i) stabilizing transition states for the proton migrations and providing easy intramolecular H-transfers in the absence of any N,O-ligands and (ii) saturating the Re coordination sphere what leads to a decrease of the activation barrier for the formation of HOO(*). The activation energy of the radical formation calculated for [MeReO(3)] (17.7 kcal/mol) is compatible with that determined experimentally [Shul'pin et al. J. Chem. Soc., Perkin Trans. 2 2001, 1351 .] for oxo-V-based catalytic systems (17 +/- 2 kcal/mol), and the overall type of mechanism proposed for such V catalysts is also effective for [MeReO(3)]. PMID:19049432

  11. Cyclopentadienone Oxidation Reaction Kinetics and Thermochemistry for the Alcohols, Hydroperoxides, and Vinylic, Alkoxy, and Alkylperoxy Radicals.

    PubMed

    Yommee, Suriyakit; Bozzelli, Joseph W

    2016-01-28

    Cyclopentadienone has one carbonyl and two olefin groups resulting in 4n + 2 π-electrons in a cyclic five-membered ring structure. Thermochemical and kinetic parameters for the initial reactions of cyclopentadienone radicals with O2 and the thermochemical properties for cyclopentadienone-hydroperoxides, alcohols, and alkenyl, alkoxy, and peroxy radicals were determined by use of computational chemistry. The CBS-QB3 composite and B3LYP density functional theory methods were used to determine the enthalpies of formation (ΔfH°298) using the isodesmic reaction schemes with several work reactions for each species. Entropy and heat capacity, S°(T) and Cp°(T) (50 K ≤ T ≤ 5000 K) are determined using geometric parameters, internal rotor potentials, and frequencies from B3LYP/6-31G(d,p) calculations. Standard enthalpies of formation are reported for parent molecules as cyclopentadienone, cyclopentadienone with alcohol, hydroperoxide substituents, and the cyclopentadienone-yl vinylic, alkoxy, and peroxy radicals corresponding to loss of a hydrogen atom from the carbon and oxygen sites. Entropy and heat capacity vs temperature also are reported for the parent molecules and for radicals. The thermochemical analysis shows The R(•) + O2 well depths are deep, on the order of 50 kcal mol(-1), and the R(•) + O2 reactions to RO + O (chain branching products) for cyclopentadienone-2-yl and cyclopentadienone-3-yl have unusually low reaction (ΔHrxn) enthalpies, some 20 or so kcal/mol below the entrance channels. Chemical activation kinetics using quantum RRK analysis for k(E) and master equation for falloff are used to show that significant chain branching as a function of temperature and pressure can occur when these vinylic radicals are formed. PMID:26784854

  12. From allylic alcohols to aldols through a new nickel-mediated tandem reaction: synthetic and mechanistic studies.

    PubMed

    Cuperly, David; Petrignet, Julien; Crévisy, Christophe; Grée, René

    2006-04-12

    Nickel hydride type complexes have been successfully developed as catalysts for the tandem isomerization-aldolization reaction of allylic alcohols with aldehydes. Optimization of the reaction conditions has shown that a cocatalyst, such as MgBr2, has a very positive effect on the kinetics of the reaction and in the yields of aldols. Under such optimized conditions {[NiHCl(dppe)] + MgBr(2) at 3-5 mol %)}, this reaction affords the aldols in good to excellent yields. It is a full-atom-economy-type reaction that occurs under mild conditions. Furthermore, it has a broad scope for the allylic alcohols and it is compatible with a wide range of aldehydes, including very bulky derivatives. The reaction is completely regioselective, but it exhibits a low stereoselectivity, except for allylic alcohols with a bulky substituent at the carbinol center. The use of chiral nonracemic catalysts was not successful, affording only racemic compounds. However, it was possible to use asymmetric synthesis for the preparation of optically active aldols. Various mechanistic studies have been performed using, for instance, a deuterated alcohol or a deuterated catalyst. They gave strong support to a mechanism involving first a transition-metal-mediated isomerization of the allylic alcohol into the free enol, followed by the addition of the latter intermediate onto the aldehyde in an "hydroxyl-carbonyl-ene" type reaction. These results confirm that allylic alcohols can be considered as new and useful partners in the development of the aldol reaction. PMID:16506253

  13. A new hypothesis about the relationship between free radical reactions and hemorheological properties in vivo.

    PubMed

    Mo, J; Fan, J; Guo, Z; Hunag, C; Yan, B; Wang, F; Wang, D; Sun, S

    1993-12-01

    This paper is concerned with a hypothesis that disturbance of free radical reactions may lead to abnormality of hemorheological properties in vivo, and so the free radicals generated in vivo may damage certain tissue cells indirectly by reducing the supply of oxygen and nutrients to these cells through slowing the circulation of blood. This hypothesis is based on the following evidence: A. We have found that the whole blood viscosity at low shear rate correlates to the lipid peroxidation in the patients suffering from certain cardio- or cerebrovascular diseases, and in dogs during liver ischemia reperfusion or hemorrhagic pancreatitis. B. Reports have shown that several alterations of hemorheological properties may take place as a result of free radical reactions, such as lipid peroxidation. For instance, lipid peroxidation may lead to decrease of deformability of red cells, increase of aggregation of red cells, formation of liquid thrombin, etc. C. We have demonstrated that some alterations of hemorheological properties involve the role of free radicals in rats suffering from intestinal ischemia/reperfusion. As evidence for this conclusion, superoxide dismutase (SOD) used as a specific scavenger of superoxide anion radical (O2-) can significantly prevent the intestinal ischemia/reperfusion induced changes of lipid peroxidation, red cell aggregation, Cassion's viscosity and whole blood viscosity at low shear rate in rats. PMID:8183128

  14. Multiple re-encounter approach to radical pair reactions and the role of nonlinear master equations

    SciTech Connect

    Clausen, Jens; Tiersch, Markus; Briegel, Hans J.; Guerreschi, Gian Giacomo

    2014-08-07

    We formulate a multiple-encounter model of the radical pair mechanism that is based on a random coupling of the radical pair to a minimal model environment. These occasional pulse-like couplings correspond to the radical encounters and give rise to both dephasing and recombination. While this is in agreement with the original model of Haberkorn and its extensions that assume additional dephasing, we show how a nonlinear master equation may be constructed to describe the conditional evolution of the radical pairs prior to the detection of their recombination. We propose a nonlinear master equation for the evolution of an ensemble of independently evolving radical pairs whose nonlinearity depends on the record of the fluorescence signal. We also reformulate Haberkorn's original argument on the physicality of reaction operators using the terminology of quantum optics/open quantum systems. Our model allows one to describe multiple encounters within the exponential model and connects this with the master equation approach. We include hitherto neglected effects of the encounters, such as a separate dephasing in the triplet subspace, and predict potential new effects, such as Grover reflections of radical spins, that may be observed if the strength and time of the encounters can be experimentally controlled.

  15. Reactions of reducing and oxidizing radicals with caffeic acid:. a pulse radiolysis and theoretical study

    NASA Astrophysics Data System (ADS)

    Li, Xifeng; Cai, Zhongli; Katsumura, Yosuke; Wu, Guozhong; Muroya, Yusa

    2001-01-01

    Molecular calculations coupled with pulse radiolysis studies are performed to understand the reactions of radicals with caffeic acid. From molecular calculation, we find that e aq- and ·OH tend to form adducts with caffeic acid, while N 3rad tends to abstract H from 4-hydroxyl group in benzene ring, generating a semi-quinoid radical. Based on comparison of the heat of formation, the most favorable radical attack sites and the most stable radical structures are predicted. The calculation results suggest that the stability of the electron adducts radicals < ·OH adducts of caffeic ions, in good agreement with their experimental second-order decay rate constants (2 k=(1.1±0.2)×10 9, (6.0±0.4)×10 7 and (2.0±0.2)×10 7 M -1 s -1, respectively), determined by pulse radiolysis. Molecular calculations seem to be a powerful tool to predict the stability and structures of transient radicals.

  16. Addition reaction of alkyl radical to C60 fullerene: Density functional theory study

    NASA Astrophysics Data System (ADS)

    Tachikawa, Hiroto; Kawabata, Hiroshi

    2016-02-01

    Functionalized fullerenes are known as a high-performance molecules. In this study, the alkyl-functionalized fullerenes (denoted by R-C60) have been investigated by means of the density functional theory (DFT) method to elucidate the effects of functionalization on the electronic states of fullerene. Also, the reaction mechanism of alkyl radicals with C60 was investigated. The methyl, ethyl, propyl, and butyl radicals (denoted by n = 1-4, where n means the number of carbon atoms in the alkyl radical) were examined as alkyl radicals. The DFT calculation showed that the alkyl radical binds to the carbon atom of C60 at the on-top site, and a strong C-C single bond is formed. The binding energies of alkyl radicals to C60 were distributed in the range of 31.8-35.1 kcal mol-1 at the CAM-B3LYP/6-311G(d,p) level. It was found that the activation barrier exists before alkyl addition, the barrier heights were calculated to be 2.1-2.8 kcal mol-1. The electronic states of R-C60 complexes were discussed on the basis of the theoretical results.

  17. Laser flash photolysis studies of radical-radical reaction kinetics: The HO{sub 2} + IO reaction

    SciTech Connect

    Cronkhite, J.M.; Stickel, R.E.; Nicovich, J.M.; Wine, P.H.

