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Sample records for identify reaction intermediate

  1. Reactions of stabilized Criegee Intermediates

    NASA Astrophysics Data System (ADS)

    Vereecken, Luc; Harder, Hartwig; Novelli, Anna

    2014-05-01

    Carbonyl oxides (Criegee intermediates) were proposed as key intermediates in the gas phase ozonolysis of alkenes in 1975 by Rudolf Criegee. Despite the importance of ozonolysis in atmospheric chemistry, direct observation of these intermediates remained elusive, with only indirect experimental evidence for their role in the oxidation of hydrocarbons, e.g. through scavenging experiments. Direct experimental observation of stabilized CI has only been achieved since 2008. Since then, a concerted effort using experimental and theoretical means is in motion to characterize the chemistry and kinetics of these reactive intermediates. We present the results of theoretical investigations of the chemistry of Criegee intermediates with a series of coreactants which may be of importance in the atmosphere, in experimental setups, or both. This includes the CI+CI cross-reaction, which proceeds with a rate coefficient near the collision limit and can be important in experimental conditions. The CI + alkene reactions show strong dependence of the rate coefficient depending on the coreactants, but is generally found to be rather slow. The CI + ozone reaction is sufficiently fast to occur both in experiment and the free troposphere, and acts as a sink for CI. The reaction of CI with hydroperoxides, ROOH, is complex, and leads both to the formation of oligomers, as to the formation of reactive etheroxides, with a moderately fast rate coefficient. The importance of these reactions is placed in the context of the reaction conditions in different atmospheric environments ranging from unpolluted to highly polluted.

  2. Kinetics, mechanisms and products of reactions of Criegee intermediates

    NASA Astrophysics Data System (ADS)

    Orr-Ewing, Andrew

    The atmospheric ozonolysis of alkenes such as isoprene produces Criegee intermediates which are increasingly recognized as important contributors to oxidation chemistry in the Earth's troposphere. Stabilized Criegee intermediates are conveniently produced in the laboratory by ultraviolet photolysis of diiodoalkanes in the presence of O2, and can be detected by absorption spectroscopy using their strong electronic bands in the near ultraviolet region. We have used these techniques to study a wide range of reactions of Criegee intermediates, including their self-reactions, and reactions with carboxylic acids and various other trace atmospheric constituents. In collaboration with the Sandia National Laboratory group led by Drs C.A. Taatjes and D.L. Osborn, we have used photoionization and mass spectrometry methods, combined with electronic structure calculations, to characterize the products of several of these reactions. Our laboratory studies determine rate coefficients for the Criegee intermediate reactions, many of which prove to be fast. In the case of reactions with carboxylic acids, a correlation between the dipole moments of the reactants and the reaction rate coefficients suggests a dipole-capture controlled reaction and allows us to propose a structure-activity relationship to predict the rates of related processes. The contributions of these various Criegee intermediate reactions to the chemistry of the troposphere have been assessed using the STOCHEM-CRI global atmospheric chemistry model. This work was supported by NERC grant NE/K004905/1.

  3. Investigation of Unexpected Reaction Intermediates in the Alkaline Hydrolysis of Methyl 3,5-Dinitrobenzoate

    ERIC Educational Resources Information Center

    Silva, Clesia C.; Silva, Ricardo O.; Navarro, Daniela M. A. F.; Navarro, Marcelo

    2009-01-01

    An experimental project aimed at identifying stable reaction intermediates is described. Initially, the studied reaction appears to involve the simple hydrolysis, by aqueous sodium hydroxide, of methyl 3,5-dinitrobenzoate dissolved in dimethyl sulfoxide. On mixing the substrates, however, the reaction mixture unexpectedly turns an intense red in…

  4. Ligand Intermediates in Metal-Catalyzed Reactions

    SciTech Connect

    Gladysz, John A.

    1999-07-31

    The longest-running goal of this project has been the synthesis, isolation, and physical chemical characterization of homogeneous transition metal complexes containing ligand types believed to be intermediates in the metal-catalyzed conversion of CO/H{sub 2}, CO{sub 2}, CH{sub 4}, and similar raw materials to organic fuels, feedstocks, etc. In the current project period, complexes that contain unusual new types of C{sub x}(carbide) and C{sub x}O{sub y} (carbon oxide) ligands have been emphasized. A new program in homogeneous fluorous phase catalysis has been launched as described in the final report.

  5. Visualizing biological reaction intermediates with DNA curtains

    NASA Astrophysics Data System (ADS)

    Zhao, Yiling; Jiang, Yanzhou; Qi, Zhi

    2017-04-01

    Single-molecule approaches have tremendous potential analyzing dynamic biological reaction with heterogeneity that cannot be effectively accessed via traditional ensemble-level biochemical approaches. The approach of deoxyribonucleic acid (DNA) curtains developed by Dr Eric Greene and his research team at Columbia University is a high-throughput single-molecule technique that utilizes fluorescent imaging to visualize protein–DNA interactions directly and allows the acquisition of statistically relevant information from hundreds or even thousands of individual reactions. This review aims to summarize the past, present, and future of DNA curtains, with an emphasis on its applications to solve important biological questions.

  6. Reaction Intermediates in Aromatic Fuel Combustion.

    DTIC Science & Technology

    2014-09-26

    distribution is unlimited. 5 ,:-,-,: ;;: , , , ’ : - ..-.. ,., ., ; -.. < ?-’.;.o .’.’.:<. .7/ ABSTRACT 4he oxidation of benzene under fuel-lean conditions has...sensitively on the rate- limiting unimolecular decomposition of benzene & C6H6 4 C6H5 + H The rate constant obtained for the initiation reaction using a...considerable current interest ia the kiuetios and mechanism of benzene oxidatiom because of the iacreasing us* of aromatics as fuel components. Partly’due to

  7. (Ligand intermediates in metal-catalyzed reactions)

    SciTech Connect

    Not Available

    1992-01-01

    This report consists of sections on sigma bond complexes of alkenes, a new carbon-hydrogen bond activation reaction of alkene complexes, carbon-hydrogen bond migrations in alkylidene complexes, carbon- hydrogen bond migrations in alkyne complexes, synthesis, structure and reactivity of C{sub x} complexes, synthesis and reactivity of alcohol and ether complexes, new catalysts for the epimerization of secondary alcohols; carbon-hydrogen bond activation in alkoxide complexes, pi/sigma equilibria in metal/O=CXX' complexes, and other hydrocarbon ligands; miscellaneous.(WET)

  8. The phosphorylated intermediate in the phosphoglyceromutase reaction

    PubMed Central

    Zwaig, N.; Milstein, C.

    1966-01-01

    1. High-voltage paper-electrophoresis methods have been used for the separation of 32P-labelled phosphoesters. 2. Evidence is presented which indicates that 32P-labelled phosphopeptides, obtained after acid hydrolysis of phosphoglyceromutase incubated with impure 2,3-di[32P]phosphoglycerate, are derived from phosphoglucomutase contamination. 3. The hydrolysis of 2,3-di[32P]phosphoglycerate by phosphoglyceromutase has been studied. After an apparent instantaneous hydrolysis of 1 mole of coenzyme/mole of enzyme the reaction proceeds at a very low rate. 4. This hydrolysis seems to be due to the destruction of an enzyme–coenzyme complex. The proportions of the decomposition products of the complex vary according to further handling (pH of ionophoresis). 5. The inorganic [32P]phosphate produced by the hydrolysis of the complex and the inorganic [32P]phosphate produced by the slow phosphatase activity can be differentiated by the ability of the former to be incorporated into non-radioactive substrate before enzyme denaturation. 6. The effect of enzyme concentration on the stoicheiometry of the slow phosphatase hydrolysis of the diphosphoglycerate is described and this suggests that it may occur via two independent reactions, one of them being the decomposition of the enzyme–coenzyme complex on standing. PMID:5941332

  9. Photocatalytic degradation of paracetamol: intermediates and total reaction mechanism.

    PubMed

    Moctezuma, Edgar; Leyva, Elisa; Aguilar, Claudia A; Luna, Raúl A; Montalvo, Carlos

    2012-12-01

    The advanced oxidation of paracetamol (PAM) promoted by TiO(2)/UV system in aqueous medium was investigated. Monitoring this reaction by HPLC and TOC, it was demonstrated that while oxidation of paracetamol is quite efficient under these conditions, its mineralization is not complete. HPLC indicated the formation of hydroquinone, benzoquinone, p-aminophenol and p-nitrophenol in the reaction mixtures. Further evidence of p-nitrophenol formation was obtained following the reaction by UV-vis spectroscopy. Continuous monitoring by IR spectroscopy demonstrated the breaking of the aromatic amide present in PAM and subsequent formation of several aromatic intermediate compounds such as p-aminophenol and p-nitrophenol. These aromatic compounds were eventually converted into trans-unsaturated carboxylic acids. Based on these experimental results, an alternative deacylation mechanism for the photocatalytic oxidation of paracetamol is proposed. Our studies also demonstrated IR spectroscopy to be a useful technique to investigate oxidative mechanisms of pharmaceutical compounds.

  10. Computational analysis of the mechanism of chemical reactions in terms of reaction phases: hidden intermediates and hidden transition States.

    PubMed

    Kraka, Elfi; Cremer, Dieter

    2010-05-18

    Computational approaches to understanding chemical reaction mechanisms generally begin by establishing the relative energies of the starting materials, transition state, and products, that is, the stationary points on the potential energy surface of the reaction complex. Examining the intervening species via the intrinsic reaction coordinate (IRC) offers further insight into the fate of the reactants by delineating, step-by-step, the energetics involved along the reaction path between the stationary states. For a detailed analysis of the mechanism and dynamics of a chemical reaction, the reaction path Hamiltonian (RPH) and the united reaction valley approach (URVA) are an efficient combination. The chemical conversion of the reaction complex is reflected by the changes in the reaction path direction t(s) and reaction path curvature k(s), both expressed as a function of the path length s. This information can be used to partition the reaction path, and by this the reaction mechanism, of a chemical reaction into reaction phases describing chemically relevant changes of the reaction complex: (i) a contact phase characterized by van der Waals interactions, (ii) a preparation phase, in which the reactants prepare for the chemical processes, (iii) one or more transition state phases, in which the chemical processes of bond cleavage and bond formation take place, (iv) a product adjustment phase, and (v) a separation phase. In this Account, we examine mechanistic analysis with URVA in detail, focusing on recent theoretical insights (with a variety of reaction types) from our laboratories. Through the utilization of the concept of localized adiabatic vibrational modes that are associated with the internal coordinates, q(n)(s), of the reaction complex, the chemical character of each reaction phase can be identified via the adiabatic curvature coupling coefficients, A(n,s)(s). These quantities reveal whether a local adiabatic vibrational mode supports (A(n,s) > 0) or resists

  11. Accomplishing structural change: identifying intermediate indicators of success.

    PubMed

    Miller, Robin Lin; Reed, Sarah J; Francisco, Vincent

    2013-03-01

    Coalitions are routinely employed across the United States as a method of mobilizing communities to improve local conditions that impact on citizens' well-being. Success in achieving specific objectives for environmental or structural community change may not quickly translate into improved population outcomes in the community, posing a dilemma for coalitions that pursue changes that focus on altering community conditions. Considerable effort by communities to plan for and pursue structural change objectives, without evidence of logical and appropriate intermediate markers of success could lead to wasted effort. Yet, the current literature provides little guidance on how coalitions might select intermediate indicators of achievement to judge their progress and the utility of their effort. The current paper explores the strengths and weaknesses of various indicators of intermediate success in creating structural changes among a sample of 13 coalitions organized to prevent exposure to HIV among high-risk adolescents in their local communities.

  12. Direct measurement of Criegee intermediate (CH2OO) reactions with acetone, acetaldehyde, and hexafluoroacetone.

    PubMed

    Taatjes, Craig A; Welz, Oliver; Eskola, Arkke J; Savee, John D; Osborn, David L; Lee, Edmond P F; Dyke, John M; Mok, Daniel W K; Shallcross, Dudley E; Percival, Carl J

    2012-08-14

    Criegee biradicals, i.e., carbonyl oxides, are critical intermediates in ozonolysis and have been implicated in autoignition chemistry and other hydrocarbon oxidation systems, but until recently the direct measurement of their gas-phase kinetics has not been feasible. Indirect determinations of Criegee intermediate kinetics often rely on the introduction of a scavenger molecule into an ozonolysis system and analysis of the effects of the scavenger on yields of products associated with Criegee intermediate reactions. Carbonyl species, in particular hexafluoroacetone (CF(3)COCF(3)), have often been used as scavengers. In this work, the reactions of the simplest Criegee intermediate, CH(2)OO (formaldehyde oxide), with three carbonyl species have been measured by laser photolysis/tunable synchrotron photoionization mass spectrometry. Diiodomethane photolysis produces CH(2)I radicals, which react with O(2) to yield CH(2)OO + I. The formaldehyde oxide is reacted with a large excess of a carbonyl reactant and both the disappearance of CH(2)OO and the formation of reaction products are monitored. The rate coefficient for CH(2)OO + hexafluoroacetone is k(1) = (3.0 ± 0.3) × 10(-11) cm(3) molecule(-1) s(-1), supporting the use of hexafluoroacetone as a Criegee-intermediate scavenger. The reactions with acetaldehyde, k(2) = (9.5 ± 0.7) × 10(-13) cm(3) molecule(-1) s(-1), and with acetone, k(3) = (2.3 ± 0.3) × 10(-13) cm(3) molecule(-1) s(-1), are substantially slower. Secondary ozonides and products of ozonide isomerization are observed from the reactions of CH(2)OO with acetone and hexafluoroacetone. Their photoionization spectra are interpreted with the aid of quantum-chemical and Franck-Condon-factor calculations. No secondary ozonide was observable in the reaction of CH(2)OO with acetaldehyde, but acetic acid was identified as a product under the conditions used (4 Torr and 293 K).

  13. Characterization of Anionic Cluster Nucleophilic Substitution Reaction Intermediates

    NASA Astrophysics Data System (ADS)

    Cyr, Donna Marie

    Recent theoretical and experimental developments in the arena of the gas phase S_{rm N}2 reaction (X^- + RY to RX + Y^-) has rekindled interest in this classic chemical reaction. Consideration of the gas phase S_{rm N} 2 double minima potential surface from a valence bond perspective, advocated by Shaik et. al., predicts the presence of a low lying excited electronic state corresponding to electron transfer. In this work we take advantage of long range ion-molecule induced forces to stabilize the S_{rm N}2 reactants in a complex, X^-cdot RY, allowing us to search for this charge transfer excited state from the well defined location on the potential energy surface. Photoelectron spectroscopy of X^ - cdot RY confirms the identification of the species as essentially charge-localized. Vibrational fine structure observed in the case of I^- cdot CH_3I is found to be consistent with small distortions of the CH_3I neutral upon complexation to form a stable intermediate in the S_{rm N}2 identity reaction. A narrow photofragmentation band lies just below the vertical electron detachment energy and is assigned to the X^- cdot RY to X cdotcdot (RY) ^- charge transfer excited state. More detailed study of the photofragmentation band reveals the photoexcitation mechanism is not direct charge transfer but is mediated by a weakly bound negative ion state. The excited state photochemistry of the X ^- cdot RY reaction intermediates is characterized by the formation of the endothermic halide abstraction product XY^-. Trends in the formation of the dihalide product are strongly dependent of the nature of the R group and these results are consistent with a preferential ion binding site in the complex. Search for the XY^- dihalide product in the bimolecular ground state reaction at supra-thermal collision energies revealed halide abstraction as a competitive product channel to the well known Walden inversion mechanism. All of these results are integrated in the development a picture of

  14. 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.

  15. The Biological Methane-Forming Reaction: Mechanism Confirmed Through Spectroscopic Characterization of a Key Intermediate.

    PubMed

    Shima, Seigo

    2016-10-24

    Find your path: Methyl-coenzyme M reductase (MCR, turquoise) reversibly catalyzes the reduction of methyl-coenzyme M (methyl-S-CoM) with coenzyme B (CoB-SH) to form methane and the heterodisulfide. Recently, spectroscopic methods were used to detect trapped intermediates in a stopped-flow system, and CoM-S-Ni(II) was identified after half a turnover of the MCR reaction (F430 =nickel porphinoid). This finding supports a methyl-radical catalytic mechanism.

  16. Kinetics and mechanisms of reactions involving small aromatic reactive intermediates

    SciTech Connect

    Lin, M.C.

    1993-12-01

    Small aromatic radicals such as C{sub 6}H{sub 5}, C{sub 6}H{sub 5}O and C{sub 6}H{sub 4} are key prototype species of their homologs. C{sub 6}H{sub 5} and its oxidation product, C{sub 6}H{sub 5}O are believed to be important intermediates which play a pivotal role in hydrocarbon combustion, particularly with regard to soot formation. Despite their fundamental importance, experimental data on the reaction mechanisms and reactivities of these species are very limited. For C{sub 6}H{sub 5}, most kinetic data except its reactions with NO and NO{sub 2}, were obtained by relative rate measurements. For C{sub 6}H{sub 5}O, the authors have earlier measured its fragmentation reaction producing C{sub 5}H{sub 5} + CO in shock waves. For C{sub 6}H{sub 4}, the only rate constant measured in the gas phase is its recombination rate at room temperature. The authors have proposed to investigate systematically the kinetics and mechanisms of this important class of molecules using two parallel laser diagnostic techniques--laser resonance absorption (LRA) and resonance enhanced multiphoton ionization mass spectrometry (REMPI/MS). In the past two years, study has been focused on the development of a new multipass adsorption technique--the {open_quotes}cavity-ring-down{close_quotes} technique for kinetic applications. The preliminary results of this study appear to be quite good and the sensitivity of the technique is at least comparable to that of the laser-induced fluorescence method.

  17. Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction

    SciTech Connect

    Heroux, A.; Bozinovski, D; Valley, M; Fitzpatrick, P; Orville, A

    2009-01-01

    The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 {angstrom} resolution or better of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct are described. The D402N enzyme has no detectable activity with neutral nitroalkanes. The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped (Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062-2066). The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2'-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle.

  18. Reaction intermediates in the catalytic Gif-type oxidation from nuclear inelastic scattering

    NASA Astrophysics Data System (ADS)

    Rajagopalan, S.; Asthalter, T.; Rabe, V.; Laschat, S.

    2016-12-01

    Nuclear inelastic scattering (NIS) of synchrotron radiation, also known as nuclear resonant vibrational spectroscopy (NRVS), has been shown to provide valuable insights into metal-centered vibrations at Mössbauer-active nuclei. We present a study of the iron-centered vibrational density of states (VDOS) during the first step of the Gif-type oxidation of cyclohexene with a novel trinuclear Fe3(μ 3-O) complex as catalyst precursor. The experiments were carried out on shock-frozen solutions for different combinations of reactants: Fe3(μ 3-O) in pyridine solution, Fe3(μ 3-O) plus Zn/acetic acid in pyridine without and with addition of either oxygen or cyclohexene, and Fe3(μ 3-O)/Zn/acetic acid/pyridine/cyclohexene (reaction mixture) for reaction times of 1 min, 5 min, and 30 min. The projected VDOS of the Fe atoms was calculated on the basis of pseudopotential density functional calculations. Two possible reaction intermediates were identified as [Fe(III)(C5H5N)2(O2CCH3)2]+ and Fe(II)(C5H5N)4(O2CCH3)2, yielding evidence that NIS (NRVS) allows to identify the presence of iron-centered intermediates also in complex reaction mixtures.

  19. Identifying Criegee Intermediates As Potential Oxidants In The Troposphere

    NASA Astrophysics Data System (ADS)

    Novelli, A.; Hens, K.; Tatum Ernest, C.; Martinez, M.; Nölscher, A. C.; Sinha, V.; Paasonen, P.; Petäjä, T.; Sipilä, M.; Elste, T.; Plass-Duelmer, C.; Kubistin, D.; Phillips, G. J.; Williams, J.; Vereecken, L.; Lelieveld, J.; Harder, H.

    2015-12-01

    Criegee intermediates (CI) are formed during the ozonolysis of unsaturated compounds and have been intensively studied in the last few years due to their possible role as oxidants in the troposphere. Stabilised CI (SCI) are now known to react very rapidly, k(298 K) = 10-12 to 10-10 cm3 molecule-1 s-1, with a large number of trace gases (SO2, NO2, organic acids, water dimers). An assessment of their effective oxidative capacity remain challenging as, CI chemistry is complex, it spans a large range of rate coefficients for different SCI conformers reacting with water dimers and trace gases, and in addition, no reliable measurement technique able to detect ambient SCI concentrations is currently available. In this study, we examine the extensive dataset from the HUMPPA-COPEC 2010 and the HOPE 2012 field campaigns, aided by literature data, to estimate the abundance of SCI in the lower troposphere. The budget of SCI is analyzed using four different approaches: 1) based on an observed yet unexplained H2SO4 production; 2) from the measured concentrations of unsaturated volatile organic compounds (VOC); 3) from OH reactivity measurements; 4) from the unexplained production rate of OH. A SCI concentration range between 5 x 103 and 2 x 106 molecule cm-3 is calculated for the two environments. The weighted mean estimate of the SCI concentration over the boreal forest of ~ 5 x 104 molecules cm-3 implies a significant impact on the conversion of SO2 into H2SO4. In addition, we present measurements obtained using our inlet pre-injector laser-induced fluorescence assay by gas expansion technique (IPI-LIF-FAGE) for the above-mentioned campaigns. A recent laboratory study performed with the same instrumental setup showed that the IPI-LIF-FAGE system is sensitive to the detection of the OH formed from unimolecular decomposition of SCI. In order to investigate the applicability of the laboratory findings to the ambient data, measurement of the background OH (OHbg), the signal

  20. Unstable Reaction Intermediates and Hysteresis during the Catalytic Cycle of 5-Aminolevulinate Synthase

    PubMed Central

    Stojanovski, Bosko M.; Hunter, Gregory A.; Jahn, Martina; Jahn, Dieter; Ferreira, Gloria C.

    2014-01-01

    5-Aminolevulinate (ALA), an essential metabolite in all heme-synthesizing organisms, results from the pyridoxal 5′-phosphate (PLP)-dependent enzymatic condensation of glycine with succinyl-CoA in non-plant eukaryotes and α-proteobacteria. The predicted chemical mechanism of this ALA synthase (ALAS)-catalyzed reaction includes a short-lived glycine quinonoid intermediate and an unstable 2-amino-3-ketoadipate intermediate. Using liquid chromatography coupled with tandem mass spectrometry to analyze the products from the reaction of murine erythroid ALAS (mALAS2) with O-methylglycine and succinyl-CoA, we directly identified the chemical nature of the inherently unstable 2-amino-3-ketoadipate intermediate, which predicates the glycine quinonoid species as its precursor. With stopped-flow absorption spectroscopy, we detected and confirmed the formation of the quinonoid intermediate upon reacting glycine with ALAS. Significantly, in the absence of the succinyl-CoA substrate, the external aldimine predominates over the glycine quinonoid intermediate. When instead of glycine, l-serine was reacted with ALAS, a lag phase was observed in the progress curve for the l-serine external aldimine formation, indicating a hysteretic behavior in ALAS. Hysteresis was not detected in the T148A-catalyzed l-serine external aldimine formation. These results with T148A, a mALAS2 variant, which, in contrast to wild-type mALAS2, is active with l-serine, suggest that active site Thr-148 modulates ALAS strict amino acid substrate specificity. The rate of ALA release is also controlled by a hysteretic kinetic mechanism (observed as a lag in the ALA external aldimine formation progress curve), consistent with conformational changes governing the dissociation of ALA from ALAS. PMID:24920668

  1. Structural characterization of the reaction pathway in phosphoserine phosphatase: Crystallographic 'snapshots' of intermediate states.

    SciTech Connect

    Wang, Weiru; Cho, Ho S.; Kim, Rosalind; Jancarik, Jaru; Yokota, Hisao; Nguyen, Henry H.; Grigoriev, Igor V.; Wemmer, David E.; Kim, Sung-Hou

    2004-04-12

    Phosphoserine phosphatase (PSP) is a member of a large class of enzymes that catalyze phosphoester hydrolysis using a phosphoaspartate enzyme intermediate. PSP is a likely regulator of the steady-state-serine level in the brain, which is a critical co-agonist of the N-methyl--aspartate type of glutamate receptors. Here, we present high-resolution (1.5 1.9 Angstrom) structures of PSP from Methanococcus jannaschii, which define the open state prior to substrate binding, the complex with phosphoserine substrate bound (with a D to N mutation in the active site), and the complex with AlF3, a transition-state analog for the phospho-transfer steps in the reaction. These structures, together with those described for the BeF3- complex (mimicking the phospho-enzyme) and the enzyme with phosphate product in the active site, provide a detailed structural picture of the full reaction cycle. The structure of the apostate indicates partial unfolding of the enzyme to allow substrate binding, with refolding in the presence of substrate to provide specificity. Interdomain and active-site conformational changes are identified. The structure with the transition state analog bound indicates a ''tight'' intermediate. A striking structure homology, with significant sequence conservation, among PSP, P-type ATPases and response regulators suggests that the knowledge of the PSP reaction mechanism from the structures determined will provide insights into the reaction mechanisms of the other enzymes in this family.

  2. Structural Insights into Intermediate Steps in the Sir2 Deacetylation Reaction

    SciTech Connect

    Hawse, William F.; Hoff, Kevin G.; Fatkins, David G.; Daines, Alison; Zubkova, Olga V.; Schramm, Vern L.; Zheng, Weiping; Wolberger, Cynthia

    2010-07-22

    Sirtuin enzymes comprise a unique class of NAD{sup +}-dependent protein deacetylases. Although structures of many sirtuin complexes have been determined, structural resolution of intermediate chemical steps are needed to understand the deacetylation mechanism. We report crystal structures of the bacterial sirtuin, Sir2Tm, in complex with an S-alkylamidate intermediate, analogous to the naturally occurring O-alkylamidate intermediate, and a Sir2Tm ternary complex containing a dissociated NAD{sup +} analog and acetylated peptide. The structures and biochemical studies reveal critical roles for the invariant active site histidine in positioning the reaction intermediate, and for a conserved phenylalanine residue in shielding reaction intermediates from base exchange with nicotinamide. The new structural and biochemical studies provide key mechanistic insight into intermediate steps of the Sir2 deacetylation reaction.

  3. 18F-Labelled Intermediates for Radiosynthesis by Modular Build-Up Reactions: Newer Developments

    PubMed Central

    Ermert, Johannes

    2014-01-01

    This brief review gives an overview of newer developments in 18F-chemistry with the focus on small 18F-labelled molecules as intermediates for modular build-up syntheses. The short half-life (<2 h) of the radionuclide requires efficient syntheses of these intermediates considering that multistep syntheses are often time consuming and characterized by a loss of yield in each reaction step. Recent examples of improved synthesis of 18F-labelled intermediates show new possibilities for no-carrier-added ring-fluorinated arenes, novel intermediates for tri[18F]fluoromethylation reactions, and 18F-fluorovinylation methods. PMID:25343144

  4. Ozonation of benzotriazole and methylindole: Kinetic modeling, identification of intermediates and reaction mechanisms.

    PubMed

    Benitez, F Javier; Acero, Juan L; Real, Francisco J; Roldán, Gloria; Rodríguez, Elena

    2015-01-23

    The ozonation of 1H-benzotriazole (BZ) and 3-methylindole (ML), two emerging contaminants that are frequently present in aquatic environments, was investigated. The experiments were performed with the contaminants (1μM) dissolved in ultrapure water. The kinetic study led to the determination of the apparent rate constants for the ozonation reactions. In the case of 1H-benzotriazole, these rate constants varied from 20.1 ± 0.4M(-1)s(-1) at pH=3 to 2143 ± 23 M(-1)s(-1) at pH=10. Due to its acidic nature (pKa=8.2), the degree of dissociation of this pollutant was determined at every pH of work, and the specific rate constants of the un-dissociated and dissociated species were evaluated, being the values of these rate constants 20.1 ± 2.0 and 2.0 ± 0.3 × 10(3)M(-1)s(-1), respectively. On the contrary, 3-methylindole does not present acidic nature, and therefore, it can be proposed an average value for its rate constant of 4.90 ± 0.7 × 10(5)M(-1)s(-1) in the whole pH range 3-10. Further experiments were performed to identify the main degradation byproducts (10 mg L(-1) of contaminants, 0.023 gh(-1) of ozone). Up to 8 intermediates formed in the ozonation of 3-methylindole were identified by LC-TOFMS, while 6 intermediates were identified in the ozonation of 1H-benzotriazole. By considering these intermediate compounds, the reaction mechanisms were proposed and discussed. Finally, evaluated rate constants allowed to predict and modeling the oxidation of these micropollutants in general aquatic systems.

  5. 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.

  6. Atomic-scale insight into the formation, mobility and reaction of Ullmann coupling intermediates.

    PubMed

    Lewis, Emily A; Murphy, Colin J; Liriano, Melissa L; Sykes, E Charles H

    2014-01-28

    The Ullmann reaction of bromobenzene, the simplest coupling reagent, to form biphenyl on a Cu surface proceeds via a highly mobile organometallic intermediate in which two phenyl groups extract and bind a single surface Cu atom.

  7. Photocatalytic degradation of pesticide methomyl: determination of the reaction pathway and identification of intermediate products.

    PubMed

    Tamimi, M; Qourzal, S; Assabbane, A; Chovelon, J-M; Ferronato, C; Ait-Ichou, Y

    2006-05-01

    The degradation of pesticide methomyl in aqueous solution by UV-irradiation in the presence of TiO2 "Degussa P-25" has been studied. It was found that mineralisation to carbon dioxide, water, sulfate and ammonia took place during the process. The rate of photodecomposition of methomyl was measured using high performance liquid chromatography (HPLC), while its mineralization was followed using ion chromatography (IC), and total organic carbon (TOC) analysis. The identification of reaction intermediate products was carried out using coupled techniques HPLC-MS (electrospray ionization in positive mode) and a degradation pathway was proposed. Under our conditions, complete disappearance of 1.23 x 10(-4) mol l(-1) of pure pesticide occurred within 45 min of illumination and 80% TOC removal occurred in less than 4 h. Three main intermediates were identified resulting from (i) the rupture of the ester bond (or the N-O bond), (ii) the hydroxylation of methyl group borne by the nitrogen atom and (iii) the product resulting from the decarboxylation of the oxidized hydroxylated methyl group (photo-Kolbe reaction). In order to be sure that the photocatalytic results were consistent, hydrolysis and photolysis tests were performed. Photocatalysis proved to be an excellent new advanced oxidation technology (AOT) to eliminate methomyl present in water.

  8. Reaction of Stabilized Criegee Intermediates from Ozonolysis of Limonene with Water: Ab Initio and DFT Study

    PubMed Central

    Jiang, Lei; Lan, Ru; Xu, Yi-Sheng; Zhang, Wen-Jie; Yang, Wen

    2013-01-01

    The mechanism of the chemical reaction of H2O with three stabilized Criegee intermediates (stabCI-OO, stabCI-CH3-OO and stabCIx-OO) produced via the limonene ozonolysis reaction has been investigated using ab initio and DFT (Density Functional Theory) methods. It has been shown that the formation of the hydrogen-bonded complexes is followed by two different reaction pathways, leading to the formation of either OH radicals via water-catalyzed H migration or of α-hydroxy hydroperoxide. Both pathways were found to be essential sources of atmospheric OH radical and H2O2 making a significant contribution to the formation of secondary aerosols in the Earth’s atmosphere. The activation energies at the CCSD(T)/6-31G(d) + CF level of theory were found to be in the range of 14.70–21.98 kcal mol−1. The formation of α-hydroxy hydroperoxide for the reaction of stabCIx-OO and H2O with the activation energy of 14.70 kcal mol−1 is identified as the most favorable pathway. PMID:23481640

  9. Investigation of the intermediate-energy deuteron breakup reaction

    SciTech Connect

    Divadeenam, M.; Ward, T.E.; Mustafa, M.G.; Udagawa, T.; Tamura, T.

    1989-01-01

    The Udagawa-Tamura formalism is employed to calculate the proton singles both in the bound and unbound regions. Both the Elastic-Breakup (EB) and the Breakup-Fusion (BF) processes are considered to calculate the doubly-differential cross section for light and intermediate mass nuclei. The calculated spectra for 25 and 56 MeV deuterons reproduce the experimental spectra very well except for the spectra at large angle and at low energies, of the outgoing particle. Contributions due to precompound and evaporation processes are estimated to supplement the spectral results based on the Elastic-Breakup and Breakup-Fusion mechanisms. An extension of the model calculations to higher deuteron energies is being made to test the (EB + BF) model limitations. 5 refs., 1 fig.

  10. Incomplete Combustion of Hydrogen: Trapping a Reaction Intermediate

    ERIC Educational Resources Information Center

    Mattson, Bruce; Hoette, Trisha

    2007-01-01

    The combustion of hydrogen in air is quite complex with at least 28 mechanistic steps and twelve reaction species. Most of the species involved are radicals (having unpaired electrons) in nature. Among the various species generated, a few are stable, including hydrogen peroxide. In a normal hydrogen flame, the hydrogen peroxide goes on to further…

  11. Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome

    SciTech Connect

    Yang, Xiaojing; Ren, Zhong; Kuk, Jane; Moffat, Keith

    2012-03-27

    Light is a fundamental signal that regulates important physiological processes such as development and circadian rhythm in living organisms. Phytochromes form a major family of photoreceptors responsible for red light perception in plants, fungi and bacteria. They undergo reversible photoconversion between red-absorbing (Pr) and far-red-absorbing (Pfr) states, thereby ultimately converting a light signal into a distinct biological signal that mediates subsequent cellular responses. Several structures of microbial phytochromes have been determined in their dark-adapted Pr or Pfr states. However, the structural nature of initial photochemical events has not been characterized by crystallography. Here we report the crystal structures of three intermediates in the photoreaction of Pseudomonas aeruginosa bacteriophytochrome (PaBphP). We used cryotrapping crystallography to capture intermediates, and followed structural changes by scanning the temperature at which the photoreaction proceeded. Light-induced conformational changes in PaBphP originate in ring D of the biliverdin (BV) chromophore, and E-to-Z isomerization about the C{sub 15} = C{sub 16} double bond between rings C and D is the initial photochemical event. As the chromophore relaxes, the twist of the C{sub 15} methine bridge about its two dihedral angles is reversed. Structural changes extend further to rings B and A, and to the surrounding protein regions. These data indicate that absorption of a photon by the Pfr state of PaBphP converts a light signal into a structural signal via twisting and untwisting of the methine bridges in the linear tetrapyrrole within the confined protein cavity.

  12. Atmospheric chemistry. Direct kinetic measurement of the reaction of the simplest Criegee intermediate with water vapor.

    PubMed

    Chao, Wen; Hsieh, Jun-Ting; Chang, Chun-Hung; Lin, Jim Jr-Min

    2015-02-13

    Carbonyl oxides, or Criegee intermediates, are important transient species formed in the reactions of unsaturated hydrocarbons with ozone. Although direct detection of Criegee intermediates has recently been realized, the main atmospheric sink of Criegee intermediates remains unclear. We report ultraviolet absorption spectroscopic measurements of the lifetime of the simplest Criegee intermediate, CH2OO, at various relative humidity levels up to 85% at 298 kelvin. An extremely fast decay rate of CH2OO was observed at high humidity. The observed quadratic dependence of the decay rate on water concentration implied a predominant reaction with water dimer. On the basis of the water dimer equilibrium constant, the effective rate coefficient of the CH2OO + (H2O)2 reaction was determined to be 6.5 (±0.8) × 10(-12) cubic centimeters per second. This work would help modelers to better constrain the atmospheric concentrations of CH2OO.

  13. Cycloaddition reactions of allenes with N-phenylmaleimide. A two-step, diradical-intermediate process

    SciTech Connect

    Pasto, D.J.; Heid, P.F.; Warren, S.E.

    1982-06-30

    The stereoselectivities, chemoselectivities, relative reactivities, and kinetic isotope effects have been determined in the cycloaddition reactions of substituted allenes with N-phenylmaleimide. The comparison of these results with those derived from the studies of the cycloaddition of 1,1-dichloro-2,2-difluoroethene and the radical-chain addition of benzenethiol to allenes strongly indicates that the cycloadditions with N-phenylmaleimide occur via a two-step, diradical-intermediate process. The stereochemical features controlling the formation of the stereoisomeric diradical intermediates and their ring closures are discussed. In addition to the cycloaddition processes, competitive ene reactions occur to produce intermediate dienes, which react further to produce 1:2 adducts or nonreactive alkyne-containing 1:1 adducts. These ene reactions also appear to proceed via diradical intermediates.

  14. Computational insight into the reaction intermediates in the glycosylation reaction assisted by donor heteroatoms.

    PubMed

    Bravo, Fernando; Viso, Antonio; Alcázar, Eva; Molas, Pineda; Bo, Carles; Castillón, Sergio

    2003-02-07

    We studied the geometric and electronic structure of several cations (9 and 18-23) that are usually proposed as intermediates for glycosylation reactions using DFT methods. For ions 9 and 18-23 the geometries obtained corresponded to an open ion (6b type) irrespective of the exocyclic heteroatom (S, Se, I) and the size of the cycle (furanoses as well as pyranoses). We studied how substituents bonded to the exocyclic heteroatom (R in SR and SeR) affect the structure of ions and found that the geometry approached that of episulfonium and episelenonium ions (6a type) when the substituents were electron donors. The tert-butyl group and the 2,4,6-trimethyl- and 2,4,6-trimethoxyphenyl and trimethylsilyl groups produced the strongest of these effects. The presence of an electron-withdrawing group (CO-CF(3)) bonded to the hydroxymethyl group produced a similar but weaker effect. We analyzed this behavior in terms of molecular orbital interactions.

  15. Nucleon radiative capture and the inverse reaction at intermediate energies

    SciTech Connect

    Halpern, I.

    1991-01-01

    The processes which can lead to the radiative capture of fast nucleons include direct transitions in the nuclear potential, transitions in which coherent multipole resonances are excited, transitions by nucleons which are excited in early intranuclear collisions, bremsstrahlung from nucleon-nucleon collisions and photon evaporation'' from a thermally equilibrated nucleus. Corresponding processes occur when an energetic photon ejects fast nucleons from a nucleus. As experimental information from capture and photoreactions has become more detailed, inconsistencies and uncertainties have appeared which reflect difficulties in identifying and separating the responsible processes. This has led to more sophisticated and more complicated theoretical treatments which in turn have promoted new and more demanding experiments. 38 refs. 10 figs.

  16. Solving the Structure of Reaction Intermediates by Time-Resolved Synchrotron X-ray Absorption Spectroscopy

    SciTech Connect

    Wang, Q.; Hanson, J; Frenkel, A

    2008-01-01

    We present a robust data analysis method of time-resolved x-ray absorption spectroscopy experiments suitable for chemical speciation and structure determination of reaction intermediates. Chemical speciation is done by principal component analysis (PCA) of the time-resolved x-ray absorption near-edge structure data. Structural analysis of intermediate phases is done by theoretical modeling of their extended x-ray absorption fine-structure data isolated by PCA. The method is demonstrated using reduction and reoxidation of Cu-doped ceria catalysts where we detected reaction intermediates and measured fine details of the reaction kinetics. This approach can be directly adapted to many time-resolved x-ray spectroscopy experiments where new rapid throughput data collection and analysis methods are needed.

  17. Forming a Two-Ring Polycyclic Aromatic Hydrocarbon without a Benzene Intermediate: the Reaction of Propargyl with Acetylene

    NASA Astrophysics Data System (ADS)

    Osborn, David; Savee, John; Selby, Talitha; Welz, Oliver; Taatjes, Craig

    The reaction of acetylene (HCCH) with a resonance-stabilized free radical is a commonly invoked mechanism for the generation of polycyclic aromatic hydrocarbons (PAH), which are likely precursors of soot particles in combustion. In this work, we examine the sequential addition of acetylene to the propargyl radical (H2CCCH) at temperatures of 800 and 1000 K. Using time-resolved multiplexed photoionization mass spectrometry with tunable ionizing radiation, we identified the isomeric forms of the C5H5 and C7H7 intermediates in this reaction sequence, and confirmed that the final C9H8 product is the two-ring aromatic compound indene. We identified two different resonance-stabilized C5H5 intermediates, with different temperature dependencies. Furthermore, the C7H7 intermediate is the tropyl radical (c-C7H7) , not the benzyl radical (C6H5CH2) , as is usually assumed in combustion environments. These experimental results are in general agreement with the latest electronic structure / master equation results of da Silva et al. This work shows a pathway for PAH formation that bypasses benzene / benzyl intermediates.

  18. Ferritin reactions: direct identification of the site for the diferric peroxide reaction intermediate.

    PubMed

    Liu, Xiaofeng; Theil, Elizabeth C

    2004-06-08

    Ferritins managing iron-oxygen biochemistry in animals, plants, and microorganisms belong to the diiron carboxylate protein family and concentrate iron as ferric oxide approximately 10(14) times above the ferric K(s). Ferritin iron (up to 4,500 atoms), used for iron cofactors and heme, or to trap DNA-damaging oxidants in microorganisms, is concentrated in the protein nanocage cavity (5-8 nm) formed during assembly of polypeptide subunits, 24 in maxiferritins and 12 in miniferritins/DNA protection during starvation proteins. Direct identification of ferritin ferroxidase (F(ox)) sites, complicated by multiple types of iron-ferritin interactions, is now achieved with chimeric proteins where putative F(ox) site residues were introduced singly and cumulatively into an inactive host, an L maxiferritin. A dimagnesium ferritin cocrystal model guided site design and the diferric peroxo F(ox) intermediates (A at 650 nm) monitored activity. Diferric peroxo formation in chimeric and WT proteins had similar K(app) values and Hill coefficients. Catalytic activity required cooperative ferrous substrate binding to two sites A (E, EXXH) and B (E, QXXD). The weaker B sites in ferritin contrast with stronger B sites (E, EXXH) in diiron carboxylate oxygenases, explaining diferric oxo/hydroxo product release in ferritin vs. diiron cofactor retention in oxygenases. Codons for Q/H and D/E differ by single nucleotides, suggesting simple DNA mutations relate site B diiron substrate sites and diiron cofactor sites in proteins. The smaller k(cat) values in chimeras indicate the absence of second-shell residues important for ferritin substrate-product channeling that, when identified, will outline the entire iron path from ferritin pores through the F(ox) site to the mineral cavity.

  19. Asymmeric Formal [3+3]-Cycloaddition Reactions of Nitrones with Electrophilic Vinylcarbene Intermediates

    PubMed Central

    Wang, Xiaochen; Xu, Xinfang; Zavalij, Peter Y.; Doyle, Michael P.

    2011-01-01

    With metal carbene access to dipolar intermediates, 3,6-dihydro-1,2-oxazines are produced in high yields by dirhodium(II) carboxylate catalyzed reactions between nitrones and a β-TBSO-substituted vinyldiazoacetate. High enantiocontrol occurs with catalysis by N-phthaloyl-(S)-(amino acid)-ligated dirhodium carboxylates for [3+3]-cycloaddition reactions with both acyclic and cyclic nitrones. PMID:21932856

  20. Reaction cross sections of intermediate energy {alpha} particles within a relativistic optical model

    SciTech Connect

    Ait-Tahar, S.; Nedjadi, Y.

    1995-07-01

    The suggestion made recently by H. Abele {ital et} {ital al}. that relativistic effects in the interaction of alpha particles with various nuclei at intermediate energies may remove the existing discrepancy between the theoretical predictions and the experimental data for the reaction cross section is investigated. We use a relativistic model based on the Kemmer-Duffin-Petiau equation and find that relativistic effects do not lead to a reduction in the reaction cross section within the present approach. Alternative explanations are discussed.

  1. Structure of hemiaminal intermediate of the reaction of diethylamine with cyclobutanone

    NASA Astrophysics Data System (ADS)

    Yufit, Dmitry S.; Howard, Judith A. K.

    2010-12-01

    The intermediate of the reaction between cyclobutanone and diethylamine has been crystallized in situ in form of co-crystal with diethylamine and its structure has been determined by X-ray crystallography. The study made possible to have an insight in the mechanism of the reaction and reveals the potential of in situ cryo-crystallization technique as an additional tool for studying the mechanisms of chemical reactions. The related structure of co-crystal of diethylamine with adipic acid, which is a product of cyclohexanone oxidative cleavage, is also reported.

  2. Controlling the ambiphilic nature of σ-arylpalladium intermediates in intramolecular cyclization reactions.

    PubMed

    Solé, Daniel; Fernández, Israel

    2014-01-21

    The reactivity of main group organometallics, such as organolithium compounds (RLi) and Grignard reagents (RMgX), is quite straightforward. In these species the R group usually exhibits nucleophilic reactivity without any possibility of inducing electrophilic character. In contrast, in organopalladium complexes, researchers can switch the reactivity from electrophilic to nucleophilic relatively simply. Although σ-aryl and σ-vinylpalladium complexes are commonly used as electrophiles in C-C bond-forming reactions, recent research has demonstrated that they can also react with carbon-heteroatom multiple bonds in a nucleophilic manner. Nevertheless, researchers have completely ignored the issue of controlling the ambiphilic nature of such species. This Account describes our efforts toward selectively promoting the same starting materials toward either electrophilic α-arylation or nucleophilic addition reactions to different carbonyl groups. We could tune the properties of the σ-arylpalladium intermediates derived from amino-tethered aryl halides and carbonyl compounds to achieve chemoselective transformations. Therefore, chemists can control the ambiphilic nature of such intermediates and, consequently, the competition between the alternative reaction pathways by the adequate selection of the reaction conditions and additives (base, presence/absence of phenol, bidentate phosphines). The nature of the carbonyl group (aldehydes, ketones, esters, and amides) and the length of the tether connecting it to the aniline moiety also play an important role in the outcome of these processes. Our joint computational and experimental efforts to elucidate the reaction mechanism of these palladium-catalyzed transformations suggest that beyond the formation of the four-membered azapalladacycle, two major factors help to control the dual character of the palladium(II) intermediates derived from 2-haloanilines. First, their high nucleophilicity strongly modifies the interaction of

  3. 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.

  4. The role of phosphate in a multistep enzymatic reaction: reactions of the substrate and intermediate in pieces.

    PubMed

    Kholodar, Svetlana A; Allen, C Leigh; Gulick, Andrew M; Murkin, Andrew S

    2015-02-25

    Several mechanistically unrelated enzymes utilize the binding energy of their substrate's nonreacting phosphoryl group to accelerate catalysis. Evidence for the involvement of the phosphodianion in transition state formation has come from reactions of the substrate in pieces, in which reaction of a truncated substrate lacking its phosphorylmethyl group is activated by inorganic phosphite. What has remained unknown until now is how the phosphodianion group influences the reaction energetics at different points along the reaction coordinate. 1-Deoxy-D-xylulose-5-phosphate (DXP) reductoisomerase (DXR), which catalyzes the isomerization of DXP to 2-C-methyl-D-erythrose 4-phosphate (MEsP) and subsequent NADPH-dependent reduction, presents a unique opportunity to address this concern. Previously, we have reported the effect of covalently linked phosphate on the energetics of DXP turnover. Through the use of chemically synthesized MEsP and its phosphate-truncated analogue, 2-C-methyl-D-glyceraldehyde, the current study revealed a loss of 6.1 kcal/mol of kinetic barrier stabilization upon truncation, of which 4.4 kcal/mol was regained in the presence of phosphite dianion. The activating effect of phosphite was accompanied by apparent tightening of its interactions within the active site at the intermediate stage of the reaction, suggesting a role of the phosphodianion in disfavoring intermediate release and in modulation of the on-enzyme isomerization equilibrium. The results of kinetic isotope effect and structural studies indicate rate limitation by physical steps when the covalent linkage is severed. These striking differences in the energetics of the natural reaction and the reactions in pieces provide a deeper insight into the contribution of enzyme-phosphodianion interactions to the reaction coordinate.

  5. Insights into the Mechanism of Type I Dehydroquinate Dehydratases from Structures of Reaction Intermediates

    SciTech Connect

    Light, Samuel H.; Minasov, George; Shuvalova, Ludmilla; Duban, Mark-Eugene; Caffrey, Michael; Anderson, Wayne F.; Lavie, Arnon

    2012-02-27

    The biosynthetic shikimate pathway consists of seven enzymes that catalyze sequential reactions to generate chorismate, a critical branch point in the synthesis of the aromatic amino acids. The third enzyme in the pathway, dehydroquinate dehydratase (DHQD), catalyzes the dehydration of 3-dehydroquinate to 3-dehydroshikimate. We present three crystal structures of the type I DHQD from the intestinal pathogens Clostridium difficile and Salmonella enterica. Structures of the enzyme with substrate and covalent pre- and post-dehydration reaction intermediates provide snapshots of successive steps along the type I DHQD-catalyzed reaction coordinate. These structures reveal that the position of the substrate within the active site does not appreciably change upon Schiff base formation. The intermediate state structures reveal a reaction state-dependent behavior of His-143 in which the residue adopts a conformation proximal to the site of catalytic dehydration only when the leaving group is present. We speculate that His-143 is likely to assume differing catalytic roles in each of its observed conformations. One conformation of His-143 positions the residue for the formation/hydrolysis of the covalent Schiff base intermediates, whereas the other conformation positions the residue for a role in the catalytic dehydration event. The fact that the shikimate pathway is absent from humans makes the enzymes of the pathway potential targets for the development of non-toxic antimicrobials. The structures and mechanistic insight presented here may inform the design of type I DHQD enzyme inhibitors.

  6. A kinetic study of the CH2OO Criegee intermediate self-reaction, reaction with SO2 and unimolecular reaction using cavity ring-down spectroscopy.

    PubMed

    Chhantyal-Pun, Rabi; Davey, Anthony; Shallcross, Dudley E; Percival, Carl J; Orr-Ewing, Andrew J

    2015-02-07

    Criegee intermediates are important species formed during the ozonolysis of alkenes. Reaction of stabilized Criegee intermediates with various species like SO2 and NO2 may contribute significantly to tropospheric chemistry. In the laboratory, self-reaction can be an important loss pathway for Criegee intermediates and thus needs to be characterized to obtain accurate bimolecular reaction rate coefficients. Cavity ring-down spectroscopy was used to perform kinetic measurements for various reactions of CH2OO at 293 K and under low pressure (7 to 30 Torr) conditions. For the reaction CH2OO + CH2OO (8), a rate coefficient k8 = (7.35 ± 0.63) × 10(-11) cm(3) molecule(-1) s(-1) was derived from the measured CH2OO decay rates, using an absorption cross section value reported previously. A rate coefficient of k4 = (3.80 ± 0.04) × 10(-11) cm(3) molecule(-1) s(-1) was obtained for the CH2OO + SO2 (4) reaction. An upper limit for the unimolecular CH2OO loss rate coefficient of 11.6 ± 8.0 s(-1) was deduced from studies of reaction (4). SO2 catalysed CH2OO isomerization or intersystem crossing is proposed to occur with a rate coefficient of (3.53 ± 0.32) × 10(-11) cm(3) molecule(-1) s(-1).

  7. Oxidation reactions performed by soluble methane monooxygenase hydroxylase intermediates H(peroxo) and Q proceed by distinct mechanisms.

    PubMed

    Tinberg, Christine E; Lippard, Stephen J

    2010-09-14

    Soluble methane monooxygenase is a bacterial enzyme that converts methane to methanol at a carboxylate-bridged diiron center with exquisite control. Because the oxidizing power required for this transformation is demanding, it is not surprising that the enzyme is also capable of hydroxylating and epoxidizing a broad range of hydrocarbon substrates in addition to methane. In this work we took advantage of this promiscuity of the enzyme to gain insight into the mechanisms of action of H(peroxo) and Q, two oxidants that are generated sequentially during the reaction of reduced protein with O(2). Using double-mixing stopped-flow spectroscopy, we investigated the reactions of the two intermediate species with a panel of substrates of varying C-H bond strength. Three classes of substrates were identified according to the rate-determining step in the reaction. We show for the first time that an inverse trend exists between the rate constant of reaction with H(peroxo) and the C-H bond strength of the hydrocarbon examined for those substrates in which C-H bond activation is rate-determining. Deuterium kinetic isotope effects revealed that reactions performed by Q, but probably not H(peroxo), involve extensive quantum mechanical tunneling. This difference sheds light on the observation that H(peroxo) is not a sufficiently potent oxidant to hydroxylate methane, whereas Q can perform this reaction in a facile manner. In addition, the reaction of H(peroxo) with acetonitrile appears to proceed by a distinct mechanism in which a cyanomethide anionic intermediate is generated, bolstering the argument that H(peroxo) is an electrophilic oxidant that operates via two-electron transfer chemistry.

  8. Reactions of acetone oxide stabilized Criegee intermediate with SO2, NO2, H2O and O3

    NASA Astrophysics Data System (ADS)

    Kukui, Alexandre; Chen, Hui; Xiao, Shan; Mellouki, Wahid; Daële, Veronique

    2015-04-01

    Atmospheric aerosol particles represent a critical component of the atmosphere, impacting global climate, regional air pollution, and human health. The formation of new atmospheric particles and their subsequent growth to larger sizes are the key processes for understanding of the aerosol effects. Sulphuric acid, H2SO4, has been identified to play the major role in formation of new atmospheric particles and in subsequent particle growth. Until recently the reaction of OH with SO2 has been considered as the only important source of H2SO4 in the atmosphere. However, recently it has been suggested that the oxidation of SO2 by Criegee biradicals can be a significant additional atmospheric source of H2SO4 comparable with the reaction of SO2 with OH. Here we present some results about the reactions of the acetone oxide stabilized Criegee intermediate, (CH3)2=OO, produced in the reaction of 2,3-dimethyl-butene (TME) with O3. The formation of the H2SO4 in the reaction of acetone oxide with SO2 was investigated in the specially constructed atmospheric pressure laminar flow reactor. The Criegee intermediate was generated by ozonolysis of TME. The H2SO4, generated by addition of SO2, was directly monitored with Chemical Ionization Mass Spectrometer (SAMU, LPC2E). Relative rates of reactions of acetone oxide with SO2, NO2, H2O and ozone were determined from the dependencies of the H2SO4 yield at different concentrations of the reactants. Atmospheric applications of the obtained results are discussed in relation to the importance of this additional H2SO4 formation pathway compared to the reaction of OH with SO2.

  9. 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.

  10. Multifragment azimuthal correlation functions: Probes for reaction dynamics in collisions of intermediate energy heavy ions

    SciTech Connect

    Lacey, R.A.; Elmaani, A.; Lauret, J.; Li, T.; Bauer, W.; Craig, D.; Cronqvist, M.; Gualtieri, E.; Hannuschke, S.; Reposeur, T.; Vander Molen, A.; Westfall, G.D.; Wilson, W.K.; Winfield, J.S.; Yee, J.; Yennello, S.; Nadasen, A.; Tickle, R.S.; Norbeck, E. National Superconducting Cyclotron Laboratory Department of Physics, Michigan State University, East Lansing, Michigan 48824-1321 Department of Physics, University of Michigan at Dearborn, Dearborn, Michigan 48128 Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1120 Department of Physics, University of Iowa, Iowa City, Iowa 52242 )

    1993-03-01

    Multifragment azimuthal correlation functions have been measured as a function of beam energy and impact parameter for the Ar+Sc system ([ital E]/[ital A]=35 to 115 MeV). The observed azimuthal correlation functions---which do not require corrections for dispersion of the reaction plane---exhibit strong asymmetries which are dependent on impact parameter and beam energy. Rotational collective motion and flow seem to dominate the correlation functions at low beam energies. It is proposed that multifragment azimuthal correlation functions can provide a useful probe for intermediate energy heavy ion reaction dynamics.

  11. Transient Absorption Spectroscopy of C1 and C2 Criegee Intermediates: UV Spectrum and Reaction Kinetics

    NASA Astrophysics Data System (ADS)

    Smith, M. C.; Chao, W.; Ting, A.; Chang, C. H.; Lin, L. C.; Takahashi, K.; Boering, K. A.; Lin, J. J. M.

    2015-12-01

    Atmospheric production and removal rates of Criegee intermediates produced in alkene ozonolysis must be understood to constrain the importance of these species in VOC oxidation and other processes. To estimate these rates, reliable detection methods and laboratory measurements of the UV absorption spectra and reaction kinetics of Criegee intermediates are needed. Here, transient absorption spectroscopy was used to directly measure the UV spectrum of the C2 Criegee intermediate CH3CHOO in a flow reactor at 295 K. The UV spectrum was scaled to the absolute absorption cross section at 308 nm determined by laser depletion measurements in a molecular beam, resulting in a peak UV cross section of (1.27±0.11) × 10-17 cm2 molecule-1 at 328 nm. This spectrum represents the absorption of the syn and anti conformers of CH3CHOO under near-atmospheric conditions, both of which contribute to CH3CHOO atmospheric removal due to UV photolysis. Transient UV absorption was also used to measure the kinetics of the reaction of the C1 Criegee intermediate CH2OO with water vapor at temperatures from 283 to 324 K. The observed CH2OO decay is quadratic with respect to the H2O concentration, indicating that reaction with water dimer is the primary process affecting CH2OO loss. The rate coefficient for the reaction of CH2OO with water dimer exhibits a strong negative temperature dependence with an Arrhenius activation energy of -8.1±0.6 kcal mol-1. The temperature dependence increases the effective loss rate for CH2OO (relative to 298 K) by a factor of ˜2.5 at 278 K and 70% relative humidity, and decreases the loss rate by a factor of ˜2 at 313 K and 30% humidity, which demonstrates that variations in reaction rate due to temperature differences should be included in estimates of Criegee intermediate removal via reactions with water dimer in the atmosphere.

  12. Random sampling of the Green's Functions for reversible reactions with an intermediate state

    NASA Astrophysics Data System (ADS)

    Plante, Ianik; Devroye, Luc; Cucinotta, Francis A.

    2013-06-01

    Exact random variate generators were developed to sample Green's functions used in Brownian Dynamics (BD) algorithms for the simulations of chemical systems. These algorithms, which use less than a kilobyte of memory, provide a useful alternative to the table look-up method that has been used in similar work. The cases that are studied with this approach are (1) diffusion-influenced reactions; (2) reversible diffusion-influenced reactions and (3) reactions with an intermediate state such as enzymatic catalysis. The results are validated by comparison with those obtained by the Independent Reaction Times (IRT) method. This work is part of our effort in developing models to understand the role of radiation chemistry in the radiation effects on human body and may eventually be included in event-based models of space radiation risk.

  13. Random sampling of the Green’s Functions for reversible reactions with an intermediate state

    SciTech Connect

    Plante, Ianik; Devroye, Luc; Cucinotta, Francis A.

    2013-06-01

    Exact random variate generators were developed to sample Green’s functions used in Brownian Dynamics (BD) algorithms for the simulations of chemical systems. These algorithms, which use less than a kilobyte of memory, provide a useful alternative to the table look-up method that has been used in similar work. The cases that are studied with this approach are (1) diffusion-influenced reactions; (2) reversible diffusion-influenced reactions and (3) reactions with an intermediate state such as enzymatic catalysis. The results are validated by comparison with those obtained by the Independent Reaction Times (IRT) method. This work is part of our effort in developing models to understand the role of radiation chemistry in the radiation effects on human body and may eventually be included in event-based models of space radiation risk.

  14. LC/MS/MS structure elucidation of reaction intermediates formed during the TiO2 photocatalysis of microcystin-LR

    EPA Science Inventory

    Microcystin-LR (MC-LR), a cyanotoxin and emerging drinking water contaminant, was treated with TiO(2) photocatalysts immobilized on stainless steel plates as an alternative to nanoparticles in slurry. The reaction intermediates of MC-LR were identified with mass spectrometry (MS)...

  15. A Computational Re-examination of the Criegee Intermediate-Sulfur Dioxide Reaction.

    PubMed

    Kuwata, Keith T; Guinn, Emily J; Hermes, Matthew R; Fernandez, Jenna A; Mathison, Jon M; Huang, Ke

    2015-10-15

    The atmospheric oxidation of sulfur dioxide by the parent and dimethyl Criegee intermediates (CIs) may be an important source of sulfuric acid aerosol, which has a large impact on radiative forcing and therefore upon climate. A number of computational studies have considered how the CH2OOS(O)O heteroozonide (HOZ) adduct formed in the CI + SO2 reaction converts SO2 to SO3. In this work we use the CBS-QB3 quantum chemical method along with equation-of-motion spin-flip CCSD(dT) and MCG3 theories to reveal new details regarding the formation and decomposition of the endo and exo conformers of the HOZ. Although ∼75% of the parent CI + SO2 reaction is initiated by formation of the exo HOZ, hyperconjugation preferentially stabilizes many of the endo intermediates and transition structures by 1-5 kcal mol(-1). Our quantum chemical calculations, in conjunction with statistical rate theory models, predict a rate coefficient for the parent CI + SO2 reaction of 3.68 × 10(-11) cm(3) molecule(-1) s(-1), in good agreement with recent experimental measurements. RRKM/master equation simulations based on our quantum chemical data predict a prompt carbonyl + SO3 yield of >95% for the reaction of both the parent and dimethyl CI with SO2. The existence of concerted cycloreversion transition structures 10-15 kcal mol(-1) higher in energy than the HOZ accounts for most of the predicted SO3 formation.

  16. Structural Analysis of Substrate, Reaction Intermediate, and Product Binding in Haemophilus influenzae Biotin Carboxylase.

    PubMed

    Broussard, Tyler C; Pakhomova, Svetlana; Neau, David B; Bonnot, Ross; Waldrop, Grover L

    2015-06-23

    Acetyl-CoA carboxylase catalyzes the first and regulated step in fatty acid synthesis. In most Gram-negative and Gram-positive bacteria, the enzyme is composed of three proteins: biotin carboxylase, a biotin carboxyl carrier protein (BCCP), and carboxyltransferase. The reaction mechanism involves two half-reactions with biotin carboxylase catalyzing the ATP-dependent carboxylation of biotin-BCCP in the first reaction. In the second reaction, carboxyltransferase catalyzes the transfer of the carboxyl group from biotin-BCCP to acetyl-CoA to form malonyl-CoA. In this report, high-resolution crystal structures of biotin carboxylase from Haemophilus influenzae were determined with bicarbonate, the ATP analogue AMPPCP; the carboxyphosphate intermediate analogues, phosphonoacetamide and phosphonoformate; the products ADP and phosphate; and the carboxybiotin analogue N1'-methoxycarbonyl biotin methyl ester. The structures have a common theme in that bicarbonate, phosphate, and the methyl ester of the carboxyl group of N1'-methoxycarbonyl biotin methyl ester all bound in the same pocket in the active site of biotin carboxylase and as such utilize the same set of amino acids for binding. This finding suggests a catalytic mechanism for biotin carboxylase in which the binding pocket that binds tetrahedral phosphate also accommodates and stabilizes a tetrahedral dianionic transition state resulting from direct transfer of CO₂ from the carboxyphosphate intermediate to biotin.

  17. Investigation of the dp Breakup and dp Elastic Reactions at Intermediate Energies at Nuclotron

    NASA Astrophysics Data System (ADS)

    Janek, Marian; Ladygin, Vladimir P.; Piyadin, Semen M.; Batyuk, Pavel N.; Gurchin, Yuri V.; Isupov, Alexander Yu.; Karachuk, Julia-Tatiana; Kurilkin, Alexei K.; Kurilkin, Pavel K.; Livanov, Alexei N.; Martinska, Gabriela; Merts, Sergei P.; Reznikov, Sergei G.; Tarjanyiova, Gabriela; Terekhin, Arkadyi A.; Vnukov, Igor E.

    2017-03-01

    The main goal of the deuteron spin structure project is to investigate the spin structure of nucleon-nucleon and three nucleon short-range correlations via the measurements of the polarization observables in the deuteron induced reactions at intermediate energies at Nuclotron (Dubna, Russia). In this framework, dp nonmesonic breakup and dp elastic reactions are investigated using internal target station. The dp breakup data are obtained with the detection of two outgoing protons at the angles of 19°-54° in lab. frame at the deuteron energies of 300-500 MeV. The data of dp elastic scattering for the deuteron energies up to 2000 MeV are obtained in angular range 70°-120° in cm. The further perspectives of the investigations using polarized deuteron beam as well as the studies of the {}^3{He}(d,p){}^4{He} reaction are discussed.

  18. Identifying Understudied Nuclear Reactions by Text-mining the EXFOR Experimental Nuclear Reaction Library

    NASA Astrophysics Data System (ADS)

    Hirdt, J. A.; Brown, D. A.

    2016-01-01

    The EXFOR library contains the largest collection of experimental nuclear reaction data available as well as the data's bibliographic information and experimental details. We text-mined the REACTION and MONITOR fields of the ENTRYs in the EXFOR library in order to identify understudied reactions and quantities. Using the results of the text-mining, we created an undirected graph from the EXFOR datasets with each graph node representing a single reaction and quantity and graph links representing the various types of connections between these reactions and quantities. This graph is an abstract representation of the connections in EXFOR, similar to graphs of social networks, authorship networks, etc. We use various graph theoretical tools to identify important yet understudied reactions and quantities in EXFOR. Although we identified a few cross sections relevant for shielding applications and isotope production, mostly we identified charged particle fluence monitor cross sections. As a side effect of this work, we learn that our abstract graph is typical of other real-world graphs.

  19. Identifying Understudied Nuclear Reactions by Text-mining the EXFOR Experimental Nuclear Reaction Library

    SciTech Connect

    Hirdt, J.A.; Brown, D.A.

    2016-01-15

    The EXFOR library contains the largest collection of experimental nuclear reaction data available as well as the data's bibliographic information and experimental details. We text-mined the REACTION and MONITOR fields of the ENTRYs in the EXFOR library in order to identify understudied reactions and quantities. Using the results of the text-mining, we created an undirected graph from the EXFOR datasets with each graph node representing a single reaction and quantity and graph links representing the various types of connections between these reactions and quantities. This graph is an abstract representation of the connections in EXFOR, similar to graphs of social networks, authorship networks, etc. We use various graph theoretical tools to identify important yet understudied reactions and quantities in EXFOR. Although we identified a few cross sections relevant for shielding applications and isotope production, mostly we identified charged particle fluence monitor cross sections. As a side effect of this work, we learn that our abstract graph is typical of other real-world graphs.

  20. Criegee intermediate reaction with CO: mechanism, barriers, conformer-dependence, and implications for ozonolysis chemistry.

    PubMed

    Kumar, Manoj; Busch, Daryle H; Subramaniam, Bala; Thompson, Ward H

    2014-03-13

    Density functional theory and transition state theory rate constant calculations have been performed to gain insight into the bimolecular reaction of the Criegee intermediate (CI) with carbon monoxide (CO) that is proposed to be important in both atmospheric and industrial chemistry. A new mechanism is suggested in which the CI acts as an oxidant by transferring an oxygen atom to the CO, resulting in the formation of a carbonyl compound (aldehyde or ketone depending upon the CI) and carbon dioxide. Fourteen different CIs, including ones resulting from biogenic ozonolysis, are considered. Consistent with previous reports for other CI bimolecular reactions, the anti conformers are found to react faster than the syn conformers. However, this can be attributed to steric effects and not hyperconjugation as generally invoked. The oxidation reaction is slow, with barrier heights between 6.3 and 14.7 kcal/mol and estimated reaction rate constants 6-12 orders-of-magnitude smaller than previously reported literature estimates. The reaction is thus expected to be unimportant in the context of tropospheric oxidation chemistry. However, the reaction mechanism suggests that CO could be exploited in ozonolysis to selectively obtain industrially important carbonyl compounds.

  1. Palladacycles: Effective Catalysts for a Multicomponent Reaction with Allylpalladium(II)-Intermediates

    PubMed Central

    Shiota, Atsushi; Malinakova, Helena C.

    2012-01-01

    Palladium(II) complexes with an auxiliary bidentate ligand featuring one C-Pd bond and a Pd-N-donor bond (palladacycles) have been shown to afford improved yields of homoallylic amines from a three-component coupling of boronic acids, allenes and imines in comparison to the yields of homoallylic amines achieved with the originally reported catalyst (Pd(OAc)2/P(t-Bu)3), thus extending the scope of the reaction. 31P NMR monitoring studies indicate that distinct intermediates featuring Pd-P bonds originate in the reactions catalyzed by either Pd(OAc)2/P(t-Bu)3 or the pallada(II)cycle/P(t-Bu)3 systems, suggesting that the role of the pallada(II)cycles is more complex than just precatalysts. The importance of an additional phosphine ligand in the reactions catalyzed the pallada(II)cycles was established, and its role in the catalytic cycle has been proposed. Insights into the nature of the reactive intermediates that limit the performance of the originally reported catalytic systems has been gained. PMID:24371362

  2. Direct kinetic measurements of reactions between the simplest Criegee intermediate CH2OO and alkenes.

    PubMed

    Buras, Zachary J; Elsamra, Rehab M I; Jalan, Amrit; Middaugh, Joshua E; Green, William H

    2014-03-20

    The simplest Criegee Intermediate (CH2OO), a well-known biradical formed in alkene ozonolysis, is known to add across double bonds. Here we report direct experimental rate measurements of the simplest Criegee Intermediate reacting with C2–C4 alkenes obtained using the laser flash photolysis technique probing the recently measured B(1)A′ ← X(1)A′ transition in CH2OO. The measured activation energy (298–494 K) for CH2OO + alkenes is Ea ≈ 3500 ± 1000 J mol(–1) for all alkyl substituted alkenes and Ea = 7000 ± 900 J mol(–1) for ethene. The measured Arrhenius pre-exponential factors (A) vary between (2 ± 1) × 10(–15) and (11 ± 3) × 10(–15) cm(3) molecule(–1) s(–1). Quantum chemical calculations of the corresponding rate coefficients reproduce qualitative reactivity trends but overestimate the absolute rate coefficients. Despite the small Ea's, the CH2OO + alkene rate coefficients are almost 2 orders of magnitude smaller than those of similar reactions between CH2OO and carbonyl compounds. Using the rate constants measured here, we estimate that, under typical atmospheric conditions, reaction with alkenes does not represent a significant sink of CH2OO. In environments rich in C═C double bonds, however, such as ozone-exposed rubber or emission plumes, these reactions can play a significant role.

  3. Near-threshold absolute photoionization cross-sections of some reaction intermediates in combustion

    NASA Astrophysics Data System (ADS)

    Wang, Juan; Yang, Bin; Cool, Terrill A.; Hansen, Nils; Kasper, Tina

    2008-02-01

    The use of photoionization mass spectrometry for the development of quantitative kinetic models for the complex combustion chemistry of both conventional hydrocarbon fuels and oxygenated biofuels requires near-threshold measurements of absolute photoionization cross-sections for numerous reaction intermediates. Near-threshold absolute cross-sections for molecular and dissociative photoionization for 20 stable reaction intermediates (methane, ethane, propane, n-butane, cyclopropane, methylcyclopentane, 1-butene, cis-2-butene, isobutene, 1-pentene, cyclohexene, 3,3-dimethyl-1-butene, 1,3-hexadiene, 1,3-cyclohexadiene, methyl acetate, ethyl acetate, tetrahydrofuran, propanal, 1-butyne, 2-butyne) are presented. Previously measured total photoionization cross-sections for 9 of these molecules are in good agreement with the present results. The measurements are performed with photoionization mass spectrometry (PIMS) using a monochromated VUV synchrotron light source with an energy resolution of 40 meV (fwhm) comparable to that used for flame-sampling molecular beam PIMS studies of flame chemistry and reaction kinetics.

  4. Use of intermediate partitioning to calculate intrinsic isotope effects for the reaction catalyzed by malic enzyme

    SciTech Connect

    Grissom, C.B.; Cleland, W.W.

    1985-02-12

    For those enzymes that proceed via a stepwise reaction mechanism with a discrete chemical intermediate and where deuterium and /sup 13/C isotope effects are on separate steps, a new method has been developed to solve for the intrinsic deuterium and /sup 13/C kinetic isotope effects that relies on directly observing the partitioning of the intermediate between the forward and reverse directions. This observed partitioning ratio, along with the values of the primary deuterium, tritium, and /sup 13/C kinetic isotope effects on V/K for the substrate with the label being followed, allows an exact solution for the intrinsic deuterium and /sup 13/C isotope effects, the forward commitment for the deuterium-sensitive step, and the partition ratio for the intermediate in the reaction. This method allows portions of the reaction coordinate diagram to be defined precisely and the relative energy levels of certain activation barriers to be assigned exactly. With chicken liver triphosphopyridine nucleotide (TPN) malic enzyme activated by Mg/sup 2 +/, the partitioning of oxalacetate to pyruvate vs. malate in the presence of TPNH, 0.47, plus previously determined isotope effects gives an intrinsic deuterium isotope effect of 5.7 on hydride transfer and a /sup 13/C isotope effect of 1.044 on decarboxylation. Reverse hydride transfer is 10 times faster than decarboxylation, and the forward commitment for hydride transfer is 3.3. The /sup 13/C isotope effect is not significantly different with reduced acetylpyridine adenine dinucleotide phosphate replacing TPNH (although the pyruvate/malate partitioning ratio for oxalactate is now 9.9), but replacement of Mg/sup 2 +/ by Mn/sup 2 +/ raises the value to 1.065 (partition ratio 0.99).

  5. Intermediate resonance excitation in the γp→pππ reaction

    NASA Astrophysics Data System (ADS)

    Gdh Collaboration; Ahrens, J.; Altieri, S.; Annand, J. R. M.; Anton, G.; Arends, H.-J.; Aulenbacher, K.; Beck, R.; Bradtke, C.; Braghieri, A.; Degrande, N.; D'Hose, N.; Dutz, H.; Goertz, S.; Grabmayr, P.; Hansen, K.; Harmsen, J.; von Harrach, D.; Hasegawa, S.; Hasegawa, T.; Heid, E.; Helbing, K.; Holvoet, H.; van Hoorebeke, L.; Horikawa, N.; Iwata, T.; Jahn, O.; Jennewein, P.; Kageya, T.; Kiel, B.; Klein, F.; Kondratiev, R.; Kossert, K.; Krimmer, J.; Lang, M.; Lannoy, B.; Leukel, R.; Lisin, V.; Matsuda, T.; McGeorge, J. C.; Meier, A.; Menze, D.; Meyer, W.; Michel, T.; Naumann, J.; Panzeri, A.; Pedroni, P.; Pinelli, T.; Preobrajenski, I.; Radtke, E.; Reichert, E.; Reicherz, G.; Rohlof, Ch.; Rosner, G.; Rostomyan, T.; Ryckbosch, D.; Sauer, M.; Schoch, B.; Schumacher, M.; Seitz, B.; Speckner, T.; Takabayashi, N.; Tamas, G.; Thomas, A.; van de Vyver, R.; Wakai, A.; Weihofen, W.; Wissmann, F.; Zapadtka, F.; Zeitler, G.

    2005-09-01

    The helicity dependence of the total cross section for the γ→p→→pππ reaction has been measured for the first time at incident photon energies from 400 to 800 MeV. The measurement, performed at the tagged photon beam facility of the MAMI accelerator in Mainz, used the large acceptance detector DAPHNE and a longitudinally polarized frozen-spin target. This channel is found to be excited predominantly when the photon and proton have a parallel spin orientation, most likely due to the intermediate production of the D(1520) resonance. However, the contribution of the antiparallel spin configuration, arising from other reaction mechanisms, is also not negligible. This result gives important new information to resolve the existing model discrepancies in the identification of the nucleon resonances contributing to this channel.

  6. Gold-Catalyzed Reactions via Cyclopropyl Gold Carbene-like Intermediates.

    PubMed

    Dorel, Ruth; Echavarren, Antonio M

    2015-08-07

    Cycloisomerizations of 1,n-enynes catalyzed by gold(I) proceed via electrophilic species with a highly distorted cyclopropyl gold(I) carbene-like structure, which can react with different nucleophiles to form a wide variety of products by attack at the cyclopropane or the carbene carbons. Particularly important are reactions in which the gold(I) carbene reacts with alkenes to form cyclopropanes either intra- or intermolecularly. In the absence of nucleophiles, 1,n-enynes lead to a variety of cycloisomerized products including those resulting from skeletal rearrangements. Reactions proceeding through cyclopropyl gold(I) carbene-like intermediates are ideally suited for the bioinspired synthesis of terpenoid natural products by the selective activation of the alkyne in highly functionalized enynes or polyenynes.

  7. Total reaction cross sections in CEM and MCNP6 at intermediate energies

    SciTech Connect

    Kerby, Leslie M.; Mashnik, Stepan G.

    2015-05-14

    Accurate total reaction cross section models are important to achieving reliable predictions from spallation and transport codes. The latest version of the Cascade Exciton Model (CEM) as incorporated in the code CEM03.03, and the Monte Carlo N-Particle transport code (MCNP6), both developed at Los Alamos National Laboratory (LANL), each use such cross sections. Having accurate total reaction cross section models in the intermediate energy region (50 MeV to 5 GeV) is very important for different applications, including analysis of space environments, use in medical physics, and accelerator design, to name just a few. The current inverse cross sections used in the preequilibrium and evaporation stages of CEM are based on the Dostrovsky et al. model, published in 1959. Better cross section models are now available. Implementing better cross section models in CEM and MCNP6 should yield improved predictions for particle spectra and total production cross sections, among other results.

  8. Gold-Catalyzed Reactions via Cyclopropyl Gold Carbene-like Intermediates

    PubMed Central

    2015-01-01

    Cycloisomerizations of 1,n-enynes catalyzed by gold(I) proceed via electrophilic species with a highly distorted cyclopropyl gold(I) carbene-like structure, which can react with different nucleophiles to form a wide variety of products by attack at the cyclopropane or the carbene carbons. Particularly important are reactions in which the gold(I) carbene reacts with alkenes to form cyclopropanes either intra- or intermolecularly. In the absence of nucleophiles, 1,n-enynes lead to a variety of cycloisomerized products including those resulting from skeletal rearrangements. Reactions proceeding through cyclopropyl gold(I) carbene-like intermediates are ideally suited for the bioinspired synthesis of terpenoid natural products by the selective activation of the alkyne in highly functionalized enynes or polyenynes. PMID:26061916

  9. Status of reactive non-heme metal-oxygen intermediates in chemical and enzymatic reactions.

    PubMed

    Ray, Kallol; Pfaff, Florian Felix; Wang, Bin; Nam, Wonwoo

    2014-10-08

    Selective functionalization of unactivated C-H bonds, water oxidation, and dioxygen reduction are extremely important reactions in the context of finding energy carriers and conversion processes that are alternatives to the current fossil-based oil for energy. A range of metalloenzymes achieve these challenging tasks in biology by using cheap and abundant transition metals, such as iron, copper, and manganese. High-valent metal-oxo and metal-dioxygen (superoxo, peroxo, and hydroperoxo) cores act as active intermediates in many of these processes. The generation of well-described model compounds can provide vital insights into the mechanisms of such enzymatic reactions. This perspective provides a focused rather than comprehensive review of the recent advances in the chemistry of biomimetic high-valent metal-oxo and metal-dioxygen complexes, which can be related to our understanding of the biological systems.

  10. Experimental investigation of dp → ppn reaction at intermediate energies at Nuclotron

    NASA Astrophysics Data System (ADS)

    Janek, M.; Ladygin, V. P.; Piyadin, S. M.; Gurchin, Yu. V.; Isupov, A. Yu.; Karachuk, J.-T.; Khrenov, A. N.; Kurilkin, A. K.; Kurilkin, P. K.; Livanov, A. N.; Martinska, G.; Reznikov, S. G.; Tarjanyiova, G.; Terekhin, A. A.; Vnukov, I. E.

    2016-11-01

    There are still discrepancies between theory and experimental data in the polarisation observables of dp → ppn reaction in the low and intermediate energies, despite of significant process in the development of theoretical models which include three and more nucleon forces and relativistic effects. The data of dp → ppn reaction have been accumulated at 300, 400 and 500 MeV in the Nuclotron (Dubna, Russia) and partially processed for some kinematic configurations including few in which possible relativistic effects can appear. Kinematic simulation in the framework of ROOT and GEANT4 package have been performed before data processing. Part of the preliminary results are obtained in the form of energy deposit correlations of the two arms working in coincidence and few in the form of kinematic S curve.

  11. Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy.

    PubMed

    Riss, Alexander; Paz, Alejandro Pérez; Wickenburg, Sebastian; Tsai, Hsin-Zon; De Oteyza, Dimas G; Bradley, Aaron J; Ugeda, Miguel M; Gorman, Patrick; Jung, Han Sae; Crommie, Michael F; Rubio, Angel; Fischer, Felix R

    2016-07-01

    Chemical transformations at the interface between solid/liquid or solid/gaseous phases of matter lie at the heart of key industrial-scale manufacturing processes. A comprehensive study of the molecular energetics and conformational dynamics that underlie these transformations is often limited to ensemble-averaging analytical techniques. Here we report the detailed investigation of a surface-catalysed cross-coupling and sequential cyclization cascade of 1,2-bis(2-ethynyl phenyl)ethyne on Ag(100). Using non-contact atomic force microscopy, we imaged the single-bond-resolved chemical structure of transient metastable intermediates. Theoretical simulations indicate that the kinetic stabilization of experimentally observable intermediates is determined not only by the potential-energy landscape, but also by selective energy dissipation to the substrate and entropic changes associated with key transformations along the reaction pathway. The microscopic insights gained here pave the way for the rational design and control of complex organic reactions at the surface of heterogeneous catalysts.

  12. Global assessment of molecularly identified Anisakis Dujardin, 1845 (Nematoda: Anisakidae) in their teleost intermediate hosts.

    PubMed

    Kuhn, Thomas; Hailer, Frank; Palm, Harry W; Klimpel, Sven

    2013-05-01

    Here, we present the ITS ribosomal DNA (rDNA) sequence data on 330 larvae of nematodes of the genus Anisakis Dujardin, 1845 collected from 26 different bony fish species from 21 sampling locations and different climatic zones. New host records are provided for Anisakis simplex (Rudolphi, 1809) sensu stricto (s.s.) and A. pegreffli Campana-Rouget et Biocca, 1955 from Anoplopoma fimbria (Pallas) (Santa Barbara, East Pacific), A. typica (Diesing, 1860) from Caesio cuning (Bloch), Lepturacanthus savala (Cuvier) and Katsuwonus pelamis (Linnaeus) (Indonesia, West Pacific), A. simplex s.s. from Cololabis saira (Brevoort) (Hawaii, Central Pacific), A. simplex C of Nascetti et al. (1986) from Sebastolobus alascanus Bean (Santa Barbara, East Pacific) and A. physeteris Baylis, 1923 from Synaphobranchus kaupii Johnson (Namibia, East Atlantic). Comparison with host records from 60 previous molecular studies of Anisakis species reveals the teleost host range so far recorded for the genus. Perciform (57 species) and gadiform (21) fishes were the most frequently infected orders, followed by pleuronectiforms (15) and scorpaeniforms (15). Most commonly infected fish families were Scombridae (12), Gadidae (10), Carangidae (8) and Clupeidae (7), with Merluccius merluccius (Linnaeus) alone harbouring eight Anisakis species. Different intermediate host compositions implicate differing life cycles for the so far molecularly identified Anisakis sibling species.

  13. Fast and Sequence-Specific Palladium-Mediated Cross-Coupling Reaction Identified from Phage Display

    PubMed Central

    2015-01-01

    Fast and specific bioorthogonal reactions are highly desirable because they provide efficient tracking of biomolecules that are present in low abundance and/or involved in fast dynamic process in living systems. Toward this end, classic strategy involves the optimization of substrate structures and reaction conditions in test tubes, testing their compatibility with biological systems, devising synthetic biology schemes to introduce the modified substrates into living cells or organisms, and finally validating the superior kinetics for enhanced capacity in tracking biomolecules in vivo—a lengthy process often mired by unexpected results. Here, we report a streamlined approach in which the “microenvironment” of a bioorthogonal chemical reporter is exploited directly in biological systems via phage-assisted interrogation of reactivity (PAIR) to optimize not only reaction kinetics but also specificity. Using the PAIR strategy, we identified a short alkyne-containing peptide sequence showing fast kinetics (k2 = 13 000 ± 2000 M–1 s–1) in a palladium-mediated cross-coupling reaction. Site-directed mutagenesis studies suggested that the residues surrounding the alkyne moiety facilitate the assembly of a key palladium–alkyne intermediate along the reaction pathway. When this peptide sequence was inserted into the extracellular domain of epidermal growth factor receptor (EGFR), this reactive sequence directed the specific labeling of EGFR in live mammalian cells. PMID:25025771

  14. Reaction of a copper(II)-nitrosyl complex with hydrogen peroxide: putative formation of a copper(I)-peroxynitrite intermediate.

    PubMed

    Kalita, Apurba; Kumar, Pankaj; Mondal, Biplab

    2012-05-14

    The reaction of a Cu(II)-nitrosyl complex (1) with hydrogen peroxide at -20 °C in acetonitrile results in the formation of the corresponding Cu(I)-peroxynitrite intermediate. The reduction of the Cu(II) center was monitored by UV-visible spectroscopic studies. Formation of the peroxynitrite intermediate has been confirmed by its characteristic phenol ring nitration reaction as well as isolation of corresponding Cu(I)-nitrate (2). On air oxidation, 2 resulted in the corresponding Cu(II)-nitrate (3). Thus, these results demonstrate a possible decomposition pathway for H(2)O(2) and NO through the formation of a peroxynitrite intermediate in biological systems.

  15. The Pressure Dependency of Stabilized Criegee Intermediate Yields of Selected Ozone-Alkene Reactions

    NASA Astrophysics Data System (ADS)

    Hakala, J. P.; Donahue, N. M.

    2014-12-01

    Stabilized Criegee Intermediates (SCI) play an important role as an oxidizing species in atmospheric reactions. The ozonolysis of alkenes in the atmosphere, i.e. the mechanism by which the SCIs are produced, is a major pathway to the formation of Secondary Organic Aerosols (SOA) in the atmosphere. Just how much SCIs contribute to the SOA formation is not well known and fundamental research in the kinetics of SCI formation need to be performed to shed light on this mystery. The alkene ozonolysis is highly exothermic reaction, so a third body is needed for stabilizing the SCI, thus making the SCI yield pressure dependent. We studied the production of SCIs at different pressures by studying their ability to oxidize sulfur dioxide in a pressure controlled flow reactor. We used a mixture of ultra-high purity nitrogen, oxygen, and a selective scavenger for hydroxyl radical (OH) as a carrier gas, and injected a mixture of nitrogen, sulfur dioxide and selected alkene to the center of the flow for ozonolysis to take place. With the OH radical scavenged, the SCI yield of the reaction was measured by measuring the amount of sulfuric acid formed in the reaction between SCI and sulfur dioxide with a Chemical Ionization Mass Spectrometer (CIMS). This work was supported by NASA/ROSES grant NNX12AE54G to CMU and Academy of Finland Center of Excellence project 1118615.

  16. Strong Negative Temperature Dependence of the Simplest Criegee Intermediate CH2OO Reaction with Water Dimer.

    PubMed

    Smith, Mica C; Chang, Chun-Hung; Chao, Wen; Lin, Liang-Chun; Takahashi, Kaito; Boering, Kristie A; Lin, Jim Jr-Min

    2015-07-16

    The kinetics of the reaction of CH2OO with water vapor was measured directly with UV absorption at temperatures from 283 to 324 K. The observed CH2OO decay rate is second order with respect to the H2O concentration, indicating water dimer participates in the reaction. The rate coefficient of the CH2OO reaction with water dimer can be described by an Arrhenius expression k(T) = A exp(-Ea/RT) with an activation energy of -8.1 ± 0.6 kcal mol(-1) and k(298 K) = (7.4 ± 0.6) × 10(-12) cm(3) s(-1). Theoretical calculations yield a large negative temperature dependence consistent with the experimental results. The temperature dependence increases the effective loss rate for CH2OO by a factor of ~2.5 at 278 K and decreases by a factor of ~2 at 313 K relative to 298 K, suggesting that temperature is important for determining the impact of Criegee intermediate reactions with water in the atmosphere.

  17. Chemically activated formation of organic acids in reactions of the Criegee intermediate with aldehydes and ketones.

    PubMed

    Jalan, Amrit; Allen, Joshua W; Green, William H

    2013-10-21

    Reactions of the Criegee intermediate (CI, ˙CH2OO˙) are important in atmospheric ozonolysis models. In this work, we compute the rates for reactions between ˙CH2OO˙ and HCHO, CH3CHO and CH3COCH3 leading to the formation of secondary ozonides (SOZ) and organic acids. Relative to infinitely separated reactants, the SOZ in all three cases is found to be 48-51 kcal mol(-1) lower in energy, formed via 1,3-cycloaddition of ˙CH2OO˙ across the C=O bond. The lowest energy pathway found for SOZ decomposition is intramolecular disproportionation of the singlet biradical intermediate formed from cleavage of the O-O bond to form hydroxyalkyl esters. These hydroxyalkyl esters undergo concerted decomposition providing a low energy pathway from SOZ to acids. Geometries and frequencies of all stationary points were obtained using the B3LYP/MG3S DFT model chemistry, and energies were refined using RCCSD(T)-F12a/cc-pVTZ-F12 single-point calculations. RRKM calculations were used to obtain microcanonical rate coefficients (k(E)) and the reservoir state method was used to obtain temperature and pressure dependent rate coefficients (k(T, P)) and product branching ratios. At atmospheric pressure, the yield of collisionally stabilized SOZ was found to increase in the order HCHO < CH3CHO < CH3COCH3 (the highest yield being 10(-4) times lower than the initial ˙CH2OO˙ concentration). At low pressures, chemically activated formation of organic acids (formic acid in the case of HCHO and CH3COCH3, formic and acetic acid in the case of CH3CHO) was found to be the major product channel in agreement with recent direct measurements. Collisional energy transfer parameters and the barrier heights for SOZ reactions were found to be the most sensitive parameters determining SOZ and organic acid yield.

  18. Chemically Activated Formation of Organic Acids in Reactions of the Criegee Intermediate with Aldehydes and Ketones

    SciTech Connect

    Jalan, Amrit; Allen, Joshua W.; Green, William H.

    2013-08-08

    Reactions of the Criegee intermediate (CI, .CH2OO.) are important in atmospheric ozonolysis models. In this work, we compute the rates for reactions between .CH2OO. and HCHO, CH3CHO and CH3COCH3 leading to the formation of secondary ozonides (SOZ) and organic acids. Relative to infinitely separated reactants, the SOZ in all three cases is found to be 48–51 kcal mol-1 lower in energy, formed via 1,3- cycloaddition of .CH2OO. across the CQO bond. The lowest energy pathway found for SOZ decomposition is intramolecular disproportionation of the singlet biradical intermediate formed from cleavage of the O–O bond to form hydroxyalkyl esters. These hydroxyalkyl esters undergo concerted decomposition providing a low energy pathway from SOZ to acids. Geometries and frequencies of all stationary points were obtained using the B3LYP/MG3S DFT model chemistry, and energies were refined using RCCSD(T)-F12a/cc-pVTZ-F12 single-point calculations. RRKM calculations were used to obtain microcanonical rate coefficients (k(E)) and the reservoir state method was used to obtain temperature and pressure dependent rate coefficients (k(T, P)) and product branching ratios. At atmospheric pressure, the yield of collisionally stabilized SOZ was found to increase in the order HCHO o CH3CHO o CH3COCH3 (the highest yield being 10-4 times lower than the initial .CH2OO. concentration). At low pressures, chemically activated formation of organic acids (formic acid in the case of HCHO and CH3COCH3, formic and acetic acid in the case of CH3CHO) was found to be the major product channel in agreement with recent direct measurements. Collisional energy transfer parameters and the barrier heights for SOZ reactions were found to be the most sensitive parameters determining SOZ and organic acid yield.

  19. Snapshot of a Reaction Intermediate: Analysis of Benzoylformate Decarboxylase in Complex with a Benzoylphosphonate Inhibitor

    SciTech Connect

    Brandt, Gabriel S.; Kneen, Malea M.; Chakraborty, Sumit; Baykal, Ahmet T.; Nemeria, Natalia; Yep, Alejandra; Ruby, David I.; Petsko, Gregory A.; Kenyon, George L.; McLeish, Michael J.; Jordan, Frank; Ringe, Dagmar

    2009-04-22

    Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate- (ThDP-) dependent enzyme acting on aromatic substrates. In addition to its metabolic role in the mandelate pathway, BFDC shows broad substrate specificity coupled with tight stereo control in the carbon-carbon bond-forming reverse reaction, making it a useful biocatalyst for the production of chiral-hydroxy ketones. The reaction of methyl benzoylphosphonate (MBP), an analogue of the natural substrate benzoylformate, with BFDC results in the formation of a stable analogue (C2{alpha}-phosphonomandelyl-ThDP) of the covalent ThDP-substrate adduct C2{alpha}-mandelyl-ThDP. Formation of the stable adduct is confirmed both by formation of a circular dichroism band characteristic of the 1',4'-iminopyrimidine tautomeric form of ThDP (commonly observed when ThDP forms tetrahedral complexes with its substrates) and by high-resolution mass spectrometry of the reaction mixture. In addition, the structure of BFDC with the MBP inhibitor was solved by X-ray crystallography to a spatial resolution of 1.37 {angstrom} (PDB ID 3FSJ). The electron density clearly shows formation of a tetrahedral adduct between the C2 atom of ThDP and the carbonyl carbon atom of the MBP. This adduct resembles the intermediate from the penultimate step of the carboligation reaction between benzaldehyde and acetaldehyde. The combination of real-time kinetic information via stopped-flow circular dichroism with steady-state data from equilibrium circular dichroism measurements and X-ray crystallography reveals details of the first step of the reaction catalyzed by BFDC. The MBP-ThDP adduct on BFDC is compared to the recently solved structure of the same adduct on benzaldehyde lyase, another ThDP-dependent enzyme capable of catalyzing aldehyde condensation with high stereospecificity.

  20. [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.

  1. X-ray absorption spectroscopy of lithium sulfur battery reaction intermediates

    NASA Astrophysics Data System (ADS)

    Wujcik, Kevin; Pascal, Tod; Prendergast, David; Balsara, Nitash

    2015-03-01

    Lithium sulfur batteries have a theoretical energy density nearly five times greater than current lithium ion battery standards, but questions still remain regarding the reaction pathways through which soluble lithium polysulfide (Li2Sx, ``x'' ranging from 2 to 8) reaction intermediates are formed. Complicating spectroelectrochemical approaches to elucidate redox pathways is the challenge of obtaining spectral standards for individual Li2Sx species. Lithium polysulfides cannot be isolated as individual component and exist only in solution as a distribution of different Li2Sx molecules formed via disproportionation reactions (e.g. 2Li2S4 goes to Li2S3 + Li2S5). X-ray absorption spectroscopy (XAS) at the sulfur K-edge has recently been employed as a technique to study Li-S chemistry. We have recently obtained XAS standards for individual Li2Sx species via first principles DFT simulations and the excited electron and core hole approach. Here, experimental sulfur K-edge XAS of Li2Sx species dissolved in poly(ethylene oxide) are compared to spectra obtained from analogous theoretical calculations. The impact that polysulfide solution concentration and the presence of other lithium salts (e.g. LiNO3) have on X-ray spectra of Li2Sx species is explored via experiment and theory.

  2. Workshop on hadron structure from photo-reactions at intermediate energies: Proceedings

    SciTech Connect

    Nathan, A.M.; Sandorfi, A.M.

    1992-10-01

    This report contains papers on the following topics: The proton compton effect: Recent measurements of the electric and magnetic polorizabilities of the proton; experiments on the electric polarizability of the neutron; chiral symmetry and nucleon polarizabilities; chiral model predictions for electromagnetic polarizabilities of the nucleon, a consumer report; the polarizabilities of bound nucleons; nucleon polarizability in free space and in nuclear matter; mechanisms of photon scattering on nucleons at intermediate energies; pion polarizabilities in chiral perturbation theory; pion polarizabilities and the shielding of {sigma}(700)-meson exchange in {gamma}{gamma}{yields}{pi}{pi} processes; pion and kaon polarizabilities in the quark confinement model; radiative pion photoproduction and pion polarizabilities; pion and sigma polarizabilities and radiative transitions; the quadrupole amplitude in the {gamma}{Nu}-{Delta} transition; pion photoproduction and the {gamma}{Nu}-{Delta} amplitudes; effective- lagrangians, Watson`s theorem, and the E2/M1 mixing ratio in the excitation of the delta resonance; new measurements of the p({rvec {gamma}}, {pi}{sup o}) reaction; multipole analyses and photo-decay couplings at intermediate energies; compton scattering off the proton; connections between compton scattering and pion photoproduction in the delta region; single-pion electroproduction and the transverse one-half and scalar helicity transition form factors; relativistic effects, QCD mixing angles, and {Nu} {yields} {Nu}{gamma} and {Delta} {yields} {gamma}{Nu} transition form factors; electroproduction studies of the {Nu} {yields} {Delta} transition at bates and CEBAF.

  3. Investigation of the O+allyl addition/elimination reaction pathways from the OCH2CHCH2 radical intermediate

    NASA Astrophysics Data System (ADS)

    Fitzpatrick, Benjamin L.; Lau, Kai-Chung; Butler, Laurie J.; Lee, Shih-Huang; Lin, Jim-Min, Jr.

    2008-08-01

    These experiments study the preparation of and product channels resulting from OCH2CHCH2, a key radical intermediate in the O+allyl bimolecular reaction. The data include velocity map imaging and molecular beam scattering results to probe the photolytic generation of the radical intermediate and the subsequent pathways by which the radicals access the energetically allowed product channels of the bimolecular reaction. The photodissociation of epichlorohydrin at 193.3 nm produces chlorine atoms and c-OCH2CHCH2 radicals; these undergo a facile ring opening to the OCH2CHCH2 radical intermediate. State-selective resonance-enhanced multiphoton ionization (REMPI) detection resolves the velocity distributions of ground and spin-orbit excited state chlorine independently, allowing for a more accurate determination of the internal energy distribution of the nascent radicals. We obtain good agreement detecting the velocity distributions of the Cl atoms with REMPI, vacuum ultraviolet (VUV) photoionization at 13.8 eV, and electron bombardment ionization; all show a bimodal distribution of recoil kinetic energies. The dominant high recoil kinetic energy feature peaks near 33 kcal/mol. To elucidate the product channels resulting from the OCH2CHCH2 radical intermediate, the crossed laser-molecular beam experiment uses VUV photoionization and detects the velocity distribution of the possible products. The data identify the three dominant product channels as C3H4O (acrolein)+H, C2H4+HCO (formyl radical), and H2CO (formaldehyde)+C2H3. A small signal from C2H2O (ketene) product is also detected. The measured velocity distributions and relative signal intensities at m/e=27, 28, and 29 at two photoionization energies show that the most exothermic product channel, C2H5+CO, does not contribute significantly to the product branching. The higher internal energy onset of the acrolein+H product channel is consistent with the relative barriers en route to each of these product channels

  4. Photodegradation of 2-chloropyridine in aqueous solution: Reaction pathways and genotoxicity of intermediate products.

    PubMed

    Skoutelis, Charalambos; Antonopoulou, Maria; Konstantinou, Ioannis; Vlastos, Dimitris; Papadaki, Maria

    2017-01-05

    2-Chloropyridine, an important precursor of the chemical industry is also a persistent water pollutant. The genotoxicity of photolytically treated 2-chloropyridine aqueous solution to human lymphocytes initially increases and fluctuates during treatment finally reaching the control values after prolonged treatment. Intermediate products formed were identified; a kinetic scheme for their formation is presented. To identify the source of genotoxicity variations and the potential in vitro effects on human lymphocytes of the partially photo-treated aqueous solution, the genotoxicity of four (the only) commercially available intermediates, i.e., 1H-pyrrole-2-carboxaldehyde, 6-chloro-2-pyridinecarboxylic acid, 2,3-dichloropyridine and 2-pyridinecarbonitrile was measured; the obtained results were used for the reasoning on the variation of the solution genotoxic (including clastogenic as well as aneugenic) events and cytotoxic activity. It was found that 1H-pyrrole-2-carboxaldehyde and 6-chloro-2-pyridinecarboxylic acid were highly genotoxic even at the very low concentration measured here. Thus, they likely had a significant contribution to the photolytically treated solution genotoxicity. 2,3-Dichloropyridine was found to be genotoxic but only at concentrations higher than the ones measured in this work. Thus, it was not likely to have contributed to the solution genotoxicity. Finally, at the concentrations measured in this work 2-pyridinecarbonitrile was found to be only cytotoxic.

  5. Reaction of stabilized Criegee intermediates from ozonolysis of limonene with sulfur dioxide: ab initio and DFT study.

    PubMed

    Jiang, Lei; Xu, Yi-sheng; Ding, Ai-zhong

    2010-12-02

    The mechanism of the reaction of the sulfur dioxide (SO(2)) with four stabilized Criegee intermediates (stabCI-CH(3)-OO, stabCI-OO, stabCIx-OO, and stabCH(2)OO) produced via the ozonolysis of limonene have been investigated using ab initio and DFT (density functional theory) methods. It has been shown that the intermediate adduct formed by the initiation of these reactions may be followed by two different reaction pathways such as H migration reaction to form carboxylic acids and rearrangement of oxygen to produce the sulfur trioxide (SO(3)) from the terminal oxygen of the COO group and SO(2). We found that the reaction of stabCI-OO and stabCH(2)OO with SO(2) can occur via both the aforementioned scenarios, whereas that of stabCI-CH(3)-OO and stabCIx-OO with SO(2) is limited to the second pathway only due to the absence of migrating H atoms. It has been shown that at the CCSD(T)/6-31G(d) + CF level of theory the activation energies of six reaction pathways are in the range of 14.18-22.59 kcal mol(-1), with the reaction between stabCIx-OO and SO(2) as the most favorable pathway of 14.18 kcal mol(-1) activation energy and that the reaction of stabCI-OO and stabCH(2)OO with SO(2) occurs mainly via the second reaction path. The thermochemical analysis of the reaction between SO(2) and stabilized Criegee intermediates indicates that the reaction of SO(2) and stabilized Criegee intermediates formed from the exocyclic primary ozonide decomposition is the main pathway of the SO(3) formation. This is likely to explain the large (~100%) difference in the production rate in the favor of the exocyclic compounds observed in recent experiments on the formation of H(2)SO(4) from exocyclic and endocyclic compounds.

  6. Direct Determination of the Simplest Criegee Intermediate (CH2OO) Self Reaction Rate.

    PubMed

    Buras, Zachary J; Elsamra, Rehab M I; Green, William H

    2014-07-03

    The rate of self-reaction of the simplest Criegee intermediate, CH2OO, is of importance in many current laboratory experiments where CH2OO concentrations are high, such as flash photolysis and alkene ozonolysis. Using laser flash photolysis while simultaneously probing both CH2OO and I atom by direct absorption, we can accurately determine absolute CH2OO concentrations as well as the UV absorption cross section of CH2OO at our probe wavelength (λ = 375 nm), which is in agreement with a recently published value. Knowing absolute concentrations we can accurately measure kself = 6.0 ± 2.1 × 10(-11)cm(3) molecule(-1) s(-1) at 297 K. We are also able to put an upper bound on the rate coefficient for CH2OO + I of 1.0 × 10(-11) cm(3) molecule(-1) s(-1). Both of these rate coefficients are at least a factor of 5 smaller than other recent measurements of the same reactions.

  7. Total reaction cross sections in CEM and MCNP6 at intermediate energies

    NASA Astrophysics Data System (ADS)

    Kerby, Leslie M.; Mashnik, Stepan G.

    2015-08-01

    Accurate total reaction cross section models are important to achieving reliable predictions from spallation and transport codes. The latest version of the Cascade Exciton Model (CEM) as incorporated in the code CEM03.03, and the Monte Carlo N-Particle transport code (MCNP6), both developed at Los Alamos National Laboratory (LANL), each use such cross sections. Having accurate total reaction cross section models in the intermediate energy region (∼ 50 MeV to ∼ 5 GeV) is very important for different applications, including analysis of space environments, use in medical physics, and accelerator design, to name just a few. The current inverse cross sections used in the preequilibrium and evaporation stages of CEM are based on the Dostrovsky et al. model, published in 1959. Better cross section models are available now. Implementing better cross section models in CEM and MCNP6 should yield improved predictions for particle spectra and total production cross sections, among other results. Our current results indicate this is, in fact, the case.

  8. Total reaction cross sections in CEM and MCNP6 at intermediate energies

    DOE PAGES

    Kerby, Leslie M.; Mashnik, Stepan G.

    2015-05-14

    Accurate total reaction cross section models are important to achieving reliable predictions from spallation and transport codes. The latest version of the Cascade Exciton Model (CEM) as incorporated in the code CEM03.03, and the Monte Carlo N-Particle transport code (MCNP6), both developed at Los Alamos National Laboratory (LANL), each use such cross sections. Having accurate total reaction cross section models in the intermediate energy region (50 MeV to 5 GeV) is very important for different applications, including analysis of space environments, use in medical physics, and accelerator design, to name just a few. The current inverse cross sections used inmore » the preequilibrium and evaporation stages of CEM are based on the Dostrovsky et al. model, published in 1959. Better cross section models are now available. Implementing better cross section models in CEM and MCNP6 should yield improved predictions for particle spectra and total production cross sections, among other results.« less

  9. 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.

  10. Developing mononuclear copper-active-oxygen complexes relevant to reactive intermediates of biological oxidation reactions.

    PubMed

    Itoh, Shinobu

    2015-07-21

    Active-oxygen species generated on a copper complex play vital roles in several biological and chemical oxidation reactions. Recent attention has been focused on the reactive intermediates generated at the mononuclear copper active sites of copper monooxygenases such as dopamine β-monooxygenase (DβM), tyramine β-monooxygenase (TβM), peptidylglycine-α-hydroxylating monooxygenase (PHM), and polysaccharide monooxygenases (PMO). In a simple model system, reaction of O2 and a reduced copper(I) complex affords a mononuclear copper(II)-superoxide complex or a copper(III)-peroxide complex, and subsequent H(•) or e(-)/H(+) transfer, which gives a copper(II)-hydroperoxide complex. A more reactive species such as a copper(II)-oxyl radical type species could be generated via O-O bond cleavage of the peroxide complex. However, little had been explored about the chemical properties and reactivity of the mononuclear copper-active-oxygen complexes due to the lack of appropriate model compounds. Thus, a great deal of effort has recently been made to develop efficient ligands that can stabilize such reactive active-oxygen complexes in synthetic modeling studies. In this Account, I describe our recent achievements of the development of a mononuclear copper(II)-(end-on)superoxide complex using a simple tridentate ligand consisting of an eight-membered cyclic diamine with a pyridylethyl donor group. The superoxide complex exhibits a similar structure (four-coordinate tetrahedral geometry) and reactivity (aliphatic hydroxylation) to those of a proposed reactive intermediate of copper monooxygenases. Systematic studies based on the crystal structures of copper(I) and copper(II) complexes of the related tridentate supporting ligands have indicated that the rigid eight-membered cyclic diamine framework is crucial for controlling the geometry and the redox potential, which are prerequisites for the generation of such a unique mononuclear copper(II)-(end-on)superoxide complex

  11. Direct kinetic measurements of Criegee intermediate (CH₂OO) formed by reaction of CH₂I with O₂.

    PubMed

    Welz, Oliver; Savee, John D; Osborn, David L; Vasu, Subith S; Percival, Carl J; Shallcross, Dudley E; Taatjes, Craig A

    2012-01-13

    Ozonolysis is a major tropospheric removal mechanism for unsaturated hydrocarbons and proceeds via "Criegee intermediates"--carbonyl oxides--that play a key role in tropospheric oxidation models. However, until recently no gas-phase Criegee intermediate had been observed, and indirect determinations of their reaction kinetics gave derived rate coefficients spanning orders of magnitude. Here, we report direct photoionization mass spectrometric detection of formaldehyde oxide (CH(2)OO) as a product of the reaction of CH(2)I with O(2). This reaction enabled direct laboratory determinations of CH(2)OO kinetics. Upper limits were extracted for reaction rate coefficients with NO and H(2)O. The CH(2)OO reactions with SO(2) and NO(2) proved unexpectedly rapid and imply a substantially greater role of carbonyl oxides in models of tropospheric sulfate and nitrate chemistry than previously assumed.

  12. The thermodynamic properties of 2-aminobiphenyl (an intermediate in the carbazole/hydrogen reaction network)

    SciTech Connect

    Steele, W.V.; Chirico, R.D.; Knipmeyer, S.E.; Nguyen, A.

    1990-12-01

    Catalytic hydrodenitrogenation (HDN) is a key step in upgrading processes for conversion of heavy petroleum, shale oil, tar sands, and the products of the liquefaction of coal to economically viable products. This research program provides accurate experimental thermochemical and thermophysical properties for key organic nitrogen-containing compounds present in the range of alternative feedstocks, and applies the experimental information to thermodynamic analyses of key HDN reaction networks. This report is the first in a series that will lead to an analysis of a three-ring HDN system; the carbazole/hydrogen reaction network. 2-Aminobiphenyl is the initial intermediate in the HDN pathway for carbazole, which consumes the least hydrogen possible. Measurements leading to the calculation of the ideal-gas thermodynamic properties for 2-aminobiphenyl are reported. Experimental methods included combustion calorimetry, adiabatic heat-capacity calorimetry, comparative ebulliometry, inclined-piston gauge manometry, and differential-scanning calorimetry (d.s.c). Entropies, enthalpies, and Gibbs energies of formation were derived for the ideal gas for selected temperatures between 298.15 K and 820 K. The critical temperature and critical density were determined for 2-aminobiphenyl with the d.s.c., and the critical pressure was derived. The Gibbs energies of formation are used in thermodynamic calculations to compare the feasibility of the initial hydrogenolysis step in the carbazole/H{sub 2} network with that of its hydrocarbon and oxygen-containing analogous; i.e., fluorene/H{sub 2} and dibenzofuran/H{sub 2}. Results of the thermodynamic calculations are compared with those of batch-reaction studies reported in the literature. 57 refs., 8 figs., 18 tabs.

  13. Oligomer Formation Reactions of Criegee Intermediates in the Ozonolysis of Small Unsaturated Hydrocarbons

    NASA Astrophysics Data System (ADS)

    Sakamoto, Y.; Inomata, S.; Hirokawa, J.

    2013-12-01

    Secondary organic aerosol (SOA) constitutes a substantial fraction of atmospheric fine particulate matters and has an effect on visibility, climate and human health. One of the major oxidizing processes leading to SOA formation is an ozonolysis of unsaturated hydrocarbons (UHCs).[1] Despite of its importance, the contribution of the ozonolysis of UHCs to the SOA formation in the troposphere is not sufficiently understood due to a lack of information on reaction pathways to produce low volatile compounds. While many studies have previously been focused on SOA formation from the ozonolysis of large UHCs, SOA formation from the ozonolysis of UHCs with less than six carbon atoms have been rarely investigated because their products are expected to be too volatile to contribute to the SOA formation. Very recently, a few studies have reported the SOA formation from the ozonolysis of such small UHCs but chemical mechanisms are still unclear. [2-4] In order to understand SOA formation from the ozonolysis of the small UHCs, this study investigated gas- and particle-phase products in laboratory experiments with a Teflon bag using a negative ion chemical ionization mass spectrometry (NI-CIMS) with chloride ion transfer for chemical ionization. This technique is suitable for analysis of compounds such as carboxylic acids and hydroperoxides expected to be produced in the ozonolysis of UHCs with less fragmentation, high selectivity, and high sensitivity. In the particle-phase analysis, SOAs collected on a PTFE filter were heated, and thermally desorbed compounds were analyzed. In the gas-phase analysis, series of peaks with an interval of a mass-to-charge ratio equal to the molecular weight of a Criegee intermediate formed in their ozonolysis were observed. These peaks were attributed to oligomeric hydroperoxides composed of Criegee intermediates as a chain unit. These oligomeric hydroperoxides were also observed in the particle-phase analysis, indicating that the oligomeric

  14. ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations

    PubMed Central

    Williams II, Benfeard; Convertino, Marino; Das, Jhuma; Dokholyan, Nikolay V.

    2015-01-01

    The increased risk of developing Alzheimer’s disease (AD) is associated with the APOE gene, which encodes for three variants of Apolipoprotein E, namely E2, E3, E4, differing only by two amino acids at positions 112 and 158. ApoE4 is known to be the strongest risk factor for AD onset, while ApoE3 and ApoE2 are considered to be the AD-neutral and AD-protective isoforms, respectively. It has been hypothesized that the ApoE isoforms may contribute to the development of AD by modifying the homeostasis of ApoE physiological partners and AD-related proteins in an isoform-specific fashion. Here we find that, despite the high sequence similarity among the three ApoE variants, only ApoE4 exhibits a misfolded intermediate state characterized by isoform-specific domain-domain interactions in molecular dynamics simulations. The existence of an ApoE4-specific intermediate state can contribute to the onset of AD by altering multiple cellular pathways involved in ApoE-dependent lipid transport efficiency or in AD-related protein aggregation and clearance. We present what we believe to be the first structural model of an ApoE4 misfolded intermediate state, which may serve to elucidate the molecular mechanism underlying the role of ApoE4 in AD pathogenesis. The knowledge of the structure for the ApoE4 folding intermediate provides a new platform for the rational design of alternative therapeutic strategies to fight AD. PMID:26506597

  15. How to identify carbonate rock reactions in concrete

    SciTech Connect

    Katayama, Tetsuya . E-mail: katayamat@kge.co.jp

    2004-11-15

    This paper summarizes the modern petrographic techniques used to diagnose carbonate rock reactions in concrete. Concrete microbar specimens of the prototype RILEM AAR-5 test, provided by the Austrian Cement Research Institute, and typical Canadian concrete that had undergone alkali-carbonate reaction (ACR) were examined. Scanning electron microscopy, element mapping and quantitative analysis using electron-probe microanalyzer with energy-dispersive spectrometry (EPMA/EDS: around x 2000, <0.1 nA) were made of polished thin sections after completing polarizing microscopy. Dedolomitization produced a myrmekitic texture, composed of spotted brucite (<3 {mu}m) and calcite within the reaction rim, along with a carbonate halo of calcite in the surrounding cement paste. However, no evidence was detected that dedolomitization had produced the expansion cracks in the cement paste, while the classical definition of alkali-carbonate reaction postulates their development. It was found that the alkali-silica reaction (ASR) due to cryptocrystalline quartz hidden in the matrix, always associated with dedolomitization in all the carbonate aggregates tested, was responsible for the expansion of both the laboratory and field concretes, even with the Canadian dolomitic limestone from Kingston, the reference material for alkali-carbonate reaction. It is suggested that the term alkali-carbonate reaction is misleading.

  16. Aryl-phenyl scrambling in intermediate organopalladium complexes: a gas-phase study of the Mizoroki-Heck reaction.

    PubMed

    Fiebig, Lukas; Schlörer, Nils; Schmalz, Hans-Günther; Schäfer, Mathias

    2014-04-22

    The intramolecular aryl-phenyl scrambling reaction within palladium-DPPP-aryl complex (DPPP=1,3-bis(diphenylphosphino)propane) ions was analyzed by state-of-the-art tandem MS, including gas-phase ion/molecule reactions. The Mizoroki-Heck cross-coupling reaction was performed in the gas phase, and the intrinsic reactivity of important intermediates could be examined. Moreover, linear free-energy correlations were applied, and a mechanism for the scrambling reaction proceeding via phosphonium cations was assumed.

  17. Solving the 170-Year-Old Mystery About Red-Violet and Blue Transient Intermediates in the Gmelin Reaction.

    PubMed

    Gao, Yin; Toubaei, Abouzar; Kong, Xianqi; Wu, Gang

    2015-11-23

    The Gmelin reaction between nitroprusside and sulfides in aqueous solution is known to produce two transient intermediates with distinct colors: an initial red-violet intermediate that subsequently converts into a blue intermediate. In this work, we use a combination of multinuclear ((17) O, (15) N, (13) C) NMR, UV/Vis, IR spectroscopic techniques and quantum chemical computation to show unequivocally that the red-violet intermediate is [Fe(CN)5 N(O)S](4-) and the blue intermediate is [Fe(CN)5 N(O)SS)](4-) . While the formation of [Fe(CN)5 N(O)S](4-) has long been postulated in the literature, this study provides the most direct proof of its structure. In contrast, [Fe(CN)5 N(O)SS)](4-) represents the first example of any metal coordination complex containing a perthionitro ligand. The new reaction pathways found in this study not only provide clues for the mode of action of nitroprusside for its pharmacological activity, but also have broader implications to the biological role of H2 S, potential reactions between H2 S and nitric oxide donor compounds, and the possible biological function of polysulfides.

  18. Identification of a Critical Intermediate in Galvanic Exchange Reactions by Single-Nanoparticle Resolved Kinetics

    NASA Astrophysics Data System (ADS)

    Smith, Jeremy George; Jain, Prashant

    2014-06-01

    The realization of common materials transformations in nanocrystalline systems is fostering the development of novel nanostructures and allowing a deep look into the atomistic mechanisms involved. Galvanic corrosion is one such transformation. We studied galvanic replacement within individual metal nanoparticles by using plasmonic spectroscopy. This proved to be a powerful approach to studying materials transformations in the absence of ensemble averaging. Individual nanoscale units act as domains that can be interrogated optically in isolation, whereas the averaging of all such domains provides a bulk reaction trajectory. Single-nanoparticle reaction