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Sample records for radical reactions mechanistic

  1. Mechanistic studies of the reactions of nitrone spin trap PBN with glutathiyl radical.

    PubMed

    Polovyanenko, Dmitriy N; Plyusnin, Victor F; Reznikov, Vladimir A; Khramtsov, Valery V; Bagryanskaya, Elena G

    2008-04-17

    We performed mechanistic studies of the reaction of PBN with the physiologically relevant glutathiyl radical, GS*, formed upon oxidation of the intracellular antioxidant, glutathione, GSH. The scavenging rate constant of GS* by PBN has been measured directly by laser flash photolysis and indirectly by competitive EPR of the spin adduct of PBN and another spin trap, DMPO (5,5-dimethyl-1-pyrroline N-oxide), and was found to be 6.7 x 107 M(-1) s(-1). Reverse decomposition of the paramagnetic PBN-glutathiyl radical adduct to the nitrone and thiyl radical was observed for the first time. The rate constant for the reaction of the monomolecular decomposition of the radical adduct was found to be 1.7 s(-1). Diamagnetic, EPR-invisible products of PBN adduct degradation were studied by 1H NMR and 19F NMR using newly synthesized fluorine-substituted PBN.

  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. Antioxidant Activity of Magnolol and Honokiol: Kinetic and Mechanistic Investigations of Their Reaction with Peroxyl Radicals.

    PubMed

    Amorati, Riccardo; Zotova, Julija; Baschieri, Andrea; Valgimigli, Luca

    2015-11-06

    Magnolol and honokiol, the bioactive phytochemicals contained in Magnolia officinalis, are uncommon antioxidants bearing isomeric bisphenol cores substituted with allyl functions. We have elucidated the chemistry behind their antioxidant activity by experimental and computational methods. In the inhibited autoxidation of cumene and styrene at 303 K, magnolol trapped four peroxyl radicals, with a kinh of 6.1 × 10(4) M(-1) s(-1) in chlorobenzene and 6.0 × 10(3) M(-1) s(-1) in acetonitrile, and honokiol trapped two peroxyl radicals in chlorobenzene (kinh = 3.8 × 10(4) M(-1) s(-1)) and four peroxyl radicals in acetonitrile (kinh = 9.5 × 10(3) M(-1) s(-1)). Their different behavior arises from a combination of intramolecular hydrogen bonding among the reactive OH groups (in magnolol) and of the OH groups with the aromatic and allyl π-systems, as confirmed by FT-IR spectroscopy and DFT calculations. Comparison with structurally related 3,3',5,5'-tetramethylbiphenyl-4,4'-diol, 2-allylphenol, and 2-allylanisole allowed us to exclude that the antioxidant behavior of magnolol and honokiol is due to the allyl groups. The reaction of the allyl group with a peroxyl radical (C-H hydrogen abstraction) proceeds with rate constant of 1.1 M(-1) s(-1) at 303 K. Magnolol and honokiol radicals do not react with molecular oxygen and produce no superoxide radical under the typical settings of inhibited autoxidations.

  4. Mechanistic study on the reaction of the CH2ClO2 radical with NO

    NASA Astrophysics Data System (ADS)

    Lesar, Antonija

    2013-07-01

    CBS-QB3 investigation of the ground-state potential energy surface for the title reaction shows that the initial addition of the chloromethylperoxy radical, CH2ClO2, and NO leads to the CH2ClOONO intermediate formed without energy barrier. Two conformeric forms of CH2ClOONO exhibit different behavior and follow different production pathways. The calculations suggest that the CH2ClO + NO2 radicals are the major products formed through CH2ClOONO intermediate. We demonstrate that the nitrite-nitrate isomerization is significantly facilitated by the assistance of single NO2 molecule compared to the unimolecular isomerization.

  5. Elucidation of the mechanistic pathways of the hydroxyl radical scavenging reaction by daidzein using hybrid QM/MM dynamics.

    PubMed

    Chakraborty, Sandipan; Biswas, P K

    2012-08-30

    Employing a hybrid QM/MM simulation we explored the reaction dynamics of the hydroxyl radical scavenging activity of daidzein, a soy isoflavone. Our simulations illustrate that the highly reactive hydroxyl radical can participate in hydrogen abstraction reaction with both OH functional groups of daidzein and can form stable daidzein radicals. We found that the reaction involving the 4'-OH site of daidzein is energetically favorable over the other reaction pathway involving the 7-OH site of daidzein by ∼29 kcal/mol. The high enthalpic stabilization involved in daidzein radical formation at the 4'-OH site can be partly attributed to better solvation through hydrogen-bonding interactions with water and higher electron density delocalization of radical over the adjacent aromatic ring. As evident from the QM/MM dynamics, both HAT pathways led to formation of ketones at the 7-OH and 4'-OH sites of daidzein, respectively, and the adjacent aromatic rings appear in a p-quinonoid form, a highly stable resonating structure. The suitability of the QM/MM methodology to study the reaction mechanism, identification of intermediate states, and pathways of flavonoid radical stabilization reported here opens up a new possibility to study a similar reaction mechanism in other systems.

  6. Radical Reactions Induced by Visible Light in Dichloromethane Solutions of Hünig's Base: Synthetic Applications and Mechanistic Observations.

    PubMed

    Böhm, Alexander; Bach, Thorsten

    2016-10-24

    β-(3-Iodopropoxy)-substituted α,β-unsaturated lactams, lactones, and cycloalkenones (eight examples) underwent reductive radical reactions in a dichloromethane solution of N,N-diisopropylethylamine (Hünig's base) upon irradiation with visible light (λ=419 nm). Apart from plain reduction reactions (hydro-de-iodination), a significant degree of cyclization was observed in three cases. In parallel to the conversion of the substrates, the formation of intensely colored by-products was observed. Based on mass spectrometric evidence and upon comparison with known compounds, the by-products were identified as cyanine dyes. Their formation supports the hypothesis that irradiation of dichloromethane solutions of Hünig's base leads to the formation of radicals, which in turn can either initiate a radical reaction or combine with cyanine precursors. It was shown by deuterium-labelling experiments, that one equivalent of dichloromethane is incorporated into the cyanine dyes and that the reductive quenching of radical intermediates is at least partially due to hydrogen abstraction from the solvent. As a consequence, a reductive cyclization of the starting materials is favored in CD2 Cl2 solutions as shown for two β-(3-iodopropoxy)-substituted tetronates, which underwent in dichloromethane almost exclusive reduction, but gave predominantly the cyclization products in CD2 Cl2 .

  7. Mechanistic analysis of intramolecular free radical reactions toward synthesis of 7-azabicyclo[2.2.1]heptane derivatives.

    PubMed

    Soriano, Elena; Marco-Contelles, José

    2009-06-05

    The mechanisms for the formation of conformationally constrained epibatidine analogues by intramolecular free radical processes have been computationally addressed by means of DFT methods. The mechanism and the critical effect of the 7-nitrogen protecting group on the outcome of these radical-mediated cyclizations are discussed. Theoretical findings account for unexpected experimental results and can assist in the selection of proper precursors for a successful cyclization.

  8. Catalytic Radical Domino Reactions in Organic Synthesis.

    PubMed

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

    2014-02-07

    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.

  9. Formation of OH radicals in the gas-phase reaction of propene, isobutene, and isoprene with O{sub 3}: Yields and mechanistic implications

    SciTech Connect

    Neeb, P.; Moortgat, G.K.

    1999-11-11

    The gas-phase reaction of ozone with alkenes is one of the very few reactions of atmospheric interest that are initiated without free radicals. This tropospheric oxidation pathway for unsaturated compounds has received considerable attention because of the reported formation of OH radicals. OH radicals originating from the alkene-ozone reaction have been proposed as a relevant source of OH radicals in the lower troposphere. Since the reported yields of OH radicals differ considerably, the authors redetermined the OH radical yield for three terminal alkenes by performing a series of pseudo-first-order experiments. Ozonolysis studies were carried out under excess ozone conditions in the presence of different cyclohexane concentrations. The decay rate of the alkene ({kappa}{sub obs}) was followed by long-path FTIR spectroscopy. From the decrease of the effective rate constant ({kappa}{sub obs} = {kappa}{sub eff}[O{sub 3}]) upon addition of cyclohexane, the OH radical yield was determined. The OH radical yields were found to be independent of the concentration of reactants for the Criegee intermediates, which are formed in ozonolysis systems. From these results the authors conclude that OH radicals are formed in a unimolecular process, presumably from the decomposition of the excited Criegee intermediate. Determined yields of OH radical formation in the ozonolysis of propene, isobutene, and isoprene were 0.34, 0.60, and 0.26, respectively. Detailed product studies were performed to verify if the observed stable products can be explained by the assumption that OH radicals are formed via the hydroperoxide channel as proposed by Niki et al. For the isobutene-ozone system, experimental product yields were found to agree well with predictions from a chemical mechanism based on the chemistry of the acetonylperoxy radical CH{sub 3}C(O)CH{sub 2}O{sub 2}, which is formed as an important radical product from the decomposition of the (CH{sub 3}){sub 2}COO Criegee intermediate.

  10. Mechanistic Enzymology of the Radical SAM Enzyme DesII.

    PubMed

    Ruszczycky, Mark W; Liu, Hung-Wen

    2015-04-01

    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.

  11. Theoretical Mechanistic Study of the Oxidative Degradation of Benzene in the Troposphere: Reaction of Benzene-HO Radical Adduct with O2.

    PubMed

    Olivella, Santiago; Solé, Albert; Bofill, Josep M

    2009-06-09

    Competing pathways arising from the reaction of hydroxycyclohexadienyl radical (1) with O2, a key reaction in the oxidative degradation of benzene under tropospheric conditions, have been investigated by means of density functional theory (UB3LYP) and quantum-mechanical (UCCSD(T) and RCCSD(T)) electronic structure calculations. The energetic, structural, and vibrational results furnished by these calculations were subsequently used to perform conventional transition-state computations to predict the rate coefficients and evaluate the product yields. The trans stereoisomer of the peroxyl radical (4) produced by the O2 addition to position 2 of benzene ring in radical 1 is energetically more stable than the cis one, although the rate coefficients at 298 K for the formation of both isomers are predicted to be similar. The cyclization of the cis isomer of 4 to a bicyclic allyl radical (5) involves calculated barrier heights (ΔU(⧧), ΔE(⧧), ΔH(⧧), and ΔG(⧧)) significantly lower than those of the cyclization of the trans isomer of 4. This implies that the formation of the cis isomer of 4 can lead to irreversible loss of radical 1 and that the observed chemical equilibrium 1 + O2 ↔ 4 essentially involves the trans isomer of 4. Although the reaction enthalpies computed for the O2 addition to position 4 of benzene ring in radical 1, affording the cis and trans stereoisomers of a peroxyl radical (6), are similar to those for the addition to position 2, the latter addition mode is clearly preferred because it involves lower barrier heights. The barrier heights computed for the cyclization of either the cis or the trans isomers of 6 to a bicyclic radical bearing a peroxy bridge (7) are about twice those computed for the cyclization of either the cis or the trans isomers of 4. Thus, under tropospheric conditions, it is unlikely that the O2 addition to position 4 of the benzene ring in radical 1 can contribute to the formation of benzene oxidation products.

  12. 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…

  13. 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…

  14. Hydrogen abstraction reactions of OH radicals with CH₃CH₂CH₂Cl and CH₃CHClCH₃: a mechanistic and kinetic study.

    PubMed

    Wang, Li; Li, Yanjie; He, Hongqing; Zhang, Jinglai

    2012-01-05

    The hydrogen abstraction reactions of OH radicals with CH₃CH₂CH₂Cl and CH₃CHClCH₃ (R2) have been investigated theoretically by a dual-level direct dynamics method. The optimized geometries and frequencies of the stationary points are calculated at the B3LYP/6-311G(d,p) level. To improve the reaction enthalpy and potential barrier of each reaction channel, the single point energy calculation is performed by the BMC-CCSD method. Using canonical variational transition-state theory (CVT) with the small-curvature tunneling correction, the rate constants are evaluated over a wide temperature range of 200-2000 K at the BMC-CCSD//B3LYP/6-311G(d,p) level. For the reaction channels with the negative barrier heights, the rate constants are calculated by using the CVT. The calculated total rate constants are consistent with available experimental data. The results show that at lower temperatures, the tunneling correction has an important contribution in the calculation of rate constants for all the reaction channels with the positive barrier heights, while the variational effect is found negligible for some reaction channels. For reactions OH radicals with CH₃CH₂CH₂Cl (R1) and CH₃CHClCH₃ (R2), the channels of H-abstraction from -CH₂ - and -CHCl groups are the major reaction channels, respectively, at lower temperatures. With temperature increasing, contributions from other channels should be taken into account. Finally, the total rate constants are fitted by two models, i.e., three-parameter and four-parameter expressions. The enthalpies of formation of the species CH₃CHClCH₂, CH₃CHCH₂Cl, and CH₃CH₂CH₂Cl are evaluated by isodesmic reactions.

  15. Radical behaviorism and scientific frameworks. From mechanistic to relational accounts.

    PubMed

    Chiesa, M

    1992-11-01

    A substantial portion of B. F. Skinner's scholarship was devoted to developing methods and terms for a scientific study of behavior. Three concepts central to scientific accounts--cause, explanation, and theory--are examined to illustrate the distinction between mechanistic and relational frameworks and radical behaviorism's relationship to those frameworks. Informed by a scientific tradition that explicitly rejects mechanistic interpretations, radical behaviorism provides a distinctive stance in contemporary psychology. The present analysis suggests that radical behaviorism makes closer contact with the "new world view" advocated by physicists and philosophers of science than does much of contemporary psychology.

  16. 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

  17. ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning.

    PubMed

    Kayala, Matthew A; Baldi, Pierre

    2012-10-22

    Proposing reasonable mechanisms and predicting the course of chemical reactions is important to the practice of organic chemistry. Approaches to reaction prediction have historically used obfuscating representations and manually encoded patterns or rules. Here we present ReactionPredictor, a machine learning approach to reaction prediction that models elementary, mechanistic reactions as interactions between approximate molecular orbitals (MOs). A training data set of productive reactions known to occur at reasonable rates and yields and verified by inclusion in the literature or textbooks is derived from an existing rule-based system and expanded upon with manual curation from graduate level textbooks. Using this training data set of complex polar, hypervalent, radical, and pericyclic reactions, a two-stage machine learning prediction framework is trained and validated. In the first stage, filtering models trained at the level of individual MOs are used to reduce the space of possible reactions to consider. In the second stage, ranking models over the filtered space of possible reactions are used to order the reactions such that the productive reactions are the top ranked. The resulting model, ReactionPredictor, perfectly ranks polar reactions 78.1% of the time and recovers all productive reactions 95.7% of the time when allowing for small numbers of errors. Pericyclic and radical reactions are perfectly ranked 85.8% and 77.0% of the time, respectively, rising to >93% recovery for both reaction types with a small number of allowed errors. Decisions about which of the polar, pericyclic, or radical reaction type ranking models to use can be made with >99% accuracy. Finally, for multistep reaction pathways, we implement the first mechanistic pathway predictor using constrained tree-search to discover a set of reasonable mechanistic steps from given reactants to given products. Webserver implementations of both the single step and pathway versions of Reaction

  18. 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.

  19. 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.

  20. Mechanistic Aspects of Hydration of Guanine Radical Cations in DNA

    PubMed Central

    2015-01-01

    The mechanistic aspects of hydration of guanine radical cations, G•+ in double- and single-stranded oligonucleotides were investigated by direct time-resolved spectroscopic monitoring methods. The G•+ radical one-electron oxidation products were generated by SO4•– radical anions derived from the photolysis of S2O82– anions by 308 nm laser pulses. In neutral aqueous solutions (pH 7.0), after the complete decay of SO4•– radicals (∼5 μs after the actinic laser flash) the transient absorbance of neutral guanine radicals, G(-H)• with maximum at 312 nm, is dominant. The kinetics of decay of G(-H)• radicals depend strongly on the DNA secondary structure. In double-stranded DNA, the G(-H)• decay is biphasic with one component decaying with a lifetime of ∼2.2 ms and the other with a lifetime of ∼0.18 s. By contrast, in single-stranded DNA the G(-H)• radicals decay monophasically with a ∼ 0.28 s lifetime. The ms decay component in double-stranded DNA is correlated with the enhancement of 8-oxo-7,8-dihydroguanine (8-oxoG) yields which are ∼7 greater than in single-stranded DNA. In double-stranded DNA, it is proposed that the G(-H)• radicals retain radical cation character by sharing the N1-proton with the N3-site of C in the [G•+:C] base pair. This [G(-H)•:H+C ⇆ G•+:C] equilibrium allows for the hydration of G•+ followed by formation of 8-oxoG. By contrast, in single-stranded DNA, deprotonation of G•+ and the irreversible escape of the proton into the aqueous phase competes more effectively with the hydration mechanism, thus diminishing the yield of 8-oxoG, as observed experimentally. PMID:24689701

  1. Sulfur Radical-Induced Redox Modifications in Proteins: Analysis and Mechanistic Aspects.

    PubMed

    Schöneich, Christian

    2017-03-10

    The sulfur-containing amino acids cysteine (Cys) and methionine (Met) are prominent protein targets of redox modification during conditions of oxidative stress. Here, two-electron pathways have received widespread attention, in part due to their role in signaling processes. However, Cys and Met are equally prone to one-electron pathways, generating intermediary radicals and/or radial ions. These radicals/radical ions can generate various reaction products that are not commonly monitored in redox proteomic studies, but they may be relevant for the fate of proteins during oxidative stress. Recent Advances: Time-resolved kinetic studies and product analysis have expanded our mechanistic understanding of radical reaction pathways of sulfur-containing amino acids. These reactions are now studied in some detail for Met and Cys in proteins, and homocysteine (Hcy) chemically linked to proteins, and the role of protein radical reactions in physiological processes is evolving. Radical-derived products from Cys, Hcy, and Met can react with additional amino acids in proteins, leading to secondary protein modifications, which are potentially remote from initial points of radical attack. These products may contain intra- and intermolecular cross-links, which may lead to protein aggregation. Protein sequence and conformation will have a significant impact on the formation of such products, and a thorough understanding of reaction mechanisms and specifically how protein structure influences reaction pathways will be critical for identification and characterization of novel reaction products. Future studies must evaluate the biological significance of novel reaction products that are derived from radical reactions of sulfur-containing amino acids. Antioxid. Redox Signal. 26, 388-405.

  2. 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.

  3. Mechanistic investigations of the ethylene tetramerisation reaction.

    PubMed

    Overett, Matthew J; Blann, Kevin; Bollmann, Annette; Dixon, John T; Haasbroek, Daleen; Killian, Esna; Maumela, Hulisani; McGuinness, David S; Morgan, David H

    2005-08-03

    The unprecedented selective tetramerisation of ethylene to 1-octene was recently reported. In the present study various mechanistic aspects of this novel transformation were investigated. The unusually high 1-octene selectivity in chromium-catalyzed ethylene tetramerisation reactions is caused by the unique extended metallacyclic mechanism in operation. Both 1-octene and higher 1-alkenes are formed by further ethylene insertion into a metallacycloheptane intermediate, whereas 1-hexene is formed by elimination from this species as in other reported trimerisation reactions. This is supported by deuterium labeling studies, analysis of the molar distribution of 1-alkene products, and identification of secondary co-oligomerization reaction products. In addition, the formation of two C6 cyclic products, methylenecyclopentane and methylcyclopentane, is discussed, and a bimetallic disproportionation mechanism to account for the available data is proposed.

  4. Mechanistic aspects of hydration of guanine radical cations in DNA.

    PubMed

    Rokhlenko, Yekaterina; Cadet, Jean; Geacintov, Nicholas E; Shafirovich, Vladimir

    2014-04-23

    The mechanistic aspects of hydration of guanine radical cations, G(•+) in double- and single-stranded oligonucleotides were investigated by direct time-resolved spectroscopic monitoring methods. The G(•+) radical one-electron oxidation products were generated by SO4(•-) radical anions derived from the photolysis of S2O8(2-) anions by 308 nm laser pulses. In neutral aqueous solutions (pH 7.0), after the complete decay of SO4(•-) radicals (∼5 μs after the actinic laser flash) the transient absorbance of neutral guanine radicals, G(-H)(•) with maximum at 312 nm, is dominant. The kinetics of decay of G(-H)(•) radicals depend strongly on the DNA secondary structure. In double-stranded DNA, the G(-H)(•) decay is biphasic with one component decaying with a lifetime of ∼2.2 ms and the other with a lifetime of ∼0.18 s. By contrast, in single-stranded DNA the G(-H)(•) radicals decay monophasically with a ∼ 0.28 s lifetime. The ms decay component in double-stranded DNA is correlated with the enhancement of 8-oxo-7,8-dihydroguanine (8-oxoG) yields which are ∼7 greater than in single-stranded DNA. In double-stranded DNA, it is proposed that the G(-H)(•) radicals retain radical cation character by sharing the N1-proton with the N3-site of C in the [G(•+):C] base pair. This [G(-H)(•):H(+)C ⇆ G(•+):C] equilibrium allows for the hydration of G(•+) followed by formation of 8-oxoG. By contrast, in single-stranded DNA, deprotonation of G(•+) and the irreversible escape of the proton into the aqueous phase competes more effectively with the hydration mechanism, thus diminishing the yield of 8-oxoG, as observed experimentally.

  5. REVERSIBILITY OF RADICAL-OLEFIN REACTIONS.

    DTIC Science & Technology

    ALKENES, *STYRENES, *POLYVINYL CHLORIDE, CHEMICAL EQUILIBRIUM, POLYMERIZATION, POLYMERIZATION, FREE RADICALS , MOLECULAR ISOMERISM, TRACER STUDIES, CHEMICAL REACTIONS, DECOMPOSITION, SYNTHESIS(CHEMISTRY).

  6. Mechanistic and functional versatility of radical SAM enzymes.

    PubMed

    Booker, Squire J; Grove, Tyler L

    2010-07-14

    Enzymes of the radical SAM (RS) superfamily catalyze a diverse assortment of reactions that proceed via intermediates containing unpaired electrons. The radical initiator is the common metabolite S-adenosyl-l-methionine (SAM), which is reductively cleaved to generate a 5'-deoxyadenosyl 5'-radical, a universal and obligate intermediate among enzymes within this class. A bioinformatics study that appeared in 2001 indicated that this superfamily contained over 600 members, many catalyzing reactions that were rich in novel chemical transformations. Since that seminal study, the RS superfamily has grown immensely, and new details about the scope of reactions and biochemical pathways in which its members participate have emerged. This review will highlight only a few of the most significant findings from the past 2-3 years, focusing primarily on: RS enzymes involved in complex metallocofactor maturation; characterized RS enzymes that lack the canonical CxxxCxxC motif; RS enzymes containing multiple iron-sulfur clusters; RS enzymes catalyzing reactions with compelling medical implications; and the energetics and mechanism of generating the 5'-deoxyadenosyl radical. A number of significant studies of RS enzymes will unfortunately be omitted, and it is hoped that the reader will access the relevant literature - particularly a number of superb review articles recently written on the subject - to acquire a deeper appreciation of this class of enzymes.

  7. Catalysis of Radical Reactions: A Radical Chemistry Perspective.

    PubMed

    Studer, Armido; Curran, Dennis P

    2016-01-04

    The area of catalysis of radical reactions has recently flourished. Various reaction conditions have been discovered and explained in terms of catalytic cycles. These cycles rarely stand alone as unique paths from substrates to products. Instead, most radical reactions have innate chains which form products without any catalyst. How do we know if a species added in "catalytic amounts" is a catalyst, an initiator, or something else? Herein we critically address both catalyst-free and catalytic radical reactions through the lens of radical chemistry. Basic principles of kinetics and thermodynamics are used to address problems of initiation, propagation, and inhibition of radical chains. The catalysis of radical reactions differs from other areas of catalysis. Whereas efficient innate chain reactions are difficult to catalyze because individual steps are fast, both inefficient chain processes and non-chain processes afford diverse opportunities for catalysis, as illustrated with selected examples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Anodic Cyclization Reactions and the Mechanistic Strategies That Enable Optimization.

    PubMed

    Feng, Ruozhu; Smith, Jake A; Moeller, Kevin D

    2017-09-19

    Oxidation reactions are powerful tools for synthesis because they allow us to reverse the polarity of electron-rich functional groups, generate highly reactive intermediates, and increase the functionality of molecules. For this reason, oxidation reactions have been and continue to be the subject of intense study. Central to these efforts is the development of mechanism-based strategies that allow us to think about the reactive intermediates that are frequently central to the success of the reactions and the mechanistic pathways that those intermediates trigger. For example, consider oxidative cyclization reactions that are triggered by the removal of an electron from an electron-rich olefin and lead to cyclic products that are functionalized for further elaboration. For these reactions to be successful, the radical cation intermediate must first be generated using conditions that limit its polymerization and then channeled down a productive desired pathway. Following the cyclization, a second oxidation step is necessary for product formation, after which the resulting cation must be quenched in a controlled fashion to avoid undesired elimination reactions. Problems can arise at any one or all of these steps, a fact that frequently complicates reaction optimization and can discourage the development of new transformations. Fortunately, anodic electrochemistry offers an outstanding opportunity to systematically probe the mechanism of oxidative cyclization reactions. The use of electrochemical methods allows for the generation of radical cations under neutral conditions in an environment that helps prevent polymerization of the intermediate. Once the intermediates have been generated, a series of "telltale indicators" can be used to diagnose which step in an oxidative cyclization is problematic for less successful transformation. A set of potential solutions to address each type of problem encountered has been developed. For example, problems with the initial

  9. REACTIONS OF FREE RADICALS CONTAINING NITROGEN.

    DTIC Science & Technology

    deduced. The reactions of methyl and ethyl radicals with a variety of amino compounds were studied. The reactions of difluoroamino radicals in the...Hydrazines, Anilines and Cyanides were pyrolysed and the heats of formation of the resultant radicals and the strengths of the bonds formed by them

  10. 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

  11. Kinetic and Mechanistic Investigations of Atom Abstraction Reactions

    NASA Astrophysics Data System (ADS)

    Stevens, Philip Stanford

    1990-01-01

    A discharge-flow system at 1-4 torr total pressure, employing resonance fluorescence detection of Br, Cl, O, H, N, and D, and laser magnetic resonance detection of OH and ClO, was used to measure the rate constants for a number of hydrogen and non-hydrogen atom abstraction reactions. The rate constants are examined within established reactivity trends in order to reveal the dominant forces governing the potential-energy surfaces. The activation energies for the F + rm H_2O/D_2O reactions are found to be smaller than that defined by the Evans-Polyani relationship between activation energy and exothermicity. The low activation energy and enhanced kinetic isotope effect for these reactions suggests that this deviation may be the result of quantum -mechanical tunneling. The rate constants for these and other heavy-light-heavy reactions are interpreted using transition-state theory and a one-dimensional tunneling model, in conjunction with ab initio calculations, to gain insight into the mechanism of these reactions. For the reactions of X + ClOCl to Products (X = Br, Cl, F, N), the rate constants correlate with the electron affinity of the radical, indicating that these mechanisms are dominated by electron transfer from ClOCl to X, similar to the reactivity of other non -hydrogen abstractions. The reactions of O and OH with ClOCl do not follow this trend, suggesting that electron transfer is not the only driving force in these reactions. These deviations are interpreted in terms of long-range attractive forces forming stable intermediates. The ClO + O_3 to ClOO + O_2 reaction has been proposed as an additional mechanism for ozone destruction within the antarctic vortex. Upper limits for the bimolecular rate constant for the ClO + O _3 reaction were measured directly between 233 and 413 K at 1-2 torr. The rate constants are several orders-of-magnitude smaller than estimated from the trend for non-hydrogen abstractions. From these results, it is concluded that this

  12. 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 ...

  13. 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 ...

  14. Semiconductor Photocatalysis for Chemoselective Radical Coupling Reactions.

    PubMed

    Kisch, Horst

    2017-04-18

    problem of quantitative comparisons of photocatalytic activities or apparent quantum yields and propose a basic three-step mechanistic model. Finally, we address the question whether or not the unique photoredox properties of simple inorganic semiconductor powders may lead to previously unknown visible light induced organic syntheses. For that, we summarize novel radical C-C- and C-N- couplings photocatalyzed by self-prepared cadmium sulfide powders. Electron acceptor and donor substrates like imines or 1,2-diazenes, and cyclic olefins or unsaturated ethers, respectively, undergo a linear addition reaction. The hitherto unknown products have all been isolated in good to moderate yields and may be of pharmaceutical interest. In the first reaction step photogenerated electron-hole pairs produce through proton-coupled electron transfer the corresponding radicals. Their subsequent chemoselective heterocoupling affords the products, correlating with an insertion of the imine or 1,2-diazene into an allylic C(sp(3))-H bond of the donor substrate. In the absence of an imine or 1,2-diazene, cyclic allyl/enol ethers are dehydrodimerized under concomitant hydrogen evolution. Even a visible light photosulfoxidation of alkanes is catalyzed by titania. In these heterogeneous photoredox reactions the role of the semiconductor photocatalyst is multifunctional. It induces favorable substrate preorientations in the surface-solvent layer, it catalyzes proton-coupled interfacial electron transfer to and from substrates generating intermediate radicals, and it enables their subsequent chemoselective coupling in the surface-solvent interface. Different from molecular photosensitizers, which enable only one one-electron transfer with one single substrate, photoexcited semiconductors induce two concerted one-electron transfer reactions with two substrates. This is because the light generated electron-hole pairs are trapped at distinct surface sites and undergo proton-coupled interfacial electron

  15. 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

  16. Tropospheric degradation of 2-hydroxy-2-methylpropanal, a photo-oxidation product of 2-methyl-3-buten-2-ol: Kinetic and mechanistic study of its photolysis and its reaction with OH radicals

    NASA Astrophysics Data System (ADS)

    Carrasco, Nathalie; Doussin, Jean-François; Picquet-Varrault, Bénédicte; Carlier, Patrick

    This article presents the first study of the chemical reactivity of a photo-oxidation product of the 2-methyl-3-buten-2-ol (MBO) in the troposphere, the 2-hydroxy-2-methylpropanal (HMPr). Experiments were performed under controlled conditions for pressure (atmospheric pressure) and temperature (296±2 K) in the LISA indoor simulation chamber and in the EUPHORE outdoor simulation chamber to understand the transformations of HMPr in the atmosphere, using FTIR spectrometry. Reaction with OH radicals was studied in the presence and in the absence of NO x. All the kinetic studies were carried out by relative rate study using isoprene and/or n-butylether as the reference compound. The rate constants found for these reactions were J=(1.01±0.39)×10 -5 s -1 and kHMPr+OH=(1.52±0.36)×10 -11 molecule -1 cm 3 s -1. For the reaction with OH radicals, an important production of acetone was observed, with a yield of Racetone=1.06±0.06.

  17. Hydroxyl radical induced oxidation of theophylline in water: a kinetic and mechanistic study.

    PubMed

    Sunil Paul, M M; Aravind, U K; Pramod, G; Saha, A; Aravindakumar, C T

    2014-08-14

    Oxidative destruction and mineralization of emerging organic pollutants by hydroxyl radicals (˙OH) is a well established area of research. The possibility of generating hazardous by-products in the case of ˙OH reaction demands extensive investigations on the degradation mechanism. A combination of pulse radiolysis and steady state photolysis (H2O2/UV photolysis) followed by high resolution mass spectrometric (HRMS) analysis have been employed to explicate the kinetic and mechanistic features of the destruction of theophylline, a model pharmaceutical compound and an identified pollutant, by ˙OH in the present study. The oxidative destruction of this molecule, for intermediate product studies, was initially achieved by H2O2/UV photolysis. The transient absorption spectrum corresponding to the reaction of ˙OH with theophylline at pH 6, primarily caused by the generation of (T8-OH)˙, was characterised by an absorption band at 330 nm (k2 = (8.22 ± 0.03) × 10(9) dm(3) mol(-1) s(-1)). A significantly different spectrum (λmax: 340 nm) was observed at highly alkaline pH (10.2) due to the deprotonation of this radical (pKa∼ 10.0). Specific one electron oxidants such as sulphate radical anions (SO4˙(-)) and azide radicals (N3˙) produce the deprotonated form (T(-H)˙) of the radical cation (T˙(+)) of theophylline (pKa 3.1) with k2 values of (7.51 ± 0.04) × 10(9) dm(3) mol(-1) s(-1) and (7.61 ± 0.02) × 10(9) dm(3) mol(-1) s(-1) respectively. Conversely, oxide radicals (O˙(-)) react with theophylline via a hydrogen abstraction protocol with a rather slow k2 value of (1.95 ± 0.02) × 10(9) dm(3) mol(-1) s(-1). The transient spectral studies were complemented by the end product profile acquired by HRMS analysis. Various transformation products of theophylline induced by ˙OH were identified by this technique which include derivatives of uric acids (i, iv & v) and xanthines (ii, iii & vi). Further breakdown of the early formed product due to ˙OH attack leads to

  18. Potential energy surface crossings and the mechanistic spectrum for intramolecular electron transfer in organic radical cations.

    PubMed

    Blancafort, L; Jolibois, F; Olivucci, M; Robb, M A

    2001-01-31

    The structure of the potential energy surface for the intramolecular electron transfer (IET) of four different model radical cations has been determined by using reaction path mapping and conical intersection optimization at the ab initio CASSCF level of theory. We show that, remarkably, the calculated paths reside in regions of the ground-state energy surface whose structure can be understood in terms of the position and properties of a surface crossing between the ground and the first excited state of the reactant. Thus, in the norbornadiene radical cation and in an analogue compound formed by two cyclopentene units linked by a norbornyl bridge, IET proceeds along direct-overlap and super-exchange concerted paths, respectively, that are located far from a sloped conical intersection point and in a region where the excited-state and ground-state surfaces are well separated. A second potential energy surface structure has been documented for 1,2-diamino ethane radical cation and features two parallel concerted (direct) and stepwise (chemical) paths. In this case a peaked conical intersection is located between the two paths. Finally, a third type of energy surface is documented for the bismethyleneadamantane radical cation and occurs when there is, effectively, a seam of intersection points (not a conical intersection) which separates the reactant and product regions. Since the reaction path cannot avoid the intersection, IET can only occur nonadiabatically. These IET paths indicate that quite different IET mechanisms may operate in radical cations, revealing an unexpectedly enriched and flexible mechanistic spectrum. We show that the origin of each path can be analyzed and understood in terms of the one-dimensional Marcus-Hush model.

  19. Adenosyl radical: reagent and catalyst in enzyme reactions.

    PubMed

    Marsh, E Neil G; Patterson, Dustin P; Li, Lei

    2010-03-22

    Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors: ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B(12), AdoCbl) or by single-electron reduction of S-adenosylmethionine (AdoMet) complexed to an iron-sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosine's role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen, which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations; nevertheless, mechanistic insights gained from studying these enzymes have proved extremely valuable in understanding how enzymes generate and control highly reactive free radical intermediates. In contrast, there has been a recent explosion in the number of radical-AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions; here there is much still to learn about their mechanisms. Although all the radical-AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes might be active in aerobic organisms including humans.

  20. 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.

  1. Laser Studies of Gas Phase Radical Reactions.

    DTIC Science & Technology

    1989-01-01

    Acremonium chrysogenum , was prepared according to the published procedure [6]. This fungal enzyme had a specific activity of 0.023 IUmg1, and was estimated to...Dist-lbitionj Avdielbiity Codes jAvail atidjor Dist 6a A-I . p -1- Laser Studies of Gas Phase Radical Reactions G. Hancock Physical Chemistry...some additional experiments concerning the formation of carbene radicals in liquid phase enzyme cleavage studies are described. Keywords Laser

  2. [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.

  3. New mechanistic studies on the proline-catalyzed aldol reaction

    PubMed Central

    List, Benjamin; Hoang, Linh; Martin, Harry J.

    2004-01-01

    The mechanism of the proline-catalyzed aldol reaction has stimulated considerable debate, and despite limited experimental data, at least five different mechanisms have been proposed. Complementary to recent theoretical studies we have initiated an experimental program with the goal of clarifying some of the basic mechanistic questions concerning the proline-catalyzed aldol reaction. Here we summarize our discoveries in this area and provide further evidence for the involvement of enamine intermediates. PMID:15073330

  4. Reactivity of γ-Terpinene with NO3 radicals: experimental approach for kinetic and mechanistic study.

    NASA Astrophysics Data System (ADS)

    Fouqueau, Axel; Cirtog, Manuela; Le Quilleuc, Meryll; Cazaunau, Mathieu; Pangui, Edouard; Duncianu, Marius; Doussin, Jean-François; Picquet-Varrault, Bénédicte

    2017-04-01

    Biogenic Volatile Organic Compounds (BVOC) are highly emitted by vegetation and play a key role in atmospheric chemistry. They are very reactive with atmospheric oxidants (OH, NO3, ozone) and significantly contribute to the formation of Secondary Organic Aerosol (SOA) at the global scale [1]. In addition, night-time chemistry initiated by NO3 radicals leads to the formation of organic nitrates which behave as reservoirs for reactive nitrogen. However, the reactivity of NO3 radical with BVOCs other than isoprene and α- and β-pinene, remains poorly understood. Among the BVOCs, γ-Terpinene is one of the most emitted by vegetation[2]. Two kinetic works were previously published on γ-Terpinene [3] [4], but mechanistic has never been studied. Thus, the aim of this work is to study the reactivity of γ-Terpinene with NO3 by performing experiments in simulation chambers. Kinetic, mechanism and SOA yield will be investigated. For this purpose, two different simulation chambers have been used: - First one, consisting of a Pyrex reactor of 1 m3 [5] coupled to a long path in situ FTIR spectrometer and a Proton Transfer Reaction Time of Flight Mass Spectrometer (PTR-ToF-MS) in NO+ mode which was internally developed in LISA, to measure organic nitrates concentration. - Second one, the CESAM chamber (http://cesam.cnrs.fr) [6] is a 4.2 m3 stainless steel chamber which permits to conduct SOA experiments at different temperature and relative humidity. In situ FTIR and PTR-ToF-MS are used to measure gaseous concentrations, and a SMPS was used to characterize particulate phase. Kinetic and mechanistic results will be discussed and compared with the literature values. References [1] Brown S. S., Stutz J., Nighttime radical observations and chemistry. Chem. Soc. Rev. (2012) 41, 6405-6447 [2] Helmig D., Klinger L.F., et al., Biogenic volatile organic compound emissions (BVOCs) I. Identifications from three continental sites in the U.S. Chemosphere. (1999), Vol. 38, No. 9, pp. 2163

  5. 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.

  6. Laser Studies of Gas Phase Radical Reaction.

    DTIC Science & Technology

    1985-11-30

    1nai Irvest-aator Or.G. Hancock gn; FILE CO, Contr3ctor : Oxford University . Physical Chemistry Laboratory. South Parks Road.AD-A 193 689 Oxfor o~d...HIF spectrum and study of reaction of this and the CCI radical with atoms vi) sea;rchtrr; f(r FC) ’ndlict of the 0 *CF, reaction. OXFORD UNIVERSITY -. - SOUTH...0 Awtilability Codes I Avail ’and/or Dis Spcal0 Spoo OXFORD UNIVERSITY Tt SOUTH PARKS ROAD OXFCRD OXFORD � X3Z U.S. Army Contract DAJA45-85-C-0034

  7. 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

  8. Proton-coupled electron transfer: the mechanistic underpinning for radical transport and catalysis in biology.

    PubMed

    Reece, Steven Y; Hodgkiss, Justin M; Stubbe, JoAnne; Nocera, Daniel G

    2006-08-29

    Charge transport and catalysis in enzymes often rely on amino acid radicals as intermediates. The generation and transport of these radicals are synonymous with proton-coupled electron transfer (PCET), which intrinsically is a quantum mechanical effect as both the electron and proton tunnel. The caveat to PCET is that proton transfer (PT) is fundamentally limited to short distances relative to electron transfer (ET). This predicament is resolved in biology by the evolution of enzymes to control PT and ET coordinates on highly different length scales. In doing so, the enzyme imparts exquisite thermodynamic and kinetic controls over radical transport and radical-based catalysis at cofactor active sites. This discussion will present model systems containing orthogonal ET and PT pathways, thereby allowing the proton and electron tunnelling events to be disentangled. Against this mechanistic backdrop, PCET catalysis of oxygen-oxygen bond activation by mono-oxygenases is captured at biomimetic porphyrin redox platforms. The discussion concludes with the case study of radical-based quantum catalysis in a natural biological enzyme, class I Escherichia coli ribonucleotide reductase. Studies are presented that show the enzyme utilizes both collinear and orthogonal PCET to transport charge from an assembled diiron-tyrosyl radical cofactor to the active site over 35A away via an amino acid radical-hopping pathway spanning two protein subunits.

  9. Taming the free radical shrew - learning to control homolytic reactions at higher heteroatoms.

    PubMed

    Schiesser, Carl H

    2006-10-21

    Free radical chemistry has come a long way in a relatively short period of time. Armed with mechanistic and rate constant data, the synthetic practitioner can now apply free radical chemistry to the synthesis of many different classes of target molecule with confidence. This Feature Article highlights progress made in the understanding and application of free radical reactions at main group higher heteroatoms and demonstrates how this knowledge can be used to construct interesting higher heterocycles, many of which exhibit biological activity, through the use of intramolecular homolytic substitution chemistry.

  10. Kinetics Studies of Radical-Radical Reactions: The NO2 + N2H3 System

    DTIC Science & Technology

    2013-10-01

    investigating the kinetics of this elementary reaction . 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES...Viewgraph 3. DATES COVERED (From - To) September 2013- October 2013 4. TITLE AND SUBTITLE Kinetics Studies of Radical-Radical Reactions (I): The NO2...characteristics in relevant operating environments. Here we report theoretical results obtained on the prototypical radical- radical reaction : NO2 + N2H3

  11. Radical addition-initiated domino reactions of conjugated oxime ethers.

    PubMed

    Ueda, Masafumi

    2014-01-01

    The application of conjugated oxime ethers to the synthesis of complex chemical scaffolds using domino radical reactions has been described in detail. The triethylborane-mediated hydroxysulfenylation reaction allows for the regioselective construction of a carbon-sulfur bond and a carbon-oxygen bond in a single operation for the formation of β-hydroxy sulfides. This reaction proceeds via a radical pathway involving regioselective thiyl addition and the subsequent trapping of the resulting α-imino radical with O₂, where the imino group enhances the stability of the intermediate radical. Hydroxyalkylation reactions that occur via a carbon radical addition reaction followed by the hydroxylation of the resulting N-borylenamine with O₂ have also been developed. We investigated sequential radical addition aldol-type reactions in detail to explore the novel domino reactions that occur via the generation of N-borylenamine. The radical reaction of a conjugated oxime ether with triethylborane in the presence of an aldehyde affords γ-butyrolactone via sequential processes including ethyl radical addition, the generation of N-borylenamine, an aldol-type reaction with an aldehyde, and a lactonization reaction. A novel domino reaction has also been developed involving the [3,3]-sigmatropic rearrangement of N-boryl-N-phenoxyenamine. The triethylborane-mediated domino reactions of O-phenyl-conjugated oxime ethers afforded the corresponding benzofuro[2,3-b]pyrrol-2-ones via a radical addition/[3,3]-sigmatropic rearrangement/cyclization/lactamization cascade.

  12. Mechanistic Insights into Two-Phase Radical C–H Arylations

    PubMed Central

    2015-01-01

    Kinetic, spectroscopic, and computational studies of radical C–H arylations highlight the interplay between chemical and physical rate processes in these multiphase reactions. Anomalous concentration dependences observed here may be reconciled by considering the role of phase transfer processes that mediate concentrations in each phase. In addition, understanding interactions through phase boundaries enables their use in optimization of reaction performance. PMID:26640819

  13. Mechanistic insight into the photoredox catalysis of anti-Markovnikov alkene hydrofunctionalization reactions

    SciTech Connect

    Romero, Nathan A.; Nicewicz, David A.

    2014-11-12

    Here, 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.

  14. Mechanistic insight into the photoredox catalysis of anti-Markovnikov alkene hydrofunctionalization reactions

    DOE PAGES

    Romero, Nathan A.; Nicewicz, David A.

    2014-11-12

    Here, 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 usingmore » 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.« less

  15. 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

  16. Mechanistic insight into the photoredox catalysis of anti-markovnikov alkene hydrofunctionalization reactions.

    PubMed

    Romero, Nathan A; Nicewicz, David A

    2014-12-10

    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.

  17. 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.

  18. Degradation of atrazine in aqueous medium by electrocatalytically generated hydroxyl radicals. A kinetic and mechanistic study.

    PubMed

    Balci, Beytul; Oturan, Nihal; Cherrier, Richard; Oturan, Mehmet A

    2009-04-01

    Oxidative degradation of atrazine by hydroxyl radicals (()OH) was studied in aqueous medium. ()OH were formed in situ from electrochemically generating Fenton's reagent by an indirect electrochemical advanced oxidation process. Identification and evolution of seven main aromatic metabolites and four short-chain carboxylic acids were performed by using liquid chromatography analyses. Total organic carbon (TOC) and ionic chromatography were used in order to evaluate the mineralization efficiency of treated aqueous solutions. A high mineralization rate of 82% (never reported until now) was obtained. The oxidative degradation of cyanuric acid, the ultimate product of atrazine degradation, was highlighted for the first time. The absolute rate constant of the reaction between atrazine and hydroxyl radicals was evaluated by competition kinetics method as (2.54+/-0.22)x10(9)M(-1)s(-1). Considering all oxidation reaction intermediates and end products a general reaction sequence for atrazine degradation by hydroxyl radicals was proposed.

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

    PubMed

    Zhang, Li; Yang, Huan; Jiao, Lei

    2016-06-08

    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.

  20. Reactions of hydrated electron with various radicals: spin factor in diffusion-controlled reactions.

    PubMed

    Ichino, Takatoshi; Fessenden, Richard W

    2007-04-05

    The reactions of hydrated electron (eaq-) with various radicals have been studied in pulse radiolysis experiments. These radicals are hydroxyl radical (*OH), sulfite radical anion (*SO3-), carbonate radical anion (CO3*-), carbon dioxide radical anion (*CO2-), azidyl radical (*N3), dibromine radical anion (Br2*-), diiodine radical anion (I2*-), 2-hydroxy-2-propyl radical (*C(CH3)2OH), 2-hydroxy-2-methyl-1-propyl radical ((*CH2)(CH3)2COH), hydroxycyclohexadienyl radical (*C6H6OH), phenoxyl radical (C6H5O*), p-methylphenoxyl radical (p-(H3C)C6H4O*), p-benzosemiquinone radical anion (p-OC6H4O*-), and phenylthiyl radical (C6H5S*). The kinetics of eaq- was followed in the presence of the counter radicals in transient optical absorption measurements. The rate constants of the eaq- reactions with radicals have been determined over a temperature range of 5-75 degrees C from the kinetic analysis of systems of multiple second-order reactions. The observed high rate constants for all the eaq- + radical reactions have been analyzed with the Smoluchowski equation. This analysis suggests that many of the eaq- + radical reactions are diffusion-controlled with a spin factor of 1/4, while other reactions with *OH, *N3, Br2*-, I2*-, and C6H5S* have spin factors significantly larger than 1/4. Spin dynamics for the eaq-/radical pairs is discussed to explain the different spin factors. The reactions with *OH, *N3, Br2*-, and I2*- have also been found to have apparent activation energies less than that for diffusion control, and it is suggested that the spin factors for these reactions decrease with increasing temperature. Such a decrease in spin factor may reflect a changing competition between spin relaxation/conversion and diffusive escape from the radical pairs.

  1. The reaction of formyl radical with chlorine atom

    NASA Astrophysics Data System (ADS)

    Qu, Zhang-Wang; Dong, Feng; Zhang, Qiyuan; Kong, Fanao

    2004-03-01

    The radical-radical reaction of formyl radical with chlorine atom has been investigated by the time-resolved infrared emission spectroscopy and by the theoretical calculations at the UB3LYP/6-31++G(d,p) and single-point UCCSD(T)/6-311++G(d,p) levels. The products have been verified as the vibrationally excited CO ( v⩽4) and HCl. The reaction is initiated by radical-radical recombination forming an intermediate of formaldehyde chloride, which further dissociates into the products of HCl and CO.

  2. Intermediate Q from soluble methane monooxygenase hydroxylates the mechanistic substrate probe norcarane: evidence for a stepwise reaction.

    PubMed

    Brazeau, B J; Austin, R N; Tarr, C; Groves, J T; Lipscomb, J D

    2001-12-05

    Norcarane is a valuable mechanistic probe for enzyme-catalyzed hydrocarbon oxidation reactions because different products or product distributions result from concerted, radical, and cation based reactions. Soluble methane monooxygenase (sMMO) from Methylosinus trichosporium OB3b catalyzes the oxidation of norcarane to afford 3-hydroxymethylcyclohexene and 3-cycloheptenol, compounds characteristic of radical and cationic intermediates, respectively, in addition to 2- and 3-norcaranols. Past single turnover transient kinetic studies have identified several optically distinct intermediates from the catalytic cycle of the hydroxylase component of sMMO. Thus, the reaction between norcarane and key reaction intermediates can be directly monitored. The presence of norcarane increases the rate of decay of only one intermediate, the high-valent bis-mu-oxo Fe(IV)(2) cluster-containing species compound Q, showing that it is responsible for the majority of the oxidation chemistry. The observation of products from both radical and cationic intermediates from norcarane oxidation catalyzed by sMMO is consistent with a mechanism in which an initial substrate radical intermediate is formed by hydrogen atom abstraction. This intermediate then undergoes either oxygen rebound, intramolecular rearrangement followed by oxygen rebound, or loss of a second electron to yield a cationic intermediate to which OH(-) is transferred. The estimated lower limit of 20 ps for the lifetime of the putative radical intermediate is in accord with values determined from previous studies of sterically hindered sMMO probes.

  3. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse.

    PubMed

    Agarwal, Vinayak; Miles, Zachary D; Winter, Jaclyn M; Eustáquio, Alessandra S; El Gamal, Abrahim A; Moore, Bradley S

    2017-01-20

    Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.

  4. Flow Giese reaction using cyanoborohydride as a radical mediator

    PubMed Central

    Fukuyama, Takahide; Kawamoto, Takuji; Kobayashi, Mikako

    2013-01-01

    Summary Tin-free Giese reactions, employing primary, secondary, and tertiary alkyl iodides as radical precursors, ethyl acrylate as a radical trap, and sodium cyanoborohydride as a radical mediator, were examined in a continuous flow system. With the use of an automated flow microreactor, flow reaction conditions for the Giese reaction were quickly optimized, and it was found that a reaction temperature of 70 °C in combination with a residence time of 10–15 minutes gave good yields of the desired addition products. PMID:24062844

  5. 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.

  6. Product detection of the CH radical reaction with acetaldehyde.

    PubMed

    Goulay, Fabien; Trevitt, Adam J; Savee, John D; Bouwman, Jordy; Osborn, David L; Taatjes, Craig A; Wilson, Kevin R; Leone, Stephen R

    2012-06-21

    The reaction of the methylidyne radical (CH) with acetaldehyde (CH(3)CHO) is studied at room temperature and at a pressure of 4 Torr (533.3 Pa) using a multiplexed photoionization mass spectrometer coupled to the tunable vacuum ultraviolet synchrotron radiation of the Advanced Light Source at Lawrence Berkeley National Laboratory. The CH radicals are generated by 248 nm multiphoton photolysis of CHBr(3) and react with acetaldehyde in an excess of helium and nitrogen gas flow. Five reaction exit channels are observed corresponding to elimination of methylene (CH(2)), elimination of a formyl radical (HCO), elimination of carbon monoxide (CO), elimination of a methyl radical (CH(3)), and elimination of a hydrogen atom. Analysis of the photoionization yields versus photon energy for the reaction of CH and CD radicals with acetaldehyde and CH radical with partially deuterated acetaldehyde (CD(3)CHO) provides fine details about the reaction mechanism. The CH(2) elimination channel is found to preferentially form the acetyl radical by removal of the aldehydic hydrogen. The insertion of the CH radical into a C-H bond of the methyl group of acetaldehyde is likely to lead to a C(3)H(5)O reaction intermediate that can isomerize by β-hydrogen transfer of the aldehydic hydrogen atom and dissociate to form acrolein + H or ketene + CH(3), which are observed directly. Cycloaddition of the radical onto the carbonyl group is likely to lead to the formation of the observed products, methylketene, methyleneoxirane, and acrolein.

  7. 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.

  8. Reactions of allylic radicals that impact molecular weight growth kinetics.

    PubMed

    Wang, Kun; Villano, Stephanie M; Dean, Anthony M

    2015-03-07

    The reactions of allylic radicals have the potential to play a critical role in molecular weight growth (MWG) kinetics during hydrocarbon oxidation and/or pyrolysis. Due to their stability (when compared to alkyl radicals), they can accumulate to relatively high concentrations. Thus, even though the rate coefficients for their various reactions are small, the rates of these reactions may be significant. In this work, we use electronic structure calculations to examine the recombination, addition, and abstraction reactions of allylic radicals. For the recombination reaction of allyl radicals, we assign a high pressure rate rule that is based on experimental data. Once formed, the recombination product can potentially undergo an H-atom abstraction reaction followed by unimolecular cyclization and β-scission reactions. Depending upon the conditions (e.g., higher pressures) these pathways can lead to the formation of stable MWG species. The addition of allylic radicals to olefins can also lead to MWG species formation. Once again, cyclization of the adduct followed by β-scission is an important energy accessible route. Since the recombination and addition reactions produce chemically-activated adducts, we have explored the pressure- and temperature-dependence of the overall rate constants as well as that for the multiple product channels. We describe a strategy for estimating these pressure-dependencies for systems where detailed electronic structure information is not available. We also derive generic rate rules for hydrogen abstraction reactions from olefins and diolefins by methyl and allyl radicals.

  9. Rate constants of the reaction of C2-C4 peroxy radicals with OH radicals

    NASA Astrophysics Data System (ADS)

    Assaf, Emmanuel; Tanaka, Shisei; Kajii, Yoshizumi; Schoemaecker, Coralie; Fittschen, Christa

    2017-09-01

    The rate constants for the reaction of three peroxy radicals with OH have been measured using different precursors. Peroxy radicals have been prepared by either the reaction of Cl-atoms with C2H6, C3H8 and n-C4H10 or through photolysis of the corresponding alkyliodide. Using Cl-atoms, the following rate constants have been measured: Experiments using 248 nm photolysis of the corresponding alkyliodides as precursor enhances the rate constants by a factor of two, bringing up the suspicion of a fast reaction between I-atoms and OH radicals.

  10. Bimolecular self-reactions of ketyl radicals of acetophenone and diphenylaminyl radicals

    NASA Astrophysics Data System (ADS)

    Khudyakov, I. V.; Koroli, L. L.

    1984-01-01

    The rate constants of self-reactions of ketyl radicals of acetophenone in n-heptane [2 k = (3.2 ± 0.5) × 10 9 M -1 s -1] and diphenylaminyl radicals in toluene [2 k = (3.3 ± 0.5) × 10 7 M -1 s -1] have been determined at 298 K using the flash photolysis technique. The rate constant of ketyl radicals is equal to the calculated diffusion constant and, therefore, this reaction is diffusion-controlled. The aminyl radical recombination rate is independent of the viscosity of the toluene/vaseline oil binary mixture (0.55 ⩽ η ⩽ 12 cP) and this reaction is activation-controlled. Reactivity anisotropy averaging due to the cage effect has been considered for ketyl and some other radicals. On the basis of the analysis it has been proposed that ketyl recombination involves formation of not only pinacol, but also iso-pinacols.

  11. Oxysterols from Free Radical Chain Oxidation of 7-Dehydrocholesterol: Product and Mechanistic Studies

    PubMed Central

    Xu, Libin; Korade, Zeljka; Porter, Ned A.

    2010-01-01

    Free radical chain oxidation of highly oxidizable 7-dehydrocholesterol (7-DHC) initiated by 2,2′-azobis(4-methoxy-2,4-dimethylvaleronitrile) was carried out at 37°C in benzene for 24 hours. Fifteen oxysterols derived from 7-DHC were isolated and characterized with 1D- and 2D-NMR spectroscopy and mass spectrometry. A mechanism that involves abstraction of hydrogen atoms at C-9 and/or C-14 is proposed to account for the formation of all of the oxysterols and the reaction progress profile. In either the H-9 or H-14 mechanism, a pentadienyl radical intermediate is formed after abstraction of H-9 or H-14 by a peroxyl radical. This step is followed by the well-precedented transformations observed in peroxidation reactions of polyunsaturated fatty acids such as oxygen addition, peroxyl radical 5-exo cyclization, and SHi carbon radical attack on the peroxide bond. The mechanism for peroxidation of 7-DHC also accounts for the formation of numerous oxysterol natural products isolated from fungal species, marine sponges, and cactaceous species. In a cell viability test, the oxysterol mixture from 7-DHC peroxidation was found to be cytotoxic to Neuro2a neuroblastoma cells in the micromolar concentration range. We propose that the high reactivity of 7-DHC and the oxysterols generated from its peroxidation may play important roles in the pathogenesis of Smith-Lemli-Opitz syndrome (SLOS), X-linked dominant chondrodysplasia punctata (CDPX2), and cerebrotendinous xanthomatosis (CTX), all of these being metabolic disorders having an elevated level of 7-DHC. PMID:20121089

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

    SciTech Connect

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

    2000-02-01

    Remediation of hydrophobic pollutants is complicated by sorption of these compounds to hydrophobic sites of dissolved natural organic matter (NOM), suspended particulates, soil, and sediment. This sorption causes the pollutants to be less easily degraded by remediation techniques. 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 (H{sub 2}O{sub 2} + Fe{sup 2+} {yields} Fe{sup 3+} + HO{sup {minus}} + HO{sm_bullet}). 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 first-order in pyrene to one that was apparently second-order 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.

  13. Bimetallic oxidative addition involving radical intermediates in nickel-catalyzed alkyl-alkyl Kumada coupling reactions.

    PubMed

    Breitenfeld, Jan; Ruiz, Jesus; Wodrich, Matthew D; Hu, Xile

    2013-08-14

    Many nickel-based catalysts have been reported for cross-coupling reactions of nonactivated alkyl halides. The mechanistic understanding of these reactions is still primitive. Here we report a mechanistic study of alkyl-alkyl Kumada coupling catalyzed by a preformed nickel(II) pincer complex ([(N2N)Ni-Cl]). The coupling proceeds through a radical process, involving two nickel centers for the oxidative addition of alkyl halide. The catalysis is second-order in Grignard reagent, first-order in catalyst, and zero-order in alkyl halide. A transient species, [(N2N)Ni-alkyl(2)](alkyl(2)-MgCl), is identified as the key intermediate responsible for the activation of alkyl halide, the formation of which is the turnover-determining step of the catalysis.

  14. 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.

  15. On the mechanism of reaction of radicals with tirapazamine.

    PubMed

    Shi, Xiaofeng; Mandel, Sarah M; Platz, Matthew S

    2007-04-18

    Ketyl radicals produced by photolysis of ketones or di-tert-butyl peroxide (DTBP) in alcohol solvents react rapidly with tirapazamine (TPZ). The acetone ketyl radical (ACOH) reacts with TPZ with an absolute second-order rate constant of (9.7 +/- 0.4) x 108 M-1 s-1. The reaction kinetics can be followed by monitoring the bleaching of TPZ absorption at 475 nm or the formation of a reaction product which absorbs at 320 and 410 nm. The ACOD radical reacts with TPZ in 2-propanol-OD with an absolute rate constant of (6.7 +/- 0.5) x 108 M-1 s-1, corresponding to a kinetic isotope effect (KIE) of 1.4. Deuteration of the radical on carbon (ACOH-d6) retards the reaction of the radical with TPZ even further (absolute rate constant = (4.8 +/- 0.04) x 108 M-1 s-1). This result corresponds to a KIE of 2.0. Radicals derived from dioxane and diisopropyl ether by flash photolysis of DTBP in ethereal solvent react with TPZ more slowly than do ketyl radicals. It is concluded that ketyl radicals react, in part, with TPZ in organic solvents by transfer of a hydrogen atom from the OH and CH3 groups of the ketyl radical to the oxygen atom at the N4 position of TPZ to form acetone or acetone enol and a radical derivative of TPZ (TPZH). The latter species absorbs at 320 and 405 nm, has a lifetime of hundreds of microseconds in alcohol solvents, and decays by disproportionation to form TPZ and a reduced heterocycle. The reduced heterocycle eventually forms a desoxytirapazamine by a polar mechanism. The results are supported by density functional theory calculations. It is proposed that dioxanyl radical will also react, in part, with TPZ by transfer of a hydrogen atom from the carbon adjacent to the radical center to the oxygen atom at the N4 position of TPZ. This produces the enol ether and the previously mentioned TPZH radical. It is further posited that ether radicals react a bit more slowly than ketyl radicals because they lack the second mode of hydrogen transfer (from the OH group

  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. 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…

  18. Pathways of arachidonic acid peroxyl radical reactions and product formation with guanine radicals.

    PubMed

    Crean, Conor; Geacintov, Nicholas E; Shafirovich, Vladimir

    2008-02-01

    Peroxyl radicals were derived from the one-electron oxidation of polyunsaturated fatty acids by sulfate radicals that were generated by the photodissociation of peroxodisulfate anions in air-equilibrated aqueous solutions. Reactions of these peroxyl and neutral guanine radicals, also generated by oxidation with sulfate radicals, were investigated by laser kinetic spectroscopy, and the guanine oxidation products were identified by HPLC and mass spectrometry methods. Sulfate radicals rapidly oxidize arachidonic (ArAc), linoleic (LnAc), and palmitoleic (PmAc) acids with similar rate constants, (2-4) x 10 (9) M (-1) s (-1). The C-centered radicals derived from the oxidation of ArAc and LnAc include nonconjugated Rn(.) ( approximately 80%) and conjugated bis-allylic Rba(.) ( approximately 20%) radicals. The latter were detectable in the absence of oxygen by their prominent, narrow absorption band at 280 nm. The Rn(.) radicals of ArAc (containing three bis-allylic sites) transform to the Rba(.) radicals via an intramolecular H-atom abstraction [rate constant (7.5 +/- 0.7) x 10 (4) s (-1)]. In contrast, the Rn(.) radicals of LnAc that contain only one bis-allylic site do not transform intramolecularly to the Rba(.) radicals. In the case of PmAc, which contains only one double bond, the Rba(.) radicals are not observed. The Rn(.) radicals of PmAc rapidly combine with oxygen with a rate constant of (3.8 +/- 0.4) x 10(9) M(-1) s(-1). The Rba(.) radicals of ArAc are less reactive and react with oxygen with a rate constant of (2.2 +/- 0.2) x 10 (8) M (-1) s (-1). The ArAc peroxyl radicals formed spontaneously eliminate superoxide radical anions [rate constant = (3.4 +/- 0.3) x 10 (4) M (-1) s (-1)]. The stable oxidative lesions derived from the 2',3',5'-tri- O-acetylguanosine or 2',3',5'-tri- O-acetyl-8-oxo-7,8-dihydroguanosine radicals and their subsequent reactions with ArAc peroxyl radicals were also investigated. The major products found were the 2,5-diamino-4 H

  19. Chemical and radiation-chemical radical reactions in lignocellulose materials

    NASA Astrophysics Data System (ADS)

    Kuzina, Svetlana I.; Shilova, Irina A.; Mikhailov, Al'fa I.

    2011-09-01

    Chemical and radiation-chemical radical reactions in lignocellulose materials were explored by 3-cm and 2-mm ESR spectroscopy. Background (intrinsic) singlet signals at g=2.003 from wood pulp and lignin and those arising during reaction of lignocellulose materials with acids and chlorine were attributed to radicals with conjugated CC bonds. The 2-mm ESR signal with 3D anisotropy of g-factor from o-semiquinone radical ions formed in reaction of lignin with NaOH was recorded for the first time. The singlet signals derived from cellulose γ-irradiated at 77 K and marked out during post-thermal reactions were assigned to radicals with conjugated bonds. In wetted cellulose, a triplet signal with αβH≅2.7 mT and imposed quadruplet structure (0.5-0.7 mT) from three γ-protons was detected at 300 K and attributed to С 4-radicals. The triplet signals derived from С 2- and С 3-radicals in pyranose cycles of cellulose exhibited higher values of αβH (3.0-3.2 mT) and lower thermal stability (up to 250 K). In radiolyzed cotton pulp, detected were ESR signals derived from formyl radicals formed upon rupture of the С 5С 6 bond in pyranose cycles. Heating up irradiated samples under О 2 was accompanied by formation of peroxide radicals. Photoinduced recombination of trapped electrons with С 1-radicals was found to proceed as a chain reaction with a kinetic length of about 25 units. Photolysis ( λ≥360 nm) of radiolyzed cellulose enhanced the disclosure of pyranose cycles and, as a result, the evolution of CO 2 by a factor of 2-2.5.

  20. 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

  1. Probing Complex Free-Radical Reaction Pathways of Fuel Model Compounds

    SciTech Connect

    Buchanan III, A C; Kidder, Michelle; Beste, Ariana; Britt, Phillip F

    2012-01-01

    Fossil (e.g. coal) and renewable (e.g. woody biomass) organic energy resources have received considerable attention as possible sources of liquid transportation fuels and commodity chemicals. Knowledge of the reactivity of these complex materials has been advanced through fundamental studies of organic compounds that model constituent substructures. In particular, an improved understanding of thermochemical reaction pathways involving free-radical intermediates has arisen from detailed experimental kinetic studies and, more recently, advanced computational investigations. In this presentation, we will discuss our recent investigations of the fundamental pyrolysis pathways of model compounds that represent key substructures in the lignin component of woody biomass with a focus on molecules representative of the dominant beta-O-4 aryl ether linkages. Additional mechanistic insights gleaned from DFT calculations on the kinetics of key elementary reaction steps will also be presented, as well as a few thoughts on the significant contributions of Jim Franz to this area of free radical chemistry.

  2. Tropospheric aqueous-phase free-radical chemistry: radical sources, spectra, reaction kinetics and prediction tools.

    PubMed

    Herrmann, Hartmut; Hoffmann, Dirk; Schaefer, Thomas; Bräuer, Peter; Tilgner, Andreas

    2010-12-17

    The most important radicals which need to be considered for the description of chemical conversion processes in tropospheric aqueous systems are the hydroxyl radical (OH), the nitrate radical (NO(3)) and sulphur-containing radicals such as the sulphate radical (SO(4)(-)). For each of the three radicals their generation and their properties are discussed first in the corresponding sections. The main focus herein is to summarize newly published aqueous-phase kinetic data on OH, NO(3) and SO(4)(-) radical reactions relevant for the description of multiphase tropospheric chemistry. The data compilation builds up on earlier datasets published in the literature. Since the last review in 2003 (H. Herrmann, Chem. Rev. 2003, 103, 4691-4716) more than hundred new rate constants are available from literature. In case of larger discrepancies between novel and already published rate constants the available kinetic data for these reactions are discussed and recommendations are provided when possible. As many OH kinetic data are obtained by means of the thiocyanate (SCN(-)) system in competition kinetic measurements of OH radical reactions this system is reviewed in a subchapter of this review. Available rate constants for the reaction sequence following the reaction of OH+SCN(-) are summarized. Newly published data since 2003 have been considered and averaged rate constants are calculated. Applying competition kinetics measurements usually the formation of the radical anion (SCN)(2)(-) is monitored directly by absorption measurements. Within this subchapter available absorption spectra of the (SCN)(2)(-) radical anion from the last five decades are presented. Based on these spectra an averaged (SCN)(2)(-) spectrum was calculated. In the last years different estimation methods for aqueous phase kinetic data of radical reactions have been developed and published. Such methods are often essential to estimate kinetic data which are not accessible from the literature. Approaches for

  3. 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. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. 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.

  5. Hydroxyl radical reaction with trans-resveratrol: initial carbon radical adduct formation followed by rearrangement to phenoxyl radical.

    PubMed

    Li, Dan-Dan; Han, Rui-Min; Liang, Ran; Chen, Chang-Hui; Lai, Wenzhen; Zhang, Jian-Ping; Skibsted, Leif H

    2012-06-21

    In the reaction between trans-resveratrol (resveratrol) and the hydroxyl radical, kinetic product control leads to a short-lived hydroxyl radical adduct with an absorption maximum at 420 nm and a lifetime of 0.21 ± 0.01 μs (anaerobic acetonitrile at 25 °C) as shown by laser flash photolysis using N-hydroxypyridine-2(1H)-thione (N-HPT) as a "photo-Fenton" reagent. The transient spectra of the radical adduct are in agreement with density functional theory (DFT) calculations showing an absorption maximum at 442 or 422 nm for C2 and C6 hydroxyl adducts, respectively, and showing the lowest energy for the transition state leading to the C2 adduct compared to other radical products. From this initial product, the relative long-lived 4'-phenoxyl radical of resveratrol (τ = 9.9 ± 0.9 μs) with an absorption maximum at 390 nm is formed in a process with a time constant (τ = 0.21 ± 0.01 μs) similar to the decay constant for the C2 hydroxyl adduct (or a C2/C6 hydroxyl adduct mixture) and in agreement with thermodynamics identifying this product as the most stable resveratrol radical. The hydroxyl radical adduct to phenoxyl radical conversion with concomitant water dissociation has a rate constant of 5 × 10(6) s(-1) and may occur by intramolecular hydrogen atom transfer or by stepwise proton-assisted electron transfer. Photolysis of N-HPT also leads to a thiyl radical which adds to resveratrol in a parallel reaction forming a sulfur radical adduct with a lifetime of 0.28 ± 0.04 μs and an absorption maximum at 483 nm.

  6. 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.

  7. Radical Reactions Affecting Polar Groups in Threonine Peptide Ions.

    PubMed

    Nguyen, Huong T H; Andrikopoulos, Prokopis C; Bím, Daniel; Rulíšek, Lubomír; Dang, Andy; Tureček, František

    2017-07-13

    Peptide cation-radicals containing the threonine residue undergo radical-induced dissociations upon collisional activation and photon absorption in the 210-400 nm range. Peptide cation-radicals containing a radical defect at the N-terminal residue, [(•)Ala-Thr-Ala-Arg+H](+), were generated by electron transfer dissociation (ETD) of peptide dications and characterized by UV-vis photodissociation action spectroscopy combined with time-dependent density functional theory (TD-DFT) calculations of absorption spectra, including thermal vibronic band broadening. The action spectrum of [(•)Ala-Thr-Ala-Arg+H](+) ions was indicative of the canonical structure of an N-terminally deaminated radical whereas isomeric structures differing in the position of the radical defect and amide bond geometry were excluded. This indicated that exothermic electron transfer to threonine peptide ions did not induce radical isomerizations in the fragment cation-radicals. Several isomeric structures, ion-molecule complexes, and transition states for isomerizations and dissociations were generated and analyzed by DFT and Møller-Plesset perturbational ab initio calculations to aid interpretation of the major dissociations by loss of water, hydroxyl radical, C3H6NO(•), C3H7NO, and backbone cleavages. Born-Oppenheimer molecular dynamics (BOMD) in combination with DFT gradient geometry optimizations and intrinsic reaction coordinate analysis were used to search for low-energy cation-radical conformers and transition states. BOMD was also employed to analyze the reaction trajectory for loss of water from ion-molecule complexes.

  8. 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.

  9. Roaming dynamics in radical addition-elimination reactions.

    PubMed

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

    2014-06-06

    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.

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

    PubMed

    Mutoh, Katsuya; Abe, Jiro

    2014-09-07

    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.

  11. Direct assembly of multiply oxygenated carbon chains by decarbonylative radical-radical coupling reactions.

    PubMed

    Masuda, Kengo; Nagatomo, Masanori; Inoue, Masayuki

    2017-03-01

    Pentoses and hexoses contain more than three oxygen-bearing stereocentres and are ideal starting materials for the synthesis of multiply oxygenated natural products such as sagittamide D, maitotoxin and hikizimycin. Here we demonstrate new radical-radical homocoupling reactions of sugar derivatives with minimal perturbation of their chiral centres. The radical exchange procedure using Et3B/O2 converted sugar-derived α-alkoxyacyl tellurides into α-alkoxy radicals via decarbonylation and rapidly dimerized the monomeric radicals. The robustness of this process was demonstrated by a single-step preparation of 12 stereochemically diverse dimers with 6-10 secondary hydroxy groups, including the C5-C10 stereohexad of sagittamide D and the enantiomer of the C51-C60 stereodecad of maitotoxin. Furthermore, the optimally convergent radical-radical cross-coupling reaction achieved a one-step assembly of the protected C1-C11 oxygenated carbon chain of the anthelmintic hikizimycin. These exceptionally efficient homo- and heterocoupling methods together provide a powerful strategy for the expedited total synthesis of contiguously hydroxylated natural products.

  12. Direct assembly of multiply oxygenated carbon chains by decarbonylative radical-radical coupling reactions

    NASA Astrophysics Data System (ADS)

    Masuda, Kengo; Nagatomo, Masanori; Inoue, Masayuki

    2016-10-01

    Pentoses and hexoses contain more than three oxygen-bearing stereocentres and are ideal starting materials for the synthesis of multiply oxygenated natural products such as sagittamide D, maitotoxin and hikizimycin. Here we demonstrate new radical-radical homocoupling reactions of sugar derivatives with minimal perturbation of their chiral centres. The radical exchange procedure using Et3B/O2 converted sugar-derived α-alkoxyacyl tellurides into α-alkoxy radicals via decarbonylation and rapidly dimerized the monomeric radicals. The robustness of this process was demonstrated by a single-step preparation of 12 stereochemically diverse dimers with 6-10 secondary hydroxy groups, including the C5-C10 stereohexad of sagittamide D and the enantiomer of the C51-C60 stereodecad of maitotoxin. Furthermore, the optimally convergent radical-radical cross-coupling reaction achieved a one-step assembly of the protected C1-C11 oxygenated carbon chain of the anthelmintic hikizimycin. These exceptionally efficient homo- and heterocoupling methods together provide a powerful strategy for the expedited total synthesis of contiguously hydroxylated natural products.

  13. Oxygen switch in visible-light photoredox catalysis: radical additions and cyclizations and unexpected C-C-bond cleavage reactions.

    PubMed

    Zhu, Shaoqun; Das, Arindam; Bui, Lan; Zhou, Hanjun; Curran, Dennis P; Rueping, Magnus

    2013-02-06

    Visible light photoredox catalyzed inter- and intramolecular C-H functionalization reactions of tertiary amines have been developed. Oxygen was found to act as chemical switch to trigger two different reaction pathways and to obtain two different types of products from the same starting material. In the absence of oxygen, the intermolecular addition of N,N-dimethyl-anilines to electron-deficient alkenes provided γ-amino nitriles in good to high yields. In the presence of oxygen, a radical addition/cyclization reaction occurred which resulted in the formation of tetrahydroquinoline derivatives in good yields under mild reaction conditions. The intramolecular version of the radical addition led to the unexpected formation of indole-3-carboxaldehyde derivatives. Mechanistic investigations of this reaction cascade uncovered a new photoredox catalyzed C-C bond cleavage reaction.

  14. The Reaction of Acetyl Peroxy Radical with Aldehyde: Impact on the OH Radical Model Simulation

    NASA Astrophysics Data System (ADS)

    Huang, D.; Chen, Z.

    2014-12-01

    Understanding the budget of OH (hydroxyl radical) is very important for investigating the atmospheric oxidation capacity, aerosol formation and climate change. Recent studies indicate that there may be a great gap between the modeled and measured OH concentrations in some rural forest areas. This gap may result from our incomplete knowledge about the oxidation mechanism of volatile organic compounds (VOCs). Here, we suggest that acetyl peroxy radical (CH3C(O)OO•), the OH-initiated oxidation intermediate of most VOCs, can take the H-atom from the aldehyde group to form corresponding peroxy carboxylic acids. This reaction has not been concerned in the atmosphere. The acetyl peroxy radical may share the "oxidation responsibility" of OH, and help saving OH from being consumed by aldehyde. Using a box model coupled with the isoprene-OH reaction mechanism selected from MCM v3.2, we get OH saving ratio (SROH) when we compare the modeled OH levels in the presence and absence of the reaction of acetyl peroxy radical with aldehyde. We find that SROH is not a constant but a function of OH production rate, reaction time, isoprene concentration and the ratio of aldehyde to isoprene. It is expected that CH3C(O)OO• radical, a non-OH oxidant, plays an important role in maintaining the oxidation capacity of the troposphere.

  15. Mechanistic insight into degradation of endocrine disrupting chemical by hydroxyl radical: An experimental and theoretical approach.

    PubMed

    Xiao, Ruiyang; Gao, Lingwei; Wei, Zongsu; Spinney, Richard; Luo, Shuang; Wang, Donghong; Dionysiou, Dionysios D; Tang, Chong-Jian; Yang, Weichun

    2017-09-13

    Advanced oxidation processes (AOPs) based on formation of free radicals at ambient temperature and pressure are effective for treating endocrine disrupting chemicals (EDCs) in waters. In this study, we systematically investigated the degradation kinetics of bisphenol A (BPA), a representative EDC by hydroxyl radical (OH) with a combination of experimental and theoretical approaches. The second-order rate constant (k) of BPA with OH was experimentally determined to be 7.2 ± 0.34 × 10(9) M(-1) s(-1) at pH 7.55. We also calculated the thermodynamic and kinetic behaviors for the bimolecular reactions by density functional theory (DFT) using the M05-2X method with 6-311++G** basis set and solvation model based on density (SMD). The results revealed that H-abstraction on the phenol group is the most favorable pathway for OH. The theoretical k value corrected by the Collins-Kimball approach was determined to be 1.03 × 10(10) M(-1) s(-1), which is in reasonable agreement with the experimental observation. These results are of fundamental and practical importance in understanding the chemical interactions between OH and BPA, and aid further AOPs design in treating EDCs during wastewater treatment processes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. 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. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Radical reactions in pyrolysis of triethylarsine and diethylarsine

    NASA Astrophysics Data System (ADS)

    Li, S. H.; Larsen, C. A.; Stringfellow, G. B.

    1991-06-01

    Pyrolysis of triethylarsine (TEAs) and diethylarsine (DEAsH) has been studied at atmospheric pressure in a flow tube reactor using mass spectrometry. He and D 2 were selected as the carrier gases to determine the ambient effects and to isotopically label the pyrolysis products. For some experiments, supplemental C 2H 5 radicals, produced from pyrolysis of a co-reactant azoethane ((C 2H 5) 2N 2), were added to investigate the role of C 2H 5 in the pyrolysis reactions of the ethylarsines. A significant ambient effect was observed for pyrolysis of TEAs, but not for DEAsH. The pyrolysis of DEAsH was enhanced by adding C 2H 5 radicals while the TEAs pyrolysis was nearly unaffected. DEAsD, rather than DEAsH, was a product for TEAs pyrolysis in D 2; however, the DEAsH pyrolysis produced TEAs in either ambient. This demonstrates that the β-elimination reaction is not a major step. Instead, radical reactions are more likely to dominate the pyrolysis process. Reaction mechanisms for pyrolysis of TEAs and DEAsH in both ambients have been proposed. The rate constants for the reactions involved were determined. In addition, consistency between the proposed reaction pathways and the experimental data has been examined using computer modelling.

  18. 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.

  19. Mechanistic Study of the Validity of Using Hydroxyl Radical Probes To Characterize Electrochemical Advanced Oxidation Processes.

    PubMed

    Jing, Yin; Chaplin, Brian P

    2017-02-21

    The detection of hydroxyl radicals (OH(•)) is typically accomplished by using reactive probe molecules, but prior studies have not thoroughly investigated the suitability of these probes for use in electrochemical advanced oxidation processes (EAOPs), due to the neglect of alternative reaction mechanisms. In this study, we investigated the suitability of four OH(•) probes (coumarin, p-chlorobenzoic acid, terephthalic acid, and p-benzoquinone) for use in EAOPs. Experimental results indicated that both coumarin and p-chlorobenzoic acid are oxidized via direct electron transfer reactions, while p-benzoquinone and terephthalic acid are not. Coumarin oxidation to form the OH(•) adduct product 7-hydroxycoumarin was found at anodic potentials lower than that necessary for OH(•) formation. Density functional theory (DFT) simulations found a thermodynamically favorable and non-OH(•) mediated pathway for 7-hydroxycoumarin formation, which is activationless at anodic potentials > 2.10 V/SHE. DFT simulations also provided estimates of E° values for a series of OH(•) probe compounds, which agreed with voltammetry results. Results from this study indicated that terephthalic acid is the most appropriate OH(•) probe compound for the characterization of electrochemical and catalytic systems.

  20. Bromine radical-mediated sequential radical rearrangement and addition reaction of alkylidenecyclopropanes.

    PubMed

    Kippo, Takashi; Hamaoka, Kanako; Ryu, Ilhyong

    2013-01-16

    Bromine radical-mediated cyclopropylcarbinyl-homoallyl rearrangement of alkylidenecyclopropanes was effectively accomplished by C-C bond formation with allylic bromides, which led to the syntheses of 2-bromo-1,6-dienes. A three-component coupling reaction comprising alkylidenecyclopropanes, allylic bromides, and carbon monoxide also proceeded well to give 2-bromo-1,7-dien-5-ones in good yield.

  1. Catalytic reactions of titanium alkoxides with Grignard reagents and imines: a mechanistic study.

    PubMed

    Kumar, Akshai; Samuelson, Ashoka G

    2010-08-02

    The reactivity of Grignard reagents towards imines in the presence of catalytic and stoichiometric amounts of titanium alkoxides is reported. Alkylation, reduction, and coupling of imines take place. Whereas reductive coupling is the major reaction in stoichiometric reactions, alkylation is favored in catalytic reactions. Mechanistic studies clearly indicate that intermediates involved in the two reactions are different. Catalytic reactions involve a metal-alkyl complex. This has been confirmed by reactions of deuterium-labeled substrates and different alkylating agents. Under the stoichiometric conditions, however, titanium olefin complexes are formed through reductive elimination, probably through a multinuclear intermediate.

  2. 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.

  3. 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

  4. Radicals in 5-methylcytosine induced by ionizing radiation. Electron magnetic resonance for structural and mechanistic analyses.

    PubMed

    Krivokapić, André; Ohman, Kjell Tage; Munthe, Morten; Nelson, William H; Hole, Eli O; Sagstuen, Einar

    2010-05-01

    Single crystals of 5-methylcytosine hemihydrate and 5-methylcytosine hydrochloride were X-irradiated and studied at 10 K and at higher temperatures using X- and K-band EPR, ENDOR and EIE spectroscopy. In the hemihydrate crystals, four radicals were identified at 10 K, one of them being the recently reported N1-deprotonated one-electron oxidation product (Krivokapić et al., J. Phys. Chem. A 113, 9633-9640, 2009). The other radicals were the 3alphaH radical and the C6 and C5 H-addition radicals (the 5-yl and 6-yl radicals, respectively). After irradiation at 295 K, only the 3alphaH and the 5-yl radicals were observed. In the hydrochloride crystals, at least seven different radicals were present after irradiation at 10 K. These were the N1-deprotonated one-electron oxidation product, the 3alphaH radical, three different one-electron reduction products, and the 5- and 6-yl radicals. DFT calculations were used to assist in assigning the observed couplings. The 3alphaH and 5-yl radicals were dominant after thermal annealing to room temperature. In neither crystal system did the N1-deprotonated oxidation product transform into the 3alphaH radical upon warming. The radical yield was significantly greater after irradiation at 300 K compared to that after irradiation at 10 K followed by warming to 300 K and was also considerably greater in the hydrochloride crystals than in the hemihydrate crystals.

  5. Adenosyl radical: reagent and catalyst in enzyme reactions

    PubMed Central

    Patterson, Dustin P.

    2010-01-01

    Lead in Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors; ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B12, AdoCbl) or by single-electron reduction of S-adenosylmethionine (AdoMet) complexed to an iron-sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosine’s role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations. In contrast, there has been a recent explosion in the number radical AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions. Although all the radical AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes may be active in aerobic organisms including humans. PMID:20191656

  6. Firefly bioluminescence: a mechanistic approach of luciferase catalyzed reactions.

    PubMed

    Marques, Simone M; Esteves da Silva, Joaquim C G

    2009-01-01

    Luciferase is a general term for enzymes catalyzing visible light emission by living organisms (bioluminescence). The studies carried out with Photinus pyralis (firefly) luciferase allowed the discovery of the reaction leading to light production. It can be regarded as a two-step process: the first corresponds to the reaction of luciferase's substrate, luciferin (LH(2)), with ATP-Mg(2+) generating inorganic pyrophosphate and an intermediate luciferyl-adenylate (LH(2)-AMP); the second is the oxidation and decarboxylation of LH(2)-AMP to oxyluciferin, the light emitter, producing CO(2), AMP, and photons of yellow-green light (550- 570 nm). In a dark reaction LH(2)-AMP is oxidized to dehydroluciferyl-adenylate (L-AMP). Luciferase also shows acyl-coenzyme A synthetase activity, which leads to the formation of dehydroluciferyl-coenzyme A (L-CoA), luciferyl-coenzyme A (LH(2)-CoA), and fatty acyl-CoAs. Moreover luciferase catalyzes the synthesis of dinucleoside polyphosphates from nucleosides with at least a 3'-phosphate chain plus an intact terminal pyrophosphate moiety. The LH(2) stereospecificity is a particular feature of the bioluminescent reaction where each isomer, D-LH(2) or L-LH(2), has a specific function. Practical applications of the luciferase system, either in its native form or with engineered proteins, encloses the analytical assay of metabolites like ATP and molecular biology studies with luc as a reporter gene, including the most recent and increasing field of bioimaging.

  7. 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...

  8. Hydroxyl radical reactions and the radical scavenging activity of β-carboline alkaloids.

    PubMed

    Herraiz, Tomás; Galisteo, Juan

    2015-04-01

    β-Carbolines are bioactive pyridoindole alkaloids occurring in foods, plants and the human body. Their activity as hydroxyl radical (OH) scavengers is reported here by using three different methods: deoxyribose degradation, hydroxylation of benzoate and hydroxylation of 2'-deoxyguanosine to give 8-hydroxy-2'-deoxyguanosine (8-OHdG) as assessed by RP-HPLC (MS). Fenton reactions (Fe(2+)/Fe(3+) plus H2O2) were used for OH generation, and the radical increased in the presence of ascorbic acid or 6-hydroxydopamine as pro-oxidants. β-Carbolines were scavengers of OH in the three assays and in the presence of pro-oxidants. Tetrahydro-β-carboline-3-carboxylic acids were active against the hydroxylation of 2'-deoxyguanosine. β-Carbolines reacted with hydroxyl radicals (OH) affording hydroxy-β-carbolines, whereas tetrahydro-β-carbolines gave oxidative and degradation products. On the basis of IC50 and reaction rates (k), β-carbolines (norharman and harman), and tetrahydro-β-carbolines (tetrahydro-β-carboline, 1-methyltetrahydro-β-carboline and pinoline) were good OH radical scavengers and their activity was comparable to that of the indole, melatonin, which is an effective hydroxyl radical scavenger and antioxidant.

  9. Products of reaction of OH radicals with α-pinene

    NASA Astrophysics Data System (ADS)

    Aschmann, Sara M.; Atkinson, Roger; Arey, Janet

    2002-07-01

    Products of the gas-phase reaction of α-pinene with OH radicals in the presence of NO have been investigated using gas chromatography with flame ionization detection to quantify pinonaldehyde and in situ atmospheric pressure ionization mass spectrometry in the negative ion mode to quantify selected other products as their NO2- adducts by utilizing C6-dihydroxycarbonyls and C6-hydroxynitrates formed in situ from the reaction of OH radicals with 1-hexene as an internal standard. The products quantified, and their molar formation yields, were: pinonaldehyde, 28 +/- 5% molecular weight 184 product (dihydroxycarbonyl), 19% (with an estimated uncertainty of a factor of ~2) molecular weight 200 product, 11% (with an estimated uncertainty of a factor of ~2). Together with a very approximate yield from our API-MS analyses for the formation of organic nitrates (~1%) and literature data for acetone (plus coproducts), ~65-70% of the reaction products and pathways are accounted for.

  10. 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.

  11. 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

  12. Radical oxidation reactions of the purine moiety of 2'-deoxyribonucleosides and DNA by iron-containing minerals.

    PubMed

    Berger, M; de Hazen, M; Nejjari, A; Fournier, J; Guignard, J; Pezerat, H; Cadet, J

    1993-01-01

    The radical oxidation capability of several classes of iron minerals, including biotite, hematite, magnetite, minette, nemalite, pyrite, vivianite and two chrysotiles (asbestos), was investigated by using a double experimental approach. One involved the electron spin resonance spin-trapping measurement of organic radicals obtained by the reaction of activated oxygen species, released upon incubation of the minerals in phosphate buffered solutions with formate used as the target molecule. In addition, the formation of mineral-mediated oxidation purine decomposition products, including 7,8-dihydro-8-oxo-2'-deoxyguanosine and 7,8-dihydro-8-oxo-2'-deoxyadenosine, was searched within nucleosides and DNA by using specific and sensitive HPLC electrochemical assays. Emphasis was placed on the mechanistic aspects of the radical oxidation reactions involved in the formation of the two C(8) hydroxylated purine decomposition products.

  13. 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.

  14. Theoretical modeling of hydroxyl-radical-induced lipid peroxidation reactions.

    PubMed

    Tejero, Ismael; Gonzalez-Lafont, Angels; Lluch, José M; Eriksson, Leif A

    2007-05-24

    The OH-radical-induced mechanism of lipid peroxidation, involving hydrogen abstraction followed by O2 addition, is explored using the kinetically corrected hybrid density functional MPWB1K in conjunction with the MG3S basis set and a polarized continuum model to mimic the membrane interior. Using a small nonadiene model of linoleic acid, it is found that hydrogen abstraction preferentially occurs at the mono-allylic methylene groups at the ends of the conjugated segment rather than at the central bis-allylic carbon, in disagreement with experimental data. Using a full linoleic acid, however, abstraction is correctly predicted to occur at the central carbon, giving a pentadienyl radical. The Gibbs free energy for abstraction at the central C11 is approximately 8 kcal/mol, compared to 9 kcal/mol at the end points (giving an allyl radical). Subsequent oxygen addition will occur at one of the terminal atoms of the pentadienyl radical fragment, giving a localized peroxy radical and a conjugated butadiene fragment, but is associated with rather high free energy barriers and low exergonicity at the CPCM-MPWB1K/MG3S level. The ZPE-corrected potential energy surfaces obtained without solvent effects, on the other hand, display considerably lower barriers and more exergonic reactions.

  15. Hypersensitive radical probe studies of chloroperoxidase-catalyzed hydroxylation reactions.

    PubMed

    Toy, P H; Newcomb, M; Hager, L P

    1998-07-01

    The oxidation of hypersensitive radical probes by chloroperoxidase from Caldariomyces fumago (CPO) was studied in an attempt to "time" a putative radical intermediate. Oxidation of (trans-2-phenylcyclopropyl)methane, previously studied by Zaks and Dodds [Zaks, A., and Dodds, D. R. (1995) J. Am. Chem. Soc. 115, 10419-10424] was reinvestigated. Unrearranged oxidation products were found as previously reported, and control experiments demonstrated that the cyclic alcohol from oxidation at the cyclopropylcarbinyl position, while subject to further oxidation, survives CPO oxidation as detectable species. However, in contrast to the report by Zaks and Dodds, the rearranged alcohol product expected from ring opening of a cyclopropylcarbinyl radical intermediate was shown to be unstable toward the enzyme oxidation reaction. Because of this instability, two new hypersensitive radical probes, (trans-2-phenylcyclopropyl)ethane and 2-(trans-2-phenylcyclopropyl)propane, and their potential cyclic and acyclic products from oxidation at the cyclopropylcarbinyl position were synthesized and tested. Oxidation of both of these probes at the cyclopropylcarbinyl position by CPO gave unrearranged alcohol products only, but control experiments again demonstrated that the rearranged alcohol products were unstable toward CPO oxidation conditions. From the combination of the probe and control studies, the lifetime of a putative radical intermediate must be less than 3 ps. Whereas the results are consistent with an insertion mechanism for production of alcohol product, they do not exclude a very short-lived intermediate.

  16. Students' Interpretations of Mechanistic Language in Organic Chemistry before Learning Reactions

    ERIC Educational Resources Information Center

    Galloway, Kelli R.; Stoyanovich, Carlee; Flynn, Alison B.

    2017-01-01

    Research on mechanistic thinking in organic chemistry has shown that students attribute little meaning to the electron-pushing (i.e., curved arrow) formalism. At the University of Ottawa, a new curriculum has been developed in which students are taught the electron-pushing formalism prior to instruction on specific reactions--this formalism is…

  17. Toluene combustion: reaction paths, thermochemical properties, and kinetic analysis for the methylphenyl radical + O2 reaction.

    PubMed

    da Silva, Gabriel; Chen, Chiung-Chu; Bozzelli, Joseph W

    2007-09-06

    Aromatic compounds such as toluene and xylene are major components of many fuels. Accurate kinetic mechanisms for the combustion of toluene are, however, incomplete, as they do not accurately model experimental results such as strain rates and ignition times and consistently underpredict conversion. Current kinetic mechanisms for toluene combustion neglect the reactions of the methylphenyl radicals, and we believe that this is responsible, in part, for the shortcomings of these models. We also demonstrate how methylphenyl radical formation is important in the combustion and pyrolysis of other alkyl-substituted aromatic compounds such as xylene and trimethylbenzene. We have studied the oxidation reactions of the methylphenyl radicals with O2 using computational ab initio and density functional theory methods. A detailed reaction submechanism is presented for the 2-methylphenyl radical + O2 system, with 16 intermediates and products. For each species, enthalpies of formation are calculated using the computational methods G3 and G3B3, with isodesmic work reactions used to minimize computational errors. Transition states are calculated at the G3B3 level, yielding high-pressure limit elementary rate constants as a function of temperature. For the barrierless methylphenyl + O2 and methylphenoxy + O association reactions, rate constants are determined from variational transition state theory. Multichannel, multifrequency quantum Rice-Ramsperger-Kassel (qRRK) theory, with master equation analysis for falloff, provides rate constants as a function of temperature and pressure from 800 to 2400 K and 1 x 10(-4) to 1 x 10(3) atm. Analysis of our results shows that the dominant pathways for reaction of the three isomeric methylphenyl radicals is formation of methyloxepinoxy radicals and subsequent ring opening to methyl-dioxo-hexadienyl radicals. The next most important reaction pathway involves formation of methylphenoxy radicals + O in a chain branching process. At lower

  18. 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.

  19. 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.

  20. Free radical reactions of monochloramine and hydroxylamine in aqueous solution

    NASA Astrophysics Data System (ADS)

    Johnson, Heather D.; Cooper, William J.; Mezyk, Stephen P.; Bartels, David M.

    2002-11-01

    The use of Advanced Oxidation Technologies to destroy organic contaminants in drinking water may be impacted by the presence of disinfection chemicals such as monochloramine (NH 2Cl). To allow a quantitative evaluation of the effect of NH 2Cl on the destruction of organics in water rate constants for its reaction with the hydrated electron, the hydroxyl radical and the hydrogen atom were determined in this study. The corresponding values of (2.2±0.2)×10 10, (2.8±0.2)×10 9, and (1.2±0.1)×10 9 M -1 s -1, respectively, were incorporated into a kinetic computer model whose predictions were in good agreement with experimental chloramine removal under large scale, steady-state electron-beam irradiation conditions. Rate constants were also determined for the reaction of the hydroxyl radical and hydrogen atom with the chloramine hydration product hydroxylamine to supplement established literature data. Hydroxyl radical rate constants for the basic (NH 2OH) and acidic (NH 3OH +) forms were determined as (8.5±0.4)×10 9 and ⩽5×10 7 M -1 s -1, respectively, while for hydrogen atom reaction, corresponding rate constants of (4.5±0.1)×10 7 and (3.6±1.5)×10 5 M -1 s -1 were found.

  1. 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.

  2. Reaction Mechanism of 4-Chlorobiphenyl and the NO3 Radical: An Experimental and Theoretical Study.

    PubMed

    Shi, Jin; Bi, Wenlong; Li, Shenmin; Dong, Wenbo; Chen, Jianmin

    2017-05-11

    Experiment and theoretical chemistry calculations were conducted to elucidate the mechanism of the reaction between 4-chlorobiphenyl (4-CB) and the NO3 radical. The degradation of PCBs was investigated mechanistically through transient absorption spectroscopy technology and high-accuracy theoretical calculation by using 4-CB as the model. Laser flash photolysis (LFP) experiments were performed at 355 nm. The main intermediate was analyzed through transient absorption spectroscopy and identified to be a charge transfer complex (CTC). The final products were identified through GC-MS analysis. The ground states and excited states of the reactants were calculated through density functional theory (DFT) method. The absorption bands at 400 and 700 nm show good agreement with the experimental results. The ratio of absorbance at 400 and 700 nm is 1.6, and the experimental value is 1.8. Analysis of the charge population indicated that one unit charge transfer from 4-CB to NO3. The entire reaction process was divided into two phases. In the first phase, the CTC intermediate was formed by electrostatic attraction between 4-CB and the NO3 radical. In the second phase, the most important channel of subsequent reactions is the σ-complex as an intermediate formed by N-C coupling. The final product 4-chloro,2-nitrobiphenyl was generated with the breakage of BC-H and BN-O, and benzene derivatives were formed by other channels.

  3. Rate constants for reactions of perhaloalkylperoxyl radicals with alkenes

    SciTech Connect

    Alfassi, Z.B.; Huie, R.E.; Neta, P. )

    1993-07-01

    Trichloro- and tribromomethylperoxyl radicals were produced by radiolytic reduction of CCl[sub 4] and CBr[sub 4] in various aerated solvents. Rate constants for the reactions of these radicals with unsaturated organic compounds were determined in methanol solutions by competition kinetics, using mainly chloropromazine as a reference. The rate constants were in the range k = 10[sup 4]-10[sup 7] L mol[sup [minus]1] s[sup [minus]1], and a good correlation was obtained between log k and the Taft substituent constants [sigma]*. Steric effects were also noticeable in some cases. The reactivities of the radicals were in the order CBr[sub 3]O[sub 2][center dot] < CCl[sub 3]O[sub 2][center dot] < C[sub 4]F[sub 9]O[sub 2][center dot], which is in contrast with the order observed in electron-transfer reactions. The rate constants for reaction of CCl[sub 3]O[sub 2][center dot] with 2,3-dimethyl-2-butene (DMB) and cyclohexene (CH) were studied in 12 solvents. In all cases DMB is considerably more reactive than CH, indicating that at least in the case of DMB the reaction is predominantly via addition. The rate constant for addition of CCl[sub 3]O[sub 2][center dot] to DMB varies by a factor of 7 in the different solvents. No correlation was found between these rate constants and thermodynamic or polarity parameters of the solvents, although viscosity appears to have an effect. 19 refs., 2 figs., 2 tabs.

  4. The scavenging reactions of nitrogen dioxide radical and carbonate radical by tea polyphenol derivatives: a pulse radiolysis study

    NASA Astrophysics Data System (ADS)

    Miao, Jin-Ling; Wang, Wen-Feng; Pan, Jing-Xi; Lu, Chang-Yuan; Li, Rong-Qun; Yao, Si-De

    2001-02-01

    The reactions of tea polyphenol derivatives, including epicatechin (EC) and epigallocatechin gallate (EGCG), with nitrogen dioxide radical (NO 2rad ) and carbonate radical (CO 3rad - ) have been studied in detail using time-resolved pulse radiolysis technique. In all the cases, the corresponding phenoxyl radical was formed through electron transfer reaction. From the build-up kinetics of the phenoxyl radicals and the decay kinetics of CO 3rad - radical, the reaction rate constants of EC, EGCG with NO 2rad and CO 3rad - were determined to be 9.0×10 7, 1.2×10 8 and 5.6×10 8, 6.6×10 8 dm 3 mol -1 s -1, respectively. Therefore, tea polyphenol derivatives proved to be efficient scavengers of NO 2rad and CO 3rad - radicals.

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

    DOE PAGES

    Ruggeri, Maria Pia; Selleri, Tomasso; Nova, Isabella; ...

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  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. OH radical reactions with phenylalanine in free and peptide forms.

    PubMed

    Galano, Annia; Cruz-Torres, Armando

    2008-02-21

    Density functional theory has been used to model the reaction of OH with l-phenylalanine, as a free molecule and in the Gly-Phe-Gly peptide. The influence of the environment has been investigated using water and benzene as models for polar and non-polar surroundings, in addition to gas phase calculations. Different paths of reaction have been considered, involving H abstractions and addition reactions, with global contributions to the overall reaction around 10% and 90% respectively when Phe is in its free form. The ortho-adducts (o-tyrosine) were found to be the major products of the Phe+OH reaction, for all the modeled environments and especially in water solutions. The reactivity of phenylalanine towards OH radical attacks is predicted to be higher in its peptidic form, compared to the free molecule. The peptidic environment also changes the sites' reactivity, and for the Gly-Phe-Gly+OH reaction H abstraction becomes the major path of reaction. The good agreement found between the calculated and the available experimental data supports the methodology used in this work, as well as the data reported here for the first time.

  10. 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.

  11. Mechanistic investigation of the reaction of epoxides with heterocumulenes catalysed by a bimetallic aluminium salen complex.

    PubMed

    Beattie, Christopher; North, Michael

    2014-06-23

    The bimetallic aluminium(salen) complex [(Al(salen))2O] is known to catalyse the reaction between epoxides and heterocumulenes (carbon dioxide, carbon disulfide and isocyanates) leading to five-membered ring heterocycles. Despite their apparent similarities, these three reactions have very different mechanistic features, and a kinetic study of oxazolidinone synthesis combined with previous kinetic work on cyclic carbonate and cyclic dithiocarbonate synthesis showed that all three reactions follow different rate equations. An NMR study of [Al(salen)]2O and phenylisocyanate provided evidence for an interaction between them, consistent with the rate equation data. A variable-temperature kinetics study on all three reactions showed that cyclic carbonate synthesis had a lower enthalpy of activation and a more negative entropy of activation than the other two heterocycle syntheses. The kinetic study was extended to oxazolidinone synthesis catalysed by the monometallic complex Al(salen)Cl, and this reaction was found to have a much less negative entropy of activation than any reaction catalysed by [Al(salen)]2O, a result that can be explained by the partial dissociation of an oligomeric Al(salen)Cl complex. A mechanistic rationale for all of the results is presented in terms of [Al(salen)]2O being able to function as a Lewis acid and/or a Lewis base, depending upon the susceptibility of the heterocumulene to reaction with nucleophiles.

  12. Branching ratios for the reaction of selected carbonyl-containing peroxy radicals with hydroperoxy radicals.

    PubMed

    Hasson, Alam S; Tyndall, Geoffrey S; Orlando, John J; Singh, Sukhdeep; Hernandez, Samuel Q; Campbell, Sean; Ibarra, Yesenia

    2012-06-21

    An important chemical sink for organic peroxy radicals (RO(2)) in the troposphere is reaction with hydroperoxy radicals (HO(2)). Although this reaction is typically assumed to form hydroperoxides as the major products (R1a), acetyl peroxy radicals and acetonyl peroxy radicals have been shown to undergo other reactions (R1b) and (R1c) with substantial branching ratios: RO(2) + HO(2) → ROOH + O(2) (R1a), RO(2) + HO(2) → ROH + O(3) (R1b), RO(2) + HO(2) → RO + OH + O(2) (R1c). Theoretical work suggests that reactions (R1b) and (R1c) may be a general feature of acyl peroxy and α-carbonyl peroxy radicals. In this work, branching ratios for R1a-R1c were derived for six carbonyl-containing peroxy radicals: C(2)H(5)C(O)O(2), C(3)H(7)C(O)O(2), CH(3)C(O)CH(2)O(2), CH(3)C(O)CH(O(2))CH(3), CH(2)ClCH(O(2))C(O)CH(3), and CH(2)ClC(CH(3))(O(2))CHO. Branching ratios for reactions of Cl-atoms with butanal, butanone, methacrolein, and methyl vinyl ketone were also measured as a part of this work. Product yields were determined using a combination of long path Fourier transform infrared spectroscopy, high performance liquid chromatography with fluorescence detection, gas chromatography with flame ionization detection, and gas chromatography-mass spectrometry. The following branching ratios were determined: C(2)H(5)C(O)O(2), Y(R1a) = 0.35 ± 0.1, Y(R1b) = 0.25 ± 0.1, and Y(R1c) = 0.4 ± 0.1; C(3)H(7)C(O)O(2), Y(R1a) = 0.24 ± 0.15, Y(R1b) = 0.29 ± 0.1, and Y(R1c) = 0.47 ± 0.15; CH(3)C(O)CH(2)O(2), Y(R1a) = 0.75 ± 0.13, Y(R1b) = 0, and Y(R1c) = 0.25 ± 0.13; CH(3)C(O)CH(O(2))CH(3), Y(R1a) = 0.42 ± 0.1, Y(R1b) = 0, and Y(R1c) = 0.58 ± 0.1; CH(2)ClC(CH(3))(O(2))CHO, Y(R1a) = 0.2 ± 0.2, Y(R1b) = 0, and Y(R1c) = 0.8 ± 0.2; and CH(2)ClCH(O(2))C(O)CH(3), Y(R1a) = 0.2 ± 0.1, Y(R1b) = 0, and Y(R1c) = 0.8 ± 0.2. The results give insights into possible mechanisms for cycling of OH radicals in the atmosphere.

  13. Solution-phase mechanistic study and solid-state structure of a tris(bipyridinium radical cation) inclusion complex.

    PubMed

    Fahrenbach, Albert C; Barnes, Jonathan C; Lanfranchi, Don Antoine; Li, Hao; Coskun, Ali; Gassensmith, Jeremiah J; Liu, Zhichang; Benítez, Diego; Trabolsi, Ali; Goddard, William A; Elhabiri, Mourad; Stoddart, J Fraser

    2012-02-15

    The ability of the diradical dicationic cyclobis(paraquat-p-phenylene) (CBPQT(2(•+))) ring to form inclusion complexes with 1,1'-dialkyl-4,4'-bipyridinium radical cationic (BIPY(•+)) guests has been investigated mechanistically and quantitatively. Two BIPY(•+) radical cations, methyl viologen (MV(•+)) and a dibutynyl derivative (V(•+)), were investigated as guests for the CBPQT(2(•+)) ring. Both guests form trisradical complexes, namely, CBPQT(2(•+))⊂MV(•+) and CBPQT(2(•+))⊂V(•+), respectively. The structural details of the CBPQT(2(•+))⊂MV(•+) complex, which were ascertained by single-crystal X-ray crystallography, reveal that MV(•+) is located inside the cavity of the ring in a centrosymmetric fashion: the 1:1 complexes pack in continuous radical cation stacks. A similar solid-state packing was observed in the case of CBPQT(2(•+)) by itself. Quantum mechanical calculations agree well with the superstructure revealed by X-ray crystallography for CBPQT(2(•+))⊂MV(•+) and further suggest an electronic asymmetry in the SOMO caused by radical-pairing interactions. The electronic asymmetry is maintained in solution. The thermodynamic stability of the CBPQT(2(•+))⊂MV(•+) complex was probed by both isothermal titration calorimetry (ITC) and UV/vis spectroscopy, leading to binding constants of (5.0 ± 0.6) × 10(4) M(-1) and (7.9 ± 5.5) × 10(4) M(-1), respectively. The kinetics of association and dissociation were determined by stopped-flow spectroscopy, yielding a k(f) and k(b) of (2.1 ± 0.3) × 10(6) M(-1) s(-1) and 250 ± 50 s(-1), respectively. The electrochemical mechanistic details were studied by variable scan rate cyclic voltammetry (CV), and the experimental data were compared digitally with simulated data, modeled on the proposed mechanism using the thermodynamic and kinetic parameters obtained from ITC, UV/vis, and stopped-flow spectroscopy. In particular, the electrochemical mechanism of association

  14. Cascading radical cyclization of bis-vinyl ethers: mechanistic investigation reveals a 5-exo/3-exo/retro-3-exo/5-exo pathway.

    PubMed

    O'Rourke, Natasha F; Davies, Katherine A; Wulff, Jeremy E

    2012-10-05

    We recently described an iterative synthesis of oligo-vinyl ethers, followed by a radical cascade to provide a family of hexahydro-2H-furo[3,4-b]pyrans. Our results for the radical cascade were consistent with either a direct 6-endo-trig addition of a vinyl radical onto the first vinyl ether function or an initial 5-exo-trig addition, followed by rearrangement to the more stable anomeric radical intermediate. In this report, we describe our further mechanistic studies aimed at distinguishing between these two possibilities and conclude that the 5-exo/3-exo/retro-3-exo pathway is dominant.

  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. Reaction Paths and Chemical Activation Reactions of 2-Methyl-5-Furanyl Radical with (3)O2.

    PubMed

    Hudzik, Jason M; Bozzelli, Joseph W

    2017-10-05

    Interest in high-energy substituted furans has been increasing due to their occurrence in biofuel production and their versatility in conversion to other useful products. Methylfurans are the simplest substituted furans and understanding their reaction pathways, thermochemical properties, including intermediate species stability, and chemical kinetics would aid in the study of larger furans. Furan ring C-H bonds have been shown to be extremely strong, approximately 120 kcal mol(-1), due in part to the placement of the oxygen atom and aromatic-like resonance, both within the ring. The thermochemistry and kinetics of the oxidation of 2-methyfuran radical at position 5 of the furan ring, 2-methyl-5-furanyl radical (2MF5j), is analyzed. The resulting chemically activated species, 2MF5OOj radical, has a well depth of 51 kcal mol(-1) below the 2MF5j + O2 reactants; this is 4-5 kcal mol(-1) deeper than that of phenyl and vinyl radical plus O2, with both of these reactions known to undergo chain branching. Important, low-energy reaction pathways include chain branching dissociations, intramolecular abstractions, group transfers, and radical oxygen additions. Enthalpies of formation, entropies, and heat capacities for the stable molecules, radicals, and transition-state species are analyzed using computational methods. Calculated ΔH(°)f 298 values were determined using an isodesmic work reaction from the CBS-QB3 composite method. Elementary rate parameters are from saddle point transition-state structures and compared to variational transition-state analysis for the barrierless reactions. Temperature- and pressure-dependent rate constants which are calculated using QRRK and master equation analysis is used for falloff and stabilization.

  17. An efficient quantum mechanical method for radical pair recombination reactions

    NASA Astrophysics Data System (ADS)

    Lewis, Alan M.; Fay, Thomas P.; Manolopoulos, David E.

    2016-12-01

    The standard quantum mechanical expressions for the singlet and triplet survival probabilities and product yields of a radical pair recombination reaction involve a trace over the states in a combined electronic and nuclear spin Hilbert space. If this trace is evaluated deterministically, by performing a separate time-dependent wavepacket calculation for each initial state in the Hilbert space, the computational effort scales as O (Z2log ⁡Z ) , where Z is the total number of nuclear spin states. Here we show that the trace can also be evaluated stochastically, by exploiting the properties of spin coherent states. This results in a computational effort of O (M Z log ⁡Z ) , where M is the number of Monte Carlo samples needed for convergence. Example calculations on a strongly coupled radical pair with Z >106 show that the singlet yield can be converged to graphical accuracy using just M =200 samples, resulting in a speed up by a factor of >5000 over a standard deterministic calculation. We expect that this factor will greatly facilitate future quantum mechanical simulations of a wide variety of radical pairs of interest in chemistry and biology.

  18. 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.

  19. 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.

  20. 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.

  1. Engaging unactivated alkyl, alkenyl and aryl iodides in visible-light-mediated free radical reactions.

    PubMed

    Nguyen, John D; D'Amato, Erica M; Narayanam, Jagan M R; Stephenson, Corey R J

    2012-10-01

    Radical reactions are a powerful class of chemical transformations. However, the formation of radical species to initiate these reactions has often required the use of stoichiometric amounts of toxic reagents, such as tributyltin hydride. Recently, the use of visible-light-mediated photoredox catalysis to generate radical species has become popular, but the scope of these radical precursors has been limited. Here, we describe the identification of reaction conditions under which photocatalysts such as fac-Ir(ppy)3 can be utilized to form radicals from unactivated alkyl, alkenyl and aryl iodides. The generated radicals undergo reduction via hydrogen atom abstraction or reductive cyclization. The reaction protocol utilizes only inexpensive reagents, occurs under mild reaction conditions, and shows exceptional functional group tolerance. Reaction efficiency is maintained upon scale-up and decreased catalyst loading, and the reaction time can be significantly shortened when the reaction is performed in a flow reactor.

  2. 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.

  3. 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]•+.

  4. 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.

  5. Radical Reaction Control in the AdoMet Radical Enzyme CDG Synthase (QueE): Consolidate, Destabilize, Accelerate

    PubMed Central

    2016-01-01

    Abstract Controlling radical intermediates and thus catalysing and directing complex radical reactions is a central feature of S‐adensosylmethionine (SAM)‐dependent radical enzymes. We report ab initio and DFT calculations highlighting the specific influence of ion complexation, including Mg2+, identified as a key catalytic component on radical stability and reaction control in 7‐carboxy‐7‐deazaguanine synthase (QueE). Radical stabilisation energies (RSEs) of key intermediates and radical clock‐like model systems of the enzyme‐catalysed rearrangement of 6‐carboxytetrahydropterin (CPH4), reveals a directing role of Mg2+ in destabilising both the substrate‐derived radical and corresponding side reactions, with the effect that the experimentally‐observed rearrangement becomes dominant over possible alternatives. Importantly, this is achieved with minimal disruption of the thermodynamics of the substrate itself, affording a novel mechanism for an enzyme to both maintain binding potential and accelerate the rearrangement step. Other mono and divalent ions were probed with only dicationic species achieving the necessary radical conformation to facilitate the reaction. PMID:27859789

  6. Kinetics of the C-C bond beta scission reactions in alkyl radical reaction class.

    PubMed

    Ratkiewicz, Artur; Truong, Thanh N

    2012-06-28

    Kinetics of the β-scission in alkyl radical reaction class was studied using the reaction class transition state theory (RC-TST) combined with the linear energy relationship (LER) and the barrier height grouping (BHG) approach. All necessary parameters were derived from first-principle density functional calculations for a representative set of 21 reactions. Different error analyses and comparisons with available literature data were made. Direct comparison with available experimental data indicates that the RC-TST/LER, where only reaction energy is needed, can predict rate constants for any reaction in this reaction class with excellent accuracy. Specifically for this reaction class, the RC-TST/LER method has less than 60% systematic errors on average in the predicted rate constants when compared to explicit rate calculations.

  7. Reaction Path Bifurcation in an Electrocyclic Reaction: Ring-Opening of the Cyclopropyl Radical.

    PubMed

    Kramer, Zeb C; Carpenter, Barry K; Ezra, Gregory S; Wiggins, Stephen

    2015-06-25

    Following previous work [J. Chem. Phys. 2013, 139, 154108] on a simple model of a reaction with a post-transition state valley ridge inflection point, we study the chemically important example of the electrocyclic cyclopropyl radical ring-opening reaction using direct dynamics and a reduced dimensional potential energy surface. The overall reaction requires con- or disrotation of the methylenes, but the initial stage of the ring-opening involves substantial internal rotation of only one methylene. The reaction path bifurcation is then associated with the relative sense of rotation of the second methylene. Clear deviations of reactive trajectories from the disrotatory intrinsic reaction coordinate (IRC) for the ring-opening are observed and the dynamical mechanism is discussed. Several features observed in the model system are found to be preserved in the more complex and higher dimensional ring-opening reaction. Most notable is the sensitivity of the reaction mechanism to the shape of the potential manifested as a Newtonian kinetic isotope effect upon deuterium substitution of one of the methylene hydrogens. Dependence of the product yield on frictional dissipation representing external environmental effects is also presented. The dynamics of the post-transition state cyclopropyl radical ring-opening are discussed in detail, and the use of low dimensional models as tools to analyze complicated organic reaction mechanisms is assessed in the context of this reaction.

  8. Carbenic vs. ionic mechanistic pathway in reaction of cyclohexanone with bromoform.

    PubMed

    Vitnik, Vesna D; Vitnik, Zeljko J; Juranić, Ivan O

    2012-10-01

    The extensive computation study was done to elucidate the mechanism of formation dibromoepoxide from cyclohexanone and bromoform. In this reaction, the formation of dihaloepoxide 2 is postulated as a key step that determines the distribution and stereochemistry of products. Two mechanistic paths of reaction were investigated: the addition of dibromocarbene to carbonyl group of ketone, and the addition of tribromomethyl carbanion to the same (C=O) group. The mechanisms for the addition reactions of dibromocarbenes and tribromomethyl carbanions with cyclohexanone have been investigated using ab initio HF/6-311++G** and MP2/6-311+G* level of theory. Solvent effects on these reactions have been explored by calculations which included a continuum polarizable conductor model (CPCM) for the solvent (H₂O). The calculations showed that both mechanisms are possible and are exothermic, but have markedly different activation energies.

  9. A radical process towards the development of transition-metal-free aromatic carbon-carbon bond-forming reactions.

    PubMed

    Chan, Tek Long; Wu, Yinuo; Choy, Pui Ying; Kwong, Fuk Yee

    2013-11-18

    Transition-metal-free cross-coupling reactions have been a hot topic in recent years. With the aid of a radical initiator, a number of unactivated arene C-H bonds can be directly arylated/functionalized by using aryl halides through homolytic aromatic substitution. Commercially available or specially designed promoters (e.g. diamines, diols, and amino alcohols) have been used to make this synthetically attractive method viable. This protocol offers an inexpensive, yet efficient route to aromatic C-C bond formations since transition metal catalysts and impurities can be avoided by using this reaction system. In this article, we focus on the significance of the reaction conditions (e.g. bases and promoters), which allow this type of reaction to proceed smoothly. Substrate scope limitations and challenges, as well as mechanistic discussion are also included.

  10. Skin sensitization: reaction mechanistic applicability domains for structure-activity relationships.

    PubMed

    Aptula, Aynur O; Patlewicz, Grace; Roberts, David W

    2005-09-01

    The prediction of skin sensitization potential with minimum animal testing is currently of great importance in light of forthcoming legislation. A number of structure-activity relationships for skin sensitization have been published over the years, but their applicability has often been limited to structural classes. The concept of an applicability domain for a quantitative structure-activity relationship [(Q)SAR] is increasingly being viewed as key for the predictive application of (Q)SARs. This is particularly the case for skin sensitization if more widely applicable SARs are to be developed. In this paper, we analyze a recently published chemical data set for skin sensitization, apply reaction mechanistic criteria to domain classification, and evaluate the structure-activity trends observed within each of these mechanistic domains.

  11. Maclurin protects against hydroxyl radical-induced damages to mesenchymal stem cells: antioxidant evaluation and mechanistic insight.

    PubMed

    Li, Xican; Gao, Yaoxiang; Li, Fei; Liang, Aifeng; Xu, Zhiming; Bai, Ye; Mai, Wenqiong; Han, Lu; Chen, Dongfeng

    2014-08-05

    Maclurin, an exceptional member of phytophenol family, was found to effectively protect against mesenchymal stem cells (MSCs) oxidative damage induced by hydroxyl radical (OH) at 62.1-310.5 μM. Antioxidant assays indicated that maclurin could efficiently protect DNA from OH-induced damage at 114.6-382.2 μM, and scavenge OH, DPPH (1,1-diphenyl-2-picrylhydrazyl radical), ABTS(+) (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid radical), and bind Cu(2+) (IC50 values were respectively 122.87 ± 10.14, 10.15 ± 0.85, 0.97 ± 0.07, and 133.95 ± 11.92 μM). HPLC-DAD and HPLC-ESI-MS/MS analyses of the end-product of maclurin reaction with DPPH clearly suggested that maclurin (m/z = 261.12 [M-H](-)) donated two hydrogen atoms to DPPH (m/z = 394.06 [M](+)) to form ortho-benzoquinone moiety (λmax = 364 nm; m/z = 259.06 [M-H](-), loss of m/z = 28) and DPPH2 molecule (m/z = 395.03, 396.01), via hydrogen atom transfer (HAT) or sequential electron (e) proton transfer (SEPT), not radical adduct formation (RAF) mechanisms. Therefore, we concluded that: (i) maclurin can effectively protect against OH-induced damages to DNA and MSCs, thereby it may have a therapeutic potential in prevention of many diseases or MSCs transplantation; (ii) a possible mechanism for maclurin to protect against oxidative damages is OH radical-scavenging; (iii) maclurin scavenges OH possibly through metal-chelating, and direct radical-scavenging which is mainly via HAT or SEPT mechanisms; and (iv) the protective and antioxidant effects of maclurin can be primarily attributed to ortho-dihydroxyl groups, and ultimately to the relative stability of the ortho-benzoquinone form.

  12. Heterogeneous Reaction of HO2 Radical with Dicarboxylic Acid Particles

    NASA Astrophysics Data System (ADS)

    Taketani, F.; Kanaya, Y.

    2010-12-01

    HOx(OH+ HO2) radical plays a central role in the tropospheric chemistry. Recently, the heterogeneous loss of HO2 by aerosol particles is a potentially important HOx sink in the troposphere suggested from observation study. However, there have been few studies for loss of HO2 by aerosols. In this study, we measured the HO2 uptake coefficients for four dicarboxylic acids (succinic acid, glutaric acid, adipic acid, and pimelic acid) aerosol particles under ambient conditions (760Torr and 296K) using an aerosol flow tube(AFT) coupled with a chemical conversion /laser-induced fluorescence(CC/LIF) technique. The CC/LIF technique enabled experiments to be performed at almost the same HO2 radical concentration as that in the atmosphere(-10^8 molecules/cm^3). In this system, the effect of the self-reaction of HO2 in the gas phase can be neglected. HO2 radicals were injected into the AFT through a vertically movable Pyrex tube. Injector position dependent profiles of LIF intensity were measured as a function of aerosol concentration at 30% and 70% of relative humilities (RH). Determined HO2 uptake coefficients by succinic acid, glutaric acid, adipic acid, and pimelic acid aerosol particles at 30% RH were 0.05 +/- 0.02, 0.07 +/- 0.03, 0.02 +/- 0.01, and 0.06 +/- 0.03, respectively, while the uptake coefficients by those particles at 70% RH were 0.13 +/- 0.05, 0.13 +/- 0.03, 0.06 +/- 0.01, and 0.11 +/- 0.03, respectively. These results suggest that compositions and relative humidity are significant to the HO2 uptake. We will discuss the potential HO2 loss processes.

  13. 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.

  14. ARTICLE Mechanistic Investigation on the Reaction of O- with CH3CN Using Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Yu, Feng; Wu, Li-xia; Zhou, Xiao-guo; Liu, Shi-lin

    2010-12-01

    The potential energy profile of the reaction between the atomic oxygen radical anion and acetonitrile has been mapped at the G3MP2B3 level of theory. Geometries of the reactants, products, intermediate complexes, and transition states involved in this reaction have been optimized at the (U)B3LYP/6-31+G(d,p) level, and then their accurate relative energies have been improved using the G3MP2B3 method. The potential energy profile is confirmed via intrinsic reaction coordinate calculations of transition states. Four possible production channels are examined respectively, as H+ transfer, H-atom transfer, H2+ transfer, and bi-molecular nucleophilic substitution (SN2) reaction pathways. Based on present calculations, the H2+ transfer reaction is major among these four channels, which agrees with previous experimental conclusions.

  15. E.s.r. of spin-trapped radicals in aqueous solutions of peptides. Reactions of the hydroxyl radical.

    PubMed

    Joshi, A; Rustgi, S; Moss, H; Riesz, P

    1978-03-01

    The reactions of hydroxyl radicals with 30 dipeptides and several larger peptides were studied in aqueous solutions. The OH radicals were generated by U.V. photolysis of H2O2. The short-lived peptide radicals were spin-trapped using t-nitrosobutane and identified by e.s.r. For dipeptides containing the amino terminal residues glycine, alanine and phenylalanine, abstraction of the hydrogen from the carbon adjacent to the peptide nitrogen was the major process leading to the spin-adducts. Such radicals will be referred to as backbone radicals. Dipeptides with a carbonyl terminal serine residue and also glycylglutamic acid form both backbone and side-chain radicals, with the latter being formed in larger quantities. For dipeptides, side-chain radicals were detected on either the carboxyl or amino terminal residues of both. The effect of pD on the e.s.r. sectrum of the spin-adducts of glycylglycine was studied and the pK of the carboxyl group of this radical was determined to be 2.5. For (Ala)3 and (Ala)n, with an average value of n = 1800, backbone and minor side-chain radicals were observed. For ribonucleases-S-peptide, containing 20 amino acid residues, both backbone and side-chain radicals were detected.

  16. 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

  17. Thermochemistry, reaction paths, and kinetics on the tert-isooctane radical reaction with O2.

    PubMed

    Snitsiriwat, Suarwee; Bozzelli, Joseph W

    2014-07-03

    Thermochemical properties of tert-isooctane hydroperoxide and its radicals are determined by computational chemistry. Enthalpies are determined using isodesmic reactions with B3LYP density function and CBS QB3 methods. Application of group additivity with comparison to calculated values is illustrated. Entropy and heat capacities are determined using geometric parameters and frequencies from the B3LYP/6-31G(d,p) calculations for the lowest energy conformer. Internal rotor potentials are determined for the tert-isooctane hydroperoxide and its radicals in order to identify isomer energies. Recommended values derived from the most stable conformers of tert-isooctane hydroperoxide of are -77.85 ± 0.44 kcal mol(-1). Isooctane is a highly branched molecule, and its structure has a significant effect on its thermochemistry and reaction barriers. Intramolecular interactions are shown to have a significant effect on the enthalpy of the isooctane parent and its radicals on peroxy/peroxide systems, the R• + O2 well depths and unimolecular reaction barriers. Bond dissociation energies and well depths, for tert-isooctane hydroperoxide → R• + O2 are 33.5 kcal mol(-1) compared to values of ∼38 to 40 kcal mol(-1) for the smaller tert-butyl-O2 → R• + O2. Transition states and kinetic parameters for intramolecular hydrogen atom transfer and molecular elimination channels are characterized to evaluate reaction paths and kinetics. Kinetic parameters are determined versus pressure and temperature for the chemically activated formation and unimolecular dissociation of the peroxide adducts. Multifrequency quantum RRK (QRRK) analysis is used for k(E) with master equation analysis for falloff. The major reaction paths at 1000 K are formation of isooctane plus HO2 followed by cyclic ether plus OH. Stabilization of the tert-isooctane hydroperoxy radical becomes important at lower temperatures.

  18. 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.

  19. Further insights into the reaction of melatonin with hydroxyl radical.

    PubMed

    Horstman, Joseph A; Wrona, Monika Z; Dryhurst, Glenn

    2002-10-01

    Recent interest has focused on the use of exogenous melatonin as an antioxidant, particularly to scavenge the highly cytotoxic hydroxyl radical (HO(z.rad;)) which may be generated in many pathological conditions. However, in vitro and in vivo studies aimed at assessing the antioxidant properties of melatonin have produced conflicting results. While it is known that HO(z.rad;) reacts with melatonin at a diffusion limited rate, very little is known about the products of this reaction. In this investigation it is shown that incubation of melatonin with a Fenton-type HO(z.rad;)-generating system at pH 7.4 forms a complex mixture of primary products. These include 2-hydroxymelatonin, which was isolated as its more stable oxindole tautomer, 4- and 6-hydroxymelatonin, N-acetyl-N(2)-formyl-5-methoxykynurenine and 7,7(')-bi-(5-methoxy-N-acetyltryptamine-4-one). Reaction pathways that might lead to these products are described. The differing biological effects of these products, while currently incompletely understood, might account for the controversy concerning the antioxidant properties of melatonin.

  20. Reaction Profiles and Molecular Dynamics Simulations of Cyanide Radical Reactions Relevant to Titan's Atmosphere

    NASA Astrophysics Data System (ADS)

    Trinidad Pérez-Rivera, Danilo; Romani, Paul N.; Lopez-Encarnacion, Juan Manuel

    2016-10-01

    Titan's atmosphere is arguably the atmosphere of greatest interest that we have an abundance of data for from both ground based and spacecraft observations. As we have learned more about Titan's atmospheric composition, the presence of pre-biotic molecules in its atmosphere has generated more and more fascination about the photochemical process and pathways it its atmosphere. Our computational laboratory has been extensively working throughout the past year characterizing nitrile synthesis reactions, making significant progress on the energetics and dynamics of the reactions of .CN with the hydrocarbons acetylene (C2H2), propylene (CH3CCH), and benzene (C6H6), developing a clear picture of the mechanistic aspects through which these three reactions proceed. Specifically, first principles calculations of the reaction profiles and molecular dynamics studies for gas-phase reactions of .CN and C2H2, .CN and CH3CCH, and .CN and C6H6 have been carried out. A very accurate determination of potential energy surfaces of these reactions will allow us to compute the reaction rates which are indispensable for photochemical modeling of Titan's atmosphere.The work at University of Puerto Rico at Cayey was supported by Puerto Rico NASA EPSCoR IDEAS-ER program (2015-2016) and DTPR was sponsored by the Puerto Rico NASA Space Grant Consortium Fellowship. *E-mail: juan.lopez15@upr.edu

  1. The Prowess of Photogenerated Amine Radical Cations in Cascade Reactions: From Carbocycles to Heterocycles.

    PubMed

    Morris, Scott A; Wang, Jiang; Zheng, Nan

    2016-09-20

    Cascade reactions represent a class of ideal organic reactions because they empower efficiency, elegance, and novelty. However, development of cascade reactions remains a daunting task for synthetic chemists. Radicals are known to be well suited for cascade reactions. Compared with widely used carbon-based radicals, nitrogen-based radicals, such as neutral aminyl radicals and protonated aminyl radicals (amine radical cations), are underutilized, although they are behind some notable synthetic methods such as the Hofmann-Löffler-Freytag reaction. The constraint on their usage is generally attributed to the limited number of available stable precursors. Since amine radical cations offer increased reactivity and selectivity in chemical transformations compared with neutral aminyl radicals, their generation is of utmost importance. Recently, a surge of reports has been revealed using visible light photoredox catalysis. It has been demonstrated that amines can act as an electron donor in a reductive quenching cycle while the amine itself is oxidized to the amine radical cation. Although a number of methods exist to generate amine radical cations, the photochemical formation of these species offers many practical advantages. In this Account, we discuss our journey to the development of annulation reactions with various π-bonds and electrophilic addition reactions to alkenes using photogenerated amine radical cations. Various carbocycles and heterocycles are produced by these reactions. In our annulation work, we first show that single electron photooxidation of cyclopropylanilines to the amine radical cations triggers ring opening of the strained carbocycle, producing distonic radical cations. These odd-electron species are shown to react with alkenes and alkynes to yield the corresponding cyclopentanes and cyclopentenes in an overall redox neutral process. Further development of this annulation reaction allows us to achieve the [4 + 2] annulation of cyclobutylanilines

  2. Free radical reactions of isoxazole and pyrazole derivatives of hispolon: kinetics correlated with molecular descriptors.

    PubMed

    Shaikh, Shaukat Ali M; Barik, Atanu; Singh, Beena G; Modukuri, Ramani V; Balaji, Neduri V; Subbaraju, Gottumukkala V; Naik, Devidas B; Priyadarsini, K Indira

    2016-12-01

    Hispolon (HS), a natural polyphenol found in medicinal mushrooms, and its isoxazole (HI) and pyrazole (HP) derivatives have been examined for free radical reactions and in vitro antioxidant activity. Reaction of these compounds with one-electron oxidant, azide radicals ([Formula: see text]) and trichloromethyl peroxyl radicals ([Formula: see text]), model peroxyl radicals, studied by nanosecond pulse radiolysis technique, indicated formation of phenoxyl radicals absorbing at 420 nm with half life of few hundred microseconds (μs). The formation of phenoxyl radicals confirmed that the phenolic OH is the active centre for free radical reactions. Rate constant for the reaction of these radicals with these compounds were in the order kHI ≅ kHP > kHS. Further the compounds were examined for their ability to inhibit lipid peroxidation in model membranes and also for the scavenging of 2,2'-diphenyl-1-picrylhydrazyl (DPPH) radical and superoxide ([Formula: see text]) radicals. The results suggested that HP and HI are less efficient than HS towards these radical reactions. Quantum chemical calculations were performed on these compounds to understand the mechanism of reaction with different radicals. Lower values of adiabatic ionization potential (AIP) and elevated highest occupied molecular orbital (HOMO) for HI and HP compared with HS controlled their activity towards [Formula: see text] and [Formula: see text] radicals, whereas the contribution of overall anion concentration was responsible for higher activity of HS for DPPH, [Formula: see text], and lipid peroxyl radical. The results confirm the role of different structural moieties on the antioxidant activity of hispolon derivatives.

  3. Electron spin resonance spectroscopic studies of radical cation reactions

    SciTech Connect

    Dai, S.

    1990-01-01

    A spin Hamiltonian suitable for theoretical analyses of ESR spectra is derived using the general effective Hamiltonian theory in the usual Schroedinger 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 are derived using 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 synsesquinorbornene oxide have been characterized by ESR spectroscopy in the CFCl[sub 3] matrix at low temperature. 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 the 3-iminiopropyl distonic species(3-iminium-1-propyl radical). The nucleophilic endocylization 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-hexdiyne have resulted in characterization the 1,5-hexadiyne radical cation isomerizing to the 1,2,4,5-hexatetraene radical cation. The symmetric (C[sub 2v]) bicyclo[3.3.0]-octa-2,6-diene-4,8-diyl(a bridged 1,4-bishomobenzene species) radical cation is produced by the radiolytic oxidation of semibullvalene in Freon matrices. The ring-opening 3,4-dimethylenecyclobutene radical cation to 1,2,4,5-hexatetraene radical cation was observed in the photolysis of 3,4-dimethylenecyclobutene radical cation. The cyclooctatetraene radical cation generated by radiolytic oxidation photoisomerizes to bicyclo[3.3.0]octa-2,6-diene-4,8-diyl radical cation.

  4. Mechanistic and comparative studies of melatonin and classic antioxidants in terms of their interactions with the ABTS cation radical.

    PubMed

    Tan, Dun-xian; Hardeland, Rüdiger; Manchester, Lucien C; Poeggeler, Burkhard; Lopez-Burillo, Silvia; Mayo, Juan C; Sainz, Rosa M; Reiter, Russel J

    2003-05-01

    Melatonin and classic antioxidants possess the capacity to scavenge ABTSb+ with IC50s of 4, 11, 15.5, 15.5, 17 and 21 microm for melatonin, glutathione, vitamin C, trolox, NADH and NADPH, respectively. In terms of scavenging ABTSb+, melatonin exhibits a different profile than that of the classic antioxidants. Classic antioxidants scavenge one or less ABTSb+, while each melatonin molecule can scavenge more than one ABTSb+, probably with a maximum of four. Classic antioxidants do not synergize when combined in terms of scavenging ABTSb+. However, a synergistic action is observed when melatonin is combined with any of the classic antioxidants. Cyclic voltammetry indicates that melatonin donates an electron at the potential of 715 mV. The scavenging mechanism of melatonin on ABTSb+ may involve multiple-electron donations via intermediates through a stepwise process. Intermediates including the melatoninyl cation radical, the melatoninyl neutral radical and cyclic 3-hydroxymelatonin (cyclic 3-OHM) and N1-acetyl-N2-formyl-5-methoxykynuramine (AFMK) seem to participate in these reactions. More interestingly, the pH of the solution dramatically modifies the ABTSb+ scavenging capacity of melatonin while pH changes have no measurable influence on the scavenging activity of classic antioxidants. An acidic pH markedly reduces the ABTSb+ scavenging capacity of melatonin while an increased pH promotes the interaction of melatonin and ABTSb+. The major melatonin metabolites that develop when melatonin interacts with ABTSb+ are cyclic 3-OHM and AFMK. Cyclic 3-OHM is the intermediate between melatonin and AFMK, and cyclic 3-OHM also has the ability to scavenge ABTSb+. Melatonin and the metabolites which are generated via the interaction of melatonin with ABTSb+, i.e. the melatoninyl cation radical, melatoninyl neutral radical and cyclic 3-OHM, all scavenge ABTSb+. This unique cascade action of melatonin, in terms of scavenging, increases its efficiency to neutralized ABTSb+; this

  5. Reaction of iodine atoms with submicrometer squalane and squalene droplets: mechanistic insights into heterogeneous reactions.

    PubMed

    Popolan-Vaida, Denisia M; Wilson, Kevin R; Leone, Stephen R

    2014-11-13

    The gas-phase reaction of iodine atoms with hydrocarbon molecules is energetically unfavorable, and there is no direct evidence for iodinated product formation by either H abstraction or I addition reactions at ambient temperature. Here we consider the possible heterogeneous reaction of I atoms with submicrometer droplets composed of a saturated alkane, squalane (Sq), and an unsaturated alkene, squalene (Sqe). The investigations are performed in an atmospheric pressure photochemical flow tube reactor in conjunction with a vacuum ultraviolet photoionization aerosol mass spectrometer and a scanning mobility particle sizer. Squalane, a branched alkane, is unreactive toward I atoms within the signal-to-noise, and an upper limit of the effective reactive uptake coefficient is estimated to be γI(Sq) ≤ 8.58 × 10(–7). In contrast, the reaction of I atoms with unsaturated submicrometer squalene droplets results in observable iodinated squalene products. The effective reactive uptake coefficient of I atom with squalene particles is determined to be γI(Sqe) = (1.20 ± 0.52) × 10(–4) at an average I concentration of 1.5 × 10(14) molecules·cm(–3).

  6. The Hydroxyl Radical Reaction Rate Constant and Products of Dimethyl Succinate

    DTIC Science & Technology

    2008-03-01

    AFRL-RX-TY-TR-2008-4522 THE HYDROXYL RADICAL REACTION RATE CONSTANT AND PRODUCTS OF DIMETHYL SUCCINATE Sheryl E. Calidonna and...the gas-phase hydroxyl radical reaction with dimethyl succinate. Additional reports and publications resulting from this work unit are not described...herein but are listed below for reference. Baxley, J.Steven and J.R. Wells, “The Hydroxyl Radical Rate Constant and Atmospheric Transforamtion

  7. Catalase reaction by myoglobin mutants and native catalase: mechanistic investigation by kinetic isotope effect.

    PubMed

    Kato, Shigeru; Ueno, Takafumi; Fukuzumi, Shunichi; Watanabe, Yoshihito

    2004-12-10

    The catalase reaction has been studied in detail by using myoglobin (Mb) mutants. Compound I of Mb mutants (Mb-I), a ferryl species (Fe(IV)=O) paired with a porphyrin radical cation, is readily prepared by the reaction with a nearly stoichiometric amount of m-chloroperbenzoic acid. Upon the addition of H2O2 to an Mb-I solution, Mb-I is reduced back to the ferric state without forming any intermediates. This indicates that Mb-I is capable of performing two-electron oxidation of H2O2 (catalatic reaction). Gas chromatography-mass spectroscopy analysis of the evolved O2 from a 50:50 mixture of H2(18)O2/H2(16)O2 solution containing H64D or F43H/H64L Mb showed the formation of 18O2 (m/e = 36) and 16O2 (m/e = 32) but not 16O18O (m/e = 34). This implies that O2 is formed by two-electron oxidation of H2O2 without breaking the O-O bond. Deuterium isotope effects on the catalatic reactions of Mb mutants and catalase suggest that the catalatic reactions of Micrococcus lysodeikticus catalase and F43H/H64L Mb proceed via an ionic mechanism with a small isotope effect of less than 4.0, since the distal histidine residue is located at a proper position to act as a general acid-base catalyst for the ionic reaction. In contrast, other Mb mutants such as H64X (X is Ala, Ser, and Asp) and L29H/H64L Mb oxidize H2O2 via a radical mechanism in which a hydrogen atom is abstracted by Mb-I with a large isotope effect in a range of 10-29, due to a lack of the general acid-base catalyst.

  8. 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.

  9. Study of elementary reactions and energy transfer processes involving the NH and CN free radicals

    NASA Astrophysics Data System (ADS)

    Dagdigian, Paul J.; Alexander, Millard H.

    1991-06-01

    Collaborative theoretical and experimental studies of a variety of elementary chemical reactions and collisional energy transfer processes involving small molecular free radicals, with particular emphasis on the NH and CN molecules, have been carried out. Specific topics studied include: molecular free radicals, collisional energy transfer, chemical reactions, excited states, and molecular decomposition.

  10. 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.

  11. Rate coefficients for the reaction of formaldehyde with HO2 radicals from fluorescence spectroscopy of HOCH2OO radicals

    NASA Astrophysics Data System (ADS)

    Bunkan, Arne; Amédro, Damien; Crowley, John

    2017-04-01

    The reaction of formaldehyde with HO2 radicals constitutes a minor, but significant sink of formaldehyde in the troposphere as well as a possible interference in other formaldehyde photooxidation experiments. HCHO + HO2 ⇌ HOCH2OO (1) Due to the difficulty of simultaneously monitoring the reactant and product concentrations while preventing interfering secondary chemistry, there is a considerable uncertainty in the literature values for the reaction rate coefficients. We have used two photon, excited fragment spectroscopy (TPEFS), originally developed for monitoring HNO3 formation in kinetic experiments, to monitor the formation of the HOCH2OO radical. Dispersed and single wavelength fluorescence emission following the 193 nm photolysis of HOCH2OO have been recorded and analysed. Characterisation of the method is presented along with rate coefficients for the reaction of HCHO with HO2 radicals at tropospheric temperatures.

  12. Hydrogen atom abstraction selectivity in the reactions of alkylamines with the benzyloxyl and cumyloxyl radicals. The importance of structure and of substrate radical hydrogen bonding.

    PubMed

    Salamone, Michela; DiLabio, Gino A; Bietti, Massimo

    2011-10-19

    A time-resolved kinetic study on the hydrogen abstraction reactions from a series of primary and secondary amines by the cumyloxyl (CumO(•)) and benzyloxyl (BnO(•)) radicals was carried out. The results were compared with those obtained previously for the corresponding reactions with tertiary amines. Very different hydrogen abstraction rate constants (k(H)) and intermolecular selectivities were observed for the reactions of the two radicals. With CumO(•), k(H) was observed to decrease on going from the tertiary to the secondary and primary amines. The lowest k(H) values were measured for the reactions with 2,2,6,6-tetramethylpiperidine (TMP) and tert-octylamine (TOA), substrates that can only undergo N-H abstraction. The opposite behavior was observed for the reactions of BnO(•), where the k(H) values increased in the order tertiary < secondary < primary. The k(H) values for the reactions of BnO(•) were in all cases significantly higher than those measured for the corresponding reactions of CumO(•), and no significant difference in reactivity was observed between structurally related substrates that could undergo exclusive α-C-H and N-H abstraction. This different behavior is evidenced by the k(H)(BnO(•))/k(H)(CumO(•)) ratios that range from 55-85 and 267-673 for secondary and primary alkylamines up to 1182 and 3388 for TMP and TOA. The reactions of CumO(•) were described in all cases as direct hydrogen atom abstractions. With BnO(•) the results were interpreted in terms of the rate-determining formation of a hydrogen-bonded prereaction complex between the radical α-C-H and the amine lone pair wherein hydrogen abstraction occurs. Steric effects and amine HBA ability play a major role, whereas the strength of the substrate α-C-H and N-H bonds involved appears to be relatively unimportant. The implications of these different mechanistic pictures are discussed.

  13. Photodegradable, Photoadaptable Hydrogels via Radical-Mediated Disulfide Fragmentation Reaction

    PubMed Central

    2011-01-01

    Various techniques have been adopted to impart a biological responsiveness to synthetic hydrogels for the delivery of therapeutic agents as well as the study and manipulation of biological processes and tissue development. Such techniques and materials include polyelectrolyte gels that swell and deswell with changes in pH, thermosensitive gels that contract at physiological temperatures, and peptide cross-linked hydrogels that degrade upon peptidolysis by cell-secreted enzymes. Herein we report a unique approach to photochemically deform and degrade disulfide cross-linked hydrogels, mitigating the challenges of light attenuation and low quantum yield, permitting the degradation of hydrogels up to 2 mm thick within 120 s at low light intensities (10 mW/cm2 at 365 nm). Hydrogels were formed by the oxidation of thiol-functionalized 4-armed poly(ethylene glycol) macromolecules. These disulfide cross-linked hydrogels were then swollen in a lithium acylphosphinate photoinitiator solution. Upon exposure to light, photogenerated radicals initiate multiple fragmentation and disulfide exchange reactions, permitting and promoting photodeformation, photowelding, and photodegradation. This novel, but simple, approach to generate photoadaptable hydrogels portends the study of cellular response to mechanically and topographically dynamic substrates as well as novel encapsulations by the welding of solid substrates. The principles and techniques described herein hold implications for more than hydrogel materials but also for photoadaptable polymers more generally. PMID:21512614

  14. Unusually high reactivity of apolipoprotein B-100 among proteins to radical reactions induced in human plasma.

    PubMed

    Hashimoto, R; Narita, S; Yamada, Y; Tanaka, K; Kojo, S

    2000-01-17

    Relative reactivities of proteins to radical reactions caused in human plasma were studied for the first time utilizing an immunoblotting assay. When radical reactions were caused by Cu(2+), apolipoprotein B-100 (apoB) underwent extensive fragmentation concurrently with the decrease in alpha-tocopherol, while human serum albumin (HSA) and transferrin (TF) were not decreased at all. When radical reactions were initiated by Cu(2+) with hydrogen peroxide or 2,2'-azobis(2-amidinopropane)dihydrochloride (AAPH), alpha-tocopherol and apoB were also decreased steadily but HSA and TF were not decreased. These observations indicate that apoB is extremely reactive, even comparable to alpha-tocopherol, towards radical reactions. These results also suggest that the radical reaction of apoB is a possible process in vivo and it is involved in atherogenesis along with low density lipoprotein lipid peroxidation, which has been studied extensively.

  15. Quantum Zeno effect explains magnetic-sensitive radical-ion-pair reactions.

    PubMed

    Kominis, I K

    2009-11-01

    Chemical reactions involving radical-ion pairs are ubiquitous in biology, since not only are they at the basis of the photosynthetic reaction chain, but are also assumed to underlie the biochemical magnetic compass used by avian species for navigation. Recent experiments with magnetic-sensitive radical-ion-pair reactions provided strong evidence for the radical-ion-pair magnetoreception mechanism, verifying the expected magnetic sensitivities and chemical product yield changes. It is here shown that the theoretical description of radical-ion-pair reactions used since the 70s cannot explain the observed data, because it is based on phenomenological equations masking quantum coherence effects. The fundamental density-matrix equation derived here from basic quantum measurement theory considerations naturally incorporates the quantum Zeno effect and readily explains recent experimental observations on low- and high magnetic-field radical-ion-pair reactions.

  16. Quantum Zeno effect explains magnetic-sensitive radical-ion-pair reactions

    NASA Astrophysics Data System (ADS)

    Kominis, I. K.

    2009-11-01

    Chemical reactions involving radical-ion pairs are ubiquitous in biology, since not only are they at the basis of the photosynthetic reaction chain, but are also assumed to underlie the biochemical magnetic compass used by avian species for navigation. Recent experiments with magnetic-sensitive radical-ion-pair reactions provided strong evidence for the radical-ion-pair magnetoreception mechanism, verifying the expected magnetic sensitivities and chemical product yield changes. It is here shown that the theoretical description of radical-ion-pair reactions used since the 70s cannot explain the observed data, because it is based on phenomenological equations masking quantum coherence effects. The fundamental density-matrix equation derived here from basic quantum measurement theory considerations naturally incorporates the quantum Zeno effect and readily explains recent experimental observations on low- and high magnetic-field radical-ion-pair reactions.

  17. Mechanistic insights into a BINOL-derived phosphoric acid-catalyzed asymmetric Pictet-Spengler reaction.

    PubMed

    Overvoorde, Lois M; Grayson, Matthew N; Luo, Yi; Goodman, Jonathan M

    2015-03-06

    The reaction of tryptamine and (2-oxocyclohexyl)acetic acid can be catalyzed by 3,3'-bis(triphenylsilyl)-1,1'-bi-2-naphthol phosphoric acid to give an asymmetric β-carboline. This reaction was first studied by Holloway et al. ( Org. Lett. 2010 , 12 , 4720 - 4723 ), but their mechanistic work did not explain the high stereoselectivity achieved. This study uses density functional theory and hybrid quantum mechanics/molecular mechanics calculations to investigate this reaction and provide a model to explain its outcome. The step leading to diastereo- and enantioselectivity is an asymmetric Pictet-Spengler reaction involving an N-acyliminium ion bound to the catalyst in a bidentate fashion. This interaction occurs via hydrogen bonds between the two terminal oxygen atoms of the catalyst phosphate group and the hydrogen atoms at N and C2 of the substrate indole group. These bonds hold the transition structure rigidly and thus allow the catalyst triphenylsilyl groups to influence the enantioselectivity.

  18. 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.

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

    PubMed

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

    2016-08-05

    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.

  20. Estimating biofilm reaction kinetics using hybrid mechanistic-neural network rate function model.

    PubMed

    Kumar, B Shiva; Venkateswarlu, Ch

    2012-01-01

    This work describes an alternative method for estimation of reaction rate of a biofilm process without using a model equation. A first principles model of the biofilm process is integrated with artificial neural networks to derive a hybrid mechanistic-neural network rate function model (HMNNRFM), and this combined model structure is used to estimate the complex kinetics of the biofilm process as a consequence of the validation of its steady state solution. The performance of the proposed methodology is studied with the aid of the experimental data of an anaerobic fixed bed biofilm reactor. The statistical significance of the method is also analyzed by means of the coefficient of determination (R2) and model efficiency (ME). The results demonstrate the effectiveness of HMNNRFM for estimating the complex kinetics of the biofilm process involved in the treatment of industry wastewater. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. Development of linear free energy relationships for aqueous phase radical-involved chemical reactions.

    PubMed

    Minakata, Daisuke; Mezyk, Stephen P; Jones, Jace W; Daws, Brittany R; Crittenden, John C

    2014-12-02

    Aqueous phase advanced oxidation processes (AOPs) produce hydroxyl radicals (HO•) which can completely oxidize electron rich organic compounds. The proper design and operation of AOPs require that we predict the formation and fate of the byproducts and their associated toxicity. Accordingly, there is a need to develop a first-principles kinetic model that can predict the dominant reaction pathways that potentially produce toxic byproducts. We have published some of our efforts on predicting the elementary reaction pathways and the HO• rate constants. Here we develop linear free energy relationships (LFERs) that predict the rate constants for aqueous phase radical reactions. The LFERs relate experimentally obtained kinetic rate constants to quantum mechanically calculated aqueous phase free energies of activation. The LFERs have been applied to 101 reactions, including (1) HO• addition to 15 aromatic compounds; (2) addition of molecular oxygen to 65 carbon-centered aliphatic and cyclohexadienyl radicals; (3) disproportionation of 10 peroxyl radicals, and (4) unimolecular decay of nine peroxyl radicals. The LFERs correlations predict the rate constants within a factor of 2 from the experimental values for HO• reactions and molecular oxygen addition, and a factor of 5 for peroxyl radical reactions. The LFERs and the elementary reaction pathways will enable us to predict the formation and initial fate of the byproducts in AOPs. Furthermore, our methodology can be applied to other environmental processes in which aqueous phase radical-involved reactions occur.

  2. 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.

  3. Quantitative rate constants for radical reactions in the nanopores of cotton.

    PubMed

    Hunt, Paula; Worrall, David R; Wilkinson, Frank; Batchelor, Stephen N

    2002-07-24

    The understanding of radical reactions in nanostructured materials is important for developing new synthetic procedures and controlling degradation reactions. To develop this area, an easy method for measuring quantitative rate constants of some radical reactions in nanostructures is required. A simple method for measuring the rate constant of dye bleaching, kdye, by organic radicals in such materials is introduced, involving the measurement of microsecond bleaching kinetics by diffuse reflectance spectroscopy, following laser flash creation of the radicals. Using wet and dry cotton as model substrates, we obtained kdye of 2-hydroxy-2-propyl and 1-hydroxy-1-cyclohexyl radicals with reactive red 3 and reactive orange 4 and compared them to solution-phase values. Surprisingly, the reactions in cotton follow simple liquid-phase kinetics and are diffusion-controlled. A cage effect in cotton is also found.

  4. Highly Oxidized Second-Generation Products from the Gas-Phase Reaction of OH Radicals with Isoprene.

    PubMed

    Berndt, Torsten; Herrmann, Hartmut; Sipilä, Mikko; Kulmala, Markku

    2016-12-29

    The gas-phase reaction of OH radicals with isoprene has been investigated in an atmospheric pressure flow tube at 293 ± 0.5 K with special attention to the second-generation products. Reaction conditions were optimized to achieve a predominant reaction of RO2 radicals with HO2 radicals. Chemical ionization-atmospheric pressure interface-time-of-flight mass spectrometry served as the analytical technique in order to follow the formation of RO2 radicals and closed-shell products containing at least four O atoms in the molecule. The reaction products were detected as adducts with the reagent ions using acetate, lactate, or nitrate in the ionization process. Observed signals were attributed to a series of C5-products with multiple hydroxy, hydroperoxy, and probably carbonyl groups. H/D exchange experiments supported the product identification. The generation of the detected second-generation products can be mechanistically explained starting from the OH radical reaction of hydroxy hydroperoxide isomers, HO-C5H8-OOH. These isomers represent the dominant products of the initial OH radical attack on isoprene. Dihydroxy dihydroperoxides, (HO)2-C5H8-(OOH)2, were analyzed as the main second-generation products beside the dihydroxy epoxides. A simple kinetic analysis revealed that the observed second-generation products in total (other than dihydroxy epoxides) were formed with an estimated molar yield of 10.0-1.5(+2.1) % with respect to converted hydroxy hydroperoxides. A formation yield of 5.8-0.9(+1.3) % has been deduced for the main product (HO)2-C5H8-(OOH)2. The detected, highly oxidized isoprene products represent potential secondary organic aerosol precursors. An annual, global (HO)2-C5H8-(OOH)2 formation strength of (16-35) × 10(6) metric tons is estimated based on product measurements of this study and literature data regarding the formation of the dihydroxy epoxide isomers for an annual isoprene emission of 454 × 10(6) metric tons of carbon.

  5. 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.

  6. Mechanistic insights on platinum- and palladium-pincer catalyzed coupling and cyclopropanation reactions between olefins.

    PubMed

    Rajeev, Ramanan; Sunoj, Raghavan B

    2012-07-21

    The mechanism of M(II)-PNP-pincer catalyzed reaction between (i) ethene, (ii) trans-butene with 2-methylbut-2-ene, 2,3-dimethylbut-2-ene and tert-butylbutene is examined by using density functional theory methods (where M = Pt or Pd). All key intermediates and transition states involved in the reaction are precisely located on the respective potential energy surfaces using the popular DFT functionals such as mPW1K, M06-2X, and B3LYP in conjunction with the 6-31+G** basis set. The reaction between these olefins can lead to a linear coupling product or a substituted cyclopropane. The energetic comparison between coupling as well as cyclopropanation pathways involving four pairs of olefins for both platinum (1-4) and palladium (5-8) catalyzed reactions is performed. The key events in the lower energy pathway in the mechanistic course involves (i) a C-C bond formation between the metal bound olefin (ethene or trans-butene) and a free olefin, and (ii) two successive [1,2] hydrogen migrations in the ensuing carbocationic intermediates (1c-4c, and 1d-4d), toward the formation of the coupling product. The computed barriers for these steps in the reaction of metal bound ethene to free tert-butylbutene (or other butenes) are found to be much lower than the corresponding steps when trans-butene is bound to the metal pincer. The Gibbs free energy differences between the transition states leading to the coupling product (TS(d-e)) and that responsible for cyclopropanated product (TS(d-g)) are found to be diminishingly closer in the case of the platinum pincer as compared to that in the palladium system. The computed energetics indicate that the coupled product prefers to remain as a metal olefin complex, consistent with the earlier experimental reports.

  7. Formation of {beta}-hydroxycarbonyls from the OH radical-initiated reactions of selected alkenes

    SciTech Connect

    Aschmann, S.M.; Arey, J.; Atkinson, R.

    2000-05-01

    {beta}-Hydroxycarbonyls can be formed from the gas-phase reactions of alkenes with the OH radical, both in the presence and in the absence of NO. To date, because of analytical difficulties, few data have been reported for the formation of this class of compound from the reactions of the OH radical with alkenes. The authors have determined that {beta}-hydroxy-ketones can be readily analyzed by gas chromatography, and in this work they have shown that in 1 atm of air the {beta}-hydroxyalkoxy radicals formed in the reactions of the OH radical with trans-2-butene, trans-3-hexene, 1-butene, and {alpha}-pinene in the presence of NO primarily decompose rather than react with O{sub 2}. Rate constant ratios k{sub d}/k{sub 0{sub 2}} (or lower limits thereof), where k{sub d} and k{sub 0{sub 2}} are respectively the rate constants for the decomposition and the reaction with 0{sub 2} of the intermediate {beta}-hydroxyalkoxy radicals, have been obtained for the reactions of the CH{sub 3}CH(O)CH-(OH)CH{sub 3}, CH{sub 3}CH{sub 2}CH(O)CH{sub 2}OH, and CH{sub 3}CH{sub 2}CH(O)CH(OH)CH{sub 2}-CH{sub 3} radicals at 296 {+-} 2 K and atmospheric pressure. Using the O{sub 3} reactions with the alkenes to generate OH radicals, the reactions of the OH radical to generate OH radicals, the reactions of the OH radical with trans-2-butene, trans-3-hexene, and {alpha}-pinene in the absence of NO lead to the formation of the expected {beta}-hydroxycarbonyls and (at least for trans-2-butene) the {alpha},{beta}-diol.

  8. Detection of radicals produced by reaction of hydroperoxides with rat liver microsomal fractions.

    PubMed

    Greenley, T L; Davies, M J

    1992-04-22

    EPR spin trapping using the spin traps 5,5-dimethyl-1-pyrroline N-oxide (DMPO) and 3,5-dibromo-4-nitrosobenzene sulphonic acid (DBNBS) has been employed to examine the generation of radicals produced on reaction of a number of primary, secondary and lipid hydroperoxides with rat liver microsomal fractions in both the presence and absence of reducing equivalents. Two major mechanisms of radical generation have been elucidated. In the absence of NADPH or NADH, oxidative degradation of the hydroperoxide occurs to give initially a peroxyl radical which in the majority of cases can be detected as a spin adduct to DMPO; these radicals can undergo further reactions which result in the generation of alkoxyl and carbon-centered radicals. In the presence of NADPH (and to a lesser extent NADH) alkoxyl radicals are generated directly via reductive cleavage of the hydroperoxide. These alkoxyl radicals undergo further fragmentation and rearrangement reactions to give carbon-centered species which can be identified by trapping with DBNBS. The type of transformation that occurs is highly dependent on the structure of the alkoxyl radical with species arising from beta-scission, 1,2-hydrogen shifts and ring closure reactions being identified; these processes are in accord with previous chemical studies and are characteristic of alkoxyl radicals present in free solution. Studies using specific enzyme inhibitors and metal-ion chelators suggest that most of the radical generation occurs via a catalytic process involving haem proteins and in particular cytochrome P-450. An unusual species (an acyl radical) is observed with lipid hydroperoxides; this is believed to arise via a cage reaction after beta-scission of an initial alkoxyl radical.

  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

    2012-08-09

    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.

  10. 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.

  11. Hydrogen atom abstraction reactions from tertiary amines by benzyloxyl and cumyloxyl radicals: influence of structure on the rate-determining formation of a hydrogen-bonded prereaction complex.

    PubMed

    Salamone, Michela; DiLabio, Gino A; Bietti, Massimo

    2011-08-05

    A time-resolved kinetic study on the hydrogen atom abstraction reactions from a series of tertiary amines by the cumyloxyl (CumO(•)) and benzyloxyl (BnO(•)) radicals was carried out. With the sterically hindered triisobutylamine, comparable hydrogen atom abstraction rate constants (k(H)) were measured for the two radicals (k(H)(BnO(•))/k(H)(CumO(•)) = 2.8), and the reactions were described as direct hydrogen atom abstractions. With the other amines, increases in k(H)(BnO(•))/k(H)(CumO(•)) ratios of 13 to 2027 times were observed. k(H) approaches the diffusion limit in the reactions between BnO(•) and unhindered cyclic and bicyiclic amines, whereas a decrease in reactivity is observed with acyclic amines and with the hindered cyclic amine 1,2,2,6,6-pentamethylpiperidine. These results provide additional support to our hypothesis that the reaction proceeds through the rate-determining formation of a C-H/N hydrogen-bonded prereaction complex between the benzyloxyl α-C-H and the nitrogen lone pair wherein hydrogen atom abstraction occurs, and demonstrate the important role of amine structure on the overall reaction mechanism. Additional mechanistic information in support of this picture is obtained from the study of the reactions of the amines with a deuterated benzyloxyl radical (PhCD(2)O(•), BnO(•)-d(2)) and the 3,5-di-tert-butylbenzyloxyl radical.

  12. Contrasting reactions of hydrated electron and formate radical with 2-thio analogues of cytosine and uracil.

    PubMed

    Prasanthkumar, Kavanal P; Alvarez-Idaboy, Juan R; Kumar, Pavitra V; Singh, Beena G; Priyadarsini, K Indira

    2016-10-19

    2-Thiocytosine (TC) and 2-thiouracil (TU) were subjected to hydrated electron (eaq(-)), formate radical (CO2˙(-)) and 2-hydroxypropan-2-yl radical ((CH3)2˙COH) reactions in aqueous medium. Transients were characterized by absorption spectroscopy and the experimental findings were rationalized by DFT calculations at LC-ωPBE and M06-2X levels using a 6-311+G(d,p) basis set and SMD solvation. In eaq(-) reactions, a ring N-atom protonated radical of TC and an exocyclic O-atom protonated radical of TU were observed via addition of eaq(-) and subsequent protonation by solvent molecules. However, two competing but simultaneous mechanisms are operative in CO2˙(-) reactions with TC and TU. The first one corresponds to formations of N(O)-atom protonated radicals (similar to eaq(-) reactions); the second mechanism led to 2 center-3 electron, sulfur-sulfur bonded neutral dimer radicals, TCdim˙ and TUdim˙. DFT calculations demonstrated that H-abstraction by CO2˙(-) from TC(TU) results in S-centered radical which upon combination with TC(TU) provide the dimer radical. In some cases, DFT energy profiles were further validated by CBS-QB3//M06-2X calculations. This is the first time report for a contradictory behavior in the mechanisms of eaq(-) and CO2˙(-) reactions with any pyrimidines or their thio analogues.

  13. 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

  14. Scheme for Detection of Single-Molecule Radical Pair Reaction Using Spin in Diamond

    NASA Astrophysics Data System (ADS)

    Liu, Haibin; Plenio, Martin B.; Cai, Jianming

    2017-05-01

    The radical pair reaction underlies the magnetic field sensitivity of chemical reactions and is suggested to play an important role in both chemistry and biology. Current experimental evidence is based on ensemble measurements; however, the ability to probe the radical pair reaction at the single-molecule level would provide valuable information concerning its role in important biological processes. Here, we propose a scheme to detect the charge recombination rate in a radical pair reaction under ambient conditions by using single nitrogen-vacancy center spin in diamond. We demonstrate theoretically that it is possible to detect the effect of the geomagnetic field on the radical pair reaction and propose the present scheme as a possible hybrid model chemical compass.

  15. 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.

  16. 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.

  17. 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

  18. A catalytic reactor for the trapping of free radicals from gas phase oxidation reactions

    NASA Astrophysics Data System (ADS)

    Conte, Marco; Wilson, Karen; Chechik, Victor

    2010-10-01

    A catalytic reactor for the trapping of free radicals originating from gas phase catalytic reactions is described and discussed. Radical trapping and identification were initially carried out using a known radical generator such as dicumyl peroxide. The trapping of radicals was further demonstrated by investigating genuine radical oxidation processes, e.g., benzaldehyde oxidation over manganese and cobalt salts. The efficiency of the reactor was finally proven by the partial oxidation of cyclohexane over MoO3, Cr2O3, and WO3, which allowed the identification of all the radical intermediates responsible for the formation of the products cyclohexanol and cyclohexanone. Assignment of the trapped radicals was carried out using spin trapping technique and X-band electron paramagnetic resonance spectroscopy.

  19. 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.

  20. 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.

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

    PubMed

    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)], in contrast to previous work by Jones and Hore [J. A. Jones and P. J. Hore, Chem. Phys. Lett. 488, 90 (2010)]. 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.

  2. Mechanism of the reaction of radicals with peroxides and dimethyl sulfoxide in aqueous solution.

    PubMed

    Herscu-Kluska, Ronit; Masarwa, Alexandra; Saphier, Magal; Cohen, Haim; Meyerstein, Dan

    2008-01-01

    The reactions of methyl and methylperoxyl radicals derived from dimethyl sulfoxide (DMSO) with hydrogen peroxide, peroxymonocarbonate (HCO4 (-)), and persulfate were studied. The major reaction observed for the hydroperoxides was the abstraction of the hydrogen atom by the radicals. The radicals interact with a lone pair of electrons on the peroxide to produce methanol and formaldehyde. Furthermore, the results indicate that in RO2H and RO2R', electron-withdrawing groups cause a considerable increase in the reactivity of the peroxides towards the radicals and not only towards nucleophiles. The HO2 (.)/O2 (.-) and CO3 (.-) radicals react with DMSO to produce methyl radicals. Thus, the formation of the (.)CH3 radicals in the presence of DMSO is not proof of the formation of the (.)OH radicals in the system. These reactions must be considered when radical processes, such as in biological and catalytic systems, are studied. Especially, the plausible role of HCO4 (-) ions in biological systems as a source of oxidative stress cannot be overlooked.

  3. Kinetics and Mechanistic Investigations of Atmospheric Oxidation of HFO-1345fz by OH Radical: Insights from Theory.

    PubMed

    Rao, Pradeep Kumar; Gejji, Shridhar P

    2017-01-26

    HFO-1345fz (CF3CF2CH═CH2 or 3,3,4,4,4-pentafluoro-1-butene) belongs to a class of hydrofluoro-olefins and represents a new generation of potential foam expansion agents. Its atmospheric impact and environmental acceptability can be estimated from the studies of kinetics and mechanism of its oxidative degradation. The molecular insights accompanying the reaction pathways in terms of the characterization of intermediates or products and radiative properties should prove useful for large-scale industrial applications. Systematic mechanistic gas-phase kinetics investigations on the reactivity of HFO-1345fz with the (•)OH facilitating a variety of degradation routes have been carried out employing the M06-2x-based density functional theory. Structure and energetics of different reaction pathways such as hydrogen abstraction, (•)OH addition, isomerization-dissociation, or interaction with atmospheric O2 have been analyzed. The formation of gaseous products from the interaction of HFO-1345fz with (•)OH in the absence and presence of NOx atmospheric conditions has been reported. Calculated branching ratios have shown that the addition channel dominates such oxidative degradation, whereas the abstraction channel contributes negligibly to the global rate constant and addition of (•)OH to the terminal carbon is favored over the nonterminal one. The rate constants for all reaction channels were computed by conventional transition state theory (TST) and canonical variation transition state theory (CVT) including small curvature tunneling (SCT) over the temperature range of 200-1000 K at atmospheric pressure. The CVT calculated rate constant for the reaction at 298 K was shown to be 1.17 × 10(-12) cm(3) molecule(-1) s(-1), which compares well with the 1.24 × 10(-12) cm(3) molecule(-1) s(-1) as obtained from TST and is in excellent agreement with the experiments reported earlier. The atmospheric lifetime, radiative efficiency, and global warming potential (GWP) have

  4. Rate constant and reaction channels for the reaction of atomic nitrogen with the ethyl radical

    SciTech Connect

    Stief, L.J.; Nesbitt, F.L.; Payne, W.A. ); Kuo, S.C.; Tao, W.; Klemm, R.B. )

    1995-04-01

    The absolute rate constant and primary reaction products have been determined at [ital T]=298 K for the atom--radical reaction N([sup 4][ital S])+C[sub 2]H[sub 5] in a discharge flow system with collision-free sampling to a mass spectrometer. The rate constant measurements employed low energy electron impact ionization while the product study used dispersed synchrotron radiation as the photoionization source. The rate constant was determined under pseudo-first-order conditions by monitoring the decay of C[sub 2]H[sub 5] or C[sub 2]D[sub 5] as a function of time in the presence of excess N atoms. The result is [ital k]=(1.1[plus minus]0.3)[times]10[sup [minus]10] cm[sup 3] molecule[sup [minus]1] s[sup [minus]1]. For the reaction product experiments using photoionization mass spectrometry, products observed at 114 nm (10.9 eV) were CD[sub 3], D[sub 2]CN and C[sub 2]D[sub 4] for the N+C[sub 2]D[sub 5] reaction. The product identification is based on the unambiguous combination of product [ital m]/[ital z] values, the shift of the [ital m]/[ital z] peaks observed for the N+C[sub 2]D[sub 5] reaction products with respect to the N+C[sub 2]H[sub 5] reaction products and the photoionization threshold measured for the major products. The observed products are consistent with the occurrence of the reaction channels D[sub 2]CN+CD[sub 3](2a) and C[sub 2]D[sub 4]+ND(2c). Formation of C[sub 2]D[sub 4] product via channel (2c) accounts for approximately 65% of the C[sub 2]D[sub 5] reacted. Most, if not all, of the remaining 35% is probably accounted for by channel (2a). These rate constant and product results are compared with those for the N+CH[sub 3] reaction as well as other atom+C[sub 2]H[sub 5] reactions. The role of the N+C[sub 2]H[sub 5] reaction in the formation of HCN in the atmospheres of Titan and Neptune is briefly considered. (Abstract Truncated)

  5. Radical-mediated dehydration reactions in anaerobic bacteria.

    PubMed

    Buckel, Wolfgang; Martins, Berta M; Messerschmidt, Albrecht; Golding, Bernard T

    2005-10-01

    Most dehydratases catalyse the elimination of water from beta-hydroxy ketones, beta-hydroxy carboxylic acids or beta-hydroxyacyl-CoA. The electron-withdrawing carbonyl functionalities acidify the alpha-hydrogens to enable their removal by basic amino acid side chains. Anaerobic bacteria, however, ferment amino acids via alpha- or gamma-hydroxyacyl-CoA, dehydrations of which involve the abstraction of a beta-hydrogen, which is ostensibly non-acidic (pK ca. 40). Evidence is accumulating that beta-hydrogens are acidified via transient conversion of the CoA derivatives to enoxy radicals by one-electron transfers, which decrease the pK to 14. The dehydrations of (R)-2-hydroxyacyl-CoA to (E)-2-enoyl-CoA are catalysed by heterodimeric [4Fe-4S]-containing dehydratases, which require reductive activation by an ATP-dependent one-electron transfer mediated by a homodimeric protein with a [4Fe-4S] cluster between the two subunits. The electron is further transferred to the substrate, yielding a ketyl radical anion, which expels the hydroxyl group and forms an enoxy radical. The dehydration of 4-hydroxybutyryl-CoA to crotonyl-CoA involves a similar mechanism, in which the ketyl radical anion is generated by one-electron oxidation. The structure of the FAD- and [4Fe-4S]-containing homotetrameric dehydratase is related to that of acyl-CoA dehydrogenases, suggesting a radical-based mechanism for both flavoproteins.

  6. TiCl4-promoted Baylis-Hillman reaction: mechanistic rationale toward product distribution and stereoselectivity.

    PubMed

    Patel, Chandan; Sunoj, Raghavan B

    2010-01-15

    The mechanism of TiCl(4)-promoted Baylis-Hillman reaction between methyl vinyl ketone (MVK) and acetaldehyde, in the absence of any base, is studied using the mPW1K density functional theory. The study focuses on several mechanistic intricacies as well as selectivity issues at each step of the reaction. The minimum energy pathway for this reaction involves three major steps such as a chloride transfer resulting in a chloro-enolate, titanium-mediated aldol reaction, and elimination of HCl or HOTiCl(3). Both s-cis and s-trans conformers of MVK are considered along with various modes of chloride transfer involving different complexes between TiCl(4), aldehyde, and MVK. Chloride transfer is found to be kinetically more favored for s-cis-MVK than for s-trans-MVK. The diastereoselectivity in the next step, i.e., Ti-mediated aldol reaction between the enolate and aldehyde, is found to be dependent on the geometry of the enolate, wherein anti and syn BH products are predicted for Z and E enolates, respectively. An interesting secondary orbital interaction between the oxygen atoms of the enolate and aldehyde moieties in the transition states for the C-C bond formation is identified as one of the contributing factors toward the predicted diastereoselectivity in the formation of the alpha-chloromethyl aldol product (P2). It has earlier been reported that under different experimental conditions, any of the three products such as (i) a normal BH product (P1), (ii) 2-(chloromethyl)vinyl ketones (P3), and (iii) alpha-chloro methyl aldol could be generated (Scheme 1 ). The present study offers valuable insights toward rationalizing the observed product distribution as well as diastereoselectivity in TiCl(4)-promoted BH reaction under base-free conditions. The computed energetics indicate that when MVK is employed as the Michael acceptor, the formation of 2-(choromethyl)vinyl ketone is the preferred product rather than the corresponding normal BH product, consistent with the known

  7. Standard Gibbs free energies of reactions of ozone with free radicals in aqueous solution: quantum-chemical calculations.

    PubMed

    Naumov, Sergej; von Sonntag, Clemens

    2011-11-01

    Free radicals are common intermediates in the chemistry of ozone in aqueous solution. Their reactions with ozone have been probed by calculating the standard Gibbs free energies of such reactions using density functional theory (Jaguar 7.6 program). O(2) reacts fast and irreversibly only with simple carbon-centered radicals. In contrast, ozone also reacts irreversibly with conjugated carbon-centered radicals such as bisallylic (hydroxycylohexadienyl) radicals, with conjugated carbon/oxygen-centered radicals such as phenoxyl radicals, and even with nitrogen- oxygen-, sulfur-, and halogen-centered radicals. In these reactions, further ozone-reactive radicals are generated. Chain reactions may destroy ozone without giving rise to products other than O(2). This may be of importance when ozonation is used in pollution control, and reactions of free radicals with ozone have to be taken into account in modeling such processes.

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

    USDA-ARS?s Scientific Manuscript database

    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. Strategies for generating peptide radical cations via ion/ion reactions.

    PubMed

    Gilbert, Joshua D; Fisher, Christine M; Bu, Jiexun; Prentice, Boone M; Redwine, James G; McLuckey, Scott A

    2015-02-01

    Several approaches for the generation of peptide radical cations using ion/ion reactions coupled with either collision induced dissociation (CID) or ultraviolet photo dissociation (UVPD) are described here. Ion/ion reactions are used to generate electrostatic or covalent complexes comprised of a peptide and a radical reagent. The radical site of the reagent can be generated multiple ways. Reagents containing a carbon-iodine (C-I) bond are subjected to UVPD with 266-nm photons, which selectively cleaves the C-I bond homolytically. Alternatively, reagents containing azo functionalities are collisionally activated to yield radical sites on either side of the azo group. Both of these methods generate an initial radical site on the reagent, which then abstracts a hydrogen from the peptide while the peptide and reagent are held together by either electrostatic interactions or a covalent linkage. These methods are demonstrated via ion/ion reactions between the model peptide RARARAA (doubly protonated) and various distonic anionic radical reagents. The radical site abstracts a hydrogen atom from the peptide, while the charge site abstracts a proton. The net result is the conversion of a doubly protonated peptide to a peptide radical cation. The peptide radical cations have been fragmented via CID and the resulting product ion mass spectra are compared to the control CID spectrum of the singly protonated, even-electron species. This work is then extended to bradykinin, a more broadly studied peptide, for comparison with other radical peptide generation methods. The work presented here provides novel methods for generating peptide radical cations in the gas phase through ion/ion reaction complexes that do not require modification of the peptide in solution or generation of non-covalent complexes in the electrospray process. Copyright © 2015 John Wiley & Sons, Ltd.

  10. Restricted mass transport effects on free radical reactions

    SciTech Connect

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

    1994-09-01

    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 ({approx}Ph(CH{sub 2}){sub 3}Ph, or {approx}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 {degrees}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.

  11. 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.

  12. Reactions of hydroxyl radicals with alkenes in low-temperature matrices

    NASA Astrophysics Data System (ADS)

    Feltham, Emma J.; Almond, Matthew J.; Marston, George; Wiltshire, Karen S.; Goldberg, Nicola

    2000-11-01

    The reactions of hydroxyl radicals with a number of stable alkenes have been studied in low-temperature matrices. The reactions were initiated by broad band UV-visible irradiation of matrices containing H 2O 2 and the alkene under investigation. The hydroxyalkyl radical products were identified principally by comparison of their spectra with the spectra of corresponding stable alcohols. Accordingly, IR spectra were recorded for the following series of alcohols isolated in argon matrices — methanol, ethanol, ethanol- d6, propan-1-ol, propan-2-ol, butan-2-ol, 2-methylpropan-1-ol ( iso-butyl alcohol), 2-methylpropan-2-ol ( tert-butyl alcohol), 2-methylbutan-2-ol ( tert-amyl alcohol), 3-methylbutan-2-ol and 2,3-dimethylbutan-2-ol. The hydroxyalkyl radicals, which appear to be formed from the alkenes studied were as follows — from ethene, 2-hydroxyethyl radical; from cis- or trans-but-2-ene, 1-methyl-2-hydroxypropyl radical; from propene, 1-methyl-2-hydroxyethyl and 2-hydroxypropyl radicals; from but-1-ene, 1-hydroxymethylpropyl and 2-hydroxybutyl radicals; from 2-methylpropene ( iso-butene), 1,1-dimethyl-2-hydroxyethyl and 2-methyl-2-hydroxypropyl radicals; the radical products from buta-1,3-diene and isoprene could not be identified. In the cases, where two radical products were possible, i.e. when propene, but-1-ene or 2-methylpropene were the substrates, it was found that the concentration of the secondary or tertiary radical always exceeded that of the primary radical. However, the relative concentration of these radicals appears to be determined by subsequent photolysis to give carbonyl compounds. There seems, therefore, to be little preference for the secondary and tertiary radicals over the primary radicals in the primary addition process. Comments on the mechanism of the transformation from radical to carbonyl compound based upon identification of intermediates within the matrix and isotopic substitution experiments are made. The characterisation of the 2

  13. 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

  14. Some aspects of radical cascade and relay reactions

    PubMed Central

    Quiclet-Sire, Béatrice; Zard, Samir Z.

    2017-01-01

    The ability to create carbon–carbon bonds is at the heart of organic synthesis. Radical processes are particularly apt at creating such bonds, especially in cascade or relay sequences where more than one bond is formed, allowing for a rapid assembly of complex structures. In the present brief overview, examples taken from the authors' laboratory will serve to illustrate the strategic impact of radical-based approaches on synthetic planning. Transformations involving nitrogen-centred radicals, electron transfer from metallic nickel and the reversible degenerative exchange of xanthates will be presented and discussed. The last method has proved to be a particularly powerful tool for the intermolecular creation of carbon–carbon bonds by radical additions even to unactivated alkenes. Various functional groups can be brought into the same molecule in a convergent manner and made to react together in order to further increase the structural complexity. One important benefit of this chemistry is the so-called RAFT/MADIX technology for the manufacture of block copolymers of almost any desired architecture. PMID:28484329

  15. Reconciling disparate models of the involvement of vinyl radicals in cobalamin-mediated dechlorination reactions.

    PubMed

    Kliegman, Sarah; McNeill, Kristopher

    2009-12-01

    Inner-sphere (nonradical) and outer-sphere (radical-based) mechanisms have been suggested for cobalamin-mediated dechlorination of tetrachloroethylene (PCE) and trichloroethylene (TCE). In this study, the role of free vinyl radicals was investigated using deuterated radical traps: d(8)-isopropanol and d(8)-tetrahydrofuran. For both substrates, addition of trap resulted in production of deuterated dechlorination products, and higher concentrations of trap resulted in increased amounts of deuterated products. However, only a finite proportion of the products were trappable: 8% of the PCE-derived products and 86% of the TCE-derived products result from free radicals. The data show that the reaction does not proceed solely by either an inner-sphere or an outer-sphere mechanism and led to the hypothesis that caged radical intermediates were involved in the mechanism. The untrappable fraction of products are hypothesized to result from in-cage reactions. This hypothesis was investigated using d(5)-glycerol as a radical trap and viscogen. Although increased viscosity resulted in decreased formation of free-radical-derived products, consistent with the cage hypothesis, these data were inconclusive. The role of d(8)-isopropanol in enhancing the production of radicals in this system via an acetone ketyl radical chain mechanism was also investigated, and no evidence for such an effect was found.

  16. 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...

  17. 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...

  18. Borohydride-mediated radical addition reactions of organic iodides to electron-deficient alkenes.

    PubMed

    Kawamoto, Takuji; Uehara, Shohei; Hirao, Hidefumi; Fukuyama, Takahide; Matsubara, Hiroshi; Ryu, Ilhyong

    2014-05-02

    Cyanoborohydrides are efficient reagents in the reductive addition reactions of alkyl iodides and electron-deficient olefins. In contrast to using tin reagents, the reaction took place chemoselectively at the carbon-iodine bond but not at the carbon-bromine or carbon-chlorine bond. The reaction system was successfully applied to three-component reactions, including radical carbonylation. The rate constant for the hydrogen abstraction of a primary alkyl radical from tetrabutylammonium cyanoborohydride was estimated to be <1 × 10(4) M(-1) s(-1) at 25 °C by a kinetic competition method. This value is 3 orders of magnitude smaller than that of tributyltin hydride.

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

    PubMed

    Wang, Heng; Bozzelli, Joseph W

    2016-07-04

    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.

  20. Mechanistic insight into the reaction catalysed by bacterial type II dehydroquinases.

    PubMed

    Coderch, Claire; Lence, Emilio; Peón, Antonio; Lamb, Heather; Hawkins, Alastair R; Gago, Federico; González-Bello, Concepción

    2014-03-15

    DHQ2 (type II dehydroquinase), which is an essential enzyme in Helicobacter pylori and Mycobacterium tuberculosis and does not have any counterpart in humans, is recognized to be an attractive target for the development of new antibacterial agents. Computational and biochemical studies that help understand in atomic detail the catalytic mechanism of these bacterial enzymes are reported in the present paper. A previously unknown key role of certain conserved residues of these enzymes, as well as the structural changes responsible for triggering the release of the product from the active site, were identified. Asp89*/Asp88* from a neighbouring enzyme subunit proved to be the residue responsible for the deprotonation of the essential tyrosine to afford the catalytic tyrosinate, which triggers the enzymatic process. The essentiality of this residue is supported by results from site-directed mutagenesis. For H. pylori DHQ2, this reaction takes place through the assistance of a water molecule, whereas for M. tuberculosis DHQ2, the tyrosine is directly deprotonated by the aspartate residue. The participation of a water molecule in this deprotonation reaction is supported by solvent isotope effects and proton inventory studies. MD simulation studies provide details of the required motions for the catalytic turnover, which provides a complete overview of the catalytic cycle. The product is expelled from the active site by the essential arginine residue and after a large conformational change of a loop containing two conserved arginine residues (Arg109/Arg108 and Arg113/Arg112), which reveals a previously unknown key role for these residues. The present study highlights the key role of the aspartate residue whose blockage could be useful in the rational design of inhibitors and the mechanistic differences between both enzymes.

  1. 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

  2. Secondary organic aerosol formation from reaction of tertiary amines with nitrate radical

    NASA Astrophysics Data System (ADS)

    Erupe, M. E.; Price, D. J.; Silva, P. J.; Malloy, Q. G. J.; Qi, L.; Warren, B.; Cocker, D. R., III

    2008-09-01

    Secondary organic aerosol formation from the reaction of tertiary amines with nitrate radical was investigated in an indoor environmental chamber. Particle chemistry was monitored using a high resolution aerosol mass spectrometer while gas-phase species were detected using a proton transfer reaction mass spectrometer. Trimethylamine, triethylamine and tributylamine were studied. Results indicate that tributylamine forms the most aerosol mass followed by trimethylamine and triethylamine respectively. Spectra from the aerosol mass spectrometer indicate the formation of complex non-salt aerosol products. We propose a reaction mechanism that proceeds via abstraction of a proton by nitrate radical followed by RO2 chemistry. Rearrangement of the aminyl alkoxy radical through hydrogen shift leads to the formation of hydroxylated amides, which explain most of the higher mass ions in the mass spectra. These experiments show that oxidation of tertiary amines by nitrate radical may be an important night-time source of secondary organic aerosol.

  3. Crossed-beam dynamics studies of the radical-radical combustion reaction O((3)P) + CH3 (methyl).

    PubMed

    Balucani, Nadia; Leonori, Francesca; Bergeat, Astrid; Petrucci, Raffaele; Casavecchia, Piergiorgio

    2011-05-14

    The dynamics of the radical-radical reaction O((3)P) + CH(3), a prototypical case for the reactions of atomic oxygen with alkyl radicals of great relevance in combustion chemistry, has been investigated by means of the crossed molecular beam technique with mass spectrometric detection at a collision energy of 55.9 kJ mol(-1). The results have been examined in the light of previous kinetic and theoretical work. From product angular and velocity distribution measurements, the dynamics of the predominant H-displacement channel leading to formaldehyde formation has been characterized. This channel has been found to proceed via the formation of an osculating complex; a significant coupling between the product centre-of-mass angular and translational energy distributions has been noted. Experimental attempts to characterize the dynamics of the channel leading to HCO + H(2) have failed and it remains unclear whether HCO is formed by the reaction and/or, if formed, a part of HCO does not dissociate quickly into CO + H.

  4. Free radical reaction characteristics of coal low-temperature oxidation and its inhibition method.

    PubMed

    Li, Zenghua; Kong, Biao; Wei, Aizhu; Yang, Yongliang; Zhou, Yinbo; Zhang, Lanzhun

    2016-12-01

    Study on the mechanism of coal spontaneous combustion is significant for controlling fire disasters due to coal spontaneous combustion. The free radical reactions can explain the chemical process of coal at low-temperature oxidation. Electron spin resonance (ESR) spectroscopy was used to measure the change rules of the different sorts and different granularity of coal directly; ESR spectroscopy chart of free radicals following the changes of temperatures was compared by the coal samples applying air and blowing nitrogen, original coal samples, dry coal samples, and demineralized coal samples. The fragmentation process was the key factor of producing and initiating free radical reactions. Oxygen, moisture, and mineral accelerated the free radical reactions. Combination of the free radical reaction mechanism, the mechanical fragmentation leaded to the elevated CO concentration, fracturing of coal pillar was more prone to spontaneous combustion, and spontaneous combustion in goaf accounted for a large proportion of the fire in the mine were explained. The method of added diphenylamine can inhibit the self-oxidation of coal effectively, the action mechanism of diphenylamine was analyzed by free radical chain reaction, and this research can offer new method for the development of new flame retardant.

  5. Reaction Of Single-Wall Carbon Nanotubes With Radicals

    NASA Astrophysics Data System (ADS)

    Lobach, A. S.; Solomentsev, V. V.; Obraztsova, E. D.; Shchegolikhin, A. N.; Sokolov, V. I.

    2004-09-01

    A method for functionalizing the sidewalls of HiPco SWNT via interaction with carbon- and metal-centered radicals is presented. A number of methods: UV-vis-NIR spectroscopy, thermogravimetric analysis, TEM and Raman spectroscopy provided a direct evidence of a chemical attachment of functional groups to the tubes. Functionalization was shown to be reversible: a thermal treatment led to the recovering of pristine structure of SWNT.

  6. Gas-phase reactivity of peptide thiyl (RS•), perthiyl (RSS•), and sulfinyl (RSO•) radical ions formed from atmospheric pressure ion/radical reactions.

    PubMed

    Tan, Lei; Xia, Yu

    2013-04-01

    In this study, we demonstrated the formation of gas-phase peptide perthiyl (RSS•) and thiyl (RS•) radical ions besides sulfinyl radical (RSO•) ions from atmospheric pressure (AP) ion/radical reactions of peptides containing inter-chain disulfide bonds. The identity of perthiyl radical was verified from characteristic 65 Da (•SSH) loss in collision-induced dissociation (CID). This signature loss was further used to assess the purity of peptide perthiyl radical ions formed from AP ion/radical reactions. Ion/molecule reactions combined with CID were carried out to confirm the formation of thiyl radical. Transmission mode ion/molecule reactions in collision cell (q2) were developed as a fast means to estimate the population of peptide thiyl radical ions. The reactivity of peptide thiyl, perthiyl, and sulfinyl radical ions was evaluated based on ion/molecule reactions toward organic disulfides, allyl iodide, organic thiol, and oxygen, which followed in order of thiyl (RS•) > perthiyl (RSS•) > sulfinyl (RSO•). The gas-phase reactivity of these three types of sulfur-based radicals is consistent with literature reports from solution studies.

  7. Radical ring expansion reactions of methylenecyclopropane derivatives: a theoretical study.

    PubMed

    Ardura, Diego; Sordo, Tomas L

    2006-06-23

    The evolution of the primary radicals from 1-(3-bromopropyl)-2-ethyl-3-methylenecyclopropane, 1-(3-bromopropyl)-1-trimethylsilyl-2-methylenecyclopropane, 1-(3-bromobutyl)-2-ethyl-3-methylenecyclopropane, and 1-(3-bromobutyl)-1-trimethylsilyl-2-methylenecyclopropane was theoretically studied at the ROMP2/6-311++G(d,p)//UB3LYP/6-31G(d,p) theory level taking into account the effect of solvent through a PCM-UAHF model. For the propyl-substituted radicals, the attack of the radical center on the double bond takes place most favorably in an exo fashion. The subsequent ring expansions yield the product corresponding to the rupture of the endo C-C bond as the most favorable one in accordance with the experimental results. In the case of 1-(3-bromobutyl)-2-ethyl-3-methylenecyclopropane, the Gibbs energy barriers for the endo and exo attacks are the same, and the subsequent reversible evolution yields the product corresponding to the rupture of the exo C-C bond as the most favorable one through thermodynamic control in agreement with experiment. Finally, for 1-(3-bromobutyl)-1-trimethylsilyl-2-methylenecyclopropane, our calculations predict that the endo attack is 0.8 kcal/mol more favorable than the exo one. In the subsequent reversible ring expansion, the product corresponding to the rupture of the endo C-C bond is kinetically the most favored one in reasonable agreement with the experimental observations.

  8. 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.

  9. ESR evidence for radical production from the reaction of ozone with unsaturated lipids

    SciTech Connect

    Church, D.F.; McAdams, M.L..; Pryor, W.A. )

    1991-03-15

    The authors report electron spin resonance (ESR) spin trapping evidence for radical production by the reaction of ozone with unsaturated compounds. Soy and egg phosphatidylcholine liposomes, fatty acid emulsions, and homogeneous aqueous solutions of 3-hexenoic acid were treated with ozone in the presence of the spin trap {alpha}-phenyl-N-tert-butyl nitrone (PBN). Under these conditions, they observe spin adducts resulting from the trapping of both organic carbon- and oxygen-centered radicals. When the lipid-soluble antioxidant alpha-tocopherol is included in the liposomal systems, the formation of spin adducts is completely inhibited. The authors suggest that radicals giving rise to these spin adducts arise form the rapid decomposition of the 1,2,3-trioxolane intermediate that is initially formed when ozone reacts with the carbon-carbon double bonds of the substrates. These free radicals are not formed by the decomposition of the Criegee ozonide, since little of the ozonide is formed in the presence of water. Although hydrogen peroxide is the predominate peroxidic product of the ozone/alkene reaction, its decomposition is not responsible for the observed radical production since neither catalase nor iron chelators significantly affect the spin adduct yield. The radical yield is approximately 1%. Since a polyunsaturated fatty acid (PUFA) such as linoleic acid produces much higher concentrations of spin trappable radicals than does the monounsaturated fatty oleic acid, the results also suggest that sites in the lung containing higher levels of PUFA may be an important target for radical formation.

  10. 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.

  11. 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.

  12. Observation of multiple radical pair states in photosystem 2 reaction centers.

    PubMed

    Booth, P J; Crystall, B; Ahmad, I; Barber, J; Porter, G; Klug, D R

    1991-07-30

    Charge recombination of the primary radical pair in D1/D2 reaction centers from photosystem 2 has been studied by time-resolved fluorescence and absorption spectroscopy. The kinetics of the primary radical pair are multiexponential and exhibit at least two lifetimes of 20 and 52 ns. In addition, a third lifetime of approximately 500 ps also appears to be present. These multiexponential charge-recombination kinetics reflect either different conformational states of D1/D2 reaction centers, with the different conformers exhibiting different radical pair lifetimes, or relaxations in the free energy of the radical pair state. Whichever model is invoked, the free energies of formation of the different radical pair states exhibit a linear temperature dependence from 100 to 220 K, indicating that they are dominated by entropy with negligible enthalpy contributions. These results are in agreement with previous determinations of the thermodynamics that govern primary charge separation in both D1/D2 reaction centers [Booth, P.J., Crystall, B., Giorgi, L. B., Barber, J., Klug, D.R., & Porter, G. (1990) Biochim. Biophys. Acta 1016, 141-152] and reaction centers of purple bacteria [Woodbury, N.W.T., & Parson, W.W. (1984) Biochim. Biophys. Acta 767, 345-361]. It is possible that these observations reflect structural changes that accompanying primary charge separation and assist in stabilization of the radical pair state thus optimizing the efficiency of primary electron transfer.

  13. 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).

  14. The reaction of methyl peroxy and hydroxyl radicals as a major source of atmospheric methanol

    NASA Astrophysics Data System (ADS)

    Müller, Jean-François; Liu, Zhen; Nguyen, Vinh Son; Stavrakou, Trissevgeni; Harvey, Jeremy N.; Peeters, Jozef

    2016-10-01

    Methyl peroxy, a key radical in tropospheric chemistry, was recently shown to react with the hydroxyl radical at an unexpectedly high rate. Here, the molecular reaction mechanisms are elucidated using high-level quantum chemical methodologies and statistical rate theory. Formation of activated methylhydrotrioxide, followed by dissociation into methoxy and hydroperoxy radicals, is found to be the main reaction pathway, whereas methylhydrotrioxide stabilization and methanol formation (from activated and stabilized methylhydrotrioxide) are viable minor channels. Criegee intermediate formation is found to be negligible. Given the theoretical uncertainties, useful constraints on the yields are provided by atmospheric methanol measurements. Using a global chemistry-transport model, we show that the only explanation for the high observed methanol abundances over remote oceans is the title reaction with an overall methanol yield of ~30%, consistent with the theoretical estimates given their uncertainties. This makes the title reaction a major methanol source (115 Tg per year), comparable to global terrestrial emissions.

  15. The reaction of methyl peroxy and hydroxyl radicals as a major source of atmospheric methanol.

    PubMed

    Müller, Jean-François; Liu, Zhen; Nguyen, Vinh Son; Stavrakou, Trissevgeni; Harvey, Jeremy N; Peeters, Jozef

    2016-10-17

    Methyl peroxy, a key radical in tropospheric chemistry, was recently shown to react with the hydroxyl radical at an unexpectedly high rate. Here, the molecular reaction mechanisms are elucidated using high-level quantum chemical methodologies and statistical rate theory. Formation of activated methylhydrotrioxide, followed by dissociation into methoxy and hydroperoxy radicals, is found to be the main reaction pathway, whereas methylhydrotrioxide stabilization and methanol formation (from activated and stabilized methylhydrotrioxide) are viable minor channels. Criegee intermediate formation is found to be negligible. Given the theoretical uncertainties, useful constraints on the yields are provided by atmospheric methanol measurements. Using a global chemistry-transport model, we show that the only explanation for the high observed methanol abundances over remote oceans is the title reaction with an overall methanol yield of ∼30%, consistent with the theoretical estimates given their uncertainties. This makes the title reaction a major methanol source (115 Tg per year), comparable to global terrestrial emissions.

  16. The reaction of methyl peroxy and hydroxyl radicals as a major source of atmospheric methanol

    PubMed Central

    Müller, Jean-François; Liu, Zhen; Nguyen, Vinh Son; Stavrakou, Trissevgeni; Harvey, Jeremy N.; Peeters, Jozef

    2016-01-01

    Methyl peroxy, a key radical in tropospheric chemistry, was recently shown to react with the hydroxyl radical at an unexpectedly high rate. Here, the molecular reaction mechanisms are elucidated using high-level quantum chemical methodologies and statistical rate theory. Formation of activated methylhydrotrioxide, followed by dissociation into methoxy and hydroperoxy radicals, is found to be the main reaction pathway, whereas methylhydrotrioxide stabilization and methanol formation (from activated and stabilized methylhydrotrioxide) are viable minor channels. Criegee intermediate formation is found to be negligible. Given the theoretical uncertainties, useful constraints on the yields are provided by atmospheric methanol measurements. Using a global chemistry-transport model, we show that the only explanation for the high observed methanol abundances over remote oceans is the title reaction with an overall methanol yield of ∼30%, consistent with the theoretical estimates given their uncertainties. This makes the title reaction a major methanol source (115 Tg per year), comparable to global terrestrial emissions. PMID:27748363

  17. Radical scavenging reaction kinetics with multiwalled carbon nanotubes

    PubMed Central

    Tsuruoka, Shuji; Matsumoto, Hidetoshi; Koyama, Kenichi; Akiba, Eiji; Yanagisawa, Takashi; Cassee, Flemming R.; Saito, Naoto; Usui, Yuki; Kobayashi, Shinsuke; Porter, Dale W.; Castranova, Vincent; Endo, Morinobu

    2016-01-01

    Progress in the development of carbon nanotubes (CNTs) has stimulated great interest among industries providing new applications. Meanwhile, toxicological evaluations on nanomaterials are advancing leading to a predictive exposure limit for CNTs, which implies the possibility of designing safer CNTs. To pursue safety by design, the redox potential in reactions with CNTs has been contemplated recently. However, the chemical reactivity of CNTs has not been explored kinetically, so that there is no scheme to express a redox reaction with CNTs, though it has been investigated and reported. In addition, the reactivity of CNTs is discussed with regard to impurities that consist of transition metals in CNTs, which obfuscates the contribution of CNTs to the reaction. The present work aimed at modeling CNT scavenging in aqueous solution using a kinetic approach and a simple first-order reaction scheme. The results show that CNTs follow the redox reaction assumption in a simple chemical system. As a result, the reaction with multiwalled CNTs is semi-quantitatively denoted as redox potential, which suggests that their biological reactions may also be evaluated using a redox potential scheme. PMID:27030782

  18. Hydroxyl radical generation by a light-dependent Fenton reaction.

    PubMed

    Van der Zee, J; Krootjes, B B; Chignell, C F; Dubbelman, T M; Van Steveninck, J

    1993-02-01

    Illumination of Fe3+, with light of a wavelength varying from 250 to 450 nm, in the presence of the iron chelators ethylenediamine N,N,N',N'-tetraacetic acid (EDTA), ethyleneglycol-bis-(beta-aminoethylether)N,N,N',N'-tetraacet ic acid (EGTA), diethylenetriamine-N,N,N',N',N'-pentaacetic acid (DTPA), or citrate resulted in the reduction of Fe3+ to Fe2+. Fe2+ formation was measured by the formation of its complex with bathophenanthroline disulfonic acid. In all cases Fe2+ formation was completely dependent on the presence of the iron chelator and on the wavelength used for illumination. A correlation was found between the absorption spectrum of the iron-chelator complex and the amount of Fe3+ reduced, suggesting that the absorption of light induced an electron transfer from the chelator to the iron ion. Exposure to oxygen, either during or after illumination, resulted in degradation of the chelator molecule. Illumination of the Fe(3+)-chelator complexes in the presence of H2O2 resulted in the formation of hydroxyl radicals, which could be determined by the formation of the 5,5-dimethyl-1-pyrroline N-oxide (DMPO)-hydroxyl radical adduct, using electron spin resonance spectroscopy. Formation of the spin adduct was inhibited by addition of catalase, mannitol, ethanol, or formate, whereas superoxide dismutase had no effect.

  19. EPR and DFT Study of the Polycyclic Aromatic Radical Cations from Friedel-Crafts Alkylation Reactions

    NASA Astrophysics Data System (ADS)

    Wang, Tao; Wu, An-an; Gao, Li-guo; Wang, Han-qing

    2009-02-01

    Electron paramagnetic resonance and electron-nuclear double resonance methods were used to study the polycyclic aromatic radical cations produced in a Friedel-Crafts alkylating system, with m-xylene, or p-xylene and alkyl chloride. The results indicate that the observed electron paramagnetic resonance spectra are due to polycyclic aromatic radicals formed from the parent hydrocarbons. It is suggested that benzyl halides produced in the Friedel-Crafts alkylation reactions undergo Scholl self-condensation to give polycyclic aromatic hydrocarbons, which are converted into corresponding polycyclic aromatic radical cations in the presence of AlCl3. The identification of observed two radicals 2,6-dimethylanthracene and 1,4,5,8-tetramethylanthracene were supported by density functional theory calculations using the B3LYP/6-31G(d,p)//B3LYP/6-31G(d) approach. The theoretical coupling constants support the experimental assignment of the observed radicals.

  20. 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.

  1. 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.

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

    DOE PAGES

    Wang, Qiang; Zheng, Jianming; Walter, Eric; ...

    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

  3. Reactions of oxygen radicals with the quinone ring of coenzyme Q.

    PubMed

    Fiorentini, D; Cabrini, L; Sechi, A M; Landi, L

    1991-01-01

    Coenzyme Q, besides its role in electron transfer reactions, may act as a radical scavenger. The effect of oxygen radicals produced by ultrasonic irradiation on the quinone ring was investigated. Aqueous solutions of a Q homologue, completely lacking the side chain, were irradiated and the modifications were spectrophotometrically followed. The experimental results show that both degradation and reduction of the benzoquinone ring took place when the irradiation was performed in water. Data obtained when ultrasonic irradiation was carried out in the presence of OH. scavengers, as formate, organic and inorganic buffers, suggest: a) the responsible species for most the ubiquinol generated by sonication appeared to be the superoxide radical b) addition reactions of OH. radicals with the aromatic ring led probably to the degradation of Coenzyme Q molecules.

  4. Radical exchange reactions between vitamin E, vitamin C and phospholipids in autoxidizing polyunsaturated lipids.

    PubMed

    Lambelet, P; Saucy, F; Löliger, J

    1994-01-01

    Antioxidant reactions of mixtures of vitamin E, vitamin C and phospholipids in autoxidizing lipids at 90 degrees C have been studied by ESR spectroscopy. When the phospholipid contained a tertiary amine (e.g. phosphatidylcholine), the vitamin C and the vitamin E radicals were successively observed as these two vitamins were sequentially oxidised during lipid oxidation. In the presence of the primary amine contained in phosphatidylserine, the vitamin E oxidation was delayed for a few hours. In this case neither the vitamin C, nor the vitamin E radicals but a nitroxide radical derived from the phospholipid was observed. Similar results to those obtained with PS were obtained in the presence of either phosphatidylethanolamine or soybean lecithin. The participation in the radical reactions of phospholipids possessing a primary amine can therefore explain the synergistic effect of these phospholipids in a mixture of vitamins E and C.

  5. 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.

  6. 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.

  7. Synthetic and Mechanistic Aspects of the Regioselective Base-Mediated Reaction of Perfluoroalkyl- and Perfluoroarylsilanes with Heterocyclic N-Oxides

    PubMed Central

    Stephens, David E.; Chavez, Gabriel; Valdes, Martin; Dovalina, Monica; Arman, Hadi D.

    2014-01-01

    The scope and mechanistic implications of the direct transformation of heterocyclic N-oxides to 2-trifluoromethyl-, and related perfluoroalkyl- and perfluoroaryl-substituted N-heterocycles has been studied. The reaction is effected by perfluoroalkyl- and perfluorophenyltrimethylsilane in the presence of strong base. In situ displacement of the para-fluoro substituent in the pentafluorophenyl ring and the methoxy group in 8-methoxyquinolines with additional nucleophiles allows for further site-selective refunctionalization of the N-heterocyclic products. PMID:24993899

  8. 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

  9. 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.

  10. Total synthesis of cephalosporolide E via a tandem radical/polar crossover reaction. The use of the radical cations under nonoxidative conditions in total synthesis.

    PubMed

    Cortezano-Arellano, Omar; Quintero, Leticia; Sartillo-Piscil, Fernando

    2015-03-06

    The present work reports the first example of the use of the chemistry of radical cations under nonoxidative conditions in total synthesis. Using a late-stage tandem radical/polar crossover reaction, a highly stereoselective total synthesis of cephalosporolide E (which is typically obtained admixed with cephalosporolide F) was accomplished. The reaction of a phthalimido derivative with triphenyltin radical in refluxing toluene engenders a contact ion-pair (radical cation) that leads, in the first instance, to the cephalosporolide F, which is transformed into the cephalosporolide E via a stereocontrolled spiroketal isomerization promoted by the diphenylphosphate acid that is formed during the tandem transformation.

  11. 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.

  12. 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.

  13. Reactions of 1-hydroxy-1-methylethyl radicals with NO2-: time-resolved electron spin resonance.

    PubMed

    Filipiak, Piotr; Camaioni, Donald M; Fessenden, Richard W; Carmichael, Ian; Hug, Gordon L

    2006-09-28

    The reaction of the alpha-hydroxyalkyl radical of 2-propanol (1-hydroxy-1-methylethyl radical) with nitrite ions was characterized. A product of the reaction was assigned as the adduct nitro radical anion, [HO-C(CH(3))(2)NO(2)](*-). This radical was identified using time-resolved electron spin resonance (TRESR). The radical's magnetic parameters, the nitrogen hyperfine coupling constant (a(N) = 26.39 G), and its g-factor (2.0052) were the same as those of the nitro radical anion previously discovered in (*)OH spin-trapping experiments with the aci-anion of (CH(3))(2)CHNO(2). Production of [HO-C(CH(3))(2)NO(2)](*-) was determined to be 38% +/- 4% of the reaction of (CH(3))(2)C(*)-OH with nitrite. The reason why this fraction was less than 100% was rationalized by invoking the competitive addition at oxygen, which forms [HO-C(CH(3))(2)ONO](*-), followed by a rapid loss of (*)NO. Furthermore, by taking this mechanism into account, the bimolecular rate constant for the total reaction of (CH(3))(2)C(*)-OH with nitrite at reaction pH 7 was determined to be 1.6 x 10(6) M(-1) s(-1), using both decay traces of (CH(3))(2)C(*)-OH and growth traces of [HO-C(CH(3))(2)NO(2)](*-). This correspondence further confirms the nature of the reaction. The reaction mechanism is discussed with guidance by computations using density functional theory.

  14. 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.

  15. 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

  16. The temperature dependence of the rate constant for the reaction of hydroxyl radicals with nitric acid

    NASA Technical Reports Server (NTRS)

    Kurylo, M. J.; Cornett, K. D.; Murphy, J. L.

    1982-01-01

    The rate constant for the reaction of hydroxyl radicals with nitric acid in the 225-443 K temperature range has been measured by means of the flash photolysis resonance fluorescence technique. Above 300 K, the rate constant levels off in a way that can only be explained by the occurrence of two reaction channels, of which one, operative at low temperatures, proceeds through the formation of an adduct intermediate. The implications of these rate constant values for stratospheric reaction constants is discussed.

  17. The temperature dependence of the rate constant for the reaction of hydroxyl radicals with nitric acid

    NASA Technical Reports Server (NTRS)

    Kurylo, M. J.; Cornett, K. D.; Murphy, J. L.

    1982-01-01

    The rate constant for the reaction of hydroxyl radicals with nitric acid in the 225-443 K temperature range has been measured by means of the flash photolysis resonance fluorescence technique. Above 300 K, the rate constant levels off in a way that can only be explained by the occurrence of two reaction channels, of which one, operative at low temperatures, proceeds through the formation of an adduct intermediate. The implications of these rate constant values for stratospheric reaction constants is discussed.

  18. Kinetics and mechanism of hydroxyl radical and OH-adduct radical reactions with nitroxides and with their hydroxylamines.

    PubMed

    Samuni, Amram; Goldstein, Sara; Russo, Angelo; Mitchell, James B; Krishna, Murali C; Neta, Pedatsur

    2002-07-24

    Stable nitroxide radicals are potent antioxidants and are among the most effective non-thiol radioprotectants, although they react with hydroxyl radicals more slowly than typical phenolic antioxidants or thiols. Surprisingly, the reduced forms of cyclic nitroxides, cyclic hydroxylamines, are better reductants yet have no radioprotective activity. To clarify the reason for this difference, we studied the kinetics and mechanisms of the reactions of nitroxides and their hydroxylamines with (*)OH radicals and with OH-adducts by using pulse radiolysis, fluorimetric determination of phenolic radiation products, and electron paramagnetic resonance spectrometric determination of nitroxide concentrations following radiolysis. Competition kinetics with phenylalanine as a reference compound in pulse radiolysis experiments yielded rate constants of (4.5 +/- 0.4) x 10(9) M(-1) s(-1) for the reaction of (*)OH radical with 2,2,6,6-tetramethylpiperidine-N-oxyl (TPO), 4-hydroxy-TPO (4-OH-TPO), and 4-oxo-TPO (4-O-TPO), (3.0 +/- 0.3) x 10(9) M(-1) s(-1) for deuterated 4-O-TPO, and (1.0 +/- 0.1) x 10(9) M(-1) s(-1) for the hydroxylamine 4-OH-TPO-H. The kinetic isotope effect suggests the occurrence of both (*)OH addition to the aminoxyl moiety of 4-O-TPO and H-atom abstraction from the 2- or 6-methyl groups or from the 3- and 5-methylene positions. This conclusion was further supported by final product analysis, which demonstrated that (*)OH partially oxidizes 4-O-TPO to the corresponding oxoammonium cation. The rate constants for the reactions of the nitroxides with the OH-adducts of phenylalanine and terephthalate have been determined to be near 4 x 10(6) M(-1) s(-1), whereas the hydroxylamine reacted at least 50 times slower, if at all. These findings indicate that the reactivity toward (*)OH does not explain the differences between the radioprotective activities of nitroxides and hydroxylamines. Instead, the radioprotective activity of nitroxides, but not of hydroxylamines, can be

  19. Accurate thermochemistry of hydrocarbon radicals via an extended generalized bond separation reaction scheme.

    PubMed

    Wodrich, Matthew D; Corminboeuf, Clémence; Wheeler, Steven E

    2012-04-05

    Detailed knowledge of hydrocarbon radical thermochemistry is critical for understanding diverse chemical phenomena, ranging from combustion processes to organic reaction mechanisms. Unfortunately, experimental thermochemical data for many radical species tend to have large errors or are lacking entirely. Here we develop procedures for deriving high-quality thermochemical data for hydrocarbon radicals by extending Wheeler et al.'s "generalized bond separation reaction" (GBSR) scheme (J. Am. Chem. Soc., 2009, 131, 2547). Moreover, we show that the existing definition of hyperhomodesmotic reactions is flawed. This is because transformation reactions, in which one molecule each from the predefined sets of products and reactants can be converted to a different product and reactant molecule, are currently allowed. This problem is corrected via a refined definition of hyperhomodesmotic reactions in which there are equal numbers of carbon-carbon bond types inclusive of carbon hybridization and number of hydrogens attached. Ab initio and density functional theory (DFT) computations using the expanded GBSRs are applied to a newly derived test set of 27 hydrocarbon radicals (HCR27). Greatly reduced errors in computed reaction enthalpies are seen for hyperhomodesmotic and other highly balanced reactions classes, which benefit from increased matching of hybridization and bonding requirements. The best performing DFT methods for hyperhomodesmotic reactions, M06-2X and B97-dDsC, give average deviations from benchmark computations of only 0.31 and 0.44 (±0.90 and ±1.56 at the 95% confidence level) kcal/mol, respectively, over the test set. By exploiting the high degree of error cancellation provided by hyperhomodesmotic reactions, accurate thermochemical data for hydrocarbon radicals (e.g., enthalpies of formation) can be computed using relatively inexpensive computational methods.

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

    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 C10H7+ 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 C16H13+, C16Hn+ (with n =10-12), and C15H10+. From pressure-dependent measurements, absolute cross sections of 1.0±0.3 and 2±0.6 Å2 (at a collision energy of about 0.2 eV in the center of mass frame) are derived for channels leading to the formation of C16H12+ and C15H10+ ions, respectively. From cross section values a phenomenological total rate constant k =(5.8±1.9)×10-11 cm3 s-1 at an average collision energy of about 0.27 eV can be estimated for the process C10H7++C6H6→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, H2, CH3). A major signal relevant to the fragmentation of the initial adduct C16H13+ belongs to C15H10+. Since it is not obvious how CH3 loss from C16H13+ can take place to form the C15H10+ radical cation, a theoretical investigation focuses on possible unimolecular transformations apt to produce it. Naphthylium can act as an electrophile and add to the π system of benzene, leading to a barrierless formation of the ionic adduct with an exothermicity of about 53 kcal mol-1. From this structure, an intramolecular electrophilic addition followed by H shifts and ring opening steps leads to an overall exothermic loss (-7.1 kcal mol-1 with respect to reagents) of

  2. Computational Study of the Thermodynamics of Atmospheric Nitration of PAHs via OH-Radical-Initiated Reaction

    NASA Astrophysics Data System (ADS)

    Jariyasopit, N.; Cheong, P.; Simonich, S. L.

    2011-12-01

    Nitrated polycyclic aromatic hydrocarbons (NPAHs) are an important class of PAH derivatives that are more toxic than their parent PAHs (1) and are emitted from direct emission and secondary emission to the atmosphere. The secondary emissions, particularly the OH-radical initiated and NO3-radical-initiated reactions, have been shown to influence the NPAH concentrations in the atmosphere. Gas-phase reactions are thought to be the major sources of NPAHs containing four or fewer rings (2). Besides NPAHs, PAHs lead to a number of other products including oxygenated, hydroxy substituted and ring-opened PAH derivatives (3). For some PAHs, the OH-initiated and NO3-initiated reactions result in the formation of different NPAH isomers, allowing the ratio of these isomers to be used in the determination of direct or secondary emission sources. Previous studies have shown that the PAH gas-phase reactions with OH radical is initiated by the addition of OH radical to the aromatic ring to form hydroxycyclohexadienyl radicals (4). In the presence of NO2, these reactive intermediates readily nitrate with the elimination of water (4). The hydroxycyclohexadienyl-type radical intermediates are also prone to react with other species in the atmosphere or revert back to the original compound (3). The objective of this study was to investigate the thermodynamics of PAH nitration through day-time OH-radical-initiated reactions. The theoretical investigation were carried out using Density Functioanl Theory (B3LYP) and the 6-31G(d) basis set, as implemented in Gaussian03. A number of different PAHs were studied including fluoranthene, pyrene, as well as the molecular weight 302 PAHs such as dibenzo[a,l]pyrene. Computations were also used to predict unknown NPAHs formed by OH-radical-initiated reaction. All intermediates for the OH-radical addition and the following nitration were computed. We have discovered that the thermodynamic stability of the intermediates involved in the PAH

  3. 1,4-Addition of TMSCCl₃ to nitroalkenes: efficient reaction conditions and mechanistic understanding.

    PubMed

    Wu, Na; Wahl, Benoit; Woodward, Simon; Lewis, William

    2014-06-16

    Improved synthetic conditions allow preparation of TMSCCl3 in good yield (70%) and excellent purity. Compounds of the type NBu4X [X=Ph3SiF2 (TBAT), F (tetrabutylammonium fluoride, TBAF), OAc, Cl and Br] act as catalytic promoters for 1,4-additions to a range of cyclic and acyclic nitroalkenes, in THF at 0-25 °C, typically in moderate to excellent yields (37-95%). TBAT is the most effective promoter and bromide the least effective. Multinuclear NMR studies ((1)H, (19)F, (13)C and (29)Si) under anaerobic conditions indicate that addition of TMSCCl3 to TBAT (both 0.13 M) at -20 °C, in the absence of nitroalkene, leads immediately to mixtures of Me3SiF, Ph3SiF and NBu4CCl3. The latter is stable to at least 0 °C and does not add nitroalkene from -20 to 0 °C, even after extended periods. Nitroalkene, in the presence of TMSCCl3 (both 0.13 M at -20 °C), when treated with TBAT, leads to immediate formation of the 1,4-addition product, suggesting the reaction proceeds via a transient [Me3Si(alkene)CCl3] species, in which (alkene) indicates an Si⋅⋅⋅O coordinated nitroalkene. The anaerobic catalytic chain is propagated through the kinetic nitronate anion resulting from 1,4 CCl3(-) addition to the nitroalkene. This is demonstrated by the fact that isolated NBu4[CH2=NO2] is an efficient promoter. Use of H2C=CH(CH2)2CH=CHNO2 in air affords radical-derived bicyclic products arising from aerobic oxidation.

  4. Recent advances in the synthesis of nitrogen heterocycles via radical cascade reactions using isonitriles as radical acceptors.

    PubMed

    Zhang, Bo; Studer, Armido

    2015-06-07

    Nitrogen heterocycles belong to a highly important class of compounds which are found in various natural products, biologically active structures, and medicinally relevant compounds. Therefore, there is continuing interest in the development of novel synthetic methods for the construction of nitrogen containing heterocycles. Recently, radical insertion reactions into isonitriles have emerged as an efficient and powerful strategy for the construction of nitrogen heterocycles, such as phenanthridines, indoles, quinolines, quinoxalines, and isoquinolines. This review highlights recent advances in this fast growing research area and also includes important pioneering studies in this area.

  5. Intramolecular hydrogen transfer reactions of thiyl radicals from glutathione: formation of carbon-centered radical at Glu, Cys and Gly

    PubMed Central

    Mozziconacci, Olivier; Williams, Todd D.; Schöneich, Christian

    2013-01-01

    Glutathione thiyl radicals (GS•) were generated in H2O and D2O by either exposure of GSH to AAPH#, photoirradiation of GSH in the presence of acetone, or photoirradiation of GSSG. Detailed interpretation of the fragmentation pathways of deuterated GSH and GSH-derivatives during mass spectrometry analysis allowed us to demonstrate that reversible intramolecular H-atom transfer reactions between GS• and C-H bonds at Cys[αC], Cys[βC], and Gly[αC] are possible. PMID:22712461

  6. Direct simulation of electron transfer reactions in DNA radical cations

    PubMed Central

    Steinbrecher, Thomas; Koslowski, Thorsten; Case, David A.

    2009-01-01

    The electron transfer properties of DNA radical cations are important in DNA damage and repair processes. Fast long-range charge transfer has been demonstrated experimentally, but the subtle influences that experimental conditions as well as DNA sequences and geometries have on the details of electron transfer parameters are still poorly understood. In this work, we employ an atomistic QM/MM approach, based on a one-electron tight binding Hamiltonian and a classical molecular mechanics forcefield, to conduct nanosecond length MD simulations of electron holes in DNA oligomers. Multiple spontaneous electron transfer events were observed in 100 ns simulations with neighbouring adenine or guanine bases. Marcus parameters of charge transfer could be extracted directly from the simulations. The reorganisation energy λ for hopping between neighbouring bases was found to be ca. 25 kcal/mol and charge transfer rates of 4.1×109 s−1 for AA hopping and 1.3×109 s−1 for GG hopping were obtained. PMID:19049302

  7. Autoxidation of drugs: prediction of degradation impurities from results of reaction with radical chain initiators.

    PubMed

    Boccardi, G

    1994-06-01

    In the study of the degradation of drug substances by molecular oxygen, their specific reaction mechanisms must be taken into account. The rate-determining step is usually the reaction of the substrate with a radical chain initiator, which is often an unknown impurity. The reactivity and selectivity of autoxidation can be controlled better by using a radical chain initiator, such as AIBN, than by changing the temperature or the oxygen pressure. In this paper the products profiles of four pharmaceutical substances in a simple oxidation test with AIBN are compared with the results of long term natural stability tests or with already established stabilities.

  8. The reaction of methionine with hydroxyl radical: reactive intermediates and methanethiol production.

    PubMed

    Spasojević, Ivan; Bogdanović Pristov, Jelena; Vujisić, Ljubodrag; Spasić, Mihajlo

    2012-06-01

    The mechanisms of reaction of methionine with hydroxyl radical are not fully understood. Here, we unequivocally show using electron paramagnetic resonance spin-trapping spectroscopy and GC-FID and GC-MS, the presence of specific carbon-, nitrogen- and sulfur-centered radicals as intermediates of this reaction, as well as the liberation of methanethiol as a gaseous end product. Taking into account the many roles that methionine has in eco- and biosystems, our results may elucidate redox chemistry of this amino acid and processes that methionine is involved in.

  9. 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

  10. Detection of free radicals in low-temperature gas-grain reactions of astrophysical interest

    NASA Astrophysics Data System (ADS)

    Zhitnikov, R. A.; Dmitriev, Yu. A.

    2002-05-01

    For laboratory detection and investigation of free radicals which often appear in chemical reactions of astrophysical interest either as important intermediate or as final products, we pioneered the use of the electron paramagnetic resonance (EPR) technique, which is very effective in observing these substances. This has allowed both formyl (HCO and DCO) and methyl (CH3 and CD3) free radicals to be detected in a sequence of low-temperature gas-grain reactions of H and D atom addition in solid CO. The solid samples subjected to the EPR study were obtained by simultaneous independent deposition of CO molecules and either H or D atoms on the substrate cooled to liquid helium temperatures. The sequence of the H-atom addition gas-grain reactions in solid CO is acknowledged to be among the fundamental processes responsible for the synthesis of organic molecules in interstellar cloud dust grains. The present observation of the above free radicals confirms that the solid-state gas-grain sequence of the reactions is efficient at low temperatures; it also suggests that there should be considerable concentrations of formyl and methyl radicals in the ISM. Another study concentrated on the formation of ethyl free radicals (C2H5) in a low-temperature gas-grain reaction of H-atom abstraction from a C2H6 molecule by free H-atom in solid CH4. These experiments were carried out by deposition onto a substrate, cooled by liquid helium, of a flow of CH4 molecules containing a small amount of impurities such as ethane molecules (C2H6), free H-atoms and CH3 radicals formed in a discharge in a pure gaseous methane. EPR spectra of CH3 radicals, H-atoms, and C2H5 radicals matrix-isolated in solid CH4 were detected. The relative concentrations of the radicals were found to depend on the experimental conditions. The abstraction reaction, C2H6 + H -> C2H5 + H2, took place in CH4-ice.

  11. Disinfection of water containing natural organic matter by using ozone-initiated radical reactions.

    PubMed

    Cho, Min; Chung, Hyenmi; Yoon, Jeyong

    2003-04-01

    Ozone is widely used to disinfect drinking water and wastewater due to its strong biocidal oxidizing properties. Recently, it was reported that hydroxyl radicals ((.)OH), resulting from ozone decomposition, play a significant role in microbial inactivation when Bacillus subtilis endospores were used as the test microorganisms in pH controlled distilled water. However, it is not yet known how natural organic matter (NOM), which is ubiquitous in sources of drinking water, affects this process of disinfection by ozone-initiated radical reactions. Two types of water matrix were considered for this study. One is water containing humic acid, which is commercially available. The other is water from the Han River. This study reported that hydroxyl radicals, initiated by the ozone chain reaction, were significantly effective at B. subtilis endospore inactivation in water containing NOM, as well as in pH-controlled distilled water. The type of NOM and the pH have a considerable effect on the percentage of disinfection by hydroxyl radicals, which ranged from 20 to 50%. In addition, the theoretical T value of hydroxyl radicals for 2-log B. subtilis removal was estimated to be about 2.4 x 10(4) times smaller than that of ozone, assuming that there is no synergistic activity between ozone and hydroxyl radicals.

  12. Kinetics of the CH2Cl + CH3 and CHCl2 + CH3 radical-radical reactions.

    PubMed

    Shestov, Alexander A; Popov, Konstantin V; Knyazev, Vadim D

    2005-07-21

    The CH2Cl + CH3 (1) and CHCl2 + CH3 (2) cross-radical reactions were studied by laser photolysis/photoionization mass spectroscopy. Overall rate constants were obtained in direct real-time experiments in the temperature region 301-800 K and bath gas (helium) density (6-12) x 10(16) atom cm(-3). The observed rate constant of reaction 1 can be represented by an Arrhenius expression k1 = 3.93 x 10(-11) exp(91 K/T) cm3 molecule(-1) s(-1) (+/-25%) or as an average temperature-independent value of k1= (4.8 +/- 0.7) x 10(-11) cm3 molecule(-1) s(-1). The rate constant of reaction 2 can be expressed as k2= 1.66 x 10(-11) exp(359 K/T) cm3 molecule(-1) s(-1) (+/-25%). C2H4 and C2H3Cl were detected as the primary products of reactions 1 and 2, respectively. The experimental values of the rate constant are in reasonable agreement with the prediction based on the "geometric mean rule." A separate experimental attempt to determine the rate constants of the high-temperature CH2Cl + O2 (10) and CHCl2 + O2 (11) reaction resulted in an upper limit of 1.2 x 10(-16) cm(3) molecule(-1) s(-1) for k10 and k11 at 800 K.

  13. Kinetics Studies of Radical-Radical Reactions (I): The NO2 + N2H3 System

    DTIC Science & Technology

    2013-08-01

    PERFORMING ORGANIZATION REPORT NO. Air Force Research Laboratory (AFMC) AFRL/RQRP 10 E. Saturn Blvd. Edwards AFB CA 93524-7680 9...MMH by NO2/N2O4 at atmospheric pressure occurs via two mechanisms: (1) sequential H-abstraction and HONO formation , and (2) reaction of MMH with...asymmetric ONONO2, leading to the formation of methyl nitrate. Furthermore, they reported that all of the intermediates observed experimentally could be

  14. Hydrogen migrations in alkylcycloalkyl radicals: implications for chain-branching reactions in fuels.

    PubMed

    Davis, Alexander C; Tangprasertchai, Narin; Francisco, Joseph S

    2012-09-03

    A thorough understanding of the oxidation chemistry of cycloalkanes is integral to the development of alternative fuels and improving current fuel performance. An important class of reactions essential to this chemistry is the hydrogen migration; however, they have largely been omitted from the literature for cycloalkanes. The present work investigates all of the hydrogen migration reactions available to methylcyclopentane, ethylcyclopentane, methylcyclohexane, and ethylcyclohexane. The kinetic and thermodynamic parameters have been studied by a combination of computational methods and compared to their corresponding n-alkyl and methylalkyl counterparts to determine the effect that the cycloalkane ring has on these reactions. In particular, although the alkylcycloalkyl activation energies for the dominant 1,4, 1,5, and 1,6 H-migration are higher than in n-alkyl and methylalkyl radicals, because several of the rotors needed to form the transition state are locked into place as part of the cycloalkane ring, the A-factors are higher for the alkylcycloalkyl reactions, making the rates closer to the noncyclic systems, at higher temperatures. The results presented here suggest that the relative importance of each H-migration pathway differs from the trends predicted by either the n-alkyl or methylalkyl radical systems. Of particular interest is the observation that since the barrier height of the 1,4 H-migration is only 3-5 kcal mol(-1) higher than the 1,5 H-migration in the methyl and ethylcycloalkyl radicals, compared to a difference of roughly 7 kcal mol(-1) in similar reactions for both the n-alkyl and methylalkyl radicals, the 1,4 H-migrations in alkylcycloalkyl radicals will be more important in the overall mechanism than would be predicted based on the n-alkyl and methylalkyl radicals. These results have important combustion model implications, particularly for fuels with high cycloalkane content.

  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. Free Radical Chemistry of Disinfection Byproducts 1: Kinetics of Hydrated Electron and Hydroxyl Radical Reactions with Halonitromethanes in Water

    SciTech Connect

    B. J. Mincher; R. V. Fox; S. P. Mezyk; T. Helgeson; S. K. Cole; W. J. Cooper; P. R. Gardinali

    2006-01-01

    Halonitromethanes are disinfection-byproducts formed during ozonation and chlorine/chloramine treatment of waters that contain bromide ion and natural organic matter. In this study, the chemical kinetics of the free-radical-induced degradations of a series of halonitromethanes were determined. Absolute rate constants for hydroxyl radical, OH, and hydrated electron, eaq-, reaction with both chlorinated and brominated halonitromethanes were measured using the techniques of electron pulse radiolysis and transient absorption spectroscopy. The bimolecular rate constants obtained, k (M-1 s-1), for eaq-/OH, respectively, were the following: chloronitromethane (3.01 ± 0.40) × 1010/(1.94 ± 0.32) × 108; dichloronitromethane (3.21 ± 0.17) × 1010/(5.12 ± 0.77) × 108; bromonitromethane (3.13 ± 0.06) × 1010/(8.36 ± 0.57) × 107; dibromonitromethane (3.07 ± 0.40) × 1010/(4.75 ± 0.98) × 108; tribromonitromethane (2.29 ± 0.39) × 1010/(3.25 ± 0.67) × 108; bromochloronitromethane (2.93 ± 0.47) × 1010/(4.2 ± 1.1) × 108; bromodichloronitromethane (2.68 ± 0.13) × 1010/(1.02 ± 0.15) × 108; and dibromochloronitromethane (2.95 ± 0.43) × 1010 / (1.80 ± 0.31) × 108 at room temperature and pH ~7. Comparison data were also obtained for hydroxyl radical reaction with bromoform (1.50 ± 0.05) × 108, bromodichloromethane (7.11 ± 0.26) × 107, and chlorodibromomethane (8.31 ± 0.25) × 107 M-1 s-1, respectively. These rate constants are compared to recently obtained data for trichloronitromethane and bromonitromethane, as well as to other established literature data for analogous compounds.

  17. Laser-Initiated Free Radical Chain Reactions: Synthesis Of Hydroperoxides

    NASA Astrophysics Data System (ADS)

    Bray, R. G.; Chou, M. S.

    1984-05-01

    We have investigated the advantages of using laser-initiation for the synthesis of cumenehydroperoxide and t-butylhydroperoxide. Laser-initiation significantly improves the oxidation rates of cumene in the liquid phase and iso-butane in the vapor phase (using HBr promoters) with moderate photoefficiencies (418 and 490 respectively). The primary effect of laser-initiation is to reduce the induction period of the reaction. For the oxidation of cumene the beneficial effect of laser initiation is strongly dependent on laser wavelength, alternately enhancing (at 351 nm) or inhibiting (at 249 nm) the oxidation rate. For isobutane oxidation, laser-initiation also minimizes the HBr depletion rate relative to oxidation rate.

  18. 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.

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

    PubMed

    Sinha, Sourab; Raj, Abhijeet

    2016-03-21

    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.

  20. Untangling the Energetics and Dynamics of Boron Monoxide Radical Reactions (11BO; X2Sigma+)

    DTIC Science & Technology

    2015-04-15

    Crossed Beam Reaction of Boron Monoxide with Benzene (P6) Organyl oxoboranes (RBO) are valuable reagents in organic synthesis due to their role in...technique, phenyl oxoborane (C6H5BO) is formed through the reaction of boronyl radicals (BO) with benzene (C6H6). The reaction is indirect...Phenyloxo-borane (C6H5BO) via the Reaction of Boron Monoxide with Benzene . JOC 78, 11896- 11900 (2013). P7. R.I. Kaiser, S. Maity, B. Dangi, A,H.H

  1. Vibrationally quantum-state-specific reaction dynamics of H atom abstraction by CN radical in solution.

    PubMed

    Greaves, Stuart J; Rose, Rebecca A; Oliver, Thomas A A; Glowacki, David R; Ashfold, Michael N R; Harvey, Jeremy N; Clark, Ian P; Greetham, Gregory M; Parker, Anthony W; Towrie, Michael; Orr-Ewing, Andrew J

    2011-03-18

    Solvent collisions can often mask initial disposition of energy to the products of solution-phase chemical reactions. Here, we show with transient infrared absorption spectra obtained with picosecond time resolution that the nascent HCN products of reaction of CN radicals with cyclohexane in chlorinated organic solvents exhibit preferential excitation of one quantum of the C-H stretching mode and up to two quanta of the bending mode. On time scales of approximately 100 to 300 picoseconds, the HCN products undergo relaxation to the vibrational ground state by coupling to the solvent bath. Comparison with reactions of CN radicals with alkanes in the gas phase, known to produce HCN with greater C-H stretch and bending mode excitation (up to two and approximately six quanta, respectively), indicates partial damping of the nascent product vibrational motion by the solvent. The transient infrared spectra therefore probe solvent-induced modifications to the reaction free energy surface and chemical dynamics.

  2. 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).

  3. Room-temperature and temperature-dependent QSRR modelling for predicting the nitrate radical reaction rate constants of organic chemicals using ensemble learning methods.

    PubMed

    Gupta, S; Basant, N; Mohan, D; Singh, K P

    2016-07-01

    Experimental determinations of the rate constants of the reaction of NO3 with a large number of organic chemicals are tedious, and time and resource intensive; and the development of computational methods has widely been advocated. In this study, we have developed room-temperature (298 K) and temperature-dependent quantitative structure-reactivity relationship (QSRR) models based on the ensemble learning approaches (decision tree forest (DTF) and decision treeboost (DTB)) for predicting the rate constant of the reaction of NO3 radicals with diverse organic chemicals, under OECD guidelines. Predictive powers of the developed models were established in terms of statistical coefficients. In the test phase, the QSRR models yielded a correlation (r(2)) of >0.94 between experimental and predicted rate constants. The applicability domains of the constructed models were determined. An attempt has been made to provide the mechanistic interpretation of the selected features for QSRR development. The proposed QSRR models outperformed the previous reports, and the temperature-dependent models offered a much wider applicability domain. This is the first report presenting a temperature-dependent QSRR model for predicting the nitrate radical reaction rate constant at different temperatures. The proposed models can be useful tools in predicting the reactivities of chemicals towards NO3 radicals in the atmosphere, hence, their persistence and exposure risk assessment.

  4. Synthesis of α-Benzyloxyamino-γ-butyrolactones via a Polar Radical Crossover Cycloaddition Reaction.

    PubMed

    Cavanaugh, Cortney L; Nicewicz, David A

    2015-12-18

    A direct catalytic synthesis of substituted α-benzyloxyamino-γ-butyrolactones is reported, starting from simple oxime acids and alkenes. The substituted O-benzyloxime acid starting materials are cyclized with oxidizable alkenes, via Polar Radical Crossover Cycloaddition (PRCC) reactions. The catalytic reaction is carried out using the Fukuzumi acridinium photooxidant and substoichiometric amounts of a redox-active cocatalyst. The utility of this method has been demonstrated through the use of 3 oxime acids and 19 oxidizable olefins.

  5. Structural effects on the beta-scission reaction of alkoxyl radicals. Direct measurement of the absolute rate constants for ring opening of benzocycloalken-1-oxyl radicals.

    PubMed

    Bietti, Massimo; Lanzalunga, Osvaldo; Salamone, Michela

    2005-02-18

    [reaction: see text] The absolute rate constants for beta-scission of a series of benzocycloalken-1-oxyl radicals and of the 2-(4-methylphenyl)-2-butoxyl radical have been measured directly by laser flash photolysis. The benzocycloalken-1-oxyl radicals undergo ring opening with rates which parallel the ring strain of the corresponding cycloalkanes. In the 1-X-indan-1-oxyl radical series, ring opening is observed when X = H, Me, whereas exclusive C-X bond cleavage occurs when X = Et. The factors governing the fragmentation regioselectivity are discussed.

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

    PubMed

    Hoffmann, Reinhard W

    2016-02-07

    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.

  8. Kinetics and products of the reaction of OH radicals with 3-methoxy-3-methyl-1-butanol.

    PubMed

    Aschmann, Sara M; Arey, Janet; Atkinson, Roger

    2011-08-15

    3-Methoxy-3-methyl-1-butanol [CH(3)OC(CH(3))(2)CH(2)CH(2)OH] is used as a solvent for paints, inks, and fragrances and as a raw material for the production of industrial detergents. A rate constant of (1.64 ± 0.18) × 10(-11) cm(3) molecule(-1) s(-1) for the reaction of 3-methoxy-3-methyl-1-butanol with OH radicals has been measured at 296 ± 2 K using a relative rate method, where the indicated error is the estimated overall uncertainty. Acetone, methyl acetate, glycolaldehyde, and 3-methoxy-3-methylbutanal were identified as products of the OH radical-initiated reaction, with molar formation yields of 3 ± 1%, 35 ± 9%, 13 ± 3%, and 33 ± 7%, respectively, at an average NO concentration of 1.3 × 10(14) molecules cm(-3). Using a 12-h average daytime OH radical concentration of 2 × 10(6) molecules cm(-3), the calculated lifetime of 3-methoxy-3-methyl-1-butanol with respect to reaction with OH radicals is 8.5 h. Potential reaction mechanisms are discussed.

  9. Mechanistic studies on the reactions of platinum(II) complexes with nitrogen- and sulfur-donor biomolecules.

    PubMed

    Bugarčić, Živadin D; Bogojeski, Jovana; Petrović, Biljana; Hochreuther, Stephanie; van Eldik, Rudi

    2012-10-28

    A brief overview of mechanistic studies on the reactions of different Pt(II) complexes with nitrogen- and sulfur-donor biomolecules is presented. The first part describes the results obtained for substitution reactions of mono-functional Pt(II) complexes with different biomolecules, under various experimental conditions (temperature, pH and ionic strength). In addition, an overview of the results obtained for the substitution reactions of bi-functional Pt(II) complexes, analogous to cisplatin, with biomolecules is given. The last part of this report deals with different polynuclear Pt(II) complexes and their substitution behaviour with different biomolecules. The purpose of this perspective is to improve the understanding of the mechanism of action of Pt(II) complexes as potential anti-tumour drugs in the human body.

  10. 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…

  11. 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…

  12. Kinetics of 1,5-hydrogen migration in alkyl radical reaction class.

    PubMed

    Ratkiewicz, Artur; Bankiewicz, Barbara

    2012-01-12

    Kinetics of the 1,5-intramolecular hydrogen migration in the alkyl radicals reaction class has been studied using the reaction class transition state theory combined with the linear energy relationship (LER) and the barrier height grouping (BHG) approach. The high pressure limits of the rate constants for the reference reaction of 1-pentyl → 1-pentyl, calculated by the Canonical Variational Transition State Theory (CVT) with the Small Curvature Tunneling (SCT), are taken from the literature. Direct comparison with available experimental data indicates that the RC-TST/LER, where only reaction energy is needed, can predict rate constants for any reaction in this reaction class with excellent accuracy. Specifically for this reaction class, the RC-TST/LER method has less than 65% systematic errors in the predicted rate constants when compared to explicit rate calculations.

  13. 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.

  14. Exploring water catalysis in the reaction of thioformic acid with hydroxyl radical: a global reaction route mapping perspective.

    PubMed

    Kaur, Gurpreet; Vikas

    2014-06-12

    Hydrogen abstraction pathways, in the gas-phase reaction of tautomers of thioformic acid (TFA), TFA(thiol), and TFA(thione), with hydroxyl radical in the presence and absence of single water molecule acting as a catalyst, is investigated with high-level quantum mechanical calculations at CCSD(T)/6-311++G(2d,2p)//MP2/6-311++G(2d,2p), CCSD(T)/6-311++G(d,p)//DFT/BHandHLYP/6-311++G(d,p), and DFT/B3LYP/6-311++G(2df,2p) levels of the theory. A systematic and automated search of the potential energy surface (PES) for the reaction pathways is performed using the global reaction route mapping (GRRM) method that employs an uphill walking technique to search prereaction complexes and transition states. The computations reveal significant lowering of the PES and substantial reduction in the activation energy for the hydrogen abstraction pathway in the presence of water, thereby proving water as an efficient catalyst in the reaction of both the TFA tautomers with OH radical. The hydrogen-bonding interactions are observed to be responsible for the large catalytic effect of water. Notably, in the case of TFA(thiol), formyl hydrogen abstraction is observed to be kinetically more favorable, while acidic hydrogen abstraction is observed to be thermodynamically more feasible. Interestingly, in the case of TFA(thione), reaction pathways involving only formyl hydrogen abstraction were observed to be feasible. The water-catalyzed hydrogen abstraction reaction of TFA with hydroxyl radical, investigated in this work, can provide significant insights into the corresponding reaction in the biological systems.

  15. Kinetics and products of the OH radical-initiated reaction of 3-methyl-2-butenal.

    PubMed

    Tuazon, Ernesto C; Aschmann, Sara M; Nishino, Noriko; Arey, Janet; Atkinson, Roger

    2005-06-07

    Kinetics and products of the gas-phase reaction of OH radicals with 3-methyl-2-butenal [(CH3)2C=CHCHO] have been investigated at room temperature and atmospheric pressure of air. Using a relative rate method with methacrolein as the reference compound, a rate constant for the reaction of OH radicals with 3-methyl-2-butenal of (6.21 +/- 0.18) x 10(-11) cm3 molecule(-1) s(-1) at 296 +/- 2 K was measured, where the indicated error does not include the uncertainty in the rate constant for the methacrolein reference compound. Products of this reaction were investigated using in situ Fourier transform infrared (FT-IR) spectroscopy and solid phase microextraction (SPME) fibers coated with O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine for on-fiber derivatization of carbonyl compounds, with subsequent thermal desorption and analysis by gas chromatography. The products observed and the molar formation yields were: glyoxal, 40 +/- 3%; acetone, 74 +/- 6%; 2-hydroxy-2-methylpropanal, 4.6 +/- 0.7%; CO2, 39% initially, decreasing to 30% at greater extents of reaction; peroxyacyl nitrate(s) [RC(O)OONO2], 5-8%, increasing with the extent of reaction and with the sum of the CO2 and RC(O)OONO2 yields being 38 +/- 6%; and organic nitrates [RONO2], 8.5 +/- 2.3%. The formation of these products is readily explained by a reaction mechanism based on those previously formulated for the corresponding reactions of the alpha,beta-unsaturated aldehydes acrolein, crotonaldehyde and methacrolein. Based on the mechanism proposed, at room temperature H-atom abstraction from the CHO group accounts for 40 +/- 6% of the overall reaction, and OH radical addition to the carbon atoms of the C=C bond accounts for 53 +/- 4% of the overall reaction. Hence 93 +/- 8% of the reaction products and pathways are accounted for.

  16. 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

  17. Mechanistic diversity of the van Leusen reaction applied to 6-ketomorphinans and synthetic potential of the resulting acrylonitrile substructures.

    PubMed

    Schütz, Johannes; Windisch, Petra; Kristeva, Elka; Wurst, Klaus; Ongania, Karl-Hans; Horvath, Ulrike E I; Schottenberger, Herwig; Laus, Gerhard; Schmidhammer, Helmut

    2005-06-24

    Tosylmethyl isocyanide was used to convert 7,8-didehydro-6-ketomorphinans to 6,7-didehydromorphinan-6-carbonitriles with retainment of the 4,5-epoxy ring. However, ring opening occurred in the presence of NaH giving 5,6,7,8-tetradehydromorphinan-6-carbonitriles. Addition of nucleophiles such as Li diisopropylamide or Grignard reagents to the acrylonitrile substructure yielded ring-opened 5,6-didehydro products. Seven products were characterized by X-ray crystal structure analysis and revealed insight into the mechanistic diversity of the van Leusen reaction.

  18. 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.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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.

  1. Insights into relevant mechanistic aspects about the induction period of Cu(0)/Me(6)TREN-mediated reversible-deactivation radical polymerization.

    PubMed

    Gao, Yongsheng; Zhao, Tianyu; Zhou, Dezhong; Greiser, Udo; Wang, Wenxin

    2015-10-04

    There is a controversial debate about the mechanism of the Cu(0)-catalyzed radical polymerization. Herein, a comparative analysis of a series of reactions catalyzed by different valent copper shows that the induction period and the subsequent autoaccelerated polymerization of a Cu(0)/Me6TREN-catalyzed system originate from the accumulation of soluble copper species, and Cu(I) is still a powerful activator under its disproportionation favored conditions.

  2. Kinetic behavior of the reaction between hydroxyl radical and the SV40 minichromosome

    NASA Astrophysics Data System (ADS)

    Ly, A.; Aguilera, J. A.; Milligan, J. R.

    2007-06-01

    Aqueous solutions containing the minichromosomal form of the virus SV40 and the radical scavenger DMSO were subjected to γ-irradiation, and the resulting formation of single-strand breaks (SSB) was quantified. Under the irradiation conditions, most SSBs were produced as a consequence of hydroxyl radical ( rad OH) reactions. By controlling the competition between DMSO and the viral DNA substrate for rad OH, we are able to estimate the rate coefficient for the reaction of rad OH with the SV40 minichromosome. The results cannot be described adequately by homogeneous competition kinetics, but it is possible to describe the rate coefficient for the reaction as a function of the scavenging capacity of the solution. The experimentally determined rate coefficient lies in the range 1×10 9-2×10 9 L mol -1 s -1 at 10 7 s -1, and increases with increasing scavenging capacity.

  3. Heterogeneous reaction of particle-associated triphenylene with NO3 radicals

    NASA Astrophysics Data System (ADS)

    Zhang, Yang; Shu, Jinian; Liu, Changgeng; Zhang, Yuanxun; Yang, Bo; Gan, Jie

    2013-04-01

    Although heterogeneous reactions of polycyclic aromatic hydrocarbons (PAHs) with atmospheric oxidants may be important loss processes for PAHs, our understanding of their kinetics and products is incomplete. The study of heterogeneous reaction of suspended triphenylene particles with NO3 radicals is undertaken in a flow-tube-reactor. The time-of-flight mass spectra of particulate triphenylene and its nitration products are obtained with vacuum ultraviolet photoionization aerosol time-of-flight mass spectrometer. 1- and 2-nitrotriphenylene are identified by GC-MS analysis of the products formed from the reaction of NO3 radicals with triphenylene coated on the inner bottom surface of a conical flask. 1-Nitrotriphenylene is formed in larger yield than 2-nitrotriphenylene. This phenomenon is different from what had been observed in previous studies of the gas-phase triphenylene nitration, showing that 2-nitrotriphenylene is the major nitration product. The experimental results may reveal the discrepancies between heterogeneous and homogeneous nitrations of triphenylene.

  4. Reactions of the OOH radical with guanine: Mechanisms of formation of 8-oxoguanine and other products

    NASA Astrophysics Data System (ADS)

    Kumar, Nagendra; Shukla, P. K.; Mishra, P. C.

    2010-09-01

    The mutagenic product 8-oxoguanine (8-oxoGua) is formed due to intermediacy of peroxyl (OOR) radicals in lipid peroxidation and protein oxidation-induced DNA damage. The mechanisms of these reactions are not yet understood properly. Therefore, in the present study, the mechanisms of formation of 8-oxoGua and other related products due to the reaction of the guanine base of DNA with the hydroperoxyl radical (OOH) were investigated theoretically employing the B3LYP and BHandHLYP hybrid functionals of density functional theory and the polarizable continuum model for solvation. It is found that the reaction of the OOH radical with guanine can occur following seven different mechanisms leading to the formation of various products including 8-oxoGua, its radicals, 5-hydroxy-8-oxoguanine and CO 2. The mechanism that yields 8-oxoGua as an intermediate and 5-hydroxy-8-oxoGua as the final product was found to be energetically most favorable.

  5. 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.

  6. Preparation of various C-2 branched carbohydrates using intramolecular radical reactions.

    PubMed

    Choe, S W; Jung, M E

    2000-12-01

    A new and efficient method for the facile synthesis of C-2 branched carbohydrates has been developed using an intramolecular radical cyclization fragmentation reaction. The desired C-2 branched glucopyranosides were isolated in 40-84% yield. Additionally, an unexpected furanoside was obtained from a tributyltin iodide-promoted rearrangement of the radical intermediate. The C-2 formyl glycal was also isolated in good yield using tris(trimethylsilyl)silane (TTMSS) as the reducing agent. This method was extended to synthesize a beta C-2 branched glucopyranoside, a C-2 branched galactoside and a C-2 cyano glucopyranoside.

  7. Spin-polarized radical pairs transiently produced by the photochemical reaction of benzophenone with aromatic amines

    NASA Astrophysics Data System (ADS)

    Miyagawa, K.; Murai, H.; I'haya, Y. J.

    1984-08-01

    Spin-polarized triplet radical pairs produced by the photochemical reaction of triplet benzophenone with aromatic amines were detected in glassy matrices at 77 K using a time-resolved ESR method. By analysis of the spectra, it is concluded that the population of the Z spin sublevel of the radical pair whose principal axis is nearly parallel to the direction of the carbonyl group of benzophenone is predominant and its spin polarization is transferred from the initial polarization of the triplet state of benzophenone.

  8. Time-resolved infrared absorption studies applied to the study of radical plus molecule reactions

    SciTech Connect

    Bethardy, G.A.; Macdonald, R.G.; Northrup, F.J.

    1994-02-01

    Reaction of the cyano radical (CN) with ethane (C{sub 2}H{sub 6}) was studied using time resolved infrared absorption to monitor the product hydrogen cyanide (HCN) in individual to-vibrational states. Pulse laser photolysis was used to provide an initial excess of the CN radical and the time dependence of individual ro-vibrational states of the high frequency anti-symmetric stretching mode of HCN (0,0,v{sub 3}) was followed. These experiments reveal that the initial product state distribution of HCN is not highly excited in the HCN(0,0,{sub 3}) vibrational manifold.

  9. Kinetics and mechanism of the reaction of recombination of vinyl and hydroxyl radicals

    NASA Astrophysics Data System (ADS)

    Knyazev, Vadim D.

    2017-10-01

    The recombination of the vinyl (C2H3) and the hydroxyl (OH) radicals was studied computationally using quantum chemistry and master equation/RRKM. The reaction mechanism includes the initial addition, several isomerization steps, and decomposition via seven different channels. The spectrum of products demonstrates temperature dependence in the 300-3000 K range. At low temperatures (below 1600 K), CH3 + HCO products are dominant but at elevated temperatures vinoxy radical (CH2CHO) and hydrogen atom become more important. The acetyl (CH3CO) + H products and formation of vinylidene (CH2C:) and water products are minor but non-negligible.

  10. A theoretical investigation on kinetics, mechanism, and thermochemistry of the gas-phase reactions of methyl fluoroacetate with OH radicals and fate of alkoxy radical.

    PubMed

    Mishra, Bhupesh Kumar; Deka, Ramesh Chandra

    2014-09-25

    We theoretically investigated OH-initiated hydrogen abstraction reactions of methyl fluoroacetate (MFA) CH2FC(O)OCH3 at the MPWB1K level of theory in conjunction with the 6-31+G(d,p) basis set. Thermodynamic and kinetic data are computed using the comparatively accurate G2(MP2) method. Two most stable conformers of MFA are identified, and the energy difference between them is found to be only 0.32 kcal mol(-1). Both of them are considered for rate coefficient calculations, and the contribution from each of the conformers is found to be quite significant. We propose an indirect mechanism due to validation of pre- and post-reactive complexes. The rate parameters are determined using canonical transition state theory and energetics at the G2(MP2) level. The temperature dependence of the rate constant can be described by the Arrhenius expressions: k = 8.79 × 10(-13) exp[(-377.27 ± 64)/T] cm(3) molecule(-1) s(-1) over a temperature range of 250-450 K. The ΔfH°298 for CH2FC(O)OCH3, CH2FC(O)OC(•)H2, and C(•)HFC(O)OCH3 are also computed using an isodesmic procedure. The OH-driven atmospheric lifetime of MFA was estimated to be 24 days. A mechanistic study to shed light on the atmospheric degradation and the sole fate for the consumption of CH2FC(O)OCH2O(•) radical has also been reported.

  11. Mechanistic examination of Cβ-Cγ bond cleavages of tryptophan residues during dissociations of molecular peptide radical cations.

    PubMed

    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 [G(n)W](•+) (n = 2-4) and [GXW](•+) (X = C, S, L, F, Y, Q) species. The C(β)-C(γ) bond cleavage of a C-terminal decarboxylated tryptophan residue ([M - CO(2)](•+)) can generate [M - CO(2) - 116](+), [M - CO(2) - 117](•+), and [1H-indole](•+) (m/z 117) species as possible product ions. Competition between the formation of [M - CO(2) - 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 C(β)-C(γ) bond cleavage, can efficiently isomerize to form a more stable π-radical isomer (ion 9) as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. The C(β)-C(γ) bond cleavage of a tryptophan residue also can occur directly from peptide radical cations containing a basic residue. CID of [WG(n)R](•+) (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 C(β)-C(γ) bond cleavage to prevail over the charge-directed one. DFT calculations predicted that 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.

  12. 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.

  13. 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.

  14. Production of cold formaldehyde molecules for study and control of chemical reaction dynamics with hydroxyl radicals

    SciTech Connect

    Hudson, Eric R.; Ticknor, Christopher; Sawyer, Brian C.; Taatjes, Craig A.; Lewandowski, H. J.; Bochinski, J. R.; Bohn, J. L.; Ye Jun

    2006-06-15

    We propose a method for controlling a class of low temperature chemical reactions. Specifically, we show the hydrogen abstraction channel in the reaction of formaldehyde (H{sub 2}CO) and the hydroxyl radical (OH) can be controlled through either the molecular state or an external electric field. We also outline experiments for investigating and demonstrating control over this important reaction. To this end, we report the first Stark deceleration of H{sub 2}CO. We have decelerated a molecular beam of H{sub 2}CO essentially to rest, producing molecules at 100 mK with a density of {approx}10{sup 6} cm{sup -3}.

  15. Orientation dependence for Br formation in the reaction of oriented OH radical with HBr molecule.

    PubMed

    Tsai, Po-Yu; Che, Dock-Chil; Nakamura, Masaaki; Lin, King-Chuen; Kasai, Toshio

    2011-01-28

    The orientation dependence of Br-atom formation in the reaction of the oriented OH radical with the HBr molecule using the hexapole electrostatic field was studied. Experimental results for the orientation dependence in the reaction were analyzed using a Legendre polynomial fit. The results show two reactive sites. It was found that O-end attack is most favored for this reaction, and that H-end attack also shows a pronounced reactivity. The reactivity of the side-ways attack was found to be small. By comparing the results of the orientation dependence in the reaction with studies of inelastic collisions and theoretical calculations, two reaction pathways are proposed. Reaction by O-end attack is followed by a direct abstraction of the H-atom from the HBr molecule. The mechanism for H-end attack may have H-atom migration from HBr to form the water molecule.

  16. A mechanistic study of manganese(iii) acetate-mediated phosphonyl group additions to [60]- and [70]-fullerenes: the oxidative-ion-transfer mechanism vs. free radical addition.

    PubMed

    Tumanskii, Boris L; Sabirov, Denis S; Lyakhovetsky, Yury I

    2016-11-14

    The phosphonylation of C60 with HP(O)(OAlk)2 and Mn(OAc)3·2H2O has been considered to occur via a free radical (FR) path involving intermediate radicals ˙P(O)(OAlk)2. The present study provides evidence in support of another mechanism for the reactions, oxidative-ion-transfer (OIT). The mechanism involves the change of an acetate group in Mn(OAc)3 for the phosphonate group and oxidation of C60 by the Mn(OAc)2P(O)(OAlk)2 formed to a pair: (C60˙(+), Mn(OAc)2P(O)(OAlk)2˙(-)) followed by the transfer of the phosphonate anion to give the monophposphonylfullerenyl radical. It undergoes reversible dimerization. The polyaddition occurs analogously. Moreover, the compounds Mn(OAc)2P(O)(OAlk)2 (Alk = Et and i-Pr) obtained make novel reagents for phosphonylation of fullerenes working by the OIT mechanism. The reactions of C60 in benzene with equimolar amounts of Mn(OAc)2P(O)(OPr-i)2 or Hg[P(O)(OPr-i)2]2 which is known as working by the FR mechanism since it produces radical ˙P(O)(OPr-i)2 under UV-irradiation, furnished the same radical ˙C60P(O)(OPr-i)2. However, at a 20-fold molar excess of the reagent toward C60, a single derivative C60[P(O)(OPr-i)2]4 and a mixture of derivatives bearing between two and eight phosphonyls were obtained in the former and latter cases, respectively. With C70, the change of the mechanism produced a change in the regioselectivity: 5 and 3 isomers of ˙C70P(O)(OPr-i)2 were obtained, respectively. DFT-calculations provided the hyperfine coupling (hfc) constants of the isomers and explained the regioselectivity change.

  17. Scavenging of free-radical metabolites of aniline xenobiotics and drugs by amino acid derivatives: toxicological implications of radical-transfer reactions.

    PubMed

    Michail, Karim; Baghdasarian, Argishti; Narwaley, Malyaj; Aljuhani, Naif; Siraki, Arno G

    2013-12-16

    We investigated a novel scavenging mechanism of arylamine free radicals by poly- and monoaminocarboxylates. Free radicals of arylamine xenobiotics and drugs did not react with oxygen in peroxidase-catalyzed reactions; however, they showed marked oxygen uptake in the presence of an aminocarboxylate. These free-radical intermediates were identified using the spin trap 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) and electron paramagnetic resonance (EPR) spectrometry. Diethylenetriaminepentaacetic acid (DTPA), a polyaminocarboxylate, caused a concentration-dependent attenuation of N-centered radicals produced by the peroxidative metabolism of arylamines with the subsequent formation of secondary aliphatic carbon-centered radicals stemming from the cosubstrate molecule. Analogously, N,N-dimethylglycine (DMG) and N-methyliminodiacetate (MIDA), but not iminodiacetic acid (IDA), demonstrated a similar scavenging effect of arylamine-derived free radicals in a horseradish peroxidase/H2O2 system. Using human promyelocytic leukemia (HL-60) cell lysate as a model of human neutrophils, DTPA, MIDA, and DMG readily reduced anilinium cation radicals derived from the arylamines and gave rise to the corresponding carbon radicals. The rate of peroxidase-triggered polymerization of aniline was studied as a measure of nitrogen-radical scavenging. Although, IDA had no effect on the rate of aniline polymerization, this was almost nullified in the presence of DTPA and MIDA at half of the molar concentration of the aniline substrate, whereas a 20 molar excess of DMPO caused only a partial inhibition. Furthermore, the yield of formaldehyde, a specific reaction endproduct of the oxidation of aminocarboxylates by aniline free-radical metabolites, was quantitatively determined. Azobenzene, a specific reaction product of peroxidase-catalyzed free-radical dimerization of aniline, was fully abrogated in the presence of DTPA, as confirmed by GC/MS. Under aerobic conditions, a radical-transfer reaction

  18. Temperature-dependent, relative-rate study of the reactions of 1- and 2-butoxyl radicals

    NASA Astrophysics Data System (ADS)

    Johnson, D.; Cassanelli, P.; Cox, R. A.

    2003-04-01

    Alkoxyl radicals (RO\\cdot) are important intermediates in the chains of free radical reactions that constitute the gas-phase oxidation of volatile organic compounds (VOCs). Generally there are a number of different reaction pathways available to alkoxyl radicals and, depending on conditions of temperature and the structure of RO\\cdot, these may be in competition. The major reactions of RO\\cdot are (1) reaction with O_2 to yield a carbonyl product and a hydroperoxy, HO_2, radical, (2) decomposition to yield a carbonyl product and a radical fragment, and (3) isomerisation via a six-membered transition state to yield a d-hydroxylated radical species. Thus the chemistry of alkoxyl radicals determines the atmospheric impact of the oxidation of a given VOC, in terms of the immediate effects of closed-shell products, and as a result of the further chemistry of free radical products. HO_2 can react with NO to yield photolabile NO_2 (and hence contribute to photochemical ozone formation), and organic radical fragments act to propagate the oxidation chain of reactions. As ozone has been identified to be an important greenhouse gas in the upper troposphere/lower stratosphere (UTLS) region it is important to understand how temperature affects the relative rates of reactions (1) to (3), and thus how the presence of VOCs in the UTLS region affects the coupled chemistries of HO_x and O_3. In the present study, we have looked at the reactions of 1- and 2-butoxyl radicals (formed in the reaction of OH with butane) in terms of the relative rates of their bimolecular reactions with O_2 (1) and unimolecular processes (2,3). The two butoxyl radicals were studied separately and were formed directly from the photolysis of 1- or 2-butylnitrite. Experiments were carried out using a metre-long photochemical flow cell made of quartz. The temperature of the cell could be controlled and for the experiments carried out in the present study was operated between about 250 and 340 K. Reactant

  19. Contribution of the photo-Fenton reaction to hydroxyl radical formation rates in river and rain water samples.

    PubMed

    Nakatani, Nobutake; Ueda, Marina; Shindo, Hirotaka; Takeda, Kazuhiko; Sakugawa, Hiroshi

    2007-09-01

    The hydroxyl radical (OH radical) formation rates from the photo-Fenton reaction in river and rain water samples were determined by using deferoxamine mesylate (DFOM), which makes a stable and strong complex with Fe(III), resulting in a suppression of the photo-Fenton reaction. The difference between the OH radical formation rates with and without added DFOM denotes the rate from the photo-Fenton reaction. The photoformation rates from the photo-Fenton reaction were in the range of 0.7 - 45.8 x 10(-12) and 2.7 - 32.3 x 10(-12) M s(-1) in river and rain water samples, respectively. A strong positive correlation between the OH radical formation rate from the photo-Fenton reaction and the amount of fluorescent matter in river water suggests that fluorescent matter, such as humic substances, plays an important role in the photo-Fenton reaction. In rain water, direct photolysis of hydrogen peroxide was an important source of OH radicals as well as the photo-Fenton reaction. The contributions of the photo-Fenton reaction to the OH radical photoformation rates in river and rain water samples were in the ranges of 2 - 29 and 5 - 38%, respectively. Taking into account the photo-Fenton reaction, 33 - 110 (mean: 80) and 42 - 110 (mean: 84)% of OH radical sources in river and rain water samples, respectively, collected in Hiroshima prefecture were elucidated.

  20. Lifetimes and reaction pathways of guanine radical cations and neutral guanine radicals in an oligonucleotide in aqueous solutions.

    PubMed

    Rokhlenko, Yekaterina; Geacintov, Nicholas E; Shafirovich, Vladimir

    2012-03-14

    The exposure of guanine in the oligonucleotide 5'-d(TCGCT) to one-electron oxidants leads initially to the formation of the guanine radical cation G(•+), its deptotonation product G(-H)(•), and, ultimately, various two- and four-electron oxidation products via pathways that depend on the oxidants and reaction conditions. We utilized single or successive multiple laser pulses (308 nm, 1 Hz rate) to generate the oxidants CO(3)(•-) and SO(4)(•-) (via the photolysis of S(2)O(8)(2-) in aqueous solutions in the presence and absence of bicarbonate, respectively) at concentrations/pulse that were ∼20-fold lower than the concentration of 5'-d(TCGCT). Time-resolved absorption spectroscopy measurements following single-pulse excitation show that the G(•+) radical (pK(a) = 3.9) can be observed only at low pH and is hydrated within 3 ms at pH 2.5, thus forming the two-electron oxidation product 8-oxo-7,8-dihydroguanosine (8-oxoG). At neutral pH, and single pulse excitation, the principal reactive intermediate is G(-H)(•), which, at best, reacts only slowly with H(2)O and lives for ∼70 ms in the absence of oxidants/other radicals to form base sequence-dependent intrastrand cross-links via the nucleophilic addition of N3-thymidine to C8-guanine (5'-G*CT* and 5'-T*CG*). Alternatively, G(-H)(•) can be oxidized further by reaction with CO(3)(•-), generating the two-electron oxidation products 8-oxoG (C8 addition) and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih, by C5 addition). The four-electron oxidation products, guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp), appear only after a second (or more) laser pulse. The levels of all products, except 8-oxoG, which remains at a low constant value, increase with the number of laser pulses.

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

    PubMed

    Chen, Hsing-Yu; Jang, Soonmin; Jinn, Tzyy-Rong; Chang, Jia-Yaw; Lu, Hsiu-Feng; Li, Feng-Yin

    2012-04-24

    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. 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. 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.

  2. 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

  3. Theoretical and kinetic study of the reactions of ketones with HO2 radicals. Part I: abstraction reaction channels.

    PubMed

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

    2013-06-06

    This work presents an ab initio and chemical kinetic study of the reaction mechanisms of hydrogen atom abstraction by the HO2 radical on five ketones: dimethyl, ethyl methyl, n-propyl methyl, iso-propyl methyl, and iso-butyl methyl ketones. The Møller-Plesset method using the 6-311G(d,p) basis set has been used in the geometry optimization and the frequency calculation for all the species involved in the reactions, as well as the hindrance potential description for reactants and transition states. Intrinsic reaction coordinate calculations were carried out to validate all the connections between transition states and local minima. Energies are reported at the CCSD(T)/cc-pVTZ//MP2/6-311G(d,p) level of theory. The CCSD(T)/cc-pVXZ method (X = D, T, Q) was used for the reaction mechanism of dimethyl ketone + HO2 radical in order to benchmark the computationally less expensive method of CCSD(T)/cc-pVTZ//MP2/6-311G(d,p). High-pressure limit rate constants have been calculated for all the reaction channels by conventional transition state theory with asymmetric Eckart tunneling corrections and 1-D hindered rotor approximations in the temperature range 500-2000 K.

  4. Atmospheric reactions of gaseous mercury with ozone and hydroxyl radical: Kinetics and product studies

    NASA Astrophysics Data System (ADS)

    Biswajit, P.; Parisa, A. A.

    2003-05-01

    The dominant form of mercury in the atmosphere is Hg^0. The oxidation processes are of great importance since oxidized mercury undergoes deposition and can become subject to bioaccumulation. Experimental data on the gaseous reactions of elemental mercury are very limited with compare to the reactions of Hg^0 in solutions. We herein carried out kinetic and product studies on the reactions of gaseous Hg^0 with O3 and hydroxyl radical (HO) under near atmospheric pressure (750 ± 1 Torr) and room temperature (298 ± 1 K) in air and N2. O3 was produced in a silent discharge generator (OL 100/SB). Hydroxyl radicals were produced from the photolysis of isopropyl nitrite in the presence of NO. Kinetics of the reactions with O3/HO was studied using absolute and relative techniques by gas chromatography with mass spectroscopic detection (GCMS). The gas phase reaction between elemental Hg^0 with O3 has been studied in different surface-to-volume (s/v) ratios, and evidence for heterogeneous reactions was observed. Existence of mercuric oxide, Hg^0 by the reaction of atomic Hg^0 with O3 has been determined in the gas phase from the suspended aerosols using high temperature mass spectrometry.

  5. 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

  6. 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.

  7. 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.

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

    PubMed

    Nishikata, Takashi; Abela, Alexander R; Huang, Shenlin; Lipshutz, Bruce H

    2016-01-01

    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.

  9. 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

  10. Enantioselective Lewis Acid Catalysis in Intramolecular [2 + 2] Photocycloaddition Reactions: A Mechanistic Comparison between Representative Coumarin and Enone Substrates.

    PubMed

    Brimioulle, Richard; Bauer, Andreas; Bach, Thorsten

    2015-04-22

    The intramolecular [2 + 2] photocycloaddition of three 4-(alk-4-enyl)coumarins and three 1-(alk-4-enoyl)-2,3-dihydropyridones was studied in the absence and in the presence of Lewis acids (irradiation wavelength λ = 366 nm). Spectral and kinetic data were collected for the respective parent compounds with a pent-4-enyl and a pent-4-enoyl chain. For the substrates with a methyl group in cis- or trans-position of the terminal alkene carbon atom (hex-4-enyl and hex-4-enoyl substitution), the stereochemical outcome of the [2 + 2] photocycloaddition was investigated. The mechanistic course of the uncatalyzed coumarin reactions was found to be a singlet pathway, whereas Lewis acid-catalyzed reactions proceeded with higher reaction rates in the triplet manifold. Contrary to that, the dihydropyridones underwent a fast triplet reaction in the absence of the Lewis acid. In the presence of a chiral Lewis acid the reactions slowed down but, due to the high extinction coefficient of the Lewis acid/dihydropyridone complexes at λ = 366 nm, still resulted in high enantioselectivity.

  11. 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.

  12. 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

  13. Nonclassical aryl radicals: Intermediates or transition states for the hydrogen shift reactions?

    SciTech Connect

    Cioslowski, J.; Liu, G.; Moncrieff, D.

    1996-06-14

    Electronic properties of aryl radicals obtained by removing single hydrogen atoms from the sterically congested regions of benzo[c]phenanthrene, biphenyl, triphenylene, phenanthrene, and perylene are studied at the UBLYP/6-311G** level of theory. Two structures are considered by each radical, the classical one involving a C-H{hor_ellipsis}C arrangement of atoms and the nonclassical one possessing a three-center C-H-C linkage. The five nonclassical radicals under study are found to be transition states for degenerate 1,4- and 1,5-hydrogen shift reactions that interconvert the classical species. However, the results of the present calculations indicate that the nonclassical structures with the C-H distances in the C-H-C linkages shorter than 1.34 {angstrom} should be energy minima representing potentially observable chemical systems. The predicted energy barrier to the 1,5-hydrogen shift in the 1-benzo[c]phenanthrenyl radical is only 9.3 kcal/mol with the zero-point energies included, making the hydrogen migration in this system facile at relatively low temperatures. Rigorous analysis of the computed electronic wave functions provides a clear-cut picture of bonding in both the classical and nonclassical aryl radicals. 2 figs., 4 tabs.

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

    NASA Astrophysics Data System (ADS)

    Miranda-Rojas, Sebastián; Toro-Labbé, Alejandro

    2015-05-01

    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 SN2 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 SN2 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 SN2 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.

  15. 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.

  16. Asymmetric Morita-Baylis-Hillman Reaction: Catalyst Development and Mechanistic Insights Based on Mass Spectrometric Back-Reaction Screening.

    PubMed

    Isenegger, Patrick G; Bächle, Florian; Pfaltz, Andreas

    2016-12-05

    An efficient protocol for the evaluation of catalysts for the asymmetric Morita-Baylis-Hillman (MBH) reaction was developed. By mass spectrometric back-reaction screening of quasi-enantiomeric MBH products, an efficient bifunctional phosphine catalyst was identified that outperforms literature-known catalysts in the MBH reaction of methyl acrylate with aldehydes. The close match between the selectivities measured for the forward and back reaction and kinetic measurements provided strong evidence that the aldol step and not the subsequent proton transfer is rate- and enantioselectivity-determining.

  17. 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.

  18. 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

    2016-03-03

    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.

  19. 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.

  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. A quantum chemical study on hydrogen radical reactions with methane and silane

    NASA Astrophysics Data System (ADS)

    Sato, Kota; Kojima, Kuniharu; Kawasaki, Masashi; Matsuzaki, Yoshio; Hirano, Tsuneo; Nakano, Masatake; Koinuma, Hideomi

    1989-03-01

    A quantum chemical study on the reaction of CH4 , CF4 , SiH4 , and SiF4 with a hydrogen radical is performed on the basis of an ab initio molecular orbital calculation to predict the photochemical reactivity of methane, silane, and their analogues. The transition state geometry of the reactions is determined by employing a 3-21G basis set. The total energies of reactant molecules at the initial, transition, and final states are calculated by employing a 6-31G** basis set. The exponential parts of the rate constants of these reactions determined from these energies on the basis of the transition state theory are in good agreement with the experimentally obtained relative rates of the reaction. The present calculation was consistent with the experimental results of photochemical reactions for methane and silane derivatives.

  2. 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

  3. Cost-Effective Implementation of Multiconformer Transition State Theory for Peroxy Radical Hydrogen Shift Reactions.

    PubMed

    Møller, Kristian H; Otkjær, Rasmus V; Hyttinen, Noora; Kurtén, Theo; Kjaergaard, Henrik G

    2016-12-29

    Based on a small test system, (R)-CH(OH)(OO·)CH2CHO, we have developed a cost-effective approach to the practical implementation of multiconformer transition state theory for peroxy radical hydrogen shift reactions at atmospherically relevant temperatures. While conformer searching is crucial for accurate reaction rates, an energy cutoff can be used to significantly reduce the computational cost with little loss of accuracy. For the reaction barrier, high-level calculations are needed, but the highest level of electronic structure theory is not necessary for the relative energy between conformers. Improving the approach to both transition state theory and electronic structure theory decreases the calculated reaction rate significantly, so low-level calculations can be used to rule out slow reactions. Further computational time can be saved by approximating the tunneling coefficients for each transition state by only that of the lowest-energy transition state. Finally, we test and validate our approach using higher-level theoretical values for our test system and existing experimental results for additional peroxy radical hydrogen shift reactions in three slightly larger systems.

  4. 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.

  5. 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.

  6. 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.

  7. Heterogeneous kinetics, products, and mechanisms of ferulic acid particles in the reaction with NO3 radicals

    NASA Astrophysics Data System (ADS)

    Liu, Changgeng; Zhang, Peng; Wen, Xiaoying; Wu, Bin

    2017-03-01

    Methoxyphenols, as an important component of wood burning, are produced by lignin pyrolysis and considered to be the potential tracers for wood smoke emissions. In this work, the heterogeneous reaction between ferulic acid particles and NO3 radicals was investigated. Six products including oxalic acid, 4-vinylguaiacol, vanillin, 5-nitrovanillin, 5-nitroferulic acid, and caffeic acid were confirmed by gas chromatography-mass spectrometry (GC-MS). In addition, the reaction mechanisms were proposed and the main pathways were NO3 electrophilic addition to olefin and the meta-position to the hydroxyl group. The uptake coefficient of NO3 radicals on ferulic acid particles was 0.17 ± 0.02 and the effective rate constant under experimental conditions was (1.71 ± 0.08) × 10-12 cm3 molecule-1 s-1. The results indicate that ferulic acid degradation by NO3 can be an important sink at night.

  8. Mechanistic insights into Diels-Alder reactions in natural product biosynthesis.

    PubMed

    Hashimoto, Takuya; Kuzuyama, Tomohisa

    2016-12-01

    Natural enzymes that catalyze Diels-Alder reactions have long been sought after, yet few enzymes have been experimentally confirmed to perform this reaction. In the past five years, several stand-alone enzymes that can catalyze the Diels-Alder reaction had been identified and characterized. Among which, the crystal structures of SpnF, PyrI4 and AbyU have been determined. The structures of PyrI4 and AbyU, which are involved in spirotetronate/spirotetramate biosynthesis, are particularly informative since they shed light on how a natural catalyst captures the flexible substrate and facilitates the intramolecular Diels-Alder reaction through stabilization of the transition state in catalysis. These pioneering studies will inspire the design of artificial catalysts for Diels-Alder reactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Major mechanistic differences between the reactions of hydroxylamine with phosphate di- and tri-esters.

    PubMed

    Medeiros, Michelle; Wanderlind, Eduardo H; Mora, José R; Moreira, Raphaell; Kirby, Anthony J; Nome, Faruk

    2013-10-07

    Hydroxylamine reacts as an oxygen nucleophile, most likely via its ammonia oxide tautomer, towards both phosphate di- and triesters of 2-hydroxypyridine. But the reactions are very different. The product of the two-step reaction with the triester TPP is trapped by the NH2OH present in solution to generate diimide, identified from its expected disproportionation and trapping products. The reaction with H3N(+)-O(-) shows general base catalysis, which calculations show is involved in the breakdown of the phosphorane addition-intermediate of a two-step reaction. The reactivity of the diester anion DPP(-) is controlled by its more basic pyridyl N. Hydroxylamine reacts preferentially with the substrate zwitterion DPP(±) to displace first one then a second 2-pyridone, in concerted S(N)2(P) reactions, forming O-phosphorylated products which are readily hydrolysed to inorganic phosphate. The suggested mechanisms are tested and supported by extensive theoretical calculations.

  10. Comprehensive mechanistic study of ion pair SN2 reactions of lithium isocyanate and methyl halides

    NASA Astrophysics Data System (ADS)

    Sun, Ying-Xin; Ren, Yi; Wong, Ning-Bew; Chu, San-Yan; Xue, Ying

    The anionic SN2 reactions NCO- + CH3X and ion pair SN2 reactions LiNCO + CH3X (X = F, Cl, Br, and I) at saturated carbon with inversion and retention mechanisms were investigated at the level of MP2/6-311+G(d,p). There are two possible reaction pathways in the anionic SN2 reactions, but eight in the ion pair SN2 reactions. Calculated results suggest that the previously reported T-shaped isomer of lithium isocyanate does not exist. All the retention pathways are not favorable based on the analysis of transition structures. Two possible competitive reaction pathways proceed via two six-member ring inversion transition structures. It is found that there are two steps in the most favorable pathway, in which less stable lithium cyanate should be formed through the isomerization of lithium isocyanate and nucleophilic site (N) subsequently attacks methyl halides from the backside. The thermodynamically and kinetically favorable methyl isocyanate is predicted as major product both in the gas phase anionic and the ion pair SN2 reactions. In addition, good correlations between the overall barriers relative to separated reactants, ?H?ovr , with geometrical looseness parameter %L? and the heterolytic cleavage energies of the C bond X and Li bond N (or Li bond O) bonds are observed for the anionic and ion pair SN2 reactions. The trend of variation of the overall barriers predicts the leaving ability of X increase in the order: F < Cl < Br < I. The polarized continuum model (PCM) has been used to evaluate the solvent effects on the two inversion pathways with six-member transition structures for the reactions of LiNCO + CH3X. The calculations in solution indicate that solvent effects will retard the rate of reactions and the predicted product, methyl isocyanate, is same as the one in the gas phase.

  11. 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

  12. 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.

  13. KINETIC STUDIES OF THE REACTION OF HYDROXYL RADICALS WITH TRICHLOROETHYLENE AND TETRACHLOROETHYLENE. (R826169)

    EPA Science Inventory

    Rate coefficients are reported for the gas-phase reaction of the hydroxyl radical (OH) with C2HCl3 (k1) and C2Cl4 (k2) over an extended temperature range at 740±10 Torr in a He bath gas. These...

  14. KINETIC STUDIES OF THE REACTION OF HYDROXYL RADICALS WITH TRICHLOROETHYLENE AND TETRACHLOROETHYLENE. (R826169)

    EPA Science Inventory

    Rate coefficients are reported for the gas-phase reaction of the hydroxyl radical (OH) with C2HCl3 (k1) and C2Cl4 (k2) over an extended temperature range at 740±10 Torr in a He bath gas. These...

  15. The reaction between CH3O2 and OH radicals: Product yields and atmospheric implications

    DOE PAGES

    Assaf, Emmanuel; Sheps, Leonid; Whalley, Lisa; ...

    2017-01-25

    The reaction between CH3O2 and OH radicals has been shown to be fast and to play an appreciable role for the removal of CH3O2 radials in remote environments such as the marine boundary layer. Two different experimental techniques have been used here to determine the products of this reaction. The HO2 yield has been obtained from simultaneous time-resolved measurements of the absolute concentration of CH3O2, OH, and HO2 radicals by cw-CRDS. The possible formation of a Criegee intermediate has been measured by broadband cavity enhanced UV absorption. A yield of ΦHO2 = (0.8 ± 0.2) and an upper limit formore » ΦCriegee = 0.05 has been determined for this reaction, suggesting a minor yield of methanol or stabilized trioxide as a product. The impact of this reaction on the composition of the remote marine boundary layer has been determined by implementing these findings into a box model utilizing the Master Chemical Mechanism v3.2, and constraining the model for conditions found at the Cape Verde Atmospheric Observatory in the remote tropical Atlantic Ocean. Inclusion of the CH3O2+OH reaction into the model results in up to 30% decrease in the CH3O2 radical concentration while the HO2 concentration increased by up to 20%. Finally, production and destruction of O3 are also influenced by these changes, and the model indicates that taking into account the reaction between CH3O2 and OH leads to a 6% decrease of O3.« less

  16. The Reaction between CH3O2 and OH Radicals: Product Yields and Atmospheric Implications.

    PubMed

    Assaf, Emmanuel; Sheps, Leonid; Whalley, Lisa; Heard, Dwayne; Tomas, Alexandre; Schoemaecker, Coralie; Fittschen, Christa

    2017-02-21

    The reaction between CH3O2 and OH radicals has been shown to be fast and to play an appreciable role for the removal of CH3O2 radials in remote environments such as the marine boundary layer. Two different experimental techniques have been used here to determine the products of this reaction. The HO2 yield has been obtained from simultaneous time-resolved measurements of the absolute concentration of CH3O2, OH, and HO2 radicals by cw-CRDS. The possible formation of a Criegee intermediate has been measured by broadband cavity enhanced UV absorption. A yield of ϕHO2 = (0.8 ± 0.2) and an upper limit for ϕCriegee = 0.05 has been determined for this reaction, suggesting a minor yield of methanol or stabilized trioxide as a product. The impact of this reaction on the composition of the remote marine boundary layer has been determined by implementing these findings into a box model utilizing the Master Chemical Mechanism v3.2, and constraining the model for conditions found at the Cape Verde Atmospheric Observatory in the remote tropical Atlantic Ocean. Inclusion of the CH3O2+OH reaction into the model results in up to 30% decrease in the CH3O2 radical concentration while the HO2 concentration increased by up to 20%. Production and destruction of O3 are also influenced by these changes, and the model indicates that taking into account the reaction between CH3O2 and OH leads to a 6% decrease of O3.

  17. 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.

  18. [Spectroscopic measurement of intermediate free radicals of n-heptane in the combustion reaction].

    PubMed

    Ye, Bin; Li, Ping; Zhang, Chang-hua; Wang, Li-dong; Tang, Hong-chang; Li, Xiang-yuan

    2012-04-01

    Using an intensified spectroscopic detector CCD and a chemical shock tube, transient emission spectra of n-heptane during the reaction process of combustion were measured, with exposure time of 6 micros and a spectral range of 200 - 850 nm Experiments were conducted at an ignition temperature of 1 408 K and pressure of 2.0 atmos, with an initial fuel mole fraction of 1.0% and an equivalence ratio of 1.0. Measured emission bands were determined to be produced by OH, CH and C2 free radicals, which reveals that small OH, CH and C2 radicals are important intermediate products in the combustion process of n-heptane. Time-resolved spectra indicate that radical concentrations of OH, CH and C2 reached their peaks sharply; however, CH and C2 reduced and disappeared rapidly while the duration of OH was much longer in the reaction. This work provides experimental data for understanding the microscopic process and validating the mechanism of n-heptane combustion reaction.

  19. Reaction between radicals and N-alkoxyamines As coordinated cleavage with fragmentation

    NASA Astrophysics Data System (ADS)

    Denisov, E. T.; Shestakov, A. F.

    2015-08-01

    Quantum chemical calculations of the enthalpy and activation energy of two reactions with MeO{2/⊙} attacking the CH- and CH2-groups of 2,2,6,6-tetramethylpiperidineoxy-2'-butane are performed. It is shown that the cleavage of hydrogen atoms is accompanied by coordinated breaking of N-O-bonds in the former case and C-O-bonds in the latter. Based on the obtained results, a new scheme is proposed for the cyclic mechanism behind the cleavage of chains on nitroxyl radicals in oxidizing hydrocarbons and polymers that agrees with experimental data. At the center of this cyclic mechanism lies the fast exothermic reaction between peroxyl radicals and N-alkoxyamine with the cleavage of H atoms and the coordinated fragmentation of molecules. Using the model of intersecting parabolas, an algorithm for calculating the enthalpies, activation energies, and rate constants of these reactions with the participation of alkyl, alkoxy, aminyl, peroxyl, phenoxyl, thiyl, and hydroxyl radicals is proposed.

  20. Mechanism and stereoselectivity of biologically important oxygenation reactions of the 7-dehydrocholesterol radical.

    PubMed

    Rajeev, Ramanan; Sunoj, Raghavan B

    2013-07-19

    The mechanism of free radical oxygenation of 7-dehydrocholesterol (7-DHC), one of the biologically important sterols, is investigated by using density functional theory. The energetic origin of the product distribution and the stereoelectronic factors involved in various mechanistic pathways are delineated. The addition of triplet molecular oxygen to two types of conjugatively stabilized radicals, generated by the removal of the reactive allylic hydrogens from C9 or C14 positions, respectively denoted as H9 and H14 pathways, is studied. The distortion-interaction analysis of the C-O bond formation transition states suggests that the energetic preference toward the α prochiral face stems from reduced skeletal distortions of the cholesterol backbone as compared to that in the corresponding β prochiral face. This insight derived through a detailed quantitative analysis of the stereocontrolling transition states suggests that the commonly found interpretations solely based on steric interactions between the incoming oxygen and the protruding angular methyl groups (C10, C13 methyls) in the β face calls for adequate refinement. The relative energies of the transition states for molecular oxygen addition to C9, C5, and C14 (where spin densities are higher) and the ensuing products thereof are in agreement with the experimentally reported distribution of oxygenated 7-DHCs.

  1. Mechanistic and kinetic study on the reactions of coumaric acids with reactive oxygen species: a DFT approach.

    PubMed

    Garzón, Andrés; Bravo, Iván; Barbero, Antonio J; Albaladejo, José

    2014-10-08

    The mechanism and kinetics of reactions between coumaric acids and a series of reactive oxygen species ((•)OX) was studied through the density functional theory (DFT). H atom abstraction from -OH and -COOH groups and addition to the nonaromatic double bond were the most representative reaction pathways chosen for which free energy barriers and rate constants were calculated within the transition state theory (TST) framework. From these calculations, it was estimated that (•)OH > (•)OCH3 > (•)OOH > (•)OOCH3 is the order of reactivity of (•)OX with any coumaric acid. The highest rate constant was estimated for p-coumaric acid + (•)OH reaction, whereas the rest of the (•)OX species are more reactive with o-coumaric acid. On the basis of the calculated rate constants, H abstraction from a -OH group should be the main mechanism for the reactions involving (•)OCH3, (•)OOH, and (•)OOCH3 radicals. Nevertheless, the addition mechanism, which sometimes is not considered in theoretical studies on reactions of phenolic compounds with electrophilic species, could play a relevant role in the global mechanism of coumaric acid + (•)OH reactions.

  2. Mechanistic insight on the Diels-Alder reaction catalyzed by a self-assembled molecular capsule.

    PubMed

    Xu, Lina; Hua, Weijie; Hua, Shugui; Li, Jun; Li, Shuhua

    2013-04-19

    We combined Monte Carlo simulations and density functional theory calculations to study the mechanism of the Diels-Alder reaction of p-quinone and cyclohexadiene catalyzed by a self-assembled molecular capsule. Our calculations show that the encapsulation of the reactants into the cage is driven by hydrogen-bonding interactions and π-π stacking interactions between two reactants and the capsule. The encapsulated Diels-Alder reaction at different locations inside the capsule may have quite different reactivity due to different guest-host interactions. A comparison of the free energy profiles of the Diels-Alder reaction in the capsule and in the bulk solution reveals that the Diels-Alder reaction in the capsule is accelerated because the host-guest interaction leads to a relatively smaller barrier for the cycloaddition step.

  3. Electrochemical reactions in fluoride-ion batteries: mechanistic insights from pair distribution function analysis

    DOE PAGES

    Grenier, Antonin; Porras-Gutierrez, Ana-Gabriela; Groult, Henri; ...

    2017-07-05

    Detailed analysis of electrochemical reactions occurring in rechargeable Fluoride-Ion Batteries (FIBs) is provided by means of synchrotron X-ray diffraction (XRD) and Pair Distribution Function (PDF) analysis.

  4. 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.

  5. Histidinyl radical formation in the self-peroxidation reaction of bovine copper-zinc superoxide dismutase.

    PubMed

    Gunther, Michael R; Peters, J Andrew; Sivaneri, Meena K

    2002-03-15

    In the absence of suitable oxidizable substrates, the peroxidase reaction of copper-zinc superoxide dismutase (SOD) oxidizes SOD itself, ultimately resulting in its inactivation. A SOD-centered free radical adduct of 2-methyl-2-nitrosopropane (MNP) was detected upon incubation of SOD with the spin trap and a hydroperoxide (either H(2)O(2) or peracetic acid). Proteolysis by Pronase converted the anisotropic electron paramagnetic resonance (EPR) spectrum of MNP/(center dot)SOD to a nearly isotropic spectrum with resolved hyperfine couplings to several atoms with non-zero nuclear spin. Authentic histidinyl radical (from histidine + HO(center dot)) formed a MNP adduct with a very similar EPR spectrum to that of the Pronase-treated MNP/(center dot)SOD, suggesting that the latter was centered on a histidine residue. An additional hyperfine coupling was detected when histidine specifically (13)C-labeled at C-2 of the imidazole ring was used, providing evidence for trapping at that atom. All of the experimental spectra were convincingly simulated assuming hyperfine couplings to 2 nearly equivalent nitrogen atoms and 2 different protons, also consistent with trapping at C-2 of the imidazole ring. Free histidinyl radical consumed oxygen, implying peroxyl radical formation. MNP-inhibitable oxygen consumption was also observed when cuprous SOD but not cupric SOD was added to a H(2)O(2) solution. Formation of 2-oxohistidine, the stable product of the SOD-hydroperoxide reaction, required oxygen and was inhibited by MNP. These results support formation of a transient SOD-peroxyl radical.

  6. 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.

  7. Intramolecular Oxyl Radical Coupling Promotes O-O Bond Formation in a Homogeneous Mononuclear Mn-based Water Oxidation Catalyst: A Computational Mechanistic Investigation.

    PubMed

    Crandell, Douglas W; Xu, Song; Smith, Jeremy M; Baik, Mu-Hyun

    2017-04-04

    The mechanism of water oxidation performed by a recently discovered manganese pyridinophane catalyst [Mn(Py2N(t)Bu2)(H2O)2](2+) is studied using density functional theory methods. A complete catalytic cycle is constructed and the catalytically active species is identified to consist of a Mn(V)-bis(oxo) moiety that is generated from the resting state by a series of proton-coupled electron transfer reactions. Whereas the electronic ground state of this key intermediate is found to be a triplet, the most favorable pathway for O-O bond formation is found on the quintet potential energy surface and involves an intramolecular coupling of two oxyl radicals with opposite spins bound to the Mn-center that adopts an electronic structure most consistent formally with a high-spin Mn(III) ion. Therefore, the thermally accessible high-spin quintet state that constitutes a typical and innate property of a first-row transition metal center plays a critical role for catalysis. It enables facile electron transfer between the oxo moieties and the Mn-center and promotes O-O bond formation via a radical coupling reaction with a calculated reaction barrier of only 14.7 kcal mol(-1). This mechanism of O-O coupling is unprecedented and provides a novel possible pathway to coupling two oxygen atoms bound to a single metal site.

  8. UV light-mediated difunctionalization of alkenes through aroyl radical addition/1,4-/1,2-aryl shift cascade reactions.

    PubMed

    Zheng, Lewei; Huang, Hongli; Yang, Chao; Xia, Wujiong

    2015-02-20

    UV light-mediated difunctionalization of alkenes through an aroyl radical addition/1,4-/1,2-aryl shift has been described. The resulted aroyl radical from a photocleavage reaction added to acrylamide compounds followed by cyclization led to the formation of oxindoles, whereas the addition to cinnamic amides aroused a unique 1,4-aryl shift reaction. Furthermore, the difunctionalization of alkenes of prop-2-en-1-ols was also achieved through aroyl radical addition and a sequential 1,2-aryl shift cascade reaction.

  9. Reaction of peroxide radicals with methane on the titanium oxide surface: Effects of the composition of the initial mixture

    NASA Astrophysics Data System (ADS)

    Jalali, H. A.; Manucharova, L. A.; Tsarukyan, S. V.; Vardanyan, I. A.

    2011-03-01

    The reaction of TiO2-adsorbed methyl peroxide radicals with methane, accompanied by transfer of the products into the gas phase at ˜20°C, was studied by the kinetic methods and EPR spectroscopy. In a definite range of methane concentrations, the reaction was accompanied by an increase in the total concentration of free radicals; i.e., these active species became not only regenerated, but also multiplied. The increase in the number of peroxide radicals was explained by the chain consumption of methane initiated by the reaction being studied.

  10. Nitroxyl Radical plus Hydroxylamine Pseudo Self-Exchange Reactions: Tunneling in Hydrogen Atom Transfer

    PubMed Central

    Wu, Adam; Mader, Elizabeth A.; Datta, Ayan; Hrovat, David A.; Borden, Weston Thatcher; Mayer, James M.

    2009-01-01

    Bimolecular rate constants have been measured for reactions that involve hydrogen atom transfer (HAT) from hydroxylamines to nitroxyl radicals, using the stable radicals TEMPO• (2,2,6,6-tetramethylpiperidine-1-oxyl radical), 4-oxo-TEMPO• (2,2,6,6-tetramethyl-4-oxo-piperidine-1-oxyl radical), di-tert-butylnitroxyl (tBu2NO•), and the hydroxylamines TEMPO-H, 4-oxo-TEMPO-H, 4-MeO-TEMPO-H (2,2,6,6-tetramethyl-N-hydroxy-4-methoxy-piperidine), and tBu2NOH. The reactions have been monitored by UV-vis stopped-flow methods, using the different optical spectra of nitroxyl radicals. The HAT reactions all have |ΔGo| ≤ 1.4 kcal mol−1 and therefore are close to self-exchange reactions. The reaction of 4-oxo-TEMPO• + TEMPO-H → 4-oxo-TEMPO-H + TEMPO• occurs with k2H,MeCN = 10 ± 1 M−1 s−1 in MeCN at 298 K (K2H,MeCN = 4.5 ± 1.8). Surprisingly, the rate constant for the analogous deuterium atom transfer reaction is much slower: k2D,MeCN = 0.44 ± 0.05 M−1 s−1 with k2H,MeCN/k2D,MeCN = 23 ± 3 at 298 K. The same large kinetic isotope effect (KIE) is found in CH2Cl2, 23 ± 4, suggesting that the large KIE is not caused by solvent dynamics or hydrogen bonding to solvent. The related reaction of 4-oxo-TEMPO• with 4-MeO-TEMPO-H(D) also has a large KIE, k3H/k3D = 21 ± 3 in MeCN. For these three reactions, the EaD – EaH values, between 0.3 ± 0.6 and 1.3 ± 0.6 kcal mol−1, and the log(AH/AD) values, between 0.5 ± 0.7 and 1.1 ± 0.6, indicate that hydrogen tunneling plays an important role. The related reaction of tBu2NO• + TEMPO-H(D) in MeCN has a large KIE, 16 ± 3 in MeCN, and very unusual isotopic activation parameters, EaD – EaH = −2.6 ± 0.4 and log(AH/AD) = 3.1 ± 0.6. Computational studies, using POLYRATE, also indicate substantial tunneling in the (CH3)2NO• + (CH3)2NOH model reaction for the experimental self-exchange processes. Additional calculations on TEMPO(•/H), tBu2NO(•/H), and Ph2NO(•/H) self-exchange reactions reveal why the

  11. Theoretical mechanisms and kinetics of the hydrogen abstraction reaction of acetone by chlorine radical

    NASA Astrophysics Data System (ADS)

    Tiu, Gerald C.; Tao, Fu-Ming

    2006-09-01

    Reaction mechanisms and kinetics of the hydrogen abstraction of acetone by chlorine radical are studied by theoretical calculations. Density functional theory and ab initio methods are used to explore the reaction pathways. The hydrogen abstraction is found to be highly favored over the addition pathway, and the latter is insignificant in atmospheric conditions. Classical transition state theory with Eckart tunneling corrections is employed to obtain rate constants of the reaction from 210 K to 360 K. The reaction is characterized by a small barrier, and rate constants approximated by the expression k( T) = 6.44 × 10 -12 e (-672/ T) cm 3 molecule -1 s -1, which is in reasonable agreement with experiment.

  12. Water-catalyzed gas-phase reaction of formic acid with hydroxyl radical: A computational investigation

    NASA Astrophysics Data System (ADS)

    Luo, Yi; Maeda, Satoshi; Ohno, Koichi

    2009-02-01

    The reaction of formic acid with hydroxyl radical, which is considered to be relevant to atmospheric chemistry, has been extensively studied. A water-catalyzed process of this reaction is computationally studied here for the first time. The scaled hypersphere search method was used for global exploration of pre-reaction complexes. Calculations were performed at high level of theory, such as CCSD(T)/cc-pVTZ//B3LYP/6-311+G(2df, 2p) and CCSD(T)/cc-pVTZ//MP2/aug-cc-pVDZ. It is found that the water-catalyzed process of this reaction is more kinetically favorable than its non-catalytic process. Such catalytic process may also be of interest for atmospheric chemistry, like the non-catalytic one.

  13. Kinetics of the C-C bond beta scission reactions in alkyl radicals.

    PubMed

    Ratkiewicz, Artur

    2011-09-07

    High pressure limits of thermal rate constants of four C-C bond beta scission reactions of propyl, 1-butyl, 2-butyl and isobutyl radicals were calculated using the canonical variational transition state theory (CVT) with a multi-dimensional small-curvature tunneling (SCT) correction over the temperature range of 300-3000 K. The CCSD(T)/cc-pVDZ//BH&HLYP/cc-pVDZ method was used to provide necessary potential energy surface information. Rate constants for these reactions were used to extrapolate rate constants for reactions in larger alkyls where experimental data are available using the Reaction Class Transition State Theory (RC-TST). Excellent agreement with experimental data confirms the validity of the RC-TST methodology and the accuracy of the calculated kinetic data in this study.

  14. Preparative and Mechanistic Studies Toward the Rational Development of Catalytic, Enantioselective Selenoetherification Reactions

    PubMed Central

    Denmark, Scott E.; Kalyani, Dipannita; Collins, William R.

    2010-01-01

    A systematic investigation into the Lewis base catalyzed, asymmetric, intramolecular selenoetherification of olefins is described. A critical challenge for the development of this process was the identification and suppression of racemization pathways available to arylseleniranium ion intermediates. Toward this end, this report details a thorough study of the influences of the steric and electronic modulation of the arylselenenyl group on the configurational stability of enantioenriched seleniranium ions. These studies show that the 2-nitrophenyl group attached to the selenium atom significantly attenuates the racemization of seleniranium ions. A variety of achiral Lewis bases catalyze the intramolecular selenoetherification of alkenes using N-(2-nitrophenylselenenyl)succinimide as the electrophile along with a Brønsted acid. Preliminary mechanistic studies suggest the intermediacy of ionic Lewis base-selenium(II) adducts. Most importantly, a broad survey of chiral Lewis bases revealed that BINAM derived thiophosphoramides catalyze the cyclization of unsaturated alcohols in the presence of N-(2-nitrophenylselenenylsuccinimide and methanesulfonic acid. A variety of cyclic seleno ethers were produced in good chemical yields and in moderate to good enantioselectivities which constitutes the first, catalytic, enantioselective selenofunctionalization of unactivated olefins. PMID:20961070

  15. Reactions of isoprene and sulphoxy radical-anions - a possible source of atmospheric organosulphites and organosulphates

    NASA Astrophysics Data System (ADS)

    Rudziński, K. J.; Gmachowski, L.; Kuznietsova, I.

    2009-03-01

    Transformation of isoprene coupled with auto-oxidation of SIV in aqueous solutions was studied experimentally and by chemical-kinetic modelling over a broad range of solution acidities (pH=3-9) to complement the research on aqueous-phase and heterogeneous transformation of isoprene reported recently by many laboratories. Isoprene significantly slowed down the auto-oxidation in acidic and basic solutions, and accelerated it slightly in neutral solutions. Simultaneously, production of sulphate ions and formation of solution acidity were significantly reduced. Formation of sulphite and sulphate derivatives of isoprene - sulphurous acid mono-(2-methyl-4-oxo-but-2-enyl) ester (m/z=163), sulphurous acid mono-(4-hydroxy-2-methyl-but-2-enyl) ester (m/z=165), sulphuric acid mono-(2-methyl-4-oxo-but-2-enyl) ester (m/z=179), sulphuric acid mono-(4-hydroxy-2-methyl-but-2-enyl) ester (m/z=181), and possible structural isomers of these species - was indicated by electrospray ionisation mass spectrometric analysis of post-reaction mixtures. The experimental results were explained by changes in a subtle quantitative balance of three superimposed processes whose rates depended in different manner on the acidity of reacting solutions - the scavenging of sulphoxy radical-anions by isoprene, the formation of sulphoxy radical-anions during further reactions of isoprene radicals, and the auto-oxidation of SIV itself. A chemical mechanism based on this idea was explored numerically to show good agreement with experimental data. In basic and neutral solutions, the model overestimated the consumption of isoprene, probably because reactions of primary sulphite and sulphate derivatives of isoprene with sulphoxy radical-anions were not included. Interaction of isoprene with sulphur(IV) species and oxygen can possibly result in formation of new organosulphate and organosulphite components of atmospheric aerosols and waters, and influence the distribution of reactive sulphur and oxygen species

  16. Enantioselective Decarboxylative Alkylation Reactions: Catalyst Development, Substrate Scope, and Mechanistic Studies

    PubMed Central

    Behenna, Douglas C.; Mohr, Justin T.; Sherden, Nathaniel H.; Marinescu, Smaranda C.; Harned, Andrew M.; Tani, Kousuke; Seto, Masaki; Ma, Sandy; Novák, Zoltán; Krout, Michael R.; McFadden, Ryan M.; Roizen, Jennifer L.; Enquist, John A.; White, David E.; Levine, Samantha R.; Petrova, Krastina V.; Iwashita, Akihiko; Virgil, Scott C.; Stoltz, Brian M.

    2012-01-01

    α-Quaternary ketones are accessed through novel enantioselective alkylations of allyl and propargyl electrophiles by unstabilized prochiral enolate nucleophiles in the presence of palladium complexes with various phosphinooxazoline (PHOX) ligands. Excellent yields and high enantiomeric excesses are obtained from three classes of enolate precursors: enol carbonates, enol silanes, and racemic β-ketoesters. Each of these substrate classes functions with nearly identical efficiency in terms of yield and enantioselectivity. Catalyst discovery and development, the optimization of reaction conditions, the exploration of reaction scope, and applications in target-directed synthesis are reported. Experimental observations suggest that these alkylation reactions occur through an unusual inner-sphere mechanism involving binding of the prochiral enolate nucleophile directly to the palladium center. PMID:22083969

  17. Mechanistic insight into the hydrazine decomposition on Rh(111): effect of reaction intermediate on catalytic activity.

    PubMed

    Deng, Zhigang; Lu, Xiaoqing; Wen, Zengqiang; Wei, Shuxian; Liu, Yunjie; Fu, Dianling; Zhao, Lianming; Guo, Wenyue

    2013-10-14

    Periodic density functional theory (DFT) calculations have been performed to systematically investigate the effect of reaction intermediate on catalytic activity for hydrazine (N2H4) decomposition on Rh(111). Reaction mechanisms via intramolecular and NH2-assisted N2H4 decompositions are comparatively analyzed, including adsorption configuration, reaction energy and barrier of elementary step, and reaction network. Our results show that the most favorable N2H4 decomposition pathway starts with the initial N-N bond scission to the NH2 intermediate, followed by stepwise H stripping from adsorbed N2Hx (x = 1-4) species, and finally forms the N2 and NH3 products. Comparatively, the stepwise intramolecular dehydrogenation via N2H4→ N2H3→ N2H2→ N2H → N2, and N2H4→ NH2→ NH → N with or without NH2 promotion effect, are unfavorable due to higher energy barriers encountered. Energy barrier analysis, reaction rate constants, and electronic structures are used to identify the crucial competitive route. The promotion effect of the NH2 intermediate is structurally reflected in the weakening of the N-H bond and strengthening of the N-N bond in N2Hx in the coadsorption system; it results intrinsically from the less structural deformation of the adsorbate, and weakening of the interaction between dehydrogenated fragment and departing H in transition state. Our results highlight the crucial effect of reaction intermediate on catalytic activity and provide a theoretical approach to analyze the effect.

  18. 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.

  19. Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins.

    PubMed

    Das, A K; Meuwly, M

    2016-01-01

    Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed.

  20. Nickel-Catalyzed Allylic Alkylation with Diarylmethane Pronucleophiles: Reaction Development and Mechanistic Insights.

    PubMed

    Sha, Sheng-Chun; Jiang, Hui; Mao, Jianyou; Bellomo, Ana; Jeong, Soo A; Walsh, Patrick J

    2016-01-18

    Palladium-catalyzed allylic substitution reactions are among the most efficient methods to construct C-C bonds between sp(3)-hybridized carbon atoms. In contrast, much less work has been done with nickel catalysts, perhaps because of the different mechanisms of the allylic substitution reactions. Palladium catalysts generally undergo substitution by a "soft"-nucleophile pathway, wherein the nucleophile attacks the allyl group externally. Nickel catalysts are usually paired with "hard" nucleophiles, which attack the metal before C-C bond formation. Introduced herein is a rare nickel-based catalyst which promotes substitution with diarylmethane pronucleophiles by the soft-nucleophile pathway. Preliminary studies on the asymmetric allylic alkylation are promising.

  1. Fundamental kinetics and mechanistic pathways for oxidation reactions in supercritical water

    NASA Technical Reports Server (NTRS)

    Webley, Paul A.; Tester, Jefferson W.

    1988-01-01

    Oxidation of the products of human metabolism in supercritical water has been shown to be an efficient way to accomplish the on-board water/waste recycling in future long-term space flights. Studies of the oxidation kinetics of methane to carbon dioxide in supercritical water are presented in this paper in order to enhance the fundamental understanding of the oxidation of human waste compounds in supercritical water. It is concluded that, although the elementary reaction models remain the best hope for simulating oxidation in supercritical water, several modifications to existing mechanisms need to be made to account for the role of water in the reaction mechanism.

  2. Fundamental kinetics and mechanistic pathways for oxidation reactions in supercritical water

    NASA Technical Reports Server (NTRS)

    Webley, Paul A.; Tester, Jefferson W.

    1988-01-01

    Oxidation of the products of human metabolism in supercritical water has been shown to be an efficient way to accomplish the on-board water/waste recycling in future long-term space flights. Studies of the oxidation kinetics of methane to carbon dioxide in supercritical water are presented in this paper in order to enhance the fundamental understanding of the oxidation of human waste compounds in supercritical water. It is concluded that, although the elementary reaction models remain the best hope for simulating oxidation in supercritical water, several modifications to existing mechanisms need to be made to account for the role of water in the reaction mechanism.

  3. Proton-electron transfer pathways in the reactions of peroxyl and dpph˙ radicals with hydrogen-bonded phenols.

    PubMed

    Amorati, Riccardo; Menichetti, Stefano; Viglianisi, Caterina; Foti, Mario C

    2012-12-18

    The kinetics of the reaction of peroxyl and dpph˙ radicals with phenols H-bonded to N-bases have been studied for the first time. Electron-transfer processes are observed in MeCN but only with the dpph˙ radical.

  4. Lewis acid-Lewis acid heterobimetallic cooperative catalysis: mechanistic studies and application in enantioselective aza-Michael reaction.

    PubMed

    Yamagiwa, Noriyuki; Qin, Hongbo; Matsunaga, Shigeki; Shibasaki, Masakatsu

    2005-09-28

    The full details of a catalytic asymmetric aza-Michael reaction of methoxylamine promoted by rare earth-alkali metal heterobimetallic complexes are described, demonstrating the effectiveness of Lewis acid-Lewis acid cooperative catalysis. First, enones were used as substrates, and the 1,4-adducts were obtained in good yield (57-98%) and high ee (81-96%). Catalyst loading was successfully reduced to 0.3-3 mol % with enones. To broaden the substrate scope of the reaction to carboxylic acid derivatives, alpha,beta-unsaturated N-acylpyrroles were used as monodentate, carboxylic acid derivatives. With beta-alkyl-substituted N-acylpyrroles, the reaction proceeded smoothly and the products were obtained in high yield and good ee. Transformation of the 1,4-adducts from enones and alpha,beta-unsaturated N-acylpyrroles afforded corresponding chiral aziridines and beta-amino acids. Detailed mechanistic studies, including kinetics, NMR analysis, nonlinear effects, and rare earth metal effects, are also described. The Lewis acid-Lewis acid cooperative mechanism, including the substrate coordination mode, is discussed in detail.

  5. INTERACTIONS OF LIGHT AND CHEMICAL REACTIONS IN THE AQUATIC ENVIRONMENT: KINETIC AND MECHANISTIC ASPECTS

    EPA Science Inventory

    Changes in the ozone layer over the past two decades have resulted in increases in solar ultraviolet (UV) radiation that reaches the surface of aquatic environments. Recent studies have demonstrated that these UV increases cause changes in photochemical reactions that affect the...

  6. INTERACTIONS OF LIGHT AND CHEMICAL REACTIONS IN THE AQUATIC ENVIRONMENT: KINETIC AND MECHANISTIC ASPECTS

    EPA Science Inventory

    Changes in the ozone layer over the past two decades have resulted in increases in solar ultraviolet (UV) radiation that reaches the surface of aquatic environments. Recent studies have demonstrated that these UV increases cause changes in photochemical reactions that affect the...

  7. Mechanistic study on the replacement reaction between silver nanostructures and chloroauric acid in aqueous medium.

    PubMed

    Sun, Yugang; Xia, Younan

    2004-03-31

    The replacement reaction between silver nanostructures and an aqueous HAuCl(4) solution has recently been demonstrated as a versatile method for generating metal nanostructures with hollow interiors. Here we describe the results of a systematic study detailing the morphological, structural, compositional, and spectral changes involved in such a heterogeneous reaction on the nanoscale. Two distinctive steps have been resolved through a combination of microscopic and spectroscopic methods. In the first step, silver nanostructure (i.e., the template) is dissolved to generate gold atoms that are deposited epitaxially on the surface of each template. Silver atoms also diffuse into the gold shell (or sheath) to form a seamless, hollow nanostructure with its wall made of Au-Ag alloys. The second step involves dealloying, a process that selectively removes silver atoms from the alloyed wall, induces morphological reconstruction, and finally leads to the formation of pinholes in the walls. Reaction temperature was found to play an important role in the replacement reaction because the solubility constant of AgCl and the diffusion coefficients of Ag and Au atoms were both strongly dependent on this parameter. This work has enabled us to prepare metal nanostructures with controllable geometric shapes and structures, and thus optical properties (for example, the surface plasmon resonance peaks could be readily shifted from 500 to 1200 nm by controlling the ratio between Ag and HAuCl(4)).

  8. Kinetic and mechanistic study of the atmospheric reaction of MBO331 with Cl atoms

    NASA Astrophysics Data System (ADS)

    Rodríguez, Diana; Rodríguez, Ana; Garzón, Andrés; Granadino-Roldán, José M.; Soto, Amparo; Aranda, Alfonso; Notario, Alberto

    2012-12-01

    The present work deals with the reaction of 3-methyl-3-buten-1-ol (MBO331) with Cl atoms, which has been investigated by gas chromatography with flame ionization detection (GC-FID) at atmospheric pressure in N2 or air, using the relative rate technique. The rate constant reaction at 298 ± 1 K was found to be (5.01 ± 0.70) × 10-10 cm3 molecule-1 s-1, using cyclohexane, octane and 1-butene as a reference compounds. The temperature dependence for the reaction was studied within the 298-333 K range. Additionally, a product identification under atmospheric conditions has been performed for the first time by GC-MS, with 3-methyl-3-butenal, methacrolein and chloroacetone being observed as degradation products. A theoretical study on the reaction at the QCISD(T)/6-311G**//MP2/6-311G** level was also carried out to obtain more information on the mechanism. From the theoretical study it can be predicted that Cl addition to the double bond proceeds through lower energy barriers than H-abstraction pathways and therefore is energetically favoured. Finally, atmospheric implications of the results obtained are discussed.

  9. Farnesyl pyrophosphate synthetase. Mechanistic studies of the 1'-4 coupling reaction with 2-fluorogeranyl pyrophosphate.

    PubMed

    Poulter, C D; Argyle, J C; Mash, E A

    1978-10-25

    The mechanism of the 1'-4 coupling reaction between isopentenyl pyrophosphate and geranyl pyrophosphate catalyzed by farnesyl pyrophosphate synthetase from porcine liver was studied with the allylic substrate analogue 2-fluorogeranyl pyrophosphate. 2-Fluorogeranyl pyrophosphate is an alternate substrate for the enzyme, yielding 6-fluorofarnesyl pyrophosphate upon condensation with isopentenyl pyrophosphate. The Michaelis constant for the fluoroanalogue, Km = 1.1 micron, is similar to that measured for geranyl pyrophosphate, Km = 0.7 micron. However, the rate of condensation with the fluoroanalogue was only 8.4 X 10(-4) that of the normal reaction. A similar rate of depression (4.4 X 10(-3)) was found for solvolysis of geranyl methanesulfonate and the corresponding 2-fluoro derivative, reactions known to proceed via cationic intermediates. In contrast, displacement of chlorine from geranyl chloride and 2-fluorogeranyl chloride by cyanide showed a small (2-fold) rate enhancement for the fluoro compound. Finally, 2-fluorogeranyl pyrophosphate is a competitive inhibitor against geranyl pyrophosphate. These data are interpreted in terms of an ionization-condensation-elimination mechanism for the 1'-4 coupling reaction.

  10. Enantioselective Visible-Light-Induced Radical-Addition Reactions to 3-Alkylidene Indolin-2-ones.

    PubMed

    Lenhart, Dominik; Bauer, Andreas; Pöthig, Alexander; Bach, Thorsten

    2016-05-04

    The title compounds underwent a facile and high-yielding addition reaction (19 examples, 66-99% yield) with various N-(trimethylsilyl)methyl-substituted amines upon irradiation with visible light and catalysis by a metal complex. If the alkylidene substituent is non-symmetric and if the reaction is performed in the presence of a chiral hydrogen-bonding template, products are obtained with significant enantioselectivity (58-72% ee) as a mixture of diastereoisomers. Mechanistic studies suggest a closed catalytic cycle for the photoactive metal complex. However, the silyl transfer from the amine occurs not only to the product, but also to the substrate, and interferes with the desired chirality transfer.

  11. Can Aerosols Catalyze the Reaction of OH Radical with Volatile Organic Compounds?

    NASA Astrophysics Data System (ADS)

    Dibble, T. S.; Sorensen, M. D.; Wallington, T. J.; Hurley, M. D.; Nielsen, O. J.

    2002-12-01

    Several recent papers have suggested that aerosol particles at atmospherically relevant concentrations can catalyze the OH-initiated degradation of selected volatile organic compounds (VOCs). If the degradation of many VOCs were to be affected in this manner, there could be large effects (locally or regionally) on the production of tropospheric ozone, the processing of aerosols, and the concentration of OH radical. The relative rate technique with FTIR detection was used to determine aerosol effects on the kinetics of the reaction of OH radical with a series of alcohols and unsaturated compounds in a smog chamber at ~1 atm and 296 K. Experiments were performed with and without NaCl, (NH4)2SO4, or NH4NO3 aerosol, in particle concentrations ranging from those typical of polluted urban conditions (500 \\mu g/m3 = 4000 \\mu m2/cm3 surface area per volume) to those an order of magnitude higher. In contrast to the previous findings there was no discernable effect of aerosol on the rate of loss of the organic compounds via reaction with OH radicals. Arguments based on gas kinetic theory confirm the implausibility of the previous results, and suggest that the present conclusions may be generalized to other aerosols and VOCs.

  12. The O_2 + Ethyl Reaction in Helium Nanodroplets: Infrared Spectroscopy of the Ethylperoxy Radical

    NASA Astrophysics Data System (ADS)

    Franke, Peter R.; Douberly, Gary E.

    2017-06-01

    Helium-solvated ethylperoxy radicals (CH_3CH_2OO) are formed via the in situ reaction between ethyl radicals and ˜{X}^{3}Σ_{g}^{-} O_2. The reactants are captured sequentially through the droplet pick-up technique. Helium droplets are doped with ethyl radical via pyrolysis of di-tert-amyl peroxide or n-propylnitrite in an effusive, low-pressure source. A mid-infrared spectrum of ethylperoxy is recorded with species-selective droplet beam depletion spectroscopy. Spectral assignments in the CH stretching region are made via comparisons to second-order vibrational perturbation theory with resonances (VPT2+K) based on coupled-cluster quartic force fields. Gauche and trans conformers are predicted to be nearly isoenergetic; however, the spectrum indicates that one dominant conformer is present. Indeed, in several previous studies in our group, where chemical reactions were conducted inside droplets, only a single conformer of the product was observed. Exploration of the ethylperoxy potential energy surface, particularly along the CCOO torsional and CO stretching coordinates, motivates an explanation that is based upon an adiabatic funneling mechanism that leads to the exclusive production of one conformer. The slower torsional degree of freedom is cooled more rapidly than the higher frequency stretching and bending coordinates owing to the stronger coupling between the torsional modes and the collective modes of the helium droplet. The reactants are cooled into the torsional well that stabilizes first during their approach on the PES.

  13. Peroxyl Radical Reactions in Water Solution: A Gym for Proton-Coupled Electron-Transfer Theories.

    PubMed

    Amorati, Riccardo; Baschieri, Andrea; Morroni, Gloria; Gambino, Rossana; Valgimigli, Luca

    2016-06-01

    The reactions of alkylperoxyl radicals with phenols have remained difficult to investigate in water. We describe herein a simple and reliable method based on the inhibited autoxidation of water/THF mixtures, which we calibrated against pulse radiolysis. With this method we measured the rate constants kinh for the reactions of 2-tetrahydrofuranylperoxyl radicals with reference compounds: urate, ascorbate, ferrocenes, 2,2,5,7,8-pentamethyl-6-chromanol, Trolox, 6-hydroxy-2,5,7,8-tetramethylchroman-2-acetic acid, 2,6-di-tert-butyl-4-methoxyphenol, 4-methoxyphenol, catechol and 3,5-di-tert-butylcatechol. The role of pH was investigated: the value of kinh for Trolox and 4-methoxyphenol increased 11- and 50-fold from pH 2.1 to 12, respectively, which indicate the occurrence of a SPLET-like mechanism. H(D) kinetic isotope effects combined with pH and solvent effects suggest that different types of proton-coupled electron transfer (PCET) mechanisms are involved in water: less electron-rich phenols react at low pH by concerted electron-proton transfer (EPT) to the peroxyl radical, whereas more electron-rich phenols and phenoxide anions react by multi-site EPT in which water acts as proton relay. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Products and kinetics of the heterogeneous reaction of particulate ametryn with NO3 radicals.

    PubMed

    Liu, Chang-Geng; Shu, Ji-Nian; Yang, Bo; Zhang, Peng

    2014-12-01

    As a renowned s-triazine herbicide, ametryn is worldwide emitted into the atmosphere in both gaseous and particulate phases via spray drifts from treatments and post application emissions, but its chemical degradation in the atmosphere has not been well characterized. In this study, the heterogeneous kinetics of particulate ametryn with NO3 radicals were investigated with a mixed-phase relative rate method. A vacuum ultraviolet photoionization aerosol time-of-flight mass spectrometer (VUV-ATOFMS) and an atmospheric gas analysis mass spectrometer were synchronously used to online monitor the decays of particulate ametryn and gas-phase isoprene. The reactive uptake coefficient of NO3 radicals on ametryn particles was calculated to be 2.9 × 10(-2), according to the measured ametryn loss ratio and the average NO3 concentration. The effective rate constant for the heterogeneous reaction of particulate ametryn with NO3 radicals measured under experimental conditions was 8.4 × 10(-13) cm(3) molecule(-1) s(-1). In addition, atraton, ametryn sulfoxide and ametryn sulfone were identified as the reaction products by gas-chromatography-mass spectrometry (GC-MS) analysis. The experimental results might shed light on the chemical behavior of atmospheric ametryn at night-time.

  15. Kinetic studies of heterogeneous reactions of particulate phosmet and parathion with NO3 radicals.

    PubMed

    Liu, Changgeng; Yang, Bo; Zeng, Chenghua

    2015-01-01

    Organophosphorous pesticides (OPPs) are ubiquitous pollutants in the atmospheric environment with adverse effects on human health. In this study, heterogeneous kinetics of particulate phosmet and parathion with NO3 radicals were investigated with a mixed-phase relative rate method. A vacuum ultraviolet photoionization aerosol time-of-flight mass spectrometer (VUV-ATOFMS) and an atmospheric gas analysis mass spectrometer were used to monitor online the decays of particulate OPPs and reference compound, respectively. Reactive uptake coefficients of NO3 radicals on phosmet and parathion particles were (0.12±0.03) and (0.14±0.04), respectively, calculated according to the measured OPPs loss ratios and the average NO3 concentrations. Additionally, the average effective rate constants for heterogeneous reactions of particulate phosmet and parathion with NO3 radicals measured under experimental conditions were (2.80±0.16)×10(-12) and (2.97±0.13)×10(-12) cm(3) molecule(-1) s(-1), respectively. The experimental results of these heterogeneous reactions in the aerosol state provide supplementary knowledge for kinetic behaviors of airborne OPPs particles. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Surprisingly Long-Lived Ascorbyl Radicals in Acetonitrile: Concerted Proton-Electron Transfer Reactions and Thermochemistry

    PubMed Central

    Warren, Jeffrey J.; Mayer, James M.

    2008-01-01

    Proton-coupled electron transfer (PCET) reactions and thermochemistry of 5,6-isopropylidene ascorbate (iAscH−) have been examined in acetonitrile solvent.iAscH− is oxidized by 2,4,6-tBu3C6H2O• and by excess TEMPO• to give the corresponding 5,6-isopropylidene ascorbyl radical anion (iAsc•−), which persists for hours at 298 K in dry MeCN solution. The stability of iAsc•− is surprising in light of the transience of the ascorbyl radical in aqueous solutions, and is due to the lack of the protons needed for radical disproportionation. A concerted proton-electron transfer (CPET) mechanism is indicated for the reactions of iAscH−. Redox potential, pKa and equilibrium measurements define the thermochemical landscape for 5,6-isopropylidene ascorbic acid and its derivatives in MeCN. These measurements give an O–H bond dissociation free energy (BDFE) for iAscH−of 65.4 ± 1.5 kcal mol−1 in MeCN. Similar studies on underivatized ascorbate indicate a BDFE of 67.8 ± 1.2 kcal mol−1. These values are much lower than the aqueous BDFE for ascorbate of 74.0 ± 1.5 kcal mol−1 derived from reported data. PMID:18505256

  17. Ab initio molecular dynamics of the reaction of quercetin with superoxide radical

    NASA Astrophysics Data System (ADS)

    Lespade, Laure

    2016-08-01

    Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car-Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.

  18. Gas-Phase Reaction of Hydroxyl Radical with p-Cymene over an Extended Temperature Range.

    PubMed

    Bedjanian, Yuri; Morin, Julien; Romanias, Manolis N

    2015-11-12

    The kinetics of the reaction of OH radicals with p-cymene has been studied in the temperature range of 243-898 K using a flow reactor combined with a quadrupole mass spectrometer: OH + p-cymene → products. The reaction rate constant was determined as a result of absolute measurements, from OH decay kinetics in excess of p-cymene and employing the relative rate method with OH reactions with n-pentane, n-heptane,1,3-dioxane, HBr, and Br2 as the reference ones. For the rate coefficient of the H atom abstraction channel, the expression k1b = (3.70 ± 0.42) × 10(-11) exp[-(772 ± 72)/T] was obtained over the temperature range of 381-898 K. The total rate constant (addition + abstraction) determined at T = 243-320 K was k1 = (1.82 ± 0.48) × 10(-12) exp[(607 ± 70)/T] or, in a biexponential form, k1 = k1a + k1b = 3.7 × 10(-11) exp(-772/T) + 6.3 × 10(-13) exp(856/T), independent of the pressure between 1 and 5 Torr of helium. In addition, our results indicate that the reaction pathway involving alkyl radical elimination upon initial addition of OH to p-cymene is most probably unimportant.

  19. Gas-phase reactions of organic radicals and diradicals with ions.

    PubMed

    Zhang, Xu; Bierbaum, Veronica M; Ellison, G Barney; Kato, Shuji

    2004-02-22

    Reactions of polyatomic organic radicals with gas phase ions have been studied at thermal energy using a flowing afterglow-selected ion flow tube (FA-SIFT) instrument. A supersonic pyrolysis nozzle produces allyl radical (CH2CHCH2) and ortho-benzyne diradical (o-C6H4) for reaction with ions. We have observed: [CH2CHCH2 + H3O+ --> C3H6+ + H2O], [CH2CHCH2 + HO- --> no ion products], [o-C6H4 + H3O+ --> C6H5+ + H2O], and [o-C6H4 + HO- --> C6H3- + H2O]. The proton transfer reactions with H3O+ occur at nearly every collision (kII approximately with 10(-9) cm3 s(-1)). The exothermic proton abstraction for o-C6H4 + HO- is unexpectedly slow (kII approximately with 10(-10) cm3 s(-1)). This has been rationalized by competing associative detachment: o-C6H4 + HO- --> C6H5O + e-. The allyl + HO- reaction proceeds presumably via similar detachment pathways.

  20. Kinetics and products study of the reaction of BrO radicals with gaseous mercury

    NASA Astrophysics Data System (ADS)

    Raofie, F.; Ariya, P. A.

    2003-05-01

    Bro reactions of elemental mercury was as a major candidate for near complete depletion of elemental mercury in polar region. The kinetics of the reaction between BrO radicals with gaseous mercury was identified using relative rate method by Gas Chromatography with Mass spectroscopic Detection (GC-MS) at room temperature (298±1 K) and at atmospheric pressure 760 ± 1 Torr in the N_2 diluent. Propane, DMS and butane were used as reference molecules. The upper and lower limits rate constant for reaction of Hg^0 with BrO was estimated to be 1.0 × 10^{-13} and 1.0 × 10^{15} cm^3 molecules^{-1} s^{-1}, respectively. BrO radicals were produced from the photolysis of bromine and dibromomethane in presence of ozone and detected by MS at m/e = 95 or 97. Ozone was produced in a Silent discharged generator. Reaction products were identified using direct mass spectrometer with chemical ionization ion source.

  1. Investigation of terpinolene + ozone or terpinolene + nitrate radical reaction products using denuder/filter apparatus

    PubMed Central

    Harrison, Joel C.; Wells, J.R.

    2015-01-01

    Terpinolene’s (1-methyl-4-(propan-2-ylidene)cyclohexene) reaction with ozone or the nitrate radical was investigated using a denuder/filter apparatus in order to characterize gas-phase and particulate reaction products. Identification of the reaction products (i.e., aldehydes, ketones, dicarbonyls and carboxylic acids) was made using two derivatization methods; O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine (PFBHA) to derivatize the carbonyl products or 3-Ethyl-1-[3-(dimethylamino)propyl]carbodiimide hydrochloride (EDC) and 2,2,2-trifluoroethylamine hydrochloride (TFEA) to derivatize the carboxylic acid products. Proposed carbonyl products for ozonolysis of terpinolene are: 4-methylcyclohex-3-en-1-one, 2-hydroxy-4-methylcyclohex-3-en-1-one, glyoxal, methyl glyoxal, 3-oxobutanal, and 6-oxo-3-(propan-2-ylidene)heptanal. Proposed carbonyl products for nitrate radical reaction of terpinolene are: 2-hydroxy-4-methylcyclohex-3-en-1-one, glyoxal, methyl glyoxal, and 4-oxopentanal. No carboxylic acid products were detected with either oxidizing reactant. PMID:26527171

  2. Investigation of terpinolene + ozone or terpinolene + nitrate radical reaction products using denuder/filter apparatus.

    PubMed

    Harrison, Joel C; Wells, J R

    2013-12-01

    Terpinolene's (1-methyl-4-(propan-2-ylidene)cyclohexene) reaction with ozone or the nitrate radical was investigated using a denuder/filter apparatus in order to characterize gas-phase and particulate reaction products. Identification of the reaction products (i.e., aldehydes, ketones, dicarbonyls and carboxylic acids) was made using two derivatization methods; O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine (PFBHA) to derivatize the carbonyl products or 3-Ethyl-1-[3-(dimethylamino)propyl]carbodiimide hydrochloride (EDC) and 2,2,2-trifluoroethylamine hydrochloride (TFEA) to derivatize the carboxylic acid products. Proposed carbonyl products for ozonolysis of terpinolene are: 4-methylcyclohex-3-en-1-one, 2-hydroxy-4-methylcyclohex-3-en-1-one, glyoxal, methyl glyoxal, 3-oxobutanal, and 6-oxo-3-(propan-2-ylidene)heptanal. Proposed carbonyl products for nitrate radical reaction of terpinolene are: 2-hydroxy-4-methylcyclohex-3-en-1-one, glyoxal, methyl glyoxal, and 4-oxopentanal. No carboxylic acid products were detected with either oxidizing reactant.

  3. Investigation of terpinolene + ozone or terpinolene + nitrate radical reaction products using denuder/filter apparatus

    NASA Astrophysics Data System (ADS)

    Harrison, Joel C.; Wells, J. R.

    2013-12-01

    Terpinolene's (1-methyl-4-(propan-2-ylidene)cyclohexene) reaction with ozone or the nitrate radical was investigated using a denuder/filter apparatus in order to characterize gas-phase and particulate reaction products. Identification of the reaction products (i.e., aldehydes, ketones, dicarbonyls and carboxylic acids) was made using two derivatization methods; O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine (PFBHA) to derivatize the carbonyl products or 3-Ethyl-1-[3-(dimethylamino)propyl]carbodiimide hydrochloride (EDC) and 2,2,2-trifluoroethylamine hydrochloride (TFEA) to derivatize the carboxylic acid products. Proposed carbonyl products for ozonolysis of terpinolene are: 4-methylcyclohex-3-en-1-one, 2-hydroxy-4-methylcyclohex-3-en-1-one, glyoxal, methyl glyoxal, 3-oxobutanal, and 6-oxo-3-(propan-2-ylidene)heptanal. Proposed carbonyl products for nitrate radical reaction of terpinolene are: 2-hydroxy-4-methylcyclohex-3-en-1-one, glyoxal, methyl glyoxal, and 4-oxopentanal. No carboxylic acid products were detected with either oxidizing reactant.

  4. Effects of delocalization on intrinsic barriers for H-atom transfer: Implications for the radical hydrogen transfer reaction

    SciTech Connect

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

    1992-08-01

    PM3 calculations of transition states (TS) for both normal H-atom transfer and radical hydrogen transfer (RHT) reactions of a a wide-variety of hydrocarbon structures have enabled development of quantitative structure-reactivity relationships. Results indicate that activation barriers for RHT reactions are large enough that thermoneutral and endothermic reactions should not compete with alternative multistep pathways.

  5. EPR and NMR detection of transient radicals and reaction products. [Radiolysis of methanol and aqueous potassium acetate

    SciTech Connect

    Trifunac, A.D.

    1981-01-01

    Magnetic resonance methods in radiation chemistry are illustrated. The most recent developments in pulsed EPR and NMR studies in pulse radiolysis are outlined with emphasis on the study of transient radicals and their reaction products. 12 figures.

  6. Photo-Induced Atom-Transfer Radical Reactions Using Charge-Transfer Complex between Iodine and Tertiary Amine.

    PubMed

    Yoshioka, Eito; Kohtani, Shigeru; Hashimoto, Takurou; Takebe, Tomoko; Miyabe, Hideto

    2017-01-01

    In the presence of charge-transfer complexes between iodine and tertiary amines, the aqueous-medium atom-transfer radical reactions proceeded under visible light irradiation without the typical photocatalysts.

  7. Kinetic and mechanistic study of the reaction of atomic chlorine with dimethyl sulfide

    SciTech Connect

    Stickel, R.E.; Nicovich, J.M.; Wang, S.; Zhao, Z.; Wine, P.H.

    1992-11-26

    Time-resolved resonance fluorescence detection of Cl({sup 2}P{sub J}) following 266-nm laser flash photolysis of Cl{sub 2}CO/CH{sub 3}SCH{sub 3}(DMS)/N{sub 2} mixtures has been employed to study the kinetics of the title reaction over the temperature and pressure ranges 240-421 K and 3-700 Torr. The reaction is found to be very fast, occurring on essentially every Cl({sup 2}P{sub J}) + DMS encounter. The reaction rate increases with decreasing temperature and shows a significant pressure dependence. At 297 K, for example, the rate coefficient increases from a low-pressure limit value of approximately 1.8 x 10{sup {minus}10} cm{sup 3} molecule{sup {minus}1} s{sup {minus}1} to a value of (3.3 {+-} 0.5) x 10{sup {minus}10} cm{sup 3} molecule{sup {minus}1} s{sup {minus}1} at P = 700 Torr. A few experiments were carried out with CD{sub 3}SCD{sub 3} or C{sub 2}H{sub 5}SC{sub 2}H{sub 5} replacing DMS as the sulfide reactant; within experimental uncertainty, no dependence of the rate coefficient on the identity of the sulfide reactant was observed. In a separate study, time-resolved tunable diode laser spectroscopic detection of HCl has been coupled with 248-nm laser flash photolysis of Cl{sub 2}CO/DMS/CO{sub 2}/N{sub 2} mixtures to measure the HCl product yield from the title reaction as a function of pressure at T = 297 K. The HCl yield approaches unity as P {yields} 0 but decreases with increasing pressure to a value of {approximately}0.5 at P = 203 Torr. The yield experiments demonstrate that hydrogen abstraction is the dominant reaction mechanism in the low-pressure limit. With increasing pressure, stabilization of a (CH{sub 3}){sub 2}SCl adduct apparently becomes competitive with the hydrogen abstraction pathway. The potential role of the title reaction in marine atmospheric chemistry is discussed. 59 refs., 7 figs., 3 tabs.

  8. Cyclic Versus Linear Isomers Produced by Reaction of the Methylidyne Radical (CH) with Small Unsaturated Hydrocarbons

    SciTech Connect

    Goulay, Fabien; Trevitt, Adam J.; Meloni, Giovanni; Selby, Talitha M.; Osborn, David L.; Taatjes, Craig A.; Vereecken, Luc; Leone, Stephen R.

    2008-12-05

    The reactions of the methylidyne radical (CH) with ethylene, acetylene, allene, and methylacetylene are studied at room temperature using tunable vacuum ultraviolet (VUV) photoionization and time-resolved mass spectrometry. The CH radicals are prepared by 248 nm multiphoton photolysis of CHBr3 at 298 K and react with the selected hydrocarbon in a helium gas flow. Analysis of photoionization efficiency versus VUV photon wavelength permits isomer-specific detection of the reaction products and allows estimation of the reaction product branching ratios. The reactions proceed by either CH insertion or addition followed by H atom elimination from the intermediate adduct. In the CH + C2H4 reaction the C3H5 intermediate decays by H atom loss to yield 70(+-8)percent allene, 30(+-8)percent methylacetylene and less than 10percent cyclopropene, in agreement with previous RRKM results. In the CH + acetylene reaction, detection of mainly the cyclic C3H2 isomer is contrary to a previous RRKM calculation that predicted linear triplet propargylene to be 90percent of the total H-atom co-products. High-level CBS-APNO quantum calculations and RRKM calculation for the CH + C2H2 reaction presented in this manuscript predict a higher contribution of the cyclic C3H2 (27.0percent) versus triplet propargylene (63.5percent) than these earlier predictions. Extensive calculations on the C3H3 and C3H2D system combined with experimental isotope ratios for the CD + C2H2 reaction indicate that H-atom assisted isomerization in the present experiments is responsible for the discrepancy between the RRKM calculations and the experimental results. Cyclic isomers are also found to represent 30(+-6)percent of the detected products in the case of CH + methylacetylene, together with 33(+-6)percent 1,2,3-butatriene and 37(+-6)percent vinylacetylene. The CH + allene reaction gives 23(+-5)percent 1,2,3-butatriene and 77(+-5)percent vinylacetylene, whereas cyclic isomers are produced below the detection limit

  9. On the reaction of lupulones, hops β-acids, with 1-hydroxyethyl radical.

    PubMed

    de Almeida, Natália E C; do Nascimento, Eduardo S P; Cardoso, Daniel R

    2012-10-24

    Lupulones, hops β-acids, are one of the main constituents of the hops resin and have an important contribution to the overall bacteriostatic activity of hops during beer brewing. The use of lupulones as natural alternatives to antibiotics is increasing in the food industry and also in bioethanol production. However, lupulones are easy oxidizable and have been shown to be very reactive toward 1-hydroxyethyl radical with apparent bimolecular rate constants close to diffusion control k = 2.9 × 10(8) and 2.6 × 10(8) L mol(-1) s(-1) at 25.0 ± 0.2 °C in ethanol-water solution (10% of ethanol (v/v)) as probed by EPR and ESI-IT-MS/MS spin-trapping competitive kinetics, respectively. The free energy change for an electron-transfer mechanism is ΔG° = 106 kJ/mol as calculated from the oxidation peak potential experimentally determined for lupulones (1.1 V vs NHE) by cyclic voltammetry and the reported reduction potential for 1-hydroxyethyl radical. The major reaction products identified by LC-ESI-IT-MS/MS and ultrahigh-resolution accurate mass spectrometry (orbitrap FT-MS) are hydroxylated lupulone derivatives and 1-hydroxyethyl radical adducts. The lack of pH dependence for the reaction rate constant, the calculated free energy change for electron transfer, and the main reaction products strongly suggest the prenyl side chains at the hops β-acids as the reaction centers rather than the β,β'-triketone moiety.

  10. Reaction mechanisms and kinetics of the iminovinylidene radical with NO: Ab initio study

    SciTech Connect

    Hsiao, Ming-Kai; Chung, Yi-Hua; Hung, Yu-Ming; Chen, Hui-Lung

    2014-05-28

    The nitric oxide (NO) is a notorious compound for polluting environment. Recent year, removing nitric oxide from the atmosphere becomes a focus of the investigation. In our work, we study the iminovinylidene (HNCC) radical reacted with NO molecule. The mechanism and kinetic for reaction of the HNCC radical with the NO molecule is investigated via considering the possible channels of the N and O atoms of NO attacking the N and C atoms of the HNCC based on the high level ab initio molecular orbital calculations in conjunction with variational TST and RRKM calculations. The species involved have been optimized at the B3LYP/6-311++G(3df,2p) level and their single-point energies are refined by the CCSD(T)/aug-cc-PVQZ//B3LYP/6-311++G(3df,2p) method. The calculated potential energy surfaces indicated that energetically the most favorable channel for the HNCC + NO reaction was predicted to be the formation of HNC+CNO (P8) product via the addition reaction of the C atom of HNCC radical and the N atom of NO with the head to head orientation. To rationalize the scenario of the calculated results, we also employ the Fukui functions and HSAB theory to seek for a possible explanation. In addition, the reaction rate constants were calculated using VariFlex code, and the results show that the total rate coefficient, k{sub total}, at Ar pressure 760 Torr can be represented with an equation: k{sub total} = 6.433 × 10{sup −11} T {sup 0.100} exp(0.275 kcal mol{sup −1}/RT) at T = 298–3000 K, in units of cm{sup 3} molecule{sup −1} s{sup −1}.

  11. Detection of free radicals from low temperature ozone-olefin reactions by ESR spin trapping: evidence that the radical precursor is a trioxide

    SciTech Connect

    Pryor, W.A.; Prier, D.G.; Church, D.F.

    1983-05-04

    Free radicals are detected fom the low-temperature ozonation of a series of olefins by using an electron spin resonance (ESR) spin-trap method. The technique involves ozonation at -78/sup 0/C in Freon-11, blowing out the ozone with an inert gas, adding the spin trap at -78/sup 0/C, and then warming the solution while in the probe of the ESR spectrometer. A series of small olefins was examined, and tetramethylethylene (TME) and 2-methyl-2-pentene (2-MP) gave the highest yield of radicals. However, even thse two olefins give yields of radicals that are less than 1% on the basis of ozone consumed. Thus, our data indicate that while the nonradical Criegee ozonation process is the principal reaction for monoolefins, radical production is a significant side reaction. The temperature dependence of the appearance of spin adducts from both TME and 2-MP shows that the radical precursor in this case is a trioxidic species; specifically, we suggest that it is an alkyl hydrotroxide, ROOOH. We propose the ROOOH is formed by allylic hydride abstraction from the olefin by ozone to give a pair of caged ions that combine to form the trioxide. (Benson has proposed a similar hydride abstraction for alkanes and several other types of compounds.) The reaction may proceed through a charge-transfer complex of the olefin and ozone as an intermediate.

  12. Aqueous Secondary Organic Aerosol (aqSOA) Formation By Radical Reactions: Model Studies Comparing the Role of OH Versus Organic Radicals

    NASA Astrophysics Data System (ADS)

    Ervens, B.; Renard, P.; Reed Harris, A.; Vaida, V.; Monod, A.

    2014-12-01

    Chemical reactions in the aqueous phase are thought to significantly contribute to ambient aerosol mass under specific conditions. Results from many laboratory studies suggest that these reactions are efficiently initiated by the OH radical and lead to high molecular weight compounds (oligomers). Recent laboratory experiments have shown that methyl vinyl ketone (MVK) can form oligomers in high yield in aqueous solutions similar to aerosol water. Additional experiments have shown that the direct photolysis of pyruvic acid can generate organic radicals that initiate similar oligomer products upon oxidation of MVK (Renard et al., submitted). Sources of the OH radical in the aerosol aqueous phase include the direct uptake from the gas phase, Fenton reactions and, to a smaller extent, direct photolyses of hydrogen peroxide and nitrate. Recent model studies imply that under many conditions, aqSOA formation might be oxidant-limited since these OH(aq) sources are not sufficient to provide a continuous OH supply. This limitation can be (partially) removed if additional radical sources in the multiphase system are considered. Exemplary, we include the direct photolysis of aqueous pyruvic acid as a proxy for possible other radical sources. Model results will be shown and consequences for aqSOA formation and processing under ambient conditions will be discussed.

  13. Partial reactions and chemical rescue of site-directed mutants of Rubisco as mechanistic probes

    SciTech Connect

    Harpel, M.R.; Larimer, F.W.; Lee, E.H.; Mural, R.J.; Smith, H.B.; Soper, T.S.; Hartman, F.C.

    1991-01-01

    Given the current state of knowledge of the reaction pathways catalyzed by D-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and the elucidation of the three-dimensional structure of several different forms of the enzyme, sit-directed mutagenesis offers the potential to decipher catalytic roles of active-site residues and to unravel the functional significance of various structural elements. Especially intriguing are intersubunit, electrostatic interactions at the active site between Glu48 and Lys168 of the nonactivated (noncarbamylated) enzyme and between Glu48 and Lys329 of the activated (carbamylated) enzyme. In this paper, we describe two approaches to address the roles of electrostatic interactions at the active site and the roles of the participant residues: (1) characterization of pertinent site-directed mutants, including their abilities to catalyze partial reactions and (2) subtle alteration of the active-site microenvironment by manipulation of these proteins with exogenous reagents.

  14. Partial reactions and chemical rescue of site-directed mutants of Rubisco as mechanistic probes

    SciTech Connect

    Harpel, M.R.; Larimer, F.W.; Lee, E.H.; Mural, R.J.; Smith, H.B.; Soper, T.S.; Hartman, F.C.

    1991-12-31

    Given the current state of knowledge of the reaction pathways catalyzed by D-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and the elucidation of the three-dimensional structure of several different forms of the enzyme, sit-directed mutagenesis offers the potential to decipher catalytic roles of active-site residues and to unravel the functional significance of various structural elements. Especially intriguing are intersubunit, electrostatic interactions at the active site between Glu48 and Lys168 of the nonactivated (noncarbamylated) enzyme and between Glu48 and Lys329 of the activated (carbamylated) enzyme. In this paper, we describe two approaches to address the roles of electrostatic interactions at the active site and the roles of the participant residues: (1) characterization of pertinent site-directed mutants, including their abilities to catalyze partial reactions and (2) subtle alteration of the active-site microenvironment by manipulation of these proteins with exogenous reagents.

  15. Relative rate constants for the reactions of atomic oxygen with HO2 anad OH radicals

    NASA Technical Reports Server (NTRS)

    Keyser, L. F.

    1983-01-01

    Relative rate constants for the reactions O + HO2 - OH + O2 (1) and O + OH - H + O2 (2) were obtained by using the discharge-flow resonance fluorescence technique at 2 torr total pressure and 299 K. HO2 radicals were generated by reacting atomic hydrogen with an excess of O2. Quasi-steady-state concentrations of OH and HO2 were established in the presence of excess atomic oxygen. Observed concentration ratios, namely the ratio of the OH concentration to the HO2 concentration, resulted in a value of 1.7 + or 0.2 for k1/k2. The error limits are twice the standard deviation obtained from the data analysis. Overall experimental error is estimated to be + or - 25 percent. This result confirms earlier direct measurements of k1 and k2 which required knowledge of absolute radical or atomic oxygen concentrations.

  16. Relative rate constants for the reactions of atomic oxygen with HO2 anad OH radicals

    NASA Technical Reports Server (NTRS)

    Keyser, L. F.

    1983-01-01

    Relative rate constants for the reactions O + HO2 - OH + O2 (1) and O + OH - H + O2 (2) were obtained by using the discharge-flow resonance fluorescence technique at 2 torr total pressure and 299 K. HO2 radicals were generated by reacting atomic hydrogen with an excess of O2. Quasi-steady-state concentrations of OH and HO2 were established in the presence of excess atomic oxygen. Observed concentration ratios, namely the ratio of the OH concentration to the HO2 concentration, resulted in a value of 1.7 + or 0.2 for k1/k2. The error limits are twice the standard deviation obtained from the data analysis. Overall experimental error is estimated to be + or - 25 percent. This result confirms earlier direct measurements of k1 and k2 which required knowledge of absolute radical or atomic oxygen concentrations.

  17. Mechanistic Studies of the Solvolyses of Carbamoyl Chlorides and Related Reactions

    PubMed Central

    D’Souza, Malcolm J.; Kevill, Dennis N.

    2016-01-01

    Carbamoyl chlorides are important intermediates, both in the research laboratory and in industrial scale syntheses. The most studied and used are the disubstituted derivatives, incorporating either aryl or alkyl groups (Ar2NCOCl or R2NCOCl). Sometimes, the groups are tied back to give a ring and piperidino- and morpholino-derivatives are commonly encountered. Some studies have been made with two different groups attached. Solvolyses tend to occur at the carbonyl carbon, with replacement of the chloride ion. Studies of both rate and products are reviewed and the solvolysis reactions are usually SN1, although addition of an amine leads to a superimposable bimolecular component. Many of the studies under solvolytic conditions include the application of the extended Grunwald–Winstein equation. The monosubstituted derivatives (ArNHCOCl or RNHCOCl) are less studied. They are readily prepared by the addition of HCl to an isocyanate. In acetonitrile, they decompose to set up and reach equilibrium with the isocyanate (ArNCO or RNCO) and HCl. Considering that the structurally related formyl chloride (HOCOCl) is highly unstable (with formation of HCl + CO2), the unsubstituted carbamoyl chloride (H2NCOCl) is remarkably stable. Recommended synthetic procedures require it to survive reaction temperatures in the 300–400 °C range. There has been very little study of its reactions. PMID:26784185

  18. Mechanistic studies on norcoclaurine synthase of benzylisoquinoline alkaloid biosynthesis: an enzymatic Pictet-Spengler reaction.

    PubMed

    Luk, Louis Y P; Bunn, Shannon; Liscombe, David K; Facchini, Peter J; Tanner, Martin E

    2007-09-04

    Norcoclaurine synthase catalyzes an asymmetric Pictet-Spengler condensation of dopamine and 4-hydroxyphenylacetaldehyde to give (S)-norcoclaurine. This is the first committed step in the biosynthesis of the benzylisoquinoline alkaloids that include morphine and codeine. In this work, the gene encoding for the Thalictrum flavum norcoclaurine synthase is highly overexpressed in Escherichia coli and the resulting His-tagged recombinant enzyme is purified for the first time. A continuous assay based on circular dichroism spectroscopy is developed and used to monitor the kinetics of the enzymatic reaction. Dopamine analogues bearing a methoxy or hydrogen substituent in place of the C-1 phenolic group were readily accepted by the enzyme whereas those bearing the same substituents at C-2 were not. This supports a mechanism involving a two-step cyclization of the putative iminium ion intermediate that does not proceed via a spirocyclic intermediate. The reaction of [3,5,6-2H]dopamine was found to be slowed by a kinetic isotope effect of 1.7 +/- 0.1 on the value of kcat/KM. This is interpreted as showing that the deprotonation step causing rearomatization is partially rate determining in the overall reaction.

  19. Asymmetric recombination and electron spin relaxation in the semiclassical theory of radical pair reactions

    SciTech Connect

    Lewis, Alan M.; Manolopoulos, David E.; Hore, P. J.

    2014-07-28

    We describe how the semiclassical theory of radical pair recombination reactions recently introduced by two of us [D. E. Manolopoulos and P. J. Hore, J. Chem. Phys. 139, 124106 (2013)] can be generalised to allow for different singlet and triplet recombination rates. This is a non-trivial generalisation because when the recombination rates are different the recombination process is dynamically coupled to the coherent electron spin dynamics of the radical pair. Furthermore, because the recombination operator is a two-electron operator, it is no longer sufficient simply to consider the two electrons as classical vectors: one has to consider the complete set of 16 two-electron spin operators as independent classical variables. The resulting semiclassical theory is first validated by comparison with exact quantum mechanical results for a model radical pair containing 12 nuclear spins. It is then used to shed light on the spin dynamics of a carotenoid-porphyrin-fullerene triad containing considerably more nuclear spins which has recently been used to establish a “proof of principle” for the operation of a chemical compass [K. Maeda, K. B. Henbest, F. Cintolesi, I. Kuprov, C. T. Rodgers, P. A. Liddell, D. Gust, C. R. Timmel, and P. J. Hore, Nature (London) 453, 387 (2008)]. We find in particular that the intriguing biphasic behaviour that has been observed in the effect of an Earth-strength magnetic field on the time-dependent survival probability of the photo-excited C{sup ·+}PF{sup ·−} radical pair arises from a delicate balance between its asymmetric recombination and the relaxation of the electron spin in the carotenoid radical.

  20. Asymmetric recombination and electron spin relaxation in the semiclassical theory of radical pair reactions

    NASA Astrophysics Data System (ADS)

    Lewis, Alan M.; Manolopoulos, David E.; Hore, P. J.

    2014-07-01

    We describe how the semiclassical theory of radical pair recombination reactions recently introduced by two of us [D. E. Manolopoulos and P. J. Hore, J. Chem. Phys. 139, 124106 (2013)] can be generalised to allow for different singlet and triplet recombination rates. This is a non-trivial generalisation because when the recombination rates are different the recombination process is dynamically coupled to the coherent electron spin dynamics of the radical pair. Furthermore, because the recombination operator is a two-electron operator, it is no longer sufficient simply to consider the two electrons as classical vectors: one has to consider the complete set of 16 two-electron spin operators as independent classical variables. The resulting semiclassical theory is first validated by comparison with exact quantum mechanical results for a model radical pair containing 12 nuclear spins. It is then used to shed light on the spin dynamics of a carotenoid-porphyrin-fullerene triad containing considerably more nuclear spins which has recently been used to establish a "proof of principle" for the operation of a chemical compass [K. Maeda, K. B. Henbest, F. Cintolesi, I. Kuprov, C. T. Rodgers, P. A. Liddell, D. Gust, C. R. Timmel, and P. J. Hore, Nature (London) 453, 387 (2008)]. We find in particular that the intriguing biphasic behaviour that has been observed in the effect of an Earth-strength magnetic field on the time-dependent survival probability of the photo-excited C.+PF.- radical pair arises from a delicate balance between its asymmetric recombination and the relaxation of the electron spin in the carotenoid radical.

  1. Asymmetric recombination and electron spin relaxation in the semiclassical theory of radical pair reactions.

    PubMed

    Lewis, Alan M; Manolopoulos, David E; Hore, P J

    2014-07-28

    We describe how the semiclassical theory of radical pair recombination reactions recently introduced by two of us [D. E. Manolopoulos and P. J. Hore, J. Chem. Phys. 139, 124106 (2013)] can be generalised to allow for different singlet and triplet recombination rates. This is a non-trivial generalisation because when the recombination rates are different the recombination process is dynamically coupled to the coherent electron spin dynamics of the radical pair. Furthermore, because the recombination operator is a two-electron operator, it is no longer sufficient simply to consider the two electrons as classical vectors: one has to consider the complete set of 16 two-electron spin operators as independent classical variables. The resulting semiclassical theory is first validated by comparison with exact quantum mechanical results for a model radical pair containing 12 nuclear spins. It is then used to shed light on the spin dynamics of a carotenoid-porphyrin-fullerene triad containing considerably more nuclear spins which has recently been used to establish a "proof of principle" for the operation of a chemical compass [K. Maeda, K. B. Henbest, F. Cintolesi, I. Kuprov, C. T. Rodgers, P. A. Liddell, D. Gust, C. R. Timmel, and P. J. Hore, Nature (London) 453, 387 (2008)]. We find in particular that the intriguing biphasic behaviour that has been observed in the effect of an Earth-strength magnetic field on the time-dependent survival probability of the photo-excited C(·+)PF(·-) radical pair arises from a delicate balance between its asymmetric recombination and the relaxation of the electron spin in the carotenoid radical.

  2. Kinetics of 1,4-hydrogen migration in the alkyl radical reaction class.

    PubMed

    Bankiewicz, Barbara; Huynh, Lam K; Ratkiewicz, Artur; Truong, Thanh N

    2009-02-26

    The kinetics of the 1,4-intramolecular hydrogen migration in the alkyl radicals reaction class has been studied using reaction class transition-state theory combined with the linear energy relationship (LER) and barrier height grouping (BHG) approach. The rate constants for the reference reaction of n-C(4)H(9) were obtained by canonical variational transition-state theory (CVT) with the small curvature tunnelling (SCT) correction in the temperature range 300-3000 K with potential-energy surface information computed at the CCSD(T)/cc-pVDZ//BH&HLYP/cc-pVDZ level of theory. Error analyses indicate that RC-TST/LER, where only reaction energy is needed, and RC-TST/BHG, where no other information is needed, can predict rate constants for any reaction in this reaction class with excellent accuracy. Specifically, for this reaction class the RC-TST/LER method has less than 65% systematic errors in the predicted rate constants, while the RC-TST/BHG method has less than 80% error when compared to explicit rate calculations.

  3. CN radical reactions with hydrogen cyanide and cyanogen - Comparison of theory and experiment

    NASA Technical Reports Server (NTRS)

    Yang, D. L.; Yu, T.; Lin, M. C.; Melius, C. F.

    1992-01-01

    The method of laser photolysis/laser-induced fluorescence is used to obtain absolute rate constants for CN radical reactions with HCN and C2N2. The rate constants were found to be temperature-dependent in the range 300-740 K and pressure independent in the range 100-600 Torr. Rice-Remsperger-Kassel-Marcus theory for both reactions employing the transition state parameters obtained by the BAC-MP4 method are made. These calculations yielded reasonable results for the CN + HCN reaction, predicting both the temperature dependence and pressure independence. No pressure effect was observed in the pressure range 100-1000 Torr at temperatures below 900 K, confirming the experimental results.

  4. Theoretical study on the gas phase reaction of allyl chloride with hydroxyl radical

    NASA Astrophysics Data System (ADS)

    Zhang, Yunju; Chao, Kai; Sun, Jingyu; Zhang, Wanqiao; Shi, Haijie; Yao, Cen; Su, Zhongmin; Pan, Xiumei; Zhang, Jingping; Wang, Rongshun

    2014-02-01

    The reaction of allyl chloride with the hydroxyl radical has been investigated on a sound theoretical basis. This is the first time to gain a conclusive insight into the reaction mechanism and kinetics for important pathways in detail. The reaction mechanism confirms that OH addition to the C=C double bond forms the chemically activated adducts, IM1 (CH2CHOHCH2Cl) and IM2 (CH2OHCHCH2Cl) via low barriers, and direct H-abstraction paths may also occur. Variational transition state model and multichannel RRKM theory are employed to calculate the temperature-, pressure-dependent rate constants. The calculated rate constants are in good agreement with the experimental data. At 100 Torr with He as bath gas, IM6 formed by collisional stabilization is the major products in the temperature range 200-600 K; the production of CH2CHCHCl via hydrogen abstractions becomes dominant at high temperatures (600-3000 K).

  5. Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions.

    PubMed

    Chen, Haoyuan; Giese, Timothy J; Huang, Ming; Wong, Kin-Yiu; Harris, Michael E; York, Darrin M

    2014-10-27

    Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate-controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition-state structure and bonding optimally requires the use of theoretical models. In this work, we apply density-functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2'-O-transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well-studied series of phosphate and phosphorothioate mono-, di- and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non-enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease A, and demonstrate the reaction coordinate-KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of

  6. Low-temperature Kinetic Studies of OH Radical Reactions Relevant to Planetary Atmospheres

    NASA Astrophysics Data System (ADS)

    Townsend, T. M.; Antiñolo, M.; Ballesteros, B.; Jimenez, E.; Canosa, A.

    2011-05-01

    In the solar system, the temperature (T) of the atmosphere of giant planets or their satellites is only several tens of Kelvin (K). The temperature of the tropopause of Titan (satellite of Saturn) and the surface of Mars is 70 K and 210 K, respectively. In the Earth's atmosphere, T decreases from 298 K (surface) to 210 K close to the T-inversion region (tropopause). The principal oxidants in the Earth's lower atmosphere are ozone, the hydroxyl (OH) radical and hydrogen peroxide. A number of critical atmospheric chemical problems depend on the Earth's oxidising capacity, which is essentially the global burden of these oxidants. In the interstellar clouds and circumstellar envelopes, OH radicals have also been detected. As the chemistry of atmospheres is highly influenced by temperature, the knowledge of the T-dependence of the rate coefficients for OH-reactions (k) is the key to understanding the underlying molecular mechanisms. In general, these reactions take place on a short temporal scale. Therefore, a detection technique with high temporal resolution is required. Measurements of k at low temperatures can be achieved by maintaining a thermalised environment using either cryogenic cooling (T>200 K) or supersonic gas expansion with a Laval nozzle (several tens of K). The pulsed laser photolysis technique coupled with laser induced fluorescence detection has been widely used in our laboratory to determine the rate coefficients of OH-reactions with different volatile organic compounds, such as alcohols (1), saturated and unsaturated aliphatic aldehydes (2), linear ketones (3), as a function of temperature (260 350 K). An experimental system based on the CRESU (Cinetique de Reaction en Ecoulement Supersonique Uniforme or Reaction Kinetics in a Uniform Supersonic Flow) technique is currently under construction. This technique will allow the performance of kinetic studies of OH-reactions of astrophysical interest at temperatures lower than 200 K.

  7. Formation of dimethylketene and methacrolein by reaction of the CH radical with acetone.

    PubMed

    Goulay, Fabien; Derakhshan, Adeeb; Maher, Eamonn; Trevitt, Adam J; Savee, John D; Scheer, Adam M; Osborn, David L; Taatjes, Craig A

    2013-03-21

    The reaction of the methylidyne radical (CH) with acetone ((CH(3))(2)C[double bond, length as m-dash]O) is studied at room temperature and at a pressure of 4 Torr (533.3 Pa) using a multiplexed photoionization mass spectrometer coupled to the tunable vacuum ultraviolet synchrotron radiation of the Advanced Light Source at Lawrence Berkeley National Laboratory. The CH radicals are generated by 248 nm multiphoton photolysis of bromoform and react with acetone in an excess of helium and nitrogen gas flow. The main observed reaction exit channel is elimination of a hydrogen atom to form C(4)H(6)O isomers. Analysis of photoionization spectra identifies dimethylketene and methacrolein as the only H-elimination products. The best fit to the data gives branching ratios of 0.68 ± 0.14 for methacrolein and 0.32 ± 0.07 for dimethylketene. A methylketene spectrum measured here is used to reanalyze the photoionization spectrum obtained at m/z = 56 for the CH + acetaldehyde reaction, (Goulay et al., J. Phys. Chem. A, 2012, 116, 6091) yielding new H-loss branching ratios of 0.61 ± 0.12 for acrolein and 0.39 ± 0.08 for methylketene. The contribution from methyleneoxirane to the reaction product distribution is revised to be negligible. Coupled with additional product detection for the CD + acetone reaction, these observations pave the way for development of general set of reaction mechanisms for the addition of CH to compounds containing an acetyl subgroup.

  8. Kinetic solvent effects on hydrogen abstraction reactions from carbon by the cumyloxyl radical. The importance of solvent hydrogen-bond interactions with the substrate and the abstracting radical.

    PubMed

    Salamone, Michela; Giammarioli, Ilaria; Bietti, Massimo

    2011-06-03

    A kinetic study of the hydrogen atom abstraction reactions from propanal (PA) and 2,2-dimethylpropanal (DMPA) by the cumyloxyl radical (CumO•) has been carried out in different solvents (benzene, PhCl, MeCN, t-BuOH, MeOH, and TFE). The corresponding reactions of the benzyloxyl radical (BnO•) have been studied in MeCN. The reaction of CumO• with 1,4-cyclohexadiene (CHD) also has been investigated in TFE solution. With CHD a 3-fold increase in rate constant (k(H)) has been observed on going from benzene, PhCl, and MeCN to TFE. This represents the first observation of a sizable kinetic solvent effect for hydrogen atom abstraction reactions from hydrocarbons by alkoxyl radicals and indicates that strong HBD solvents influence the hydrogen abstraction reactivity of CumO•. With PA and DMPA a significant decrease in k(H) has been observed on going from benzene and PhCl to MeOH and TFE, indicative of hydrogen-bond interactions between the carbonyl lone pair and the solvent in the transition state. The similar k(H) values observed for the reactions of the aldehydes in MeOH and TFE point toward differential hydrogen bond interactions of the latter solvent with the substrate and the radical in the transition state. The small reactivity ratios observed for the reactions of CumO• and BnO• with PA and DMPA (k(H)(BnO•)/k(H)(CumO•) = 1.2 and 1.6, respectively) indicate that with these substrates alkoxyl radical sterics play a minor role.

  9. On the time behaviour of the concentration of pyrazinium radical cations in the early stage of the Maillard reaction

    NASA Astrophysics Data System (ADS)

    Stoesser, Reinhard; Klein, Jeannette; Peschke, Simone; Zehl, Andrea; Cämmerer, Bettina; Kroh, Lothar W.

    2007-08-01

    During the early stage of the Maillard reaction pyrazinium radical cations were detected by ESR within the reaction system D-glucose/glycine. The spectra were characterized by completely resolved hyperfine structure. The partial pressure of oxygen and the radical concentrations were measured directly in the reaction mixture by ESR using solutions of the spin probe TEMPOL and of DPPH, respectively. There are quantitative and qualitative relations of the actual concentration of the radical ions to the partial pressure of oxygen, the temperature-time regime and the mechanical mixing of the reaction system. These macroscopic parameters significantly affect both the induction period and the velocity of the time-dependent formation of free radicals. From in situ variations of p(O 2) and p(Ar) including the connected mixing effects caused by the passing the gases through the reaction mixture, steric and chemical effects of the stabilization of the radical ions were established. The determination of suitable and relevant conditions for stabilization and subsequent radical reactions contributes to the elucidation of the macroscopically known antioxidant activity of Maillard products.

  10. Detection of a tryptophan radical in the reaction of ascorbate peroxidase with hydrogen peroxide.

    PubMed

    Hiner, A N; Martínez, J I; Arnao, M B; Acosta, M; Turner, D D; Lloyd Raven, E; Rodríguez-López, J N

    2001-05-01

    The reactivity of recombinant pea cytosolic ascorbate peroxidase (rAPX) towards H2O2, the nature of the intermediates and the products of the reaction have been examined using UV/visible and EPR spectroscopies together with HPLC. Compound I of rAPX, generated by reaction of rAPX with 1 molar equivalent of H2O2, contains a porphyrin pi-cation radical. This species is unstable and, in the absence of reducing substrate, decays within 60 s to a second species, compound I*, that has a UV/visible spectrum [lambda(max) (nm) = 414, 527, 558 and 350 (sh)] similar, but not identical, to those of both horseradish peroxidase compound II and cytochrome c peroxidase compound I. Small but systematic differences were observed in the UV/visible spectra of compound I* and authentic rAPX compound II, generated by reaction of rAPX with 1 molar equivalent H2O2 in the presence of 1 molar equivalent of ascorbate [lambda(max) (nm) = 416, 527, 554, 350 (sh) and 628 (sh)]. Compound I* decays to give a 'ferric-like' species (lambda(max) = 406 nm) that is not spectroscopically identical to ferric rAPX (lambda(max) = 403 nm) with a first order rate constant, k(decay)' = (2.7 +/- 0.3) x 10(-4) s(-1). Authentic samples of compound II evolve to ferric rAPX [k(decay) = (1.1 +/- 0.2) x 10(-3) s(-1)]. Low temperature (10 K) EPR spectra are consistent with the formation of a protein-based radical, with g values for compound I* (g parallel = 2.038, g perpendicular = 2.008) close to those previously reported for the Trp191 radical in cytochrome c peroxidase (g parallel = 2.037, g perpendicular = 2.005). The EPR spectrum of rAPX compound II was essentially silent in the g = 2 region. Tryptic digestion of the 'ferric-like' rAPX followed by RP-HPLC revealed a fragment with a new absorption peak near 330 nm, consistent with the formation of a hydroxylated tryptophan residue. The results show, for the first time, that rAPX can, under certain conditions, form a protein-based radical analogous to that found

  11. Mechanistic insights into the stepwise Diels-Alder reaction of 4,6-dinitrobenzofuroxan.

    PubMed

    Linder, Mats; Johansson, Adam Johannes; Brinck, Tore

    2012-01-06

    The stepwise Diels-Alder reaction between 1-trimethylsiloxy-1,3-butadiene and 4,6-dinitrobenzofuroxan is explored using state-of-the-art computational methods. The results support a stepwise mechanism via a persistent intermediate, however, not the one previously reported (Lakhdar et al., Chem. Eur. J.2007, 16, 5681) but a heterocyclic adduct. The novel DFT functional M062X and the SCS-MP2 method were essential to reproduce a reasonable potential energy surface for this challenging system.

  12. Laser Flash Photolysis Studies of Radical-Radical Reaction Kinetics: The O((sup 3)P(sub J)) + BrO Reaction

    NASA Technical Reports Server (NTRS)

    Thorn, R. P.; Cronkhite, J. M.; Nicovich, J. M.; Wine, P. H.

    1997-01-01

    A novel dual laser flash photolysis-long path absorption-resonance fluorescence technique has been employed to study the kinetics of the important stratospheric reaction 0((sup 3)P(sub j)) + Br yields(k1) BrO((sup 2)P(sub J)) + O2 as a function of temperature (231-328 K) and pressure (25-150 Torr) in N2 buffer gas. The experimental approach preserves the principal advantages of the flash photolysis method, i.e., complete absence of surface reactions and a wide range of accessible pressures, but also employs techniques which are characteristic of the discharge flow method, namely chemical titration as a means for deducing the absolute concentration of a radical reactant and use of multiple detection axes. We find that k1 is independent of pressure, and that the temperature dependence of k1 is adequately described by the Arrhenius expression k1(T) = 1.91 x 10(exp -11)(230/J) cu cm/ molecule.s; the absolute accuracy of measured values for k1 is estimated to vary from +/- 20 percent at at T approximately 230 K to +/- 30 percent at T approximately 330 K. Our results demonstrate that the O((sup 3)P(sub j)) + BrO rate coefficient is significantly faster than previously 'guesstimated,' and suggest that the catalytic cycle with the O((sup 3)P(sub j)) + BrO reaction as its rate-limiting step is the dominant stratospheric BrO(x), odd-oxygen destruction cycle at altitudes above 24 km.

  13. Laser Flash Photolysis Studies of Radical-Radical Reaction Kinetics: The O((sup 3)P(sub J)) + BrO Reaction

    NASA Technical Reports Server (NTRS)

    Thorn, R. P.; Cronkhite, J. M.; Nicovich, J. M.; Wine, P. H.

    1997-01-01

    A novel dual laser flash photolysis-long path absorption-resonance fluorescence technique has been employed to study the kinetics of the important stratospheric reaction 0((sup 3)P(sub j)) + Br yields(k1) BrO((sup 2)P(sub J)) + O2 as a function of temperature (231-328 K) and pressure (25-150 Torr) in N2 buffer gas. The experimental approach preserves the principal advantages of the flash photolysis method, i.e., complete absence of surface reactions and a wide range of accessible pressures, but also employs techniques which are characteristic of the discharge flow method, namely chemical titration as a means for deducing the absolute concentration of a radical reactant and use of multiple detection axes. We find that k1 is independent of pressure, and that the temperature dependence of k1 is adequately described by the Arrhenius expression k1(T) = 1.91 x 10(exp -11)(230/J) cu cm/ molecule.s; the absolute accuracy of measured values for k1 is estimated to vary from +/- 20 percent at at T approximately 230 K to +/- 30 percent at T approximately 330 K. Our results demonstrate that the O((sup 3)P(sub j)) + BrO rate coefficient is significantly faster than previously 'guesstimated,' and suggest that the catalytic cycle with the O((sup 3)P(sub j)) + BrO reaction as its rate-limiting step is the dominant stratospheric BrO(x), odd-oxygen destruction cycle at altitudes above 24 km.

  14. Reaction mechanism of naphthyl radicals with molecular oxygen. 1. Theoretical study of the potential energy surface.

    PubMed

    Zhou, Chong-Wen; Kislov, Vadim V; Mebel, Alexander M

    2012-02-16

    Potential energy surfaces (PESs) of the reactions of 1- and 2-naphthyl radicals with molecular oxygen have been investigated at the G3(MP2,CC)//B3LYP/6-311G** level of theory. Both reactions are shown to be initiated by barrierless addition of O(2) to the respective radical sites of C(10)H(7). The end-on O(2) addition leading to 1- and 2-naphthylperoxy radicals exothermic by 45-46 kcal/mol is found to be more preferable thermodynamically than the side-on addition. At the subsequent reaction step, the chemically activated 1- and 2-C(10)H(7)OO adducts can eliminate an oxygen atom leading to the formation of 1- and 2-naphthoxy radical products, respectively, which in turn can undergo unimolecular decomposition producing indenyl radical + CO via the barriers of 57.8 and 48.3 kcal/mol and with total reaction endothermicities of 14.5 and 10.2 kcal/mol, respectively. Alternatively, the initial reaction adducts can feature an oxygen atom insertion into the attacked C(6) ring leading to bicyclic intermediates a10 and a10' (from 1-naphthyl + O(2)) or b10 and b10' (from 2-naphthyl + O(2)) composed from two fused six-member C(6) and seven-member C(6)O rings. Next, a10 and a10' are predicted to decompose to C(9)H(7) (indenyl) + CO(2), 1,2-C(10)H(6)O(2) (1,2-naphthoquinone) + H, and 1-C(9)H(7)O (1-benzopyranyl) + CO, whereas b10 and b10' would dissociate to C(9)H(7) (indenyl) + CO(2), 2-C(9)H(7)O (2-benzopyranyl) + CO, and 1,2-C(10)H(6)O(2) (1,2-naphthoquinone) + H. On the basis of this, the 1-naphthyl + O(2) reaction is concluded to form the following products (with the overall reaction energies given in parentheses): 1-naphthoxy + O (-15.5 kcal/mol), indenyl + CO(2) (-123.9 kcal/mol), 1-benzopyranyl + CO (-97.2 kcal/mol), and 1,2-naphthoquinone + H (-63.5 kcal/mol). The 2-naphthyl + O(2) reaction is predicted to produce 2-naphthoxy + O (-10.9 kcal/mol), indenyl + CO(2) (-123.7 kcal/mol), 2-benzopyranyl + CO (-90.7 kcal/mol), and 1,2-naphthoquinone + H (-63.2 kcal

  15. Peroxidyme-Amplified Radical Chain Reaction (PARCR): Visible Detection of a Catalytic Reporter.

    PubMed

    Goertz, John P; White, Ian M

    2017-08-29

    Peroxidyme Amplified Radical Chain Reaction (PARCR), a novel enzyme-free system that achieves exponential amplification of a visible signal, is presented. Typical enzyme-free amplification systems that produce a visible readout suffer from long reaction times, low sensitivity, and narrow dynamic range. PARCR employs photocatalyzed nonlinear signal generation, enabling unprecedented one-pot, naked-eye detection of a catalytic reporter from 1 μm down to 100 pm. In this reaction, hemin-binding peroxidase-mimicking DNAzymes ("peroxidymes") mediate the NADH-driven oxidation of a colorless, nonfluorescent phenoxazine dye (Amplex Red) to a brightly colored, strongly fluorescent product (resorufin); illumination with green light initiates multiple radical-forming positive-feedback loops, rapidly producing visible levels of resorufin. Collectively, these results demonstrate the potential of PARCR as an easy-to-use readout for a range of detection schemes, including aptamer labels, hybridization assays, and nucleic acid amplification. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Kinetic Reaction Mechanism of Sinapic Acid Scavenging NO2 and OH Radicals: A Theoretical Study

    PubMed Central

    Lu, Yang; Wang, AiHua; Shi, Peng; Zhang, Hui; Li, ZeSheng

    2016-01-01

    The mechanism and kinetics underlying reactions between the naturally-occurring antioxidant sinapic acid (SA) and the very damaging ·NO2 and ·OH were investigated through the density functional theory (DFT). Two most possible reaction mechanisms were studied: hydrogen atom transfer (HAT) and radical adduct formation (RAF). Different reaction channels of neutral and anionic sinapic acid (SA-) scavenging radicals in both atmosphere and water medium were traced independently, and the thermodynamic and kinetic parameters were calculated. We find the most active site of SA/SA- scavenging ·NO2 and ·OH is the –OH group in benzene ring by HAT mechanism, while the RAF mechanism for SA/SA- scavenging ·NO2 seems thermodynamically unfavorable. In water phase, at 298 K, the total rate constants of SA eliminating ·NO2 and ·OH are 1.30×108 and 9.20×109 M-1 S-1 respectively, indicating that sinapic acid is an efficient scavenger for both ·NO2 and ·OH. PMID:27622460

  17. Reactions of OH-radicals with procarbazine. A pulse radiolysis and computer simulation study.

    PubMed

    Delipetar-Grudl, A; Solar, S; Getoff, N

    2006-01-01

    Pulse radiolysis was applied to study the reactivity of *OH radicals with procarbazine (PC), a cytostatic agent widely used in radiation- and chemotherapy. An overall rate constant of k(*OH+PC) = 3.7 x 10(9) l.mol(-1).s(-1) was determined. The thereby formed transients had a strong absorption at 350 nm, epsilon350 = 4.46 x 10(3) l.mol(-1).cm(-1), and a weak absorption band around 530 nm. Computer simulation studies to elucidate the most probable sites of *OH attack on the PC molecule showed that *OH radical addition to the aromatic ring had the highest probability. These transients decayed by a first order reaction, k = 1.75 x 10(3) s(-1), whereby species having a maximum absorption at 300 nm and broad shoulder at 340-380 nm were formed. Similar absorptions were observed after gamma radiolysis of PC. A reaction mechanism is suggested. For the reaction of H-atoms with PC, a rate constant k(*H+PC) = 6.4 x 10(8) l.mol(-1).s(-1) was determined.

  18. Mechanistic Analysis of an Isoxazole-Oxazole Photoisomerization Reaction Using a Conical Intersection.

    PubMed

    Su, Ming-Der

    2015-09-17

    The mechanisms of the three reaction pathways for the photochemical transformation of 3,5-dimethylisoxazole (1) in its first singlet excited state (π→ π*)1 have been determined using the CASSCF (11-orbital/14-electron active space) and MP2-CAS methods with the 6-311G(d) basis set. These three reaction pathways are denoted as (i) the internal cyclization-isomerization path (path A), (ii) the ring contraction-ring expansion path (path B), and (iii) the direct path (path C). This work provides the first theoretical examinations of mechanisms for such photochemical rearrangements. The present theoretical findings suggest that the photoisomerization of 1 via path C should be much more favorable then either path A or path B. Nevertheless, the theoretical observations reveal that path B, which consists of a sequence of small geometric rearrangements, should be energetically feasible as well. Accordingly, the fleeting intermediate, acetyl nitrile ylide (4), which arises from the mechanism of path B, can be detected experimentally.

  19. Electrochemical reactions in fluoride-ion batteries: mechanistic insights from PDF analysis

    DOE PAGES

    Grenier, Antonin; Porras-Gutierrez, Ana-Gabriela; Groult, Henri; ...

    2017-08-14

    Detailed analysis of electrochemical reactions occurring in a rechargeable Fluoride-Ion Battery (FIB) is provided by means of synchrotron X-ray diffraction (XRD) and Pair Distribution Function (PDF) analysis. In this study, a symmetrical cell containing Bi-BiF3 composite electrodes was characterized after three cycles. As for Li conversionbased electrodes, our study confirms that a multi-electron redox process occurs between Bi metal and BiF3. XRD and PDF analyses show that multiple Bi oxyfluoride phases are formed due to the presence of Bi oxide in the initial Bi electrode and/or Bi oxyfluoride in the initial BiF3 electrode. Quantitative PDF analyses suggests that oxygen doesmore » not migrate through the electrolyte and that the fluoride ion is the sole charge transfer anion. Hence, we showed that oxide species are not preventing the electrochemical reactions, opening the path for the study of metal oxyfluoride as active materials for FIBs.« less

  20. Mechanistic studies of 1-aminocyclopropane-1-carboxylate deaminase: characterization of an unusual pyridoxal 5'-phosphate-dependent reaction.

    PubMed

    Thibodeaux, Christopher J; Liu, Hung-Wen

    2011-03-22

    1-Aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCD) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that cleaves the cyclopropane ring of ACC, to give α-ketobutyric acid and ammonia as products. The cleavage of the C(α)-C(β) bond of an amino acid substrate is a rare event in PLP-dependent enzyme catalysis. Potential chemical mechanisms involving nucleophile- or acid-catalyzed cyclopropane ring opening have been proposed for the unusual transformation catalyzed by ACCD, but the actual mode of cyclopropane ring cleavage remains obscure. In this report, we aim to elucidate the mechanistic features of ACCD catalysis by investigating the kinetic properties of ACCD from Pseudomonas sp. ACP and several of its mutant enzymes. Our studies suggest that the pK(a) of the conserved active site residue, Tyr294, is lowered by a hydrogen bonding interaction with a second conserved residue, Tyr268. This allows Tyr294 to deprotonate the incoming amino group of ACC to initiate the aldimine exchange reaction between ACC and the PLP coenzyme and also likely helps to activate Tyr294 for a role as a nucleophile to attack and cleave the cyclopropane ring of the substrate. In addition, solvent kinetic isotope effect (KIE), proton inventory, and (13)C KIE studies of the wild type enzyme suggest that the C(α)-C(β) bond cleavage step in the chemical mechanism is at least partially rate-limiting under k(cat)/K(m) conditions and is likely preceded in the mechanism by a partially rate-limiting step involving the conversion of a stable gem-diamine intermediate into a reactive external aldimine intermediate that is poised for cyclopropane ring cleavage. When viewed within the context of previous mechanistic and structural studies of ACCD enzymes, our studies are most consistent with a mode of cyclopropane ring cleavage involving nucleophilic catalysis by Tyr294.

  1. Rapid reaction of superoxide with insulin-tyrosyl radicals to generate a hydroperoxide with subsequent glutathione addition.

    PubMed

    Das, Andrew B; Nauser, Thomas; Koppenol, Willem H; Kettle, Anthony J; Winterbourn, Christine C; Nagy, Péter

    2014-05-01

    Tyrosine (Tyr) residues are major sites of radical generation during protein oxidation. We used insulin as a model to study the kinetics, mechanisms, and products of the reactions of radiation-induced or enzyme-generated protein-tyrosyl radicals with superoxide to demonstrate the feasibility of these reactions under oxidative stress conditions. We found that insulin-tyrosyl radicals combined to form dimers, mostly via the tyrosine at position 14 on the α chain (Tyr14). However, in the presence of superoxide, dimerization was largely outcompeted by the reaction of superoxide with insulin-tyrosyl radicals. Using pulse radiolysis, we measured a second-order rate constant for the latter reaction of (6±1) × 10(8) M(-1) s(-1) at pH 7.3, representing the first measured rate constant for a protein-tyrosyl radical with superoxide. Mass-spectrometry-based product analyses revealed the addition of superoxide to the insulin-Tyr14 radical to form the hydroperoxide. Glutathione efficiently reduced the hydroperoxide to the corresponding monoxide and also subsequently underwent Michael addition to the monoxide to give a diglutathionylated protein adduct. Although much slower, conjugation of the backbone amide group can form a bicyclic Tyr-monoxide derivative, allowing the addition of only one glutathione molecule. These findings suggest that Tyr-hydroperoxides should readily form on proteins under oxidative stress conditions where protein radicals and superoxide are both generated and that these should form addition products with thiol compounds such as glutathione.

  2. Ab initio study of the influence of resonance stabilization on intramolecular ring closure reactions of hydrocarbon radicals.

    PubMed

    Wang, Kun; Villano, Stephanie M; Dean, Anthony M

    2016-03-28

    The intramolecular ring closure reactions of unsaturated hydrocarbon radicals potentially play an important role for the formation of molecular weight growth species, especially during the pyrolysis and oxidation of alkenes under low to intermediate temperatures. In this work we investigated a series of intramolecular cycloaddition reactions of both allylic- and alkyl-type dienyl radicals. In the first set of reactions, a resonant linear radical is converted into a non-resonant cyclic radical. In the second set, a non-resonant linear alkenyl radical isomerizes to either a resonant cyclic radical or a cyclic carbinyl radical. In both cases, three different reaction schemes are examined based on the location of the partially-formed resonance structure in the cyclic transition state. For each reaction scheme, both the endo- and exo-pathways were investigated. High pressure rate parameters are obtained from the results of CBS-QB3 electronic structure calculations combined with canonical transition state theory calculations. The results are discussed in the context of a Benson-type model to examine the impact of the partially-formed resonance stabilization on both the activation energies and pre-exponential factors. The results are compared to previously reported rate parameters for cycloaddition reactions of alkenyl radicals. The differences in the activation energies are primarily due to the bimolecular component of the activation energy. However, in some cases, the presence of the partial resonance structure significantly increases the strain energy for the ring that is formed in the transition state. The pre-exponential factors are also impacted by the formation of a partial resonance structure in the transition state. Lastly, the C6H9 potential energy surface is examined to show how the trends that are outlined here can be used to estimate rate parameters, which are needed to analyze pressure-dependent reaction systems.

  3. Ethanol oxidation: kinetics of the alpha-hydroxyethyl radical + O2 reaction.

    PubMed

    da Silva, Gabriel; Bozzelli, Joseph W; Liang, Long; Farrell, John T

    2009-08-06

    Bioethanol is currently a significant gasoline additive and the major blend component of flex-fuel formulations. Ethanol is a high-octane fuel component, and vehicles designed to take advantage of higher octane fuel blends could operate at higher compression ratios than traditional gasoline engines, leading to improved performance and tank-to-wheel efficiency. There are significant uncertainties, however, regarding the mechanism for ethanol autoignition, especially at lower temperatures such as in the negative temperature coefficient (NTC) regime. We have studied an important chemical process in the autoignition and oxidation of ethanol, reaction of the alpha-hydroxyethyl radical with O2(3P), using first principles computational chemistry, variational transition state theory, and Rice-Ramsperger-Kassel-Marcus (RRKM)/master equation simulations. The alpha-hydroxyethyl + O2 association reaction is found to produce an activated alpha-hydroxy-ethylperoxy adduct with ca. 37 kcal mol(-1) of excess vibrational energy. This activated adduct predominantly proceeds to acetaldehyde + HO(2), with smaller quantities of the enol vinyl alcohol (ethenol), particularly at higher temperatures. The reaction to acetaldehyde + HO2 proceeds with such a low barrier that collision stabilization of C2O3H5 isomers is unimportant, even for high-pressure/low-temperature conditions. The short lifetimes of these radicals precludes the chain-branching addition of a second O2 molecule, responsible for NTC behavior in alkane autoignition. This result helps to explain why ignition delays for ethanol are longer than those for ethane, despite ethanol having a weaker C-C bond energy. Given its relative instability, it is also unlikely that the alpha-hydroxy-ethylperoxy radical acts as a major acetaldehyde sink in the atmosphere, as has been suggested.

  4. Rate coefficient for the OH radical reaction with HONO2 under UT/LS conditions

    NASA Astrophysics Data System (ADS)

    Winiberg, F.; Liu, Y.; Sander, S. P.

    2016-12-01

    Nitric acid (HONO2) is one of the most reactive nitrogen-containing species in our atmosphere and its oxidation chemistry plays an important role in controlling the O3 budget in the upper troposphere/lower stratosphere (UT/LS). The O3 budget in the UT/LS is largely controlled by the cycling of HOx (OH + HO2) and NOx (NO + NO2). The HONO2 reaction with OH is a net HOx radical sink and drives NOx/y partitioning chemistry by yielding NO3 radicals; therefore, understanding the rate coefficient of the OH + HONO2 reaction is critical for accurate prediction of the O3, HOx, and NOx budgets in the UT/LS. Previous studies have observed both negative temperature-dependent and pressure-dependent kinetics below, which results from the formation of a pre-reactive complex between OH and HONO2 ( 6 kcal mol-1). Currently, the JPL recommended uncertainty in kOH+HONO2 is 20% (±1σ) at STP, but under UT/LS conditions (low T and p), the uncertainty could increase to as much as ± 50%, which translates to 10 - 20% in model predictions of NOx/NOy partitioning. Previous groups have measured the concentration of HONO2 after or before the reaction cell but never in-situ, which could lead to greater uncertainties in the overall determination of the rate coefficient from heterogeneous uptake of the low volatility HONO2. Here, we present experimental results into the matrix of the temperature and pressure dependence of the OH + HONO2 rate coefficient. Specifically, our results represent the first determination of kOH+HONO2 using in-situ [HONO2] measurements coupled to a Light Induced Fluorescence (LIF) technique to probe OH radicals. Results and importance to UT/LS chemistry will be discussed. Copyright 2015, California Institute of Technology

  5. An electron spin resonance investigation of the structure and formation of sulfinyl radicals: Reaction of peroxyl radicals with thiols

    SciTech Connect

    Swarts, S.G.; Becker, D.; DeBolt, S.; Sevilla, M.D. )

    1989-01-12

    In this work we present an electron spin resonance investigation of the irradiation of the alkyl mercaptans methyl, n-butyl, and tert-butyl mercaptan and the radioprotective thiols cysteamine and dithiothreitol in a number of aqueous and organic matrices in the present of oxygen. Matrix peroxyl radicals (ROO*) are formed after the irradiation of organic matrices in the presence of oxygen at 77 K. Upon annealing, these react with added thiols to form sulfinyl radicals (RSO*). Evidence for a thiol peroxyl radical (RSOO*) intermediate is found. Hyperfine couplings and g values are reported for the sulfinyl radicals formed from the five thiols investigated. The incorporation of {sup 17}O-labeled oxygen into the RSO* radical confirms that molecular oxygen is the source of the oxygen atom in the radical. The isotropic and parallel anisotropic {sup 17}O couplings indicate slightly less than 0.5 spin density on the oxygen. The couplings and spin densities are compared to those predicted from ab inito molecular orbital calculations for CH{sub 3}SO*. Calculations for the sulfur-peroxyl intermediate, CH{sub 3}SOO*, predict that it will have similar ESR parameters as those predicted for the carbon-centered peroxyl radical, CH{sub 3}OO*.

  6. Rapid reaction of nanomolar Mn(II) with superoxide radical in seawater and simulated freshwater

    USGS Publications Warehouse

    Hansard, S.P.; Easter, H.D.; Voelker, B.M.

    2011-01-01

    Superoxide radical (O2-) has been proposed to be an important participant in oxidation-reduction reactions of metal ions in natural waters. Here, we studied the reaction of nanomolar Mn(II) with O 2- in seawater and simulated freshwater, using chemiluminescence detection of O2- to quantify the effect of Mn(II) on the decay kinetics of O2-. With 3-24 nM added [Mn(II)] and <0.7 nM [O2-], we observed effective second-order rate constants for the reaction of Mn(II) with O2- of 6 ?? 106 to 1 ?? 107 M -1???s-1 in various seawater samples. In simulated freshwater (pH 8.6), the effective rate constant of Mn(II) reaction with O 2- was somewhat lower, 1.6 ?? 106 M -1???s-1. With higher initial [O2-], in excess of added [Mn(II)], catalytic decay of O 2- by Mn was observed, implying that a Mn(II/III) redox cycle occurred. Our results show that reactions with nanomolar Mn(II) could be an important sink of O2- in natural waters. In addition, reaction of Mn(II) with superoxide could maintain a significant fraction of dissolved Mn in the +III oxidation state. ?? 2011 American Chemical Society.

  7. Controllable Chemoselectivity in Visible-Light Photoredox Catalysis: Four Diverse Aerobic Radical Cascade Reactions.

    PubMed

    Liu, Xinfei; Ye, Xinyi; Bureš, Filip; Liu, Hongjun; Jiang, Zhiyong

    2015-09-21

    Reported is the controllable selectivity syntheses of four distinct products from the same starting materials by visible-light photoredox catalysis. By employing a dicyanopyrazine-derived chromophore (DPZ) as photoredox catalyst, an aerobic radical mechanism has been developed, and allows the reactions of N-tetrahydroisoquinolines (THIQs) with N-itaconimides to through four different pathways, including addition-cyclization, addition-elimination, addition-coupling, and addition-protonation, with satisfactory chemoselectivity. The current strategy provide straightforward access to four different but valuable N-heterocyclic adducts in moderate to excellent yields. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Branching ratios in reactions of OH radicals with methylamine, dimethylamine, and ethylamine.

    PubMed

    Onel, Lavinia; Blitz, Mark; Dryden, Matthew; Thonger, Lucy; Seakins, Paul

    2014-08-19

    The branching ratios for the reaction of the OH radical with the primary and secondary alkylamines: methylamine (MA), dimethylamine (DMA), and ethylamine (EA), have been determined using the technique of pulsed laser photolysis-laser-induced fluorescence. Titration of the carbon-centered radical, formed following the initial OH abstraction, with oxygen to give HO2 and an imine, followed by conversion of HO2 to OH by reaction with NO, resulted in biexponential OH decay traces on a millisecond time scale. Analysis of the biexponential curves gave the HO2 yield, which equaled the branching ratio for abstraction at αC-H position, r(αC-H). The technique was validated by reproducing known branching ratios for OH abstraction for methanol and ethanol. For the amines studied in this work (all at 298 K): r(αC-H,MA) = 0.76 ± 0.08, r(αC-H,DMA) = 0.59 ± 0.07, and r(αC-H,EA) = 0.49 ± 0.06 where the errors are a combination in quadrature of statistical errors at the 2σ level and an estimated 10% systematic error. The branching ratios r(αC-H) for OH reacting with (CH3)2NH and CH3CH2NH2 are in agreement with those obtained for the OD reaction with (CH3)2ND (d-DMA) and CH3CH2ND2 (d-EA): r(αC-H,d-DMA) = 0.71 ± 0.12 and r(αC-H,d-EA) = 0.54 ± 0.07. A master equation analysis (using the MESMER package) based on potential energy surfaces from G4 theory was used to demonstrate that the experimental determinations are unaffected by formation of stabilized peroxy radicals and to estimate atmospheric pressure yields. The branching ratio for imine formation through the reaction of O2 with α carbon-centered radicals at 1 atm of N2 are estimated as r(CH2NH2) = 0.79 ± 0.15, r(CH2NHCH3) = 0.72 ± 0.19, and r(CH3CHNH2) = 0.50 ± 0.18. The implications of this work on the potential formation of nitrosamines and nitramines are briefly discussed.

  9. Understanding kinetic solvent effects on hydrogen abstraction reactions from carbon by the cumyloxyl radical.

    PubMed

    Bietti, Massimo; Martella, Roberto; Salamone, Michela

    2011-11-18

    A kinetic study of the hydrogen abstraction reactions from tetrahydrofuran (THF) and cyclohexane (CHX) by the cumyloxyl radical was carried out in different solvents. With THF, a 4.5-fold decrease in rate constant (k(H)) was observed on going from isooctane to 2,2,2-trifluoroethanol. An opposite behavior was observed with CHX, where k(H) increased by a factor 4 on going from isooctane to 2,2,2-trifluoroethanol. The important role of substrate structure and of the solvent hydrogen bond donor ability is discussed.

  10. Total synthesis of (±)-sacidumlignans D and A through Ueno-Stork radical cyclization reaction.

    PubMed

    Zhang, Jian-Jian; Yan, Chang-Song; Peng, Yu; Luo, Zhen-Biao; Xu, Xiao-Bo; Wang, Ya-Wen

    2013-04-21

    Efficient synthesis of (±)-sacidumlignan D (4) has been successfully achieved employing Ueno-Stork radical cyclization of α-bromo acetal 21 as a key step. Two synthetic approaches for the symmetrical diaryl ketone 19 have been discussed in detail. Notably, sacidumlignan A (1) can be also efficiently synthesized in only 7 steps with 25% overall yield, where acid triggered tandem reaction starting from analogous Ueno-Stork cyclization product 27 played an important role. Moreover, potentially biomimetic conversion from (±)-sacidumlignan D (4) to sacidumlignan A (1) could be realized.

  11. Growth of polyphenyls via ion-molecule reactions: an experimental and theoretical mechanistic study.

    PubMed

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

    2013-05-28

    The reactivity of biphenylium cations C12H9(+) with benzene C6H6 is investigated in a joint experimental and theoretical approach. Experiments are performed by using a triple quadruple mass spectrometer equipped with an atmospheric pressure chemical ion source to generate C12H9(+) via dissociative ionization of various isomers of the neutral precursor hydroxybiphenyl (C12H10O). C-C coupling reactions leading to hydrocarbon growth are observed. The most abundant ionic products are C18H15(+), C18H13(+), C17H12(+), and C8H7(+). The dependence of product ion yields on the kinetic energy of reagent ions, as well as further experiments performed using partial isotopic labelling of reagents, support the idea that the reaction proceeds via a long lived association product, presumably the covalently bound protonated terphenyl C18H15(+). Its formation is found to be exothermic and barrierless and, therefore, might occur under the low pressure and temperature conditions typical of planetary atmospheres and the interstellar medium. Theoretical calculations have focussed on the channel leading to C8H7(+) plus C10H8, identifying, as the most probable fragments, the phenylethen-1-ylium cation and naphthalene, thus suggesting that the pathway leading to them might be of particular interest for the synthesis of polycyclic aromatic hydrocarbons. Both experiments and theory agree in finding this channel exoergic but hampered by small barriers of 2.7 and 3.7 kcal mol(-1) on the singlet potential energy surface.

  12. Rates of primary electron transfer in photosynthetic reaction centres and their mechanistic implications

    NASA Astrophysics Data System (ADS)

    Fleming, G. R.; Martin, J. L.; Breton, J.

    1988-05-01

    The conversion of light energy to chemical energy during photosyn-thesis involves the transfer of electrons between pigments embedded in a membrane protein. This process occurs with high quantum efficiency, the result of extremely fast electron transfer over a long distance preventing back transfer and energy loss. Recently the three-dimensional structures of the photosynthetic reaction centres of the bacteria Rhodopseudomonas viridis1 and Rhodobacter sphaeroides2 have been determined, allowing a molecular descrip-tion of the primary charge separation process. There are two symmetrically related branches of pigments in the structure (L and M), extending from the special pair of bacteriochlorophyll molecules (P) to the two bacteriopheophytins (HL and HM) via two bacteriochlorophylls (BLand BM). Many features of the electron transfer process are poorly understood, such as the nature of the excited states involved, the identity of the primary charge separation step and the roles of the protein and of B3-13. We have determined the rates of electron transfer in isolated reaction centre complexes of Rps. viridis and Rb. sphaeroides as a function of temperature. The rates increase as temperature is decreased, which may be due to either changes in electronic coupling of the pigments or changes in the population of coupled vibrational modes, or a combination of the two. We see no evidence of a B-L intermediate, which sets a lower limit on the rate of electron transfer from BL to HL. This is so high as to rule out transfer by two non-adiabatic steps.

  13. Growth of polyphenyls via ion-molecule reactions: An experimental and theoretical mechanistic study

    SciTech Connect

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

    2013-05-28

    The reactivity of biphenylium cations C{sub 12}H{sub 9}{sup +} with benzene C{sub 6}H{sub 6} is investigated in a joint experimental and theoretical approach. Experiments are performed by using a triple quadruple mass spectrometer equipped with an atmospheric pressure chemical ion source to generate C{sub 12}H{sub 9}{sup +} via dissociative ionization of various isomers of the neutral precursor hydroxybiphenyl (C{sub 12}H{sub 10}O). C-C coupling reactions leading to hydrocarbon growth are observed. The most abundant ionic products are C{sub 18}H{sub 15}{sup +}, C{sub 18}H{sub 13}{sup +}, C{sub 17}H{sub 12}{sup +}, and C{sub 8}H{sub 7}{sup +}. The dependence of product ion yields on the kinetic energy of reagent ions, as well as further experiments performed using partial isotopic labelling of reagents, support the idea that the reaction proceeds via a long lived association product, presumably the covalently bound protonated terphenyl C{sub 18}H{sub 15}{sup +}. Its formation is found to be exothermic and barrierless and, therefore, might occur under the low pressure and temperature conditions typical of planetary atmospheres and the interstellar medium. Theoretical calculations have focussed on the channel leading to C{sub 8}H{sub 7}{sup +} plus C{sub 10}H{sub 8}, identifying, as the most probable fragments, the phenylethen-1-ylium cation and naphthalene, thus suggesting that the pathway leading to them might be of particular interest for the synthesis of polycyclic aromatic hydrocarbons. Both experiments and theory agree in finding this channel exoergic but hampered by small barriers of 2.7 and 3.7 kcal mol{sup -1} on the singlet potential energy surface.

  14. Atmospheric degradation of saturated alcohols: Room temperature rate coefficients for NO3 radical reactions

    NASA Astrophysics Data System (ADS)

    Moreno, Alberto; Salgado, Sagrario; Taccone, Raul; Martín, Pilar; Cabañas, Beatriz

    2014-10-01

    Rate coefficients for the reactions of NO3 radicals with a series of saturated alcohols are reported here using the relative rate technique. Experiments were performed using air as bath gas in a 50 L glass-pyrex reaction chamber at room temperature (298 ± 2) K with long-path FTIR spectroscopy used to monitor the reaction at atmospheric pressure (708 ± 8) Torr. The reference compounds used and their rate coefficients are: propanal kNO3 = (6.0 ± 0.6) × 10-15, methyl methacrylate kNO3 = (3.55 ± 0.62) × 10-15, acetaldehyde kNO3 = (2.62 ± 0.29) × 10-15 and propene kNO3 = (9.50 ± 1.9) × 10-15, in cm3 molecule-1 s-1. Rate coefficients obtained were (in units cm3 molecule-1 s-1): (1.87 ± 0.14) × 10-15, (2.39 ± 0.20) × 10-15, (2.28 ± 0.17) × 10-15, (1.80 ± 0.13) × 10-15 and (3.52 ± 0.19) × 10-15 for 1-butanol, 2-methyl-1-butanol, 3-methyl-1-butanol, 3,3-dimethyl-1-butanol and 3,3-dimethyl-2-butanol respectively. Reactivity trend can be explained in terms of the different types of hydrogen inside the hydrocarbon chain. The reaction occurs by an initial H-atom abstraction mainly from C-H groups of the alcohols by the NO3 radical being NO3 more reactive towards an H atom attached to a tertiary carbon than that attached to a secondary or primary carbon. Reactivity trend is compared with their similar structural 2-butanol and with the corresponding alkanes. Atmospheric implications are also discussed calculating lifetimes of the saturated alcohols studied here due to the reaction with NO3 radicals in comparison to their reactions with the other major atmospheric oxidants.

  15. Investigation of radical important in the Gyoergyi-Turanyi-Field model of the Belousov-Zhabotinskii reaction

    SciTech Connect

    Foersterling, H.D. ); Stuk, L. )

    1991-09-19

    In the Gyoergyi-Turanyi-Field (GTF) model of the Belousov-Zhabotinskii (BZ) reaction, malonyl radicals (MA) and bromomalonyl radicals (BrMA) are assumed to be important intermediates. The hydrogen abstraction reactions MA{sm bullet} + BrMA {yields} MA + BrMa{sm bullet} (a) and BrMA{sm bullet} + MA {yields} BrMA + MA{sm bullet} (b) (MA, malonic acid; BrMA, bromomalonic acid) transfer the free-radical nature of the malonyl species to the bromomalonyl species and vice versa. The rates of these two reactions determine in part the relative importance of these radical intermediates. Another key radical reaction is BrMA + Ce{sup 4+} + H{sub 2}O {yields} BrTTA + Ce{sup 3+} (c) (BrTTA, bromotartronic acid), which is a source of Br{sup {minus}} through decomposition of BrTTa in the model. It has been deduced from ESR and spectrophotometric experiments that reactions a-c do not contribute to the chemistry of the BZ reaction. Numerical integration of the GTF rate equations, omitting reactions a-c, shows no oscillations in BZ systems with high initial concentrations of BrMA. Experimentally, these systems exhibit oscillations with no induction period.

  16. Monoascorbate free radical-dependent oxidation-reduction reactions of liver Golgi apparatus membranes.

    PubMed

    Navas, Placido; Sun, Iris; Crane, Frederick L; Morré, Dorothy M; Morré, D James

    2010-04-01

    Golgi apparatus from rat liver contain an ascorbate free radical oxidoreductase that oxidizes NADH at neutral pH with monodehydroascorbate as acceptor to generate a membrane potential. At pH 5.0, the reverse reaction occurs from NAD(+). The electron spin resonance signal of the ascorbate-free radical and its disappearance upon the addition of NADH (pH 7) or NAD(+) (pH 5.0) confirms monodehydroascorbate involvement. Location of monodehydroascorbate both external to and within Golgi apparatus compartments is suggested from energization provided by inward or outward flux of electrons across the Golgi apparatus membranes. The isolated membranes are sealed, oriented cytoplasmic side out and impermeable to NAD(+) and ascorbate. NAD(+) derived through the action of Golgi apparatus beta-NADP phosphohydrolase is simultaneously reduced to NADH with monodehydroascorbate present. The response of the NADH- (NAD(+)-) ascorbate free radical oxidoreductase system to pH in Golgi apparatus provides a simple regulatory mechanism to control vesicle acidification.

  17. An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

    NASA Technical Reports Server (NTRS)

    Jackels, C. F.; Phillips, D. H.

    1986-01-01

    Ab initio quantum chemical techniques have been used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types were identified. Basic sets of polarized double-zeta quality and large scale configuration interaction wave functions have been utilized. Based upon electronic energies, the covalently-bonded HOOOH species is found to be 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen-bonded HO-HO2 species is found to have an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen-bonded form is found to be planar, to possess one relatively 'normal' hydrogen bond, and to have lowest energy 3A-prime and 1A-prime states that are essentially degenerate. The 1A-double prime and 3A-double prime excited states produced by rotation of the unpaired OH electron into the molecular plane are found to be very slightly bound.

  18. An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

    NASA Technical Reports Server (NTRS)

    Jackels, C. F.

    1985-01-01

    Ab initio quantum chemical techniques are used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types are identified. Basis sets of polarized double zeta quality and large scale configuration interaction wave functions are utilized. Based on electronic energies, the covalently bonded HOOOH species is 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen bonded HO---HO2 species has an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen bonded form is planar, possesses one relatively normal hydrogen bond, and has the lowest energy 3A' and 1A' states that are essentially degenerate. The 1A" and 3A" excited states produced by rotation of the unpaired OH electron into the molecular plane are very slightly bound.

  19. Deep Eutectic Solvents as Reaction Media for the Palladium-Catalysed C-S Bond Formation: Scope and Mechanistic Studies.

    PubMed

    Marset, Xavier; Guillena, Gabriela; Ramón, Diego J

    2017-08-04

    A unique jigsaw catalytic system based on deep eutectic solvents and palladium nanoparticles where C-S bonds are formed from aryl boronic acids and sodium metabisulfite, is introduced. The functionalization step is compatible with a broad spectrum of reagents such as nucleophiles, electrophiles or radical scavengers. This versatile approach allows the formation of different types of products in an environmentally friendly medium by selecting the components of the reaction, which engage one with another as pieces in a jigsaw. This simple procedure avoids the use of toxic volatile organic solvents allowing the formation of complex molecules in a one-pot reaction under mild conditions. Despite the fact that only 1 mol % of metal loading is used, the recyclability of the catalytic system is possible. Kinetic experiments were performed and the reaction order for all reagents, catalyst and ligand was determined. The obtained results were compared to palladium nanocrystals of different known shapes in order to shed some light on the properties of the catalyst. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Experimental evidence for a non-OH oxidant produced from the reaction of isoprene with OH radical

    NASA Astrophysics Data System (ADS)

    Huang, D.; Chen, Z.

    2013-12-01

    The OH radical initiated oxidation of alkenes is of great importance to air quality and atmospheric chemistry. Although the related mechanism is well studied over several decades, several intermediate steps, such as the recycling of OH radical, the reaction of intermediates, and the formation of peroxides, are unresolved. As we known, the traditional mechanism cannot reproduce the high measured OH radical level in the rural forests. Currently, the recycling of OH radical in the isoprene-OH reaction is considered to be a potential candidate for the explanation. Here, alternatively, we intend to know if a non-OH oxidant leads to the discrepancy between the modeled and measured OH radical in the rural forest by reacting with plenty of oxygenated products of hydrocarbon compounds, sharing the 'oxidation responsibility' of OH radical, and consequently saving the OH radical. After mixing the products produced from the isoprene-OH reaction with formaldehyde and acetaldehyde in a flow reactor in the absent of light, we found an immediate increase of the peroxy formic acid and peroxy acetic acid. Control experiment results indicated that these peroxy acids were the products of aldehyde reaction with some non-OH oxidant, which was produced from the isoprene-OH reaction. Unfortunately, we have not identified this unknown oxidant. However, based on the decrement of aldehyde during the process of mixing with isoprene products, we estimate the OH-equivalent concentration of this oxidant to be ~0.2 pptv, which is one fifth of the OH radical in the isoprene-OH reaction. This mechanism may contribute to explaining the maintenance of the oxidation capacity of the troposphere. Additionally, this mechanism might involve in the functionalization of oxygenated organic compounds and the formation of secondary organic aerosols.

  1. Methane to acetic acid over Cu-exchanged zeolites: mechanistic insights from a site-specific carbonylation reaction.

    PubMed

    Narsimhan, Karthik; Michaelis, Vladimir K; Mathies, Guinevere; Gunther, William R; Griffin, Robert G; Román-Leshkov, Yuriy

    2015-02-11

    The selective low temperature oxidation of methane is an attractive yet challenging pathway to convert abundant natural gas into value added chemicals. Copper-exchanged ZSM-5 and mordenite (MOR) zeolites have received attention due to their ability to oxidize methane into methanol using molecular oxygen. In this work, the conversion of methane into acetic acid is demonstrated using Cu-MOR by coupling oxidation with carbonylation reactions. The carbonylation reaction, known to occur predominantly in the 8-membered ring (8MR) pockets of MOR, is used as a site-specific probe to gain insight into important mechanistic differences existing between Cu-MOR and Cu-ZSM-5 during methane oxidation. For the tandem reaction sequence, Cu-MOR generated drastically higher amounts of acetic acid when compared to Cu-ZSM-5 (22 vs 4 μmol/g). Preferential titration with sodium showed a direct correlation between the number of acid sites in the 8MR pockets in MOR and acetic acid yield, indicating that methoxy species present in the MOR side pockets undergo carbonylation. Coupled spectroscopic and reactivity measurements were used to identify the genesis of the oxidation sites and to validate the migration of methoxy species from the oxidation site to the carbonylation site. Our results indicate that the Cu(II)-O-Cu(II) sites previously associated with methane oxidation in both Cu-MOR and Cu-ZSM-5 are oxidation active but carbonylation inactive. In turn, combined UV-vis and EPR spectroscopic studies showed that a novel Cu(2+) site is formed at Cu/Al <0.2 in MOR. These sites oxidize methane and promote the migration of the product to a Brønsted acid site in the 8MR to undergo carbonylation.

  2. Modelling Population Dynamics in Realistic Landscapes with Linear Elements: A Mechanistic-Statistical Reaction-Diffusion Approach

    PubMed Central

    2016-01-01

    We propose and develop a general approach based on reaction-diffusion equations for modelling a species dynamics in a realistic two-dimensional (2D) landscape crossed by linear one-dimensional (1D) corridors, such as roads, hedgerows or rivers. Our approach is based on a hybrid “2D/1D model”, i.e, a system of 2D and 1D reaction-diffusion equations with homogeneous coefficients, in which each equation describes the population dynamics in a given 2D or 1D element of the landscape. Using the example of the range expansion of the tiger mosquito Aedes albopictus in France and its main highways as 1D corridors, we show that the model can be fitted to realistic observation data. We develop a mechanistic-statistical approach, based on the coupling between a model of population dynamics and a probabilistic model of the observation process. This allows us to bridge the gap between the data (3 levels of infestation, at the scale of a French department) and the output of the model (population densities at each point of the landscape), and to estimate the model parameter values using a maximum-likelihood approach. Using classical model comparison criteria, we obtain a better fit and a better predictive power with the 2D/1D model than with a standard homogeneous reaction-diffusion model. This shows the potential importance of taking into account the effect of the corridors (highways in the present case) on species dynamics. With regard to the particular case of A. albopictus, the conclusion that highways played an important role in species range expansion in mainland France is consistent with recent findings from the literature. PMID:26986201

  3. Modelling Population Dynamics in Realistic Landscapes with Linear Elements: A Mechanistic-Statistical Reaction-Diffusion Approach.

    PubMed

    Roques, Lionel; Bonnefon, Olivier

    2016-01-01

    We propose and develop a general approach based on reaction-diffusion equations for modelling a species dynamics in a realistic two-dimensional (2D) landscape crossed by linear one-dimensional (1D) corridors, such as roads, hedgerows or rivers. Our approach is based on a hybrid "2D/1D model", i.e, a system of 2D and 1D reaction-diffusion equations with homogeneous coefficients, in which each equation describes the population dynamics in a given 2D or 1D element of the landscape. Using the example of the range expansion of the tiger mosquito Aedes albopictus in France and its main highways as 1D corridors, we show that the model can be fitted to realistic observation data. We develop a mechanistic-statistical approach, based on the coupling between a model of population dynamics and a probabilistic model of the observation process. This allows us to bridge the gap between the data (3 levels of infestation, at the scale of a French department) and the output of the model (population densities at each point of the landscape), and to estimate the model parameter values using a maximum-likelihood approach. Using classical model comparison criteria, we obtain a better fit and a better predictive power with the 2D/1D model than with a standard homogeneous reaction-diffusion model. This shows the potential importance of taking into account the effect of the corridors (highways in the present case) on species dynamics. With regard to the particular case of A. albopictus, the conclusion that highways played an important role in species range expansion in mainland France is consistent with recent findings from the literature.

  4. Some polyphenols inhibit the formation of pentyl radical and octanoic acid radical in the reaction mixture of linoleic acid hydroperoxide with ferrous ions.

    PubMed Central

    Iwahashi, H

    2000-01-01

    Effects of some polyphenols and their related compounds (chlorogenic acid, caffeic acid, quinic acid, ferulic acid, gallic acid, D-(+)-catechin, D-(-)-catechin, 4-hydroxy-3-methoxybenzoic acid, salicylic acid, L-dopa, dopamine, L-adrenaline, L-noradrenaline, o-dihydroxybenzene, m-dihydroxybenzene, and p-dihydroxybenzene) on the formation of 13-hydroperoxide octadecadienoic (13-HPODE) acid-derived radicals (pentyl radical and octanoic acid radical) were examined. The ESR spin trapping showed that chlorogenic acid, caffeic acid, gallic acid, D-(+)-catechin, D-(-)-catechin, L-dopa, dopamine, L-adrenaline, L-noradrenaline, and o-dihydroxybenzene inhibited the overall formation of 13-HPODE acid-derived radicals in the reaction mixture of 13-HPODE with ferrous ions. The ESR peak heights of alpha-(4-pyridyl-1-oxide)-N-tert-butylnitrone (4-POBN)/13-HPODE-derived radical adducts decreased to 46+/-4% (chlorogenic acid), 54+/-2% (caffeic acid), 49+/-2% (gallic acid), 55+/-1% [D-(+)-catechin], 60+/-3% [D-(-)-catechin], 42+/-1% (L-dopa), 30+/-2% (dopamine), 49+/-2% (L-adrenaline), 24+/-2% (L-noradrenaline), and 54+/-5% (o-dihydroxybenzene) of the control, respectively. The high performance liquid chromatography-electron spin resonance (HPLC-ESR) and high performance liquid chromatography-electron spin resonance-mass spectrometries (HPLC-ESR-MS) showed that caffeic acid inhibited the formation of octanoic acid radical and pentyl radical to 42+/-2% and 52+/-7% of the control, respectively. On the other hand, the polyphenols and their related compounds had few inhibitory effects on the radical formation in the presence of EDTA. Visible absorbance measurement revealed that all the polyphenols exhibiting the inhibitory effect chelate ferrous ions. Above results indicated that the chelation of ferrous ion is essential to the inhibitory effects of the polyphenols. PMID:10677343

  5. A mechanistic analysis of the Birch Reduction.

    PubMed

    Zimmerman, Howard E

    2012-02-21

    The Birch Reduction is one of the main reactions of organic chemistry. The reaction involves the reaction of dissolving metals in ammonia with aromatic compounds to produce 1,4-cyclohexadienes. Discovered by Arthur Birch in 1944, the reaction occupies 300 pages in Organic Reactions to describe its synthetic versatility. Thus, it is remarkable that the reaction mechanism has been so very controversial and only relatively recently has been firmly established. Perhaps this is not that surprising, since the reaction also has many unusual and esoteric mechanistic facets. Here, I provide a description of how I have applied ever-evolving levels of quantum mechanics and a novel experimental test to understand details of the mechanism and the origins of the selectivities observed in the Birch reduction. The reaction involves an initial radical anion resulting from introduction of an electron from the blue liquid ammonia solution of free electrons formed by the dissolution of Li or related metals. This radical anion is protonated by an alcohol and then further reduced to a carbanion. Finally, the carbanion is protonated using a second proton to afford a nonconjugated cyclohexadiene. The regiochemistry depends on substituents present. With 18 resonance structures in the case of anisole radical anion, prediction of the initial protonation site would seem difficult. Nevertheless, computational methods from Hückel theory through modern density functional calculations do correctly predict the site of protonation. An esoteric test established this mechanism experimentally. The nature of the carbanion also is of mechanistic interest, and the preponderance of the resonance structure shown was revealed from Hückel calculations involving variable bond orders. For the trianion from benzoic acid, parallel questions about structure are apparent, and have been answered. Some mechanistic questions are answered experimentally and some by modern computations. Recently, our mechanistic

  6. Reactions of the CN Radical with Benzene and Toluene: Product Detection and Low-Temperature Kinetics

    SciTech Connect

    Trevitt, Adam J.; Goulay, Fabien; Taatjes, Craig A.; Osborn, David L.; Leone, Stephen R.

    2009-12-23

    Low temperature rate coefficients are measured for the CN + benzene and CN + toluene reactions using the pulsed Laval nozzle expansion technique coupled with laser-induced fluorescence detection. The CN + benzene reaction rate coefficient at 105, 165 and 295 K is found to be relatively constant over this temperature range, 3.9 - 4.9 x 10-10 cm3 molecule-1 s-1. These rapid kinetics, along with the observed negligible temperature dependence, are consistent with a barrierless reaction entrance channel and reaction efficiencies approaching unity. The CN + toluene reaction is measured to have a slower rate coefficient of 1.3 x 10-10 cm3 molecule-1 s-1 at 105 K. At room temperature, non-exponential decay profiles are observed for this reaction that may suggest significant back-dissociation of intermediate complexes. In separate experiments, the products of these reactions are probed at room temperature using synchrotron VUV photoionization mass spectrometry. For CN + benzene, cyanobenzene (C6H5CN) is the only product recorded with no detectable evidence for a C6H5 + HCN product channel. In the case of CN + toluene, cyanotoluene (NCC6H4CH3) constitutes the only detected product. It is not possible to differentiate among the ortho, meta and para isomers of cyanotoluene because of their similar ionization energies and the ~;; 40 meV photon energy resolution of the experiment. There is no significant detection of benzyl radicals (C6H5CH2) that would suggest a H-abstraction or a HCN elimination channel is prominent at these conditions. As both reactions are measured to be rapid at 105 K, appearing to have barrierless entrance channels, it follows that they will proceed efficiently at the temperatures of Saturn?s moon Titan (~;;100 K) and are also likely to proceed at the temperature of interstellar clouds (10-20 K).

  7. Thermochemical properties and bond dissociation energies of C3-C5 cycloalkyl hydroperoxides and peroxy radicals: cycloalkyl radical + (3)O2 reaction thermochemistry.

    PubMed

    Auzmendi-Murua, Itsaso; Bozzelli, Joseph W

    2012-07-19

    Cyclic aliphatic hydrocarbons are major components in modern fuels; they can be present in the reactants, and they can be formed during the gas-phase oxidation processes. In combustion and thermal oxidation processes, these cyclics will form radicals that react with (3)O(2) to form peroxy radicals. In this study, density functional theory and higher level ab initio calculations are used to calculate thermochemical properties and bond dissociation energies of 3-5-membered cycloalkanes, corresponding hydroperoxides, hydroperoxycycloalkyl radicals, and cycloalkyl radicals that occur in these reaction systems. Geometries, vibration frequencies, and thermochemical properties, ΔH(f 298)°, are calculated with the B3LYP/6-31 g(d,p), B3LYP/6-31 g(2d,2p), composite CBS-QB3, and G3MP2B3 methods. Standard enthalpies of formation at 298 K are evaluated using isodesmic reaction schemes with several work reactions for each species. Group additivity contributions are developed, and application of group additivity with comparison to calculated values is illustrated. Entropy and heat capacities, S°(T) and C(p)°(T) (5 K ≤ T ≤ 5000), are determined using geometric parameters and frequencies from the B3LYP/6-31 g(d,p) calculations.

  8. Theoretical investigation on the mechanism of NO3 radical-initiated atmospheric reactions of phenanthrene

    NASA Astrophysics Data System (ADS)

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

    2017-07-01

    Phenanthrene is a polycyclic aromatic hydrocarbon from fossil fuel combustion with toxic properties. The products arising from atmospheric reaction can be more mutagenic and carcinogenic compared to unmodified phenanthrene, and are therefore important to be studied. The products of the specific NO3-radical reactions with phenanthrene where therefore investigated in this study by means of Density Functional Theory (DFT). The results show that the main products are proposed to be 10-(nitrooxy)-10-hydro-phenanthrene-9-one, 2,2‧-diformylbiphenyl, 9,10-phenanthrenequinone, 9-fluorenone and dibenzopyranone. 10-(nitrooxy)-10-hydro-phenanthrene-9-one and 2,2‧-diformylbiphenyl are classified as first-generation products which are subject to secondary reactions to produce 9,10-phenanthrenequinone, 9-fluorenone and dibenzopyranone. The rate constants of elementary reactions were assessed by Rice-Ramsperger-Kassel-Marcus (RRKM) theory. The atmospheric lifetime of Phe determined by the gas-phase reaction with NO3 is estimated to be 1.8 h, based on the calculated overall rate constant of 3.04 × 10-13 cm3 molecule-1 s-1 at 298 K and 1 atm. Combined with available experimental observation, this work should help to clarify the transformation and potential health risk of Phe in the atmosphere.

  9. Direct dynamics study on hydrogen abstraction reaction of CF 3CHOHCF 3 with OH radical

    NASA Astrophysics Data System (ADS)

    Wang, Ying; Liu, Jing-Yao; Li, Ze-Sheng

    2007-05-01

    Dual-level direct dynamics method is employed to investigate the H-abstraction reaction CF 3CHOHCF 3 with OH radical. Two hydrogen-abstraction reaction channels are possible: one from the methylene (-CH-) position and the other from the hydroxyl (-OH) position. The minimum energy path is calculated at the B3LYP/6-311G(d,p) level, and the energetic information is further refined by a new powerful and inexpensive BMC-CCSD method. To testify the accuracy of the structures and the energies, the recently developed hybrid density functional theory BB1K and higher level MC-QCISD are applied to this system. Hydrogen-bonded complexes are presented at both reactants and products sides of these two channels, which indicating that the reaction may proceed via an indirect mechanism. The rate constants for each reaction channel are evaluated by canonical variational transition state theory (CVT) with a small-curvature tunneling correction (SCT) over a wide range of temperatures from 200 to 2000 K. The calculated CVT/SCT rate constants are in good agreement with the available experimental values in the temperature region 250-430 K. The present results indicate that the two channels are competitive. At lower temperature, the reaction occurs mainly via the hydroxyl-H-abstraction channel, while the methylene-H-abstraction channel is preferred when the temperature is higher than 273 K.

  10. The direct observation of secondary radical chain chemistry in the heterogeneous reaction of chlorine atoms with submicron squalane droplets.

    PubMed

    Liu, Chen-Lin; Smith, Jared D; Che, Dung L; Ahmed, Musahid; Leone, Stephen R; Wilson, Kevin R

    2011-05-21

    The reaction of Cl atoms, in the presence of Cl(2) and O(2), with sub-micron squalane particles is used as a model system to explore how surface hydrogen abstraction reactions initiate chain reactions that rapidly transform the chemical composition of an organic particle. The heterogeneous reaction is measured in a photochemical flow tube reactor in which chlorine atoms are produced by the photolysis of Cl(2) at 365 nm. By monitoring the heterogeneous reaction, using a vacuum ultraviolet photoionization aerosol mass spectrometer, the effective reactive uptake coefficient and the distributions of both oxygenated and chlorinated reaction products are measured and found to depend sensitively upon O(2), Cl(2), and Cl concentrations in the flow reactor. In the absence of O(2), the effective reactive uptake coefficient monotonically increases with Cl(2) concentration to a value of ∼3, clearly indicating the presence of secondary chain chemistry occurring in the condensed phase. The effective uptake coefficient decreases with increasing O(2) approaching a diffusion corrected value of 0.65 ± 0.07, when 20% of the total nitrogen flow rate in the reactor is replaced with O(2). Using a kinetic model it is found that the amount of secondary chemistry and the product distributions in the aerosol phase are controlled by the competitive reaction rates of O(2) and Cl(2) with alkyl radicals. The role that a heterogeneous pathway might play in the reaction of alkyl radicals with O(2) and Cl(2) is investigated within a reasonable range of reaction parameters. These results show, more generally, that for heterogeneous reactions involving secondary chain chemistry, time and radical concentration are not interchangeable kinetic quantities, but rather the observed reaction rate and product formation chemistry depends sensitively upon the concentrations and time evolution of radical initiators and those species that propagate or terminate free radical chain reactions. © The Owner

  11. Kinetics of the Reactions of NO3 Radical with Methacrylate Esters.

    PubMed

    Zhou, Li; Ravishankara, A R; Brown, Steven S; Idir, Mahmoud; Zarzana, Kyle J; Daële, Véronique; Mellouki, Abdelwahid

    2017-06-15

    Two different experimental methods (relative rate and absolute rate methods) were used to measure the rate coefficients for the reactions of NO3 radical with six methacrylate esters: methyl methacrylate (MMA, k1), ethyl methacrylate (EMA, k2), propyl methacrylate (PMA, k3), isopropyl methacrylate (IPMA, k4), butyl methacrylate (BMA, k5), and isobutyl methacrylate (IBMA, k6). In the relative rate method, the loss of the esters relative to that of a reference compound was followed in a 7300 L Teflon-walled chamber at 298 ± 2 K and 1000 ± 5 hpa. In the absolute method, the temporal profiles of NO3 and N2O5 were followed by using a dual channel cavity ring-down spectrometer in the presence of an excess of ester in the 7300 L chamber. The rate coefficients from these two methods (weighted averages) in the units of 10(-15) cm(3) molecule(-1) s(-1) at 298 K are k1 = 2.98 ± 0.35, k2 = 4.67 ± 0.49, k3 = 5.23 ± 0.60, k4 = 7.91 ± 1.00, k5 = 5.91 ± 0.58, and k6 = 6.24 ± 0.66. The quoted uncertainties are at the 2σ level and include estimated systematic errors. Unweighted averages are also reported. In addition, the rate coefficient k7 for the reaction of NO3 radical with deuterated methyl methacrylate (MMA-d8) was measured by using the relative rate method to be essentially the same as k1. The trends in the measured rate coefficient with the length and nature of the alkyl group, along with the equivalence of k1 and k7, strongly suggest that the reaction of NO3 with the methacrylate esters proceeds via addition to the double bond on the methacrylate group. The present results are compared with those from previous studies. Using the measured values of the rate coefficients, along with those for reactions of these esters with OH, O3, and chlorine atoms, we calculated the atmospheric lifetimes of methacrylate esters. We suggest that NO3 radicals do contribute to the atmospheric loss of these unsaturated esters, but to a lesser extent than their reactions with OH and O3.

  12. Atmospheric degradation of pyridine: UV absorption spectrum and reaction with OH radicals and O3

    NASA Astrophysics Data System (ADS)

    Errami, M.; El Dib, G.; Cazaunau, M.; Roth, E.; Salghi, R.; Mellouki, A.; Chakir, A.

    2016-10-01

    The UV absorption spectrum of pyridine and its gas phase reactions with OH radicals and O3 were investigated. UV absorption cross-sections were determined by using a D2-lamp system in the range 200-350 nm. The kinetic studies were carried out at room temperature and atmospheric pressure of purified air. The rate coefficient for the reaction of pyridine with OH was determined relative to that with acetone while that with O3 was measured under pseudo first order conditions. The rate coefficients obtained are (in cm3 molecule-1 s-1): k(OH + pyridine) = (5.40 ± 0.80) × 10-13 and k(O3 + pyridine) = (3.28 ± 1.70) × 10-20.

  13. Heterogeneous reaction of particulate chlorpyrifos with NO3 radicals: Products, pathways, and kinetics

    NASA Astrophysics Data System (ADS)

    Li, Nana; Zhang, Peng; Yang, Bo; Shu, Jinian; Wang, Youfeng; Sun, Wanqi

    2014-08-01

    Chlorpyrifos is a typical chlorinated organophosphorus pesticide. The heterogeneous reaction of chlorpyrifos particles with NO3 radicals was investigated using a vacuum ultraviolet photoionization aerosol time-of-flight mass spectrometer (VUV-ATOFMS) and a real-time atmospheric gas analysis mass spectrometer. Chlorpyrifos oxon, 3,5,6-trichloro-2-pyridinol, O,O-diethyl O-hydrogen phosphorothioate, O,O-diethyl ester thiophosphoric acid, diethyl hydrogen phosphate and a phosphinyl disulfide compound were identified as the main degradation products. The heterogeneous reaction pathways were proposed and their kinetic processes were investigated via a mixed-phase relative rate method. The observed effective rate constant is 3.4 ± 0.2 × 10-12 cm3 molecule-1 s-1.

  14. In situ electrochemical-electron spin resonance investigations of multi-electron redox reaction for organic radical cathodes

    SciTech Connect

    Huang, Qian; Walter, Eric D.; Cosimbescu, Lelia; Choi, Daiwon; Lemmon, John P.

    2016-02-29

    Organic radical batteries (ORBs) bearing robust radical polymers as energy storage species, are emerging promisingly with durable high energy and power characteristics by unique tunable redox properties. Here we report the development and application of in situ electrochemical-electron spin resonance (ESR) methodologies to identify the charge transfer mechanism of Poly(2,2,6,6- tetramethylpiperidinyloxy-4-yl methacrylate) (PTMA) based organic radical composite cathodes in the charge-discharge process of lithium half cells. The in situ experiments allow each electrochemical state to be associated with the chemical state (or environment) of the radical species upon the cell cycling. In situ ESR spectra of the composite cathode demonstrate a two-electron redox reaction of PTMA. Moreover, two different local environments of radical species are found in the composite electrode that includes both concentrated and isolated radicals. These two types of radicals show similarities during the redox reaction process while behave quite differently in the non-faradic reaction of ion sorption/desorption on the electrode surface.

  15. Study on the multiple mechanisms underlying the reaction between hydroxyl radical and phenolic compounds by qualitative structure and activity relationship.

    PubMed

    Cheng, Zhiyong; Ren, Jie; Li, Yuanzong; Chang, Wenbao; Chen, Zhida

    2002-12-01

    The activity-structure relationships (ASR) of phenolic compounds as hydroxyl-radical scavengers have mostly been studied and discussed with regard to their iron-chelating and hydrogen-donation properties in Fenton-type system, but extensive elucidation of multiple mechanisms underlying the hydroxyl radical scavenging reaction is out of obtaining up to now. In the present paper, a series of phenolic compounds was studied for their reactivity with hydroxyl radical by computed chemistry and deoxyribose degradation assay. The rate constant (K(S)), an index dependent markedly on the reaction mechanism and intrinsic reactivity of antioxidants, was found to have good correlation with hydroxyl O-H bond strength (DeltaH(f)), electron-donating ability (ionization potential approximated by HOMO energy level), enthalpy of single electron transfer (E(a)), and spin distribution of phenoxyl radicals (Ds(r)) after H-abstraction. Moreover, the theoretical parameters were highly intercorrelated, suggesting that multiple mechanisms co-exist in the hydroxyl-radical-scavenging reaction and interact with each other. Multi-linear regression analysis indicated that, in addition to H-atom transfer, electron transfer process and stability of the resulted phenoxyl radicals also significantly influence the reactivity of quenching hydroxyl radicals. The QSAR model so established here was based on the elucidation of the complex molecular mechanisms, and may reasonably predict the antioxidant activity using simple experimental and calculated parameters.

  16. Carbonate radical ion is the only observable intermediate in the reaction of peroxynitrite with CO(2).

    PubMed

    Goldstein, S; Czapski, G; Lind, J; Merényi, G

    2001-09-01

    The reaction of ONOO(-) with CO(2) at alkaline pH was recently reported to form a transient absorption with a maximum at 640 nm and a half-life of ca. 4 ms at 10 degrees C [Meli et al. (1999) Helv. Chim. Acta 82, 722-725]. This transient absorption was hardly affected by the presence of *NO, and therefore was attributed to the adduct ONOOC(O)O(-). This conclusion contradicts all current experimental results as it suggests that the decomposition of this adduct via homolysis of the O-O bond into CO(3)(*)(-) and *NO(2) is a minor pathway. In the present work the observations of Meli et al. will be shown to be artifacts resulting from light coming from the UV region. When these experiments are carried out in the presence of appropriate cutoff filters, the only observable intermediate formed in the reaction of ONOO(-) with CO(2) at alkaline pH is the carbonate radical ion with a maximum at 600 nm. This transient absorption is not observed in the presence of *NO or ferrocyanide. In the latter case ferricyanide is formed, and its yield was determined to be 66 +/- 2% of the initial concentration of peroxynitrite. The reaction of ONOO(-) with 16 mM CO(2) with and without ferrocyanide was also studied at pH 5.6-7.7 in the presence of 0.1 M phosphate, where both the initial pH and [CO(2)] remain constant. Under these conditions the rate constant of the decay of peroxynitrite was found to be identical to that of the formation of ferricyanide, indicating that ONOOC(O)(-) does not accumulate. These results confirm our earlier observations, i.e., the reaction of peroxynitrite with excess CO(2) takes place via the formation of about 33% CO(3)(*)(-) and *NO(2) radicals in the bulk of the solution.

  17. Atmospheric chemistry of benzyl alcohol: kinetics and mechanism of reaction with OH radicals.

    PubMed

    Bernard, François; Magneron, Isabelle; Eyglunent, Grégory; Daële, Véronique; Wallington, Timothy J; Hurley, Michael D; Mellouki, Abdelwahid

    2013-04-02

    The atmospheric oxidation of benzyl alcohol has been investigated using smog chambers at ICARE, FORD, and EUPHORE. The rate coefficient for reaction with OH radicals was measured and an upper limit for the reaction with ozone was established; kOH = (2.8 ± 0.4) × 10(-11) at 297 ± 3 K (averaged value including results from Harrison and Wells) and kO(3) < 2 × 10(-19) cm(3) molecule(-1) s(-1) at 299 K. The products of the OH radical initiated oxidation of benzyl alcohol in the presence of NOX were studied. Benzaldehyde, originating from H-abstraction from the -CH(2)OH group, was identified using in situ FTIR spectroscopy, HPLC-UV/FID, and GC-PID and quantified in a yield of (24 ± 5) %. Ring retaining products originating from OH-addition to the aromatic ring such as o-hydroxybenzylalcohol and o-dihydroxybenzene as well as ring-cleavage products such as glyoxal were also identified and quantified with molar yields of (22 ± 2)%, (10 ± 3)%, and (2.7 ± 0.7)%, respectively. Formaldehyde was observed with a molar yield of (27 ± 10)%. The results are discussed with respect to previous studies and the atmospheric oxidation mechanism of benzyl alcohol.

  18. Atmospheric fate of methyl vinyl ketone: peroxy radical reactions with NO and HO2.

    PubMed

    Praske, Eric; Crounse, John D; Bates, Kelvin H; Kurtén, Theo; Kjaergaard, Henrik G; Wennberg, Paul O

    2015-05-14

    First generation product yields from the OH-initiated oxidation of methyl vinyl ketone (3-buten-2-one, MVK) under both low and high NO conditions are reported. In the low NO chemistry, three distinct reaction channels are identified leading to the formation of (1) OH, glycolaldehyde, and acetyl peroxy R2a , (2) a hydroperoxide R2b , and (3) an α-diketone R2c . The α-diketone likely results from HOx-neutral chemistry previously only known to occur in reactions of HO2 with halogenated peroxy radicals. Quantum chemical calculations demonstrate that all channels are kinetically accessible at 298 K. In the high NO chemistry, glycolaldehyde is produced with a yield of 74 ± 6.0%. Two alkyl nitrates are formed with a combined yield of 4.0 ± 0.6%. We revise a three-dimensional chemical transport model to assess what impact these modifications in the MVK mechanism have on simulations of atmospheric oxidative chemistry. The calculated OH mixing ratio over the Amazon increases by 6%, suggesting that the low NO chemistry makes a non-negligible contribution toward sustaining the atmospheric radical pool.

  19. Enhancement by cigarette smoke extract of the radical formation in a reaction mixture of 13-hydroperoxide octadecadienoic acid and ferric ions.

    PubMed

    Iimura, Sae; Iwahashi, Hideo

    2006-04-01

    The effects of cigarette smoke extract on radical formation were examined in reaction mixtures containing 13-hydroperoxide octadecadienoic acid (13-HPODE), FeCl3, cigarette smoke extract, ethylenediaminetetraacetic acid (EDTA), alpha-(4-pyridyl-1-oxide)-N-tert-butylnitrone (4-POBN), and phosphate buffer (pH 7.4). Cigarette smoke extract enhanced the formation of both 7-carboxyheptyl and pentyl radicals in the reaction. Ferric ions were reduced in the reaction mixture, suggesting that cigarette smoke extract enhances the formation of 7-carboxyheptyl and pentyl radicals by reducing ferric irons. Although there is a large body of evidence supporting the