    1999-04-29

    Reactive iodine as a potential tropospheric O{sub 3} sink has received considerable attention recently. Laser flash photolysis of Cl{sub 2}/CH{sub 3}OH/O{sub 2}/I{sub 2}/NO{sub 2}/SF{sub 6}N{sub 2} mixtures at 308 nm has been coupled with simultaneous time-resolved detection of HO{sub 2} (by infrared tunable diode laser absorption spectroscopy) and IO (by visible absorption spectroscopy) to investigate the kinetics of the atmospherically important reaction HO{sub 2} + IO {r_arrow} products over the temperature range 274--373 K in N{sub 2} buffer gas at pressures of 12 and 25 Torr. All experiments were performed under near pseudo-first-order conditions with HO{sub 2} in excess over IO. At 298 K, the rate coefficient was determined to be (9.7 {+-} 2.9) {times} 10{sup {minus}11} cm{sup 3} molecule{sup {minus}1}s{sup {minus}1}, with the primary source of uncertainty being knowledge of the infrared line strength(s) required to convert measured HO{sub 2} absorbances to absolute concentrations. The temperature dependence of the HO{sub 2} + IO rate coefficient was found to be adequately described by the Arrhenius expression k = 9.3 {times} 10{sup {minus}12} exp(680/T) cm{sup 3} molecule{sup {minus}1} s{sup {minus}1}. The results reported in this study are compared with other recent studies of HO{sub 2} + IO kinetics, and the potential roles of this reaction in atmospheric chemistry are discussed.

  18. Mechanistic Examination of Cβ–Cγ Bond Cleavages of Tryptophan Residues during Dissociations of Molecular Peptide Radical Cations

    SciTech Connect

    Song, Tao; Ma, Ching-Yung; Chu, Ivan K.; Siu, Chi-Kit; Laskin, Julia

    2013-02-14

    In this study, we used collision-induced dissociation (CID) to examine the gas-phase fragmentations of [GnW]•+ (n = 2-4) and [GXW]•+ (X = C, S, L, F, Y, Q) species. The Cβ–Cγ bond cleavage of a C-terminal decarboxylated tryptophan residue ([M - CO2]•+) can generate [M - CO2 - 116]+, [M - CO2 - 117]•+, and [1H-indole]•+ (m/z 117) species as possible product ions. Competition between the formation of [M - CO2 - 116]+ and [1H-indole]•+ systems implies the existence of a proton-bound dimer formed between the indole ring and peptide backbone. Formation of such a proton-bound dimer is facile via a protonation of the tryptophan γ-carbon atom as suggested by density functional theory (DFT) calculations. DFT calculations also suggested the initially formed ion 2--the decarboxylated species that is active against Cβ–Cγ bond cleavage -can efficiently isomerize to form a more-stable -radical isomer (ion 9) as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. The Cβ–Cγ bond cleavage of a tryptophan residue also can occur directly from peptide radical cations containing a basic residue. CID of [WGnR]•+ (n = 1-3) radical cations consistently resulted in predominant formation of [M-116]+ product ions. It appears that the basic arginine residue tightly sequesters the proton and allows the charge-remote Cβ–Cγ bond cleavage to prevail over the charge-directed one. DFT calculations predicted the barrier for the former is 6.2 kcal mol -1 lower than that of the latter. Furthermore, the pathway involving a salt-bridge intermediate also was accessible during such a bond cleavage event.

  19. Sub-millitesla magnetic field effects on the recombination reaction of flavin and ascorbic acid radicals.

    PubMed

    Evans, Emrys W; Kattnig, Daniel R; Henbest, Kevin B; Hore, P J; Mackenzie, Stuart R; Timmel, Christiane R

    2016-08-28

    Even though the interaction of a <1 mT magnetic field with an electron spin is less than a millionth of the thermal energy at room temperature (kBT), it still can have a profound effect on the quantum yields of radical pair reactions. We present a study of the effects of sub-millitesla magnetic fields on the photoreaction of flavin mononucleotide with ascorbic acid. Direct control of the reaction pathway is achieved by varying the rate of electron transfer from ascorbic acid to the photo-excited flavin. At pH 7.0, we verify the theoretical prediction that, apart from a sign change, the form of the magnetic field effect is independent of the initial spin configuration of the radical pair. The data agree well with model calculations based on a Green's function approach that allows multinuclear spin systems to be treated including the diffusive motion of the radicals, their spin-selective recombination reactions, and the effects of the inter-radical exchange interaction. The protonation states of the radicals are uniquely determined from the form of the magnetic field-dependence. At pH 3.0, the effects of two chemically distinct radical pair complexes combine to produce a pronounced response to ∼500 μT magnetic fields. These findings are relevant to the magnetic responses of cryptochromes (flavin-containing proteins proposed as magnetoreceptors in birds) and may aid the evaluation of effects of weak magnetic fields on other biologically relevant electron transfer processes. PMID:27586950

  20. Determination of the rate constant of hydroperoxyl radical reaction with phenol

    NASA Astrophysics Data System (ADS)

    Kozmér, Zsuzsanna; Arany, Eszter; Alapi, Tünde; Takács, Erzsébet; Wojnárovits, László; Dombi, András

    2014-09-01

    The rate constant of HO2rad reaction with phenol (kHO2rad +phenol) was investigated. The primary radical set produced in water γ radiolysis (rad OH, eaq- and Hrad ) was transformed to HO2rad /O2rad - by using dissolved oxygen and formate anion (in the form of either formic acid or sodium formate). The concentration ratio of HO2rad /O2rad - was affected by the pH value of the solution: under acidic conditions (using HCOOH) almost all radicals were converted to HO2rad , while under alkaline conditions (using HCOONa) to O2rad -. The degradation rate of phenol was significantly higher using HCOOH. From the ratio of reaction rates under the two reaction conditions kHO2rad +phenol was estimated to be (2.7±1.2)×103 L mol-1 s-1.

  1. Absolute rate constants of alkoxyl radical reactions in aqueous solution. [Tert-butyl hydroperoxide

    SciTech Connect

    Erben-Russ, M.; Michel, C.; Bors, W.; Saran, M.

    1987-04-23

    The pulse radiolysis technique was used to generate the alkoxyl radical derived from tert-butyl hydroperoxide (/sup t/BuOOH) in aqueous solution. The reactions of this radical with 2,2'-azinobis(3-ethyl-6-benzothiazolinesulfonate) (ABTS) and promethazine were monitored by kinetic spectroscopy. The unimolecular decay rate constant of the tert-butoxyl radical (/sup t/BuO) was determined to be 1.4 x 10/sup 6/ s/sup -1/. On the basis of this value, the rate constants for /sup t/BuO attack on quercetin, crocin, crocetin, ascorbate, isoascorbate, trolox c, glutathione, thymidine, adenosine, guanosine, and unsaturated fatty acids were determined. In addition, the reaction of /sup t/BuO with the polyunsaturated fatty acids (PUFA) was observed by directly monitoring the formation of the fatty acid pentadienyl radicals. Interestingly, the attack of /sup t/BuO on PUFA was found to be faster by about one order of magnitude as compared to the same reaction in a nonpolar solvent.

  2. Concurrent esterification and N-acetylation of amino acids with orthoesters: A useful reaction with interesting mechanistic implications.

    PubMed

    Gibson, Sarah; Romero, Dickie; Jacobs, Hollie K; Gopalan, Aravamudan S

    2010-12-22

    The concurrent esterification and N-acetylation of amino acids has been studied with triethyl orthoacetate (TEOA) and triethyl orthoformate (TEOF). In a surprising finding, only one equivalent of TEOA in refluxing toluene was necessary to convert L-proline and L-phenylalanine to the corresponding N-acetyl ethyl esters in good yield. The same transformation using TEOF was not effective. Stereochemical outcome and stoichiometric studies as well as structural variation of the amino acids in this reaction provided unexpected mechanistic insight. PMID:21286246

  3. Concurrent esterification and N-acetylation of amino acids with orthoesters: A useful reaction with interesting mechanistic implications

    PubMed Central

    Gibson, Sarah; Romero, Dickie; Jacobs, Hollie K.; Gopalan, Aravamudan S.

    2010-01-01

    The concurrent esterification and N-acetylation of amino acids has been studied with triethyl orthoacetate (TEOA) and triethyl orthoformate (TEOF). In a surprising finding, only one equivalent of TEOA in refluxing toluene was necessary to convert L-proline and L-phenylalanine to the corresponding N-acetyl ethyl esters in good yield. The same transformation using TEOF was not effective. Stereochemical outcome and stoichiometric studies as well as structural variation of the amino acids in this reaction provided unexpected mechanistic insight. PMID:21286246

  4. Computational Chemistry in the Undergraduate Laboratory: A Mechanistic Study of the Wittig Reaction

    ERIC Educational Resources Information Center

    Albrecht, Birgit

    2014-01-01

    The Wittig reaction is one of the most useful reactions in organic chemistry. Despite its prominence early in the organic chemistry curriculum, the exact mechanism of this reaction is still under debate, and this controversy is often neglected in the classroom. Introducing a simple computational study of the Wittig reaction illustrates the…

  5. Experimental and theoretical investigation of the self-reaction of phenyl radicals.

    SciTech Connect

    Tranter, R. S.; Klippenstein, S. J.; Harding, L. B.; Giri, B. R.; Yang, X.; Kiefer, J. H.; Chemical Sciences and Engineering Division; Univ. of Illinois at Chicago

    2010-08-19

    A combination of experiment and theory is applied to the self-reaction kinetics of phenyl radicals. The dissociation of phenyl iodide is observed with both time-of-flight mass spectrometry, TOF-MS, and laser schlieren, LS, diagnostics coupled to a diaphragmless shock tube for temperatures ranging from 1276 to 1853 K. The LS experiments were performed at pressures of 22 {+-} 2, 54 {+-} 7, and 122 {+-} 6 Torr, and the TOF-MS experiments were performed at pressures in the range 500-700 Torr. These observations are sensitive to both the dissociation of phenyl iodide and to the subsequent self-reaction of the phenyl radicals. The experimental observations indicate that both these reactions are more complicated than previously assumed. The phenyl iodide dissociation yields {approx}6% C{sub 6}H{sub 4} + HI in addition to the major and commonly assumed C{sub 6}H{sub 5} + I channel. The self-reaction of phenyl radicals does not proceed solely by recombination, but also through disproportionation to benzene + o-/m-/p-benzynes, with comparable rate coefficients for both. The various channels in the self-reaction of phenyl radicals are studied with ab initio transition state theory based master equation calculations. These calculations elucidate the complex nature of the C{sub 6}H{sub 5} self-reaction and are consistent with the experimental observations. The theoretical predictions are used as a guide in the development of a model for the phenyl iodide pyrolysis that accurately reproduces the observed laser schlieren profiles over the full range of the observations.

  6. Experimental study of the reactions of limonene with OH and OD radicals: kinetics and products.

    PubMed

    Braure, Tristan; Bedjanian, Yuri; Romanias, Manolis N; Morin, Julien; Riffault, Véronique; Tomas, Alexandre; Coddeville, Patrice

    2014-10-01

    The kinetics of the reactions of limonene with OH and OD radicals has been studied using a low-pressure flow tube reactor coupled with a quadrupole mass spectrometer: OH + C10H16 → products (1), OD + C10H16 → products (2). The rate constants of the title reactions were determined using four different approaches: either monitoring the kinetics of OH (OD) radicals or limonene consumption in excess of limonene or of the radicals, respectively (absolute method), and by the relative rate method using either the reaction OH (OD) + Br2 or OH (OD) + DMDS (dimethyl disulfide) as the reference one and following HOBr (DOBr) formation or DMDS and limonene consumption, respectively. As a result of the absolute and relative measurements, the overall rate coefficients, k1 = (3.0 ± 0.5) × 10(-11) exp((515 ± 50)/T) and k2 = (2.5 ± 0.6) × 10(-11) exp((575 ± 60)/T) cm(3) molecule(-1) s(-1), were determined at a pressure of 1 Torr of helium over the temperature ranges 220-360 and 233-353 K, respectively. k1 was found to be pressure independent over the range 0.5-5 Torr. There are two possible pathways for the reaction between OH (OD) and limonene: addition of the radical to one of the limonene double bonds (reactions 1a and 2a ) and abstraction of a hydrogen atom (reactions 1b and 2b ), resulting in the formation of H2O (HOD). Measurements of the HOD yield as a function of temperature led to the following branching ratio of the H atom abstraction channel: k2b/k2 = (0.07 ± 0.03) × exp((460 ± 140)/T) for T = (253-355) K. PMID:25211148

  7. Mechanistic investigation of the uncatalyzed esterification reaction of acetic acid and acid halides with methanol: a DFT study.

    PubMed

    Lawal, Monsurat M; Govender, Thavendran; Maguire, Glenn E M; Honarparvar, Bahareh; Kruger, Hendrik G

    2016-10-01

    Implementation of catalysts to drive reactions from reactants to products remains a burden to synthetic and organic chemists. In spite of investigations into the kinetics and mechanism of catalyzed esterification reactions, less effort has been made to explore the possibility of an uncatalyzed esterification process. Therefore, a comprehensive mechanistic perspective for the uncatalyzed mechanism at the molecular level is presented. Herein, we describe the non-catalyzed esterification reaction of acetic acid and its halide derivatives (XAc, where X= OH, F, Cl, Br, I) with methanol (MeOH) through a concerted process. The reaction in vacuum and methanol was performed using the density functional theory (DFT) method at M06-2X level with def2-TZVP basis set after a careful literature survey and computations. Esterification through cyclic 4- or 6-membered transition state structures in one- or two-step concerted mechanisms were investigated. The present study outlines the possible cyclic geometry conformations that may occur during experiments at simple ratio of reactants. The free energy of activation for acetic acid and acetyl chloride are 36 kcal mol(-1) and 21 kcal mol(-1), respectively. These are in good agreement with available experimental results from the literature. The selected quantum chemical descriptors proved to be useful tools in chemical reactivity prediction for the reaction mechanism. This quantum mechanics study can serve as a necessary step towards revisiting uncatalyzed reaction mechanisms in some classical organic reactions. PMID:27604278

  8. Kinetics of the reactions of SH radicals with NO2 and O2

    NASA Technical Reports Server (NTRS)

    Stachnik, R. A.; Molina, M. J.

    1987-01-01

    The SH + NO2 reaction rate constant was measured by monitoring SH concentrations with long-path optical absorption at 324 nm in a laser photolysis system. At 298 K, the rate constant was found to be (4.8 + or - 1.0) x 10 to the -11th cu cm/molecule per sec. An upper limit of 4 x 10 to the -19th cu cm/molecule per sec was inferred for the SH + O2 reaction, indicating that the atmospheric oxidation of the SH radical may occur via reaction with species such as NO2 and O3.

  9. Kinetics of CH(X 2Pi) radical reactions with cyclopropane, cyclopentane, and cyclohexane

    NASA Technical Reports Server (NTRS)

    Zabarnick, S.; Fleming, J. W.; Lin, M. C.

    1988-01-01

    Rate constants have been obtained for CH(X 2Pi) radical reactions with cyclopropane, cyclopentane, and cyclohexane in order to establish the rate of CH insertion into secondary C-H bonds in alkanes. Data indicate that there is no measurable dependence on photolysis laser energy. The reactions all exhibited rate constants that decrease with increasing temperature. It is suggested that a possible set of pathways for the cycloalkane reactions is a ring-opening process where the excited adduct decomposes to a hydrogen atom and a diene.

  10. Role of oxygen radical reactions in the browning and cross-linking of lysozyme by glucose

    SciTech Connect

    Hull, C.J.; Thorpe, S.R.; Baynes, J.W.

    1986-05-01

    Lysozyme (LZM) was used as a model protein for studies on the effects of oxygen on the Maillard reaction. During a 4 wk incubation in 0.25 M glucose (0.2 M phosphate buffer, pH 7.4, 37/sup 0/C) the kinetics of glycation of LZM were similar under air and N/sub 2/, yielding approx.2 mol Lys modified per mol LZM. Fructoselysine (FL) was the major Lys derivative formed under air and N/sub 2/, while N/sup epsilon/-carboxymethyllysine (CML) accounted for approx.30% of FL formed at 4 wk under air. A loss of 1 mol Arg per mol LZM was also observed under both air and N/sub 2/, with greater loss from LZM dimer vs. monomer, suggesting a role for Arg in the crosslinking reaction. Dimer and monomer did not differ in content of Lys, FL or CML (under air), but dimer was 4 times as fluorescent as monomer, suggesting that crosslink structures are fluorescent. Despite significant differences in kinetics of crosslinking, browning and development of fluorescence of LZM under air vs. N/sub 2/, products formed had similar absorbance and fluorescence spectra. Based on inhibition by chelators and radical scavengers, the more rapid crosslinking and development of fluorescence under air was shown to result from oxygen radical reactions. These results indicate that both radical and non-radical processes may contribute to the Maillard reaction, but that the browning, fluorescence and crosslinking of protein may proceed in the absence of oxygen and oxygen radicals.

  11. Photoinitiated electron-transfer reactions of aromatic imides with phenylcyclopropanes. Formation of radical ion pair cycloadducts. Mechanism of the reaction

    SciTech Connect

    Somich, C.; Mazzocchi, P.H.; Edwards, M.; Morgan, T.; Ammon, H.L. )

    1990-04-27

    Few investigations have addressed the cyclization of a radical anion-radical cation pair resulting from photoinitiated electron transfer. One system taht meets the criteria necessary to observe this phenomenon is the acceptor-donor pair N-methylphthalimide (NMP) and phenylcyclopropane (PC). Irradiation of NMP or N-methyl-2,3-naphthalimide (NMN) in the presence of PC in acetonitrile gave rise to two spiro tetrahydrofuranyl lactams. The regiochemistry and relative stereochemistry of these compounds were determined by NMR techniques and X-ray crystallography. The mechanism of the reaction proceeds via electron transfer from PC to the imide followed by coupling of the radical ion pair at the 1,2-position of the carbonyl to the cyclopropane ring in a stepwise fashion. Fluorescence quenching experiments, reaction efficiency, and the free energy for electron transfer using various aromatic substituted phenylcyclopropanes provided strong evidence that electron transfer occurs. The reaction of cis-2-deutero-1-phenylcyclopropane (PC-d) with NMN established that cycloaddition is stepwise rather than concerted and that both syn and anti reactive intermediates are equally accessible.

  12. Production of sulfate radical and hydroxyl radical by reaction of ozone with peroxymonosulfate: a novel advanced oxidation process.

    PubMed

    Yang, Yi; Jiang, Jin; Lu, Xinglin; Ma, Jun; Liu, Yongze

    2015-06-16

    In this work, simultaneous generation of hydroxyl radical (•OH) and sulfate radical (SO4•−) by the reaction of ozone (O3) with peroxymonosulfate (PMS; HSO5−) has been proposed and experimentally verified. We demonstrate that the reaction between the anion of PMS (i.e.,SO52−) and O3 is primarily responsible for driving O3 consumption with a measured second order rate constant of (2.12 ± 0.03) × 10(4) M(-1) s(-1). The formation of both •OH and SO4•− from the reaction between SO52− and O3 is confirmed by chemical probes (i.e., nitrobenzene for •OH and atrazine forb oth •OH and SO4•−). The yields of •OH and SO4•− are determined to be 0.43 ± 0.1 and 0.45 ± 0.1 per mol of O3 consumption, respectively. An adduct,−O3SOO− + O3 → −O3SO5−, is assumed as the first step, which further decomposes into SO5•− and O3•−. The subsequent reaction of SO5•− with O3is proposed to generate SO4•−, while O3•− converts to •OH. A definition of R(ct,•OH) and R(ct,SO4•−) (i.e., respective ratios of •OH and SO4•− exposures to O3 exposure) is adopted to quantify relative contributions of •OH and SO4•−. Increasing pH leads to increases in both values of R(ct,•OH) and R(ct,SO4•−) but does not significantly affect the ratio of R(ct,SO4•−) to R(ct,•OH) (i.e., R(ct,SO4•−)/R(ct,•OH)), which represents the relative formation of SO4•− to •OH. The presence of bicarbonate appreciably inhibits the degradation of probes and fairly decreases the relative contribution of •OH for their degradation, which may be attributed to the conversion of both •OH and SO4•− to the more selective carbonate radical (CO3•−).Humic acid promotes O3 consumption to generate •OH and thus leads to an increase in the R(ct,•OH) value in the O3/PMS process,w hile humic acid has negligible influence on the R(ct,SO4•−) value. This discrepancy is reasonably explained by the negligible effect of humic acid on SO

  13. Oxygen radical-mediated oxidation reactions of an alanine peptide motif - density functional theory and transition state theory study

    PubMed Central

    2012-01-01

    Background Oxygen-base (O-base) oxidation in protein backbone is important in the protein backbone fragmentation due to the attack from reactive oxygen species (ROS). In this study, an alanine peptide was used model system to investigate this O-base oxidation by employing density functional theory (DFT) calculations combining with continuum solvent model. Detailed reaction steps were analyzed along with their reaction rate constants. Results Most of the O-base oxidation reactions for this alanine peptide are exothermic except for the bond-breakage of the Cα-N bond to form hydroperoxy alanine radical. Among the reactions investigated in this study, the activated energy of OH α-H abstraction is the lowest one, while the generation of alkylperoxy peptide radical must overcome the highest energy barrier. The aqueous situation facilitates the oxidation reactions to generate hydroxyl alanine peptide derivatives except for the fragmentations of alkoxyl alanine peptide radical. The Cα-Cβ bond of the alkoxyl alanine peptide radical is more labile than the peptide bond. Conclusion the rate-determining step of oxidation in protein backbone is the generation of hydroperoxy peptide radical via the reaction of alkylperoxy peptide radical with HO2. The stabilities of alkylperoxy peptide radical and complex of alkylperoxy peptide radical with HO2 are crucial in this O-base oxidation reaction. PMID:22524792

  14. O(1D) Reaction with Methane Studied by State Resolved Scattering Distribution Measurements of Methyl Radicals

    NASA Astrophysics Data System (ADS)

    Suzuki, Toshinori

    2014-06-01

    The scattering distributions of state-selected methyl radicals are measured for the O(^1D_2) reaction with methane using a crossed molecular beam ion imaging method at collision energies of 0.9 - 6.8 kcal/mol. The results are compared with the reaction with deuterated methane to examine the isotope effects. The scattering distributions exhibit contributions from both the insertion and abstraction pathways respectively on the ground and excited-state potential energy surfaces. Insertion is the main pathway, and it provides a strongly forward-enhanced angular distribution of methyl radicals. Abstraction is a minor pathway, causing backward scattering of methyl radicals with a discrete speed distribution. From the collision energy dependence of the abstraction/insertion ratio, the barrier height for the abstraction pathway is estimated for O(^1D_2) with CH_4 and CD_4, respectively. The insertion pathway of the O(^1D_2) reaction with CH_4 has a narrower angular width in the forward scattering and a larger insertion/abstraction ratio than the reaction with CD_4, which indicate that the insertion reaction with CH_4 has a larger cross section and a shorter reaction time than the reaction with CD_4. Additionally, while the insertion reaction with CD_4 exhibits strong angular dependence of the CD_3 speed distribution, CH_3 exhibits considerably smaller dependence. The result suggests that, although intramolecular vibrational redistribution (IVR) within the lifetime of the methanol intermediate is restrictive in both isotopomers, relatively more extensive IVR occurs in CD_3OD than CH_3OH, presumably due to the higher vibrational state density.

  15. A resistive pyrolytic radical source for gas-surface reaction studies

    NASA Astrophysics Data System (ADS)

    Lee, David Y.; Jobbins, Matthew M.; Kandel, S. Alex

    2012-04-01

    We describe a thermal gas cracker designed to produce low fluxes of gas-phase radicals for use in radical-surface reaction studies. A resistively heated thin piece of highly oriented pyrolytic graphite is used as the pyrolysis filament, with the major advantage that this material remains inert at high temperatures. The instrument is built within an existing titanium sublimation pump, which simplifies construction and allows for self-pumping of the radical source. Thermal generation of Cl atoms from Cl2 was chosen to test the effectiveness of the instrument. 35Cl and 37Cl were generated with a concomitant decrease in parent 70Cl2 and 72Cl2 species, as monitored by a residual gas analyzer. The cracking fraction of Cl2 as a function of cell temperature is reported, with nearly full conversion achieved at high temperature.

  16. Alkyl bromides as mechanistic probes of reductive dehalogenation: reactions of vicinal dibromide stereoisomers with zerovalent metals.

    PubMed

    Totten, L A; Jans, U; Roberts, A L

    2001-06-01

    Whether reductive dehalogenation proceeds via a one- or a two-electron mechanism has been suggested to affect product distributions, hence potentially influencing the success of engineered treatment systems. In this work, we explore vicinal dibromide stereoisomers as "probes" of the concertedness of electron transfer in reduction by aqueous suspensions of iron and zinc metal. Dibromides consisted of 2,3-dibromopentane (diBP) stereoisomers and (+/-)-1,2-dibromo-1,2-diphenylethane. All dibromides reacted with metals to give the same E:Z ratio of olefins observed during dehalogenation by iodide (a two-electron reductant). Reduction by Cr(II) (a one-electron reductant) yielded distinctly different proportions of E and Z olefins. Although this might be construed as evidence that metals function as two-electron reductants, high stereo-specificity was also obtained for reduction of diBPs by Fe(II) adsorbed to goethite, a presumed one-electron reductant; this can be explained by two single-electron transfers in rapid succession, facilitated by the locally elevated concentration of reducing equivalents at the oxide-water interface. The results suggest that reduction of alkyl halides by metals is not likely to produce free radicals that persist long enough to undergo radical-radical coupling or hydrogen-atom abstraction from minor dissolved constituents. Apparent free-radical coupling products are more likely to result from (possibly surface-bound) organometallic intermediates. PMID:11414030

  17. Coherent chemical kinetics as quantum walks. II. Radical-pair reactions in Arabidopsis thaliana

    NASA Astrophysics Data System (ADS)

    Chia, A.; Górecka, A.; Kurzyński, P.; Paterek, T.; Kaszlikowski, D.

    2016-03-01

    We apply the quantum-walk approach proposed in the preceding paper [A. Chia et al., preceding paper, Phys. Rev. E 93, 032407 (2016), 10.1103/PhysRevE.93.032407] to a radical-pair reaction where realistic estimates for the intermediate transition rates are available. The well-known average hitting time from quantum walks can be adopted as a measure of how quickly the reaction occurs and we calculate this for varying degrees of dephasing in the radical pair. The time for the radical pair to react to a product is found to be independent of the amount of dephasing introduced, even in the limit of no dephasing where the transient population dynamics exhibits strong coherent oscillations. This can be seen to arise from the existence of a rate-limiting step in the reaction and we argue that in such examples, a purely classical model based on rate equations can be used for estimating the time scale of the reaction but not necessarily its population dynamics.

  18. Reactions of CH3, CH3O, and CH3O2 radicals with O3

    NASA Technical Reports Server (NTRS)

    Simonaitis, R.; Heicklen, J.

    1975-01-01

    Ozone was photolyzed at 253.7 nm at 25 and -52 degrees in the presence of CH4 and O2 to measure the reactions of O3 with CH3, CH3O, and CH3O2. The O(1D) atoms produced in the primary photochemical act react with CH4 to give CH3 radicals which in turn can react with O2 to give CH3O2 and CH3O radicals. At very high O2 to O3 concentration ratios, the quantum yield of O3 disappearance approached 1.0, indicating that O3 reactions with CH3O2 and CH3O are slow. Upper limits to the rate coefficients at 25 degrees were computed. At lower values of the concentration ratio, chain decomposition of O3 occurred which could be explained by the reaction of O3 with CH3 radicals to produce CH2O, O2, and H atoms all the time. The two routes to these products are considered, and the preferred reaction channel is found.

  19. Electronic nonadiabatic effects in low temperature radical-radical reactions. I. C(3P) + OH(2Π).

    PubMed

    Maergoiz, A I; Nikitin, E E; Troe, J

    2014-07-28

    The formation of collision complexes, as a first step towards reaction, in collisions between two open-electronic shell radicals is treated within an adiabatic channel approach. Adiabatic channel potentials are constructed on the basis of asymptotic electrostatic, induction, dispersion, and exchange interactions, accounting for spin-orbit coupling within the multitude of electronic states arising from the separated reactants. Suitable coupling schemes (such as rotational + electronic) are designed to secure maximum adiabaticity of the channels. The reaction between C((3)P) and OH((2)Π) is treated as a representative example. The results show that the low temperature association rate coefficients in general cannot be represented by results obtained with a single (generally the lowest) potential energy surface of the adduct, asymptotically reaching the lowest fine-structure states of the reactants, and a factor accounting for the thermal population of the latter states. Instead, the influence of non-Born-Oppenheimer couplings within the multitude of electronic states arising during the encounter markedly increases the capture rates. This effect extends up to temperatures of several hundred K. PMID:25084905

  20. Radical Rearrangement Catalysis in an Enzyme at 190-207 K: Mechanistic Features Revealed by Substrate ^1H/^2H Isotope Effects

    NASA Astrophysics Data System (ADS)

    Zhu, Chen; Warncke, Kurt

    2009-11-01

    The decay kinetics of both the natural abundance and [1,1,2,2-^2H4]-aminoethanol generated Co^II-substrate radical pair catalytic intermediate in ethanolamine ammonia-lyase (EAL) from Salmonella typhimrium have been measured by using time-resolved, full-spectrum X-band continuous-wave electron paramagnetic resonance (EPR) spectroscopy in frozen aqueous solution from 190 to 207 K. The decay reaction proceeds through sequential radical covalent rearrangement and hydrogen atom transfer (HT) steps. In the temperature range from 190 to 207 K, the decay is biexponential, and the two phases correspond to distinct populations [1]. The ^1H/^2H isotope effects (IE) on the fast phase and slow phase are 1.3 and 0.8, respectively. These IE are not caused by a primary kinetic IE. Therefore, HT is rapid, relative to rearrangement. We propose that the fast phase is rate-determined by the rearrangement step, and that the slow phase is rate-determined by a step after rearrangement that is associated with protein guidance of the reactions. The results reveal microscopic features of the core reaction chemistry and protein dynamics participation in the reaction, which are not accessible at ambient temperatures.[4pt] [1] Zhu, C., Warncke, K. Biophys. J. 95, 5890 (2008). Supported by grant DK54514 from NIDDK/NIH.

  1. Concerted effects of substituents in the reaction of •OH radicals with aromatics: The hydroxybenzaldehydes

    NASA Astrophysics Data System (ADS)

    Albarran, Guadalupe; Mendoza, Edith; Schuler, Robert H.

    2016-07-01

    In the present work, we have examined the distribution of products in the radiolytic hydroxylation of 2-, 3- and 4-hydroxybenzaldehyde to obtain information on the concerted effect of the -CHO and -OH groups at the addition site of •OH radicals. The •OH radical was found to selectively add to the free positions of the aromatic ring. Furthermore, the •OH radical reacts by substitution at the ipso position followed by elimination of the substituent, producing dihydroxybenzene compounds. Additionally, the formation of carboxylic acids as an initial product has been conclusively identified by retention times and UV and mass spectra. These acids are formed as a result of the radiolytic oxidation of the initial radical formed by the addition reaction of the •OH radicals to the meso position (exocyclic carbon). The identification of the products, dihydroxybenzaldehydes, dihydroxybenzenes and hydroxybenzoic acids and calculation of their yields were achieved through HPLC. The G values of each product are given, which reflect the charge distributions in the hydroxybenzaldehydes, such that the formyl group modifies the ortho-para directing effect of the -OH substituent. The 3 and 5 positions in 2- and 4-hydroxybenzaldehyde showed increased the electronic density compared to that of phenol, indicating that the formyl group has a significant effect on the electronic structure of those hydroxybenzaldehydes. In 3-hydroxybenzaldehyde, the -OH substituent had a dominant ortho-directing effect similar to that observed for phenol.

  2. Some reactions and properties of nitro radical-anions important in biology and medicine.

    PubMed Central

    Wardman, P

    1985-01-01

    Nitroaromatic compounds, ArNO2 have widespread actual or potential use in medicine and cancer therapy. There is direct proof that free-radical metabolites are involved in many applications, and an appreciation of the conceptual basis for their therapeutic differential; however, an understanding of the detailed mechanisms involved is lacking. Redox properties control most biological responses of nitro compounds, and the characteristics of the one-electron couple: ArNO2/ArNO2- are detailed. The "futile metabolism" of nitroaryl compounds characteristic of most aerobic nitroreductase systems reflects competition between natural radical-decay pathways and a one-electron transfer reaction to yield superoxide ion, O2-. Prototropic properties control the rate of radical decay, and redox properties control the rate of electron transfer to O2 or other acceptors. There are clear parallels in the chemistry of ArNO2- and O2-. While nitro radicals have frequently been invoked as damaging species, they are very unreactive (except as simple reductants). It seems likely that reductive metabolism of nitroaryl compounds, although generally involving nitro radical-anions as obligate intermediates (and this is required for therapeutic selectivity towards anaerobes), results in biological damage via reductive metabolites of higher reduction order than the one-electron product. PMID:3830700

  3. Gas-Phase Reactions of Methoxyphenols with NO3 Radicals: Kinetics, Products, and Mechanisms.

    PubMed

    Zhang, Haixu; Yang, Bo; Wang, Youfeng; Shu, Jinian; Zhang, Peng; Ma, Pengkun; Li, Zhen

    2016-03-01

    Methoxyphenols, a group of important tracers for wood smoke, are emitted to the atmosphere in large quantities, but their transformations are rarely studied. In this study, the kinetics and products of the gas-phase reactions of eugenol and 4-ethylguaiacol with NO3 radicals were investigated online using a vacuum ultraviolet photoionization gas time-of-flight mass spectrometer. The rate coefficients of the gaseous reactions of eugenol and 4-ethylguaiacol with NO3 radicals were (1.6 ± 0.4) × 10(-13) and (1.1 ± 0.2) × 10(-12) cm(3) molecule(-1) s(-1) (at 298 K), indicating that the atmospheric lifetimes of the NO3 radicals were 3.5 and 0.5 h, respectively. With the aid of gas-chromatography-mass-spectrometry analysis, several types of degradation products were identified with nitro derivatives as the major products. The configurations of the nitro-product isomers and their formation mechanisms were determined via theoretical calculations. On the basis of these products, degradation pathways of the methoxyphenols with NO3 radicals were proposed. This study determines the degradation rates and mechanisms of the methoxyphenols at night and implies the significant NO3 nighttime chemistry. PMID:26845070

  4. Characterization of the reaction rate coefficient of DNA with the hydroxyl radical

    SciTech Connect

    Milligan, J.R.; Ward, J.F.; Aguilera, J.A.

    1996-11-01

    Using agarose gel electrophoresis, we have measured the yield of single-strand breaks (SSBs) induced by {sup 137}Cs {gamma} irradiation in a variety of plasmid DNA substrates ranging in size from 2.7 kb to 38 kb irradiated in aerobic aqueous solution in the presence of the hydroxyl radical scavenger dimethyl sulfoxide (DMSO). Under these conditions DNA SSBs are caused mainly by the hydroxyl radical. Using the competition between DMSO and DNA for the hydroxyl radical, we have estimated the rate coefficient for the reaction of the hydroxyl radical with DNA. The results cannot be characterized by conventional steady-state competition kinetics. However, it is possible to describe the second-order rate constant for the reaction as a function of the scavenging capacity of the solution. The second-order rate constant increases with increasing scavenging capacity, rising from about 5x10{sup 8} dm{sup 3} mol{sup -1} s{sup -1} at 10{sup 5} s{sup -1} to about 10{sup 10} dm{sup 3} mol{sup -1} s{sup -1} at 10{sup 10} s{sup -1}. This dependence of the second-order rate constant on the scavenging capacity appears to be more pronounced for larger plasmids. 17 refs., 4 figs.

  5. Formation of polycyclic aromatic hydrocarbons from bimolecular reactions of phenyl radicals at high temperatures.

    PubMed

    Constantinidis, P; Schmitt, H-C; Fischer, I; Yan, B; Rijs, A M

    2015-11-21

    The self-reaction of the phenyl radical is one of the key reactions in combustion chemistry. Here we study this reaction in a high-temperature flow reactor by IR/UV ion dip spectroscopy, using free electron laser radiation as mid-infrared source. We identified several major reaction products based on their infrared spectra, among them indene, 1,2-dihydronaphthalene, naphthalene, biphenyl and para-terphenyl. Due to the structural sensitivity of the method, the reaction products were identified isomer-selectively. The work shows that the formation of indene and naphthalene, which was previously considered to be evidence for the HACA (hydrogen abstraction C2H2 addition) mechanism in the formation of polycyclic aromatic hydrocarbons and soot can also be understood in a phenyl addition model. PMID:26457393

  6. Free radicals: how do we stand them? Anaerobic and aerobic free radical (chain) reactions involved in the use of fluorogenic probes and in biological systems.

    PubMed

    Liochev, Stefan I

    2014-01-01

    Biologically significant conclusions have been based on the use of fluorogenic and luminogenic probes for the detection of reactive species. The basic mechanisms of the processes involved have not been satisfactorily elucidated. In the present work, the mechanism of the enzyme and photosensitized oxidation of NAD(P)H by resorufin is analyzed and appears to involve both aerobic and anaerobic free radical chain reactions. There are two major fallouts of this analysis. Many of the conclusions about the participation of radicals based on the use of probes such as resorufin and Amplex red need reevaluation. It is also concluded that anaerobic free radical reactions may be biologically significant, and the possible existence of enzymatic systems to eliminate certain free radicals is discussed. PMID:24356000

  7. Mechanistic Significance of the Si–O–Pd Bond in the Palladium-Catalyzed Cross-Coupling Reactions of Alkenylsilanolates

    PubMed Central

    2016-01-01

    Through the combination of reaction kinetics (both catalytic and stoichiometric) and solid-state characterization of arylpalladium(II) alkenylsilanolate complexes, the intermediacy of covalent adducts containing Si–O–Pd linkages in the cross-coupling reactions of organosilanolates has been unambiguously established. Two mechanistically distinct pathways have been demonstrated: (1) transmetalation via a neutral 8-Si-4 intermediate that dominates in the cross-coupling of potassium alkenylsilanolates, and (2) transmetalation via an anionic 10-Si-5 intermediate that dominates in the cross-coupling of cesium alkenylsilanolates. Arylpalladium(II) alkenylsilanolate complexes bearing various phosphine ligands (both bidentate and monodentate) have been isolated, fully characterized, and evaluated for their kinetic competence under thermal (stoichiometric) and anionic (catalytic) conditions. Comparison of the rates for thermal and anionic activation demonstrates that intermediates containing the Si–O–Pd linkage are involved in the cross-coupling process. PMID:25945390

  8. A Metal and Base-Free Chemoselective Primary Amination of Boronic Acids Using Cyanamidyl/Arylcyanamidyl Radical as Aminating Species: Synthesis and Mechanistic Studies by Density Functional Theory.

    PubMed

    Chatterjee, Nachiketa; Arfeen, Minhajul; Bharatam, Prasad V; Goswami, Avijit

    2016-06-17

    An efficient, metal and base-free, chemoselective synthesis of aryl-, heteroaryl-, and alkyl primary amines from the corresponding boronic acids has been achieved at ambient temperature mediated by [bis(trifluoroacetoxy)iodo]benzene (PIFA) and N-bromosuccinimide (NBS) using cyanamidyl/arylcyanamidyl radicals as the aminating species. The primary amine compounds were initially obtained as their corresponding ammonium trifluoroacetate salts which, on treatment with aq NaOH, provide the free amines. Finally, the primary amines were isolated through column chromatography over silica-gel using hexane-EtOAc solvent system as the eluent. The reactions are sufficiently fast, completing within 1 h. Quantum chemical calculations in combination with experimental observations validate that the ipso amination of substituted boronic acids involves the formation of cyanamidyl/arylcyanamidyl radical, followed by regiospecific interaction of its nitrile-N center with boron atom of the boronic acids, leading to chemoselective primary amination. PMID:27182931

  9. Reaction Rates of Semi-Volatile Organic Compounds with the Hydroxyl Radical.

    NASA Astrophysics Data System (ADS)

    Anderson, Philip Neal

    1995-01-01

    The atmosphere is the primary route of global dispersion of many semi-volatile organic compounds (SOCs), including polychlorinated biphenyls, dibenzo-p-dioxins, and dibenzofurans. While the long-distance atmospheric transport of these compounds has been well established, the importance of chemical reactions that may occur while SOCs are in the atmosphere is largely unknown. For most semi-volatile organic compounds in the vapor phase, the most significant atmospheric reaction is likely to be attack by the hydroxyl radical (OH). The importance of this removal pathway, relative to other loss mechanisms from the atmosphere, is dependent on the reaction rate of a given semi-volatile organic compound with OH. A system was constructed and validated to measure the reaction rate of OH with semi-volatile organic compounds in the laboratory. The system featured a small, heated, quartz chamber with on-line detection of reactants by mass spectrometry. OH radicals were generated by the 254 nm photolysis of O _3 in the presence of H_2 O. The temperature dependent reaction rates of OH with 15 polychlorinated biphenyl congeners (PCBs), containing 0-5 chlorines, were measured. Calculated atmospheric lifetimes of PCBs due to OH-initiated reactions ranged from 2 days for biphenyl to 34 days for a pentachlorobiphenyl. Using an average of reaction rates extrapolated to atmospheric temperatures, the lifetime in the atmosphere for total PCBs due to OH reaction was calculated. A model for the vertical concentration gradient of PCBs in the troposphere was developed and used to calculate the flux (16 mug m^{-2} yr^{-1}) and total global flow (8,300 tonnes yr^{-1}) of PCBs removed from the atmosphere by OH-PCB reaction. This pathway is very large in comparison to any other known permanent PCB loss processes from the environment, such as deep ocean sediment burial (240 tonnes yr^ {-1}). The reaction of PCBs with OH may be the dominant removal mechanism of PCBs from the natural environment.

  10. A shock tube study of the reactions of the hydroxyl radical with combustion species

    SciTech Connect

    Cohen, N.; Koffend, J.B.

    1993-12-01

    To extend the semi-empirical techniques of Benson and coworkers, and to extend the database of reliable high temperature measurements of OH radicals with hydrocarbons and other fuels and their decomposition products, the authors undertook a research program with both experimental and computational tasks. The experimental goal was to design a procedure for measuring, at combustion temperatures, the reaction rate coefficients of OH radicals with fuels and other species of importance in combustion or propulsion systems. The computational effort was intended to refine the semi-empirical transition-state-theory procedures for extrapolating rate coefficients of reactions of OH with combustion species of interest, for predicting rate coefficients for species not studied in the laboratory, and to examine the ability of the theory to predict rate coefficients for different pathways in the case the reagent possessed more than one nonequivalent H atoms.

  11. A shock tube study of the reactions of the hydroxyl radical with combustion species and pollutants

    SciTech Connect

    Cohen, N.

    1992-08-01

    To extend the database of reliable high temperature measurements of OH radicals with hydrocarbons and other fuels and their decomposition products, we undertook, a research program with both experimental and computational tasks. The experimental goal was to design a procedure for measuring, at combustion temperatures, the reaction rate coefficients of OH radicals with fuels and other species of importance in combustion or propulsion systems. The computational effort was intended to refine the semi-empirical thermochemical kinetics/ transition-state-theory (TK-TST) procedures for extrapolating rate coefficients of reactions of OH with combustion species of interest, for predicting rate coefficients for species not studied in the laboratory, and to examine the ability of the theory to predict rate coefficients for different pathways in cases where the reagent possessed nonequivalent H atoms.

  12. Mechanistic investigation of oxidative Mannich reaction with tert-butyl hydroperoxide. The role of transition metal salt.

    PubMed

    Ratnikov, Maxim O; Doyle, Michael P

    2013-01-30

    A general mechanism is proposed for transition metal-catalyzed oxidative Mannich reactions of N,N-dialkylanilines with tert-butyl hydroperoxide (TBHP) as the oxidant. The mechanism consists of a rate-determining single electron transfer (SET) that is uniform from 4-methoxy- to 4-cyano-N,N-dimethylanilines. The tert-butylperoxy radical is the major oxidant in the rate-determining SET step that is followed by competing backward SET and irreversible heterolytic cleavage of the carbon-hydrogen bond at the α-position to nitrogen. A second SET completes the conversion of N,N-dimethylaniline to an iminium ion that is subsequently trapped by the nucleophilic solvent or the oxidant prior to formation of the Mannich adduct. The general role of Rh(2)(cap)(4), RuCl(2)(PPh(3))(3), CuBr, FeCl(3), and Co(OAc)(2) in N,N-dialkylaniline oxidations by T-HYDRO is to initiate the conversion of TBHP to tert-butylperoxy radicals. A second pathway, involving O(2) as the oxidant, exists for copper, iron, and cobalt salts. Results from linear free-energy relationship (LFER) analyses, kinetic and product isotope effects (KIE and PIE), and radical trap experiments of N,N-dimethylaniline oxidation by T-HYDRO in the presence of transition metal catalysts are discussed. Kinetic studies of the oxidative Mannich reaction in methanol and toluene are also reported. PMID:23298175

  13. Cationic Pd(II)-catalyzed C–H activation/cross-coupling reactions at room temperature: synthetic and mechanistic studies

    PubMed Central

    Nishikata, Takashi; Abela, Alexander R; Huang, Shenlin

    2016-01-01

    Summary Cationic palladium(II) complexes have been found to be highly reactive towards aromatic C–H activation of arylureas at room temperature. A commercially available catalyst [Pd(MeCN)4](BF4)2 or a nitrile-free cationic palladium(II) complex generated in situ from the reaction of Pd(OAc)2 and HBF4, effectively catalyzes C–H activation/cross-coupling reactions between aryl iodides, arylboronic acids and acrylates under milder conditions than those previously reported. The nature of the directing group was found to be critical for achieving room temperature conditions, with the urea moiety the most effective in promoting facile coupling reactions at an ortho C–H position. This methodology has been utilized in a streamlined and efficient synthesis of boscalid, an agent produced on the kiloton scale annually and used to control a range of plant pathogens in broadacre and horticultural crops. Mechanistic investigations led to a proposed catalytic cycle involving three steps: (1) C–H activation to generate a cationic palladacycle; (2) reaction of the cationic palladacycle with an aryl iodide, arylboronic acid or acrylate, and (3) regeneration of the active cationic palladium catalyst. The reaction between a cationic palladium(II) complex and arylurea allowed the formation and isolation of the corresponding palladacycle intermediate, characterized by X-ray analysis. Roles of various additives in the stepwise process have also been studied. PMID:27340491

  14. Vitamin E analogue Trolox C. E.s.r. and pulse-radiolysis studies of free-radical reactions.

    PubMed Central

    Davies, M J; Forni, L G; Willson, R L

    1988-01-01

    The reactions between Trolox C, a water-soluble vitamin E analogue, and several oxidizing free radicals including the hydroxyl radical and various peroxy radicals were examined by using the pulse-radiolysis technique. The results demonstrate that Trolox C may undergo rapid one-electron-transfer reactions as well as hydrogen-transfer processes; the resulting phenoxyl radical is shown to be relatively stable, in common with the phenoxyl radical derived from vitamin E. The reactions between the Trolox C phenoxyl radical and a variety of biologically relevant reducing compounds were examined by using both pulse radiolysis and e.s.r. The results demonstrate that the Trolox C phenoxyl radical is readily repaired by ascorbate (k = 8.3 x 10(6) dm3.mol-1.s-1) and certain thiols (k less than 10(5) dm3.mol-1.s-1) but not by urate, NADH or propyl gallate. Evidence from e.s.r. studies indicates that thiol-containing compounds may also enter into similar repair reactions with the alpha-tocopherol phenoxyl radical. Kinetic evidence is presented that suggests that Trolox C may 'repair' proteins that have been oxidized by free radicals. PMID:2849418

  15. New Mechanistic Insights on the Selectivity of Transition-Metal-Catalyzed Organic Reactions: The Role of Computational Chemistry.

    PubMed

    Zhang, Xinhao; Chung, Lung Wa; Wu, Yun-Dong

    2016-06-21

    With new advances in theoretical methods and increased computational power, applications of computational chemistry are becoming practical and routine in many fields of chemistry. In organic chemistry, computational chemistry plays an indispensable role in elucidating reaction mechanisms and the origins of various selectivities, such as chemo-, regio-, and stereoselectivities. Consequently, mechanistic understanding improves synthesis and assists in the rational design of new catalysts. In this Account, we present some of our recent works to illustrate how computational chemistry provides new mechanistic insights for improvement of the selectivities of several organic reactions. These examples include not only explanations for the existing experimental observations, but also predictions which were subsequently verified experimentally. This Account consists of three sections discuss three different kinds of selectivities. The first section discusses the regio- and stereoselectivities of hydrosilylations of alkynes, mainly catalyzed by [Cp*Ru(MeCN)3](+) or [CpRu(MeCN)3](+). Calculations suggest a new mechanism that involves a key ruthenacyclopropene intermediate. This mechanism not only explains the unusual Markovnikov regio-selectivity and anti-addition stereoselectivity observed by Trost and co-workers, but also motivated further experimental investigations. New intriguing experimental observations and further theoretical studies led to an extension of the reaction mechanism. The second section includes three cases of meta-selective C-H activation of aryl compounds. In the case of Cu-catalyzed selective meta-C-H activation of aniline, a new mechanism that involves a Cu(III)-Ar-mediated Heck-like transition state, in which the Ar group acts as an electrophile, was proposed. This mechanism predicted a higher reactivity for more electron-deficient Ar groups, which was supported by experiments. For two template-mediated, meta-selective C-H bond activations catalyzed by

  16. Chemistry of polycyclic aromatic hydrocarbons formation from phenyl radical pyrolysis and reaction of phenyl and acetylene.

    PubMed

    Comandini, A; Malewicki, T; Brezinsky, K

    2012-03-15

    An experimental investigation of phenyl radical pyrolysis and the phenyl radical + acetylene reaction has been performed to clarify the role of different reaction mechanisms involved in the formation and growth of polycyclic aromatic hydrocarbons (PAHs) serving as precursors for soot formation. Experiments were conducted using GC/GC-MS diagnostics coupled to the high-pressure single-pulse shock tube present at the University of Illinois at Chicago. For the first time, comprehensive speciation of the major stable products, including small hydrocarbons and large PAH intermediates, was obtained over a wide range of pressures (25-60 atm) and temperatures (900-1800 K) which encompass the typical conditions in modern combustion devices. The experimental results were used to validate a comprehensive chemical kinetic model which provides relevant information on the chemistry associated with the formation of PAH compounds. In particular, the modeling results indicate that the o-benzyne chemistry is a key factor in the formation of multi-ring intermediates in phenyl radical pyrolysis. On the other hand, the PAHs from the phenyl + acetylene reaction are formed mainly through recombination between single-ring aromatics and through the hydrogen abstraction/acetylene addition mechanism. Polymerization is the common dominant process at high temperature conditions. PMID:22339468

  17. Gas-Phase Ozonolysis of Cycloalkenes: Formation of Highly Oxidized RO2 Radicals and Their Reactions with NO, NO2, SO2, and Other RO2 Radicals.

    PubMed

    Berndt, Torsten; Richters, Stefanie; Kaethner, Ralf; Voigtländer, Jens; Stratmann, Frank; Sipilä, Mikko; Kulmala, Markku; Herrmann, Hartmut

    2015-10-15

    The gas-phase reaction of ozone with C5-C8 cycloalkenes has been investigated in a free-jet flow system at atmospheric pressure and a temperature of 297 ± 1 K. Highly oxidized RO2 radicals bearing at least 5 O atoms in the molecule and their subsequent reaction products were detected in most cases by means of nitrate-CI-APi-TOF mass spectrometry. Starting from a Criegee intermediate after splitting-off an OH-radical, the formation of these RO2 radicals can be explained via an autoxidation mechanism, meaning RO2 isomerization (ROO → QOOH) and subsequently O2 addition (QOOH + O2 → R'OO). Time-dependent RO2 radical measurements concerning the ozonolysis of cyclohexene indicate rate coefficients of the intramolecular H-shifts, ROO → QOOH, higher than 1 s(-1). The total molar yield of highly oxidized products (predominantly RO2 radicals) from C5-C8 cycloalkenes in air is 4.8-6.0% affected with a calibration uncertainty by a factor of about two. For the most abundant RO2 radical from cyclohexene ozonolysis, O,O-C6H7(OOH)2O2 ("O,O" stands for two O atoms arising from the ozone attack), the determination of the rate coefficients of the reaction with NO2, NO, and SO2 yielded (1.6 ± 0.5) × 10(-12), (3.4 ± 0.9) × 10(-11), and <10(-14) cm(3) molecule(-1) s(-1), respectively. The reaction of highly oxidized RO2 radicals with other peroxy radicals (R'O2) leads to detectable accretion products, RO2 + R'O2 → ROOR' + O2, which allows to acquire information on peroxy radicals not directly measurable with the nitrate ionization technique applied here. Additional experiments using acetate as the charger ion confirm conclusively the existence of highly oxidized RO2 radicals and closed-shell products. Other reaction products, detectable with this ionization technique, give a deeper insight in the reaction mechanism of cyclohexene ozonolysis. PMID:26392132

  18. Mechanistic insights into the dehalogenation reaction of fluoroacetate/fluoroacetic acid

    SciTech Connect

    Miranda-Rojas, Sebastián; Toro-Labbé, Alejandro

    2015-05-21

    Fluoroacetate is a toxic compound whose environmental accumulation may represent an important contamination problem, its elimination is therefore a challenging issue. Fluoroacetate dehalogenase catalyzes its degradation through a two step process initiated by an S{sub N}2 reaction in which the aspartate residue performs a nucleophilic attack on the carbon bonded to the fluorine; the second step is hydrolysis that releases the product as glycolate. In this paper, we present a study based on density functional theory calculations of the S{sub N}2 initiation reaction modeled through the interaction between the substrate and the propionate anion as the nucleophile. Results are analyzed within the framework of the reaction force and using the reaction electronic flux to identify and characterize the electronic activity that drives the reaction. Our results reveal that the selective protonation of the substrate catalyzes the reaction by decreasing the resistance of the structural and electronic reorganization needed to reach the transition state. Finally, the reaction energy is modulated by the degree of stabilization of the fluoride anion formed after the S{sub N}2 reaction. In this way, a site-induced partial protonation acts as a chemical switch in a key process that determines the output of the reaction.

  19. A temperature dependent kinetic study of the reaction of the hydroxyl radical with CH2Br

    NASA Technical Reports Server (NTRS)

    Zhang, Zhengyu; Saini, Rameshwar D.; Kurylo, Michael; Huie, Robert E.

    1992-01-01

    Rate constants have been measured for the gas phase reaction of the hydroxyl radical (OH) with CH3Br over the temperature range 250 to 400 K. The Arrhenius expression k = (5.79 x 10 exp -12) exp(-1560/T) cu cm/molecule per sec was derived from the kinetic data. From the rate constant at 277 K, the tropospheric lifetime of CH3Br with respect to reaction with OH is estimated to be 2.2 years and the overall atmospheric lifetime to be 2.1 years.

  20. Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations.

    PubMed

    Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L

    2016-05-12

    An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data. PMID:27082439

  1. Rate constant calculations of H-atom abstraction reactions from ethers by HȮ2 radicals.

    PubMed

    Mendes, Jorge; Zhou, Chong-Wen; Curran, Henry J

    2014-02-27

    In this work, we detail hydrogen atom abstraction reactions from six ethers by the hydroperoxyl radical, including dimethyl ether, ethyl methyl ether, propyl methyl ether, isopropyl methyl ether, butyl methyl ether, and isobutyl methyl ether, in order to test the effect of the functional group on the rate constant calculations. The Møller-Plesset (MP2) method with the 6-311G(d,p) basis set has been employed in the geometry optimizations and frequency calculations of all of the species involved in the above reaction systems. The connections between each transition state and the corresponding local minima have been determined by intrinsic reaction coordinate calculations. Energies are reported at the CCSD(T)/cc-pVTZ level of theory and include the zero-point energy corrections. As a benchmark in the electronic energy calculations, the CCSD(T)/CBS extrapolation was used for the reactions of dimethyl ether + HȮ2 radicals. A systematic calculation of the high-pressure limit rate constants has been performed using conventional transition-state theory, including asymmetric Eckart tunneling corrections, in the temperature range of 500-2000 K. The one dimensional hindrance potentials obtained at MP2/6-311G(d,p) for the reactants and transition states have been used to describe the low frequency torsional modes. Herein, we report the calculated individual, average, and total rate constants. A branching ratio analysis for every reaction site has also been performed. PMID:24483837

  2. Synchronous vs asynchronous diffusion-reaction processes involving geminate radical pairs

    NASA Astrophysics Data System (ADS)

    Urie, Kristopher G.; Kozak, John J.; Abad, E.

    2010-10-01

    We report lattice Monte Carlo calculations to study the efficiency of diffusion-controlled reactive processes involving geminate radical pairs. Whereas our earlier study [J.J. Kozak, C. Nicolis, G. Nicolis, N.J. Turro, J. Phys. Chem. 105 (2001) 10949] focused on factors affecting the reaction efficiency when a pair of coreactants moved synchronously on a surface modeled as a d=2 dimensional square planar lattice subject to periodic boundary conditions, we document here differences in reaction efficiency when a pair of coreactants can move synchronously or asynchronously on surfaces which are topologically different but characterized by the same number N of sites. As before, the first surface is taken to be a d=2 square planar lattice; the second surface considered is a Cartesian shell, the bounded surface of a cube. When studied as a function of system size, we find that synchronous dynamics are more efficient than asynchronous dynamics in optimizing diffusion-reaction processes; and, reactions on planar, periodic surfaces are more efficient than on cubic shells. The relevance of these conclusions to experimental studies on two radiation-induced, radical decay reactions [the one cited above and A.J. Frank, M. Grätzel, J.J. Kozak, J. Am. Chem. Soc. 98 (1976) 3317] is noted and discussed.

  3. A DFT Study Toward the Reaction Mechanisms of TNT With Hydroxyl Radicals for Advanced Oxidation Processes.

    PubMed

    He, Xi; Zeng, Qun; Zhou, Yang; Zeng, Qingxuan; Wei, Xianfeng; Zhang, Chaoyang

    2016-05-26

    The degradation pathway of environmental contaminant 2,4,6-trinitrotoluene (TNT) was investigated computationally at the SMD(Pauling)/M06-2X/6-311+G(d,p) level of theory. The dominant decomposition pathway of TNT → 4,6-dinitro-o-cresol → 4,6-dinitro-2-hydroxybenzylalcohol → 4,6-dinitro-2-hydroxybenzaldehyde was provided, and the corresponding predicted products and their distributions are in a good agreement with available experimental data on TNT degradation by Fenton reaction. It was shown that the mechanism of addition-elimination is crucial for this stage of the reaction. The reaction of H atom abstraction is a minor competing pathway. The details on transition states, intermediate radicals, and free energy surfaces for all proposed reactions are given and make up for a lack of experimental knowledge. PMID:27135259

  4. Menshutkin reaction between DABCO and benzyfluoride/fluorodiphenylmethane: a mechanistic study.

    PubMed

    Singh, Amritpal; Goel, Neetu

    2014-06-01

    The microcosmic mechanism of the Menshutkin reaction between DABCO and benzyl fluoride/fluorodiphenylmethane has been investigated in both the gas and solvent phase by performing DFT calculations at B3LYP/6-31G(d,p) level of theory. The Gibbs free energy profiles to reach the possible transition states, i.e., five-membered ring transition state and SN2 transition state show that the reaction between DABCO and benzyl fluoride proceeds through SN2 transition state in accordance with previously reported studies, while the reaction between DABCO and fluorodiphenylmethane proceeds through five-membered ring transition state contrary to earlier literature. The role of solvent has been elucidated by reoptimizing the structures using SMD model of solvation. Hydrogen bonding and steric hinderance have been identified as the key factors in guiding the reaction pathway of commercially important Menshutkin reaction. PMID:24827613

  5. Explaining the atypical reaction profiles of heme enzymes with a novel mechanistic hypothesis and kinetic treatment.

    PubMed

    Manoj, Kelath Murali; Baburaj, Arun; Ephraim, Binoy; Pappachan, Febin; Maviliparambathu, Pravitha Parapurathu; Vijayan, Umesh K; Narayanan, Sivaprasad Valiyaveettil; Periasamy, Kalaiselvi; George, Ebi Ashley; Mathew, Lazar T

    2010-01-01

    Many heme enzymes show remarkable versatility and atypical kinetics. The fungal extracellular enzyme chloroperoxidase (CPO) characterizes a variety of one and two electron redox reactions in the presence of hydroperoxides. A structural counterpart, found in mammalian microsomal cytochrome P450 (CYP), uses molecular oxygen plus NADPH for the oxidative metabolism (predominantly hydroxylation) of substrate in conjunction with a redox partner enzyme, cytochrome P450 reductase. In this study, we employ the two above-mentioned heme-thiolate proteins to probe the reaction kinetics and mechanism of heme enzymes. Hitherto, a substrate inhibition model based upon non-productive binding of substrate (two-site model) was used to account for the inhibition of reaction at higher substrate concentrations for the CYP reaction systems. Herein, the observation of substrate inhibition is shown for both peroxide and final substrate in CPO catalyzed peroxidations. Further, analogy is drawn in the "steady state kinetics" of CPO and CYP reaction systems. New experimental observations and analyses indicate that a scheme of competing reactions (involving primary product with enzyme or other reaction components/intermediates) is relevant in such complex reaction mixtures. The presence of non-selective reactive intermediate(s) affords alternate reaction routes at various substrate/product concentrations, thereby leading to a lowered detectable concentration of "the product of interest" in the reaction milieu. Occam's razor favors the new hypothesis. With the new hypothesis as foundation, a new biphasic treatment to analyze the kinetics is put forth. We also introduce a key concept of "substrate concentration at maximum observed rate". The new treatment affords a more acceptable fit for observable experimental kinetic data of heme redox enzymes. PMID:20498847

  6. Explaining the Atypical Reaction Profiles of Heme Enzymes with a Novel Mechanistic Hypothesis and Kinetic Treatment

    PubMed Central

    Manoj, Kelath Murali; Baburaj, Arun; Ephraim, Binoy; Pappachan, Febin; Maviliparambathu, Pravitha Parapurathu; Vijayan, Umesh K.; Narayanan, Sivaprasad Valiyaveettil; Periasamy, Kalaiselvi; George, Ebi Ashley; Mathew, Lazar T.

    2010-01-01

    Many heme enzymes show remarkable versatility and atypical kinetics. The fungal extracellular enzyme chloroperoxidase (CPO) characterizes a variety of one and two electron redox reactions in the presence of hydroperoxides. A structural counterpart, found in mammalian microsomal cytochrome P450 (CYP), uses molecular oxygen plus NADPH for the oxidative metabolism (predominantly hydroxylation) of substrate in conjunction with a redox partner enzyme, cytochrome P450 reductase. In this study, we employ the two above-mentioned heme-thiolate proteins to probe the reaction kinetics and mechanism of heme enzymes. Hitherto, a substrate inhibition model based upon non-productive binding of substrate (two-site model) was used to account for the inhibition of reaction at higher substrate concentrations for the CYP reaction systems. Herein, the observation of substrate inhibition is shown for both peroxide and final substrate in CPO catalyzed peroxidations. Further, analogy is drawn in the “steady state kinetics” of CPO and CYP reaction systems. New experimental observations and analyses indicate that a scheme of competing reactions (involving primary product with enzyme or other reaction components/intermediates) is relevant in such complex reaction mixtures. The presence of non-selective reactive intermediate(s) affords alternate reaction routes at various substrate/product concentrations, thereby leading to a lowered detectable concentration of “the product of interest” in the reaction milieu. Occam's razor favors the new hypothesis. With the new hypothesis as foundation, a new biphasic treatment to analyze the kinetics is put forth. We also introduce a key concept of “substrate concentration at maximum observed rate”. The new treatment affords a more acceptable fit for observable experimental kinetic data of heme redox enzymes. PMID:20498847

  7. Hydroxyl Radical Generation and DNA Nuclease Activity: A Mechanistic Study Based on a Surface-Immobilized Copper Thioether Clip-Phen Derivative.

    PubMed

    Romo, Adolfo I B; Abreu, Dieric S; de F Paulo, Tércio; Carepo, Marta S P; Sousa, Eduardo H S; Lemus, Luis; Aliaga, Carolina; Batista, Alzir A; Nascimento, Otaciro R; Abruña, Héctor D; Diógenes, Izaura C N

    2016-07-11

    Coordination compounds of copper have been invoked as major actors in processes involving the reduction of molecular oxygen, mostly with the generation of radical species the assignment for which has, so far, not been fully addressed. In the present work, we have carried out studies in solution and on surfaces to gain insights into the nature of the radical oxygen species (ROS) generated by a copper(II) coordination compound containing a thioether clip-phen derivative, 1,3-bis(1,10-phenanthrolin-2-yloxy)-N-(4-(methylthio)benzylidene)propan-2-amine (2CP-Bz-SMe), enabling its adsorption/immobilization to gold surfaces. Whereas surface plasmon resonance (SPR) and electrochemistry of the adsorbed complex indicated the formation of a dimeric Cu(I) intermediate containing molecular oxygen as a bridging ligand, scanning electrochemical microscopy (SECM) and nuclease assays pointed to the generation of a ROS species. Electron paramagnetic resonance (EPR) data reinforced such conclusions, indicating that radical production was dependent on the amount of oxygen and H2 O2 , thus pointing to a mechanism involving a Fenton-like reaction that results in the production of OH(.) . PMID:27310653

  8. Mechanistic features of the copper-free Sonogashira reaction from ESI-MS.

    PubMed

    Ahmadi, Zohrab; Yunker, Lars P E; Oliver, Allen G; McIndoe, J Scott

    2015-12-21

    The mechanism of the Sonogashira reaction in methanol was studied in detail using pressurized sample infusion electrospray ionization mass spectrometry (PSI-ESI-MS). Several key intermediates were identified and their structures were assigned by MS/MS studies. Cationic and anionic charged-tagged substrates were employed to look into the mechanism of this reaction from variety of angles. A reverse kinetic isotope effect was observed in which the reaction rate is accelerated in deuterated solvents (kH/kD = 0.6). The reaction was found to be zero order with respect to the aryl iodide and first order with respect to the phenylacetylene. A Hammett parameter of ρ = 1.4 indicates that the reaction is more favorable for aryl iodides with para EWGs. No evidence of product inhibition, dimerization of palladium catalyst, or agglomeration were observed. However, catalyst decomposition was inferred from a non-zero intercept in the plot of catalyst loading versus reaction rate. Monitoring the reaction by PSI-ESI-(-)MS on neutral and negatively charged substrates at variety of concentrations and conditions did not reveal any detectable anionic palladium complexes. Likewise no evidence of carbopalladation and relevant intermediates in the absence of a base was observed. PMID:26469767

  9. Inorganic phosphate promotes redox cycling of iron in liver microsomes: effects on free radical reactions.

    PubMed

    Reinke, L A; Moore, D R; Rau, J M; McCay, P B

    1995-02-01

    The phosphate buffer concentration used in spin trapping experiments with liver microsomes markedly influenced rates of free radical formation from ethanol and dimethylsulfoxide, but not from carbon tetrachloride. Effects of phosphate concentration on ethanol radical formation were abolished by addition of deferoxamine or bathophenanthrolene, indicating that an iron-phosphate complex might be involved. High concentrations of phosphate stimulated rates of microsomal Fe+3 reduction and facilitated the mobilization of microsomal nonheme iron, but had little effect on a variety of microsomal monooxygenase enzyme activities. Although microsomal oxygen utilization and superoxide production were relatively unaffected by phosphate, hydrogen peroxide concentrations were markedly decreased in the presence of high concentrations of phosphate. Taken together, the data suggest that a ferric-phosphate complex may be enzymatically reduced by microsomal enzymes and NADPH. Reoxidation of ferrous ion is nonenzymatically promoted by phosphate and/or H2O2 produced by the microsomes. During the process of reoxidation, one or more oxidizing intermediates may be formed which initiate secondary free radical reactions. Although the reactivity of the intermediate(s) is similar to that of the hydroxyl radical, no spin trapping evidence was obtained to support this assignment. PMID:7864631

  10. Direct Excitation of the Reaction Coordinate: Overtone-Induced Predissociation of the Hydroxymethyl Radical

    NASA Astrophysics Data System (ADS)

    Reisler, Hanna; Ryazanov, Mikhail; Rodrigo, Chirantha P.

    2011-06-01

    The overtone-induced vibrational predissociation of the hydroxymethyl radical is achieved following excitation of the radical to the third O-H stretch overtone. The excited O-H stretch is also the bond that breaks; i.e. overtone excitation is in the reaction coordinate. The production of H atoms takes place via tunneling through the barrier to the H + formaldehyde channel. H-atom photofragment yield spectra in the region of the third overtone reveal two mixed bands with contributions from the third OH overtone and a combination band comprised of two quanta of OH stretch and one quantum of CH asymmetric stretch. Using velocity map imaging, sliced images of H-atom products are obtained with kinetic energy resolution sufficient to reveal the vibrational structure in the formaldehyde co-fragment. As expected, most of the formaldehyde molecules are born without vibrational excitation but some exhibit excitation in other modes, such as wagging and CO stretch. The rotational contours of the vibrational bands are well described by temperatures in the range 100-150 K. Slice imaging allows scanning the pump laser while monitoring H fragments in selected kinetic energy ranges, and in this way it is demonstrated that all the observed vibrational levels of formaldehyde have their parentage in the hydroxymethyl radical. The barrier to isomerization to methoxy is comparable to the barrier to direct dissociation and the role of isomerization is investigated by using partially deuterated radicals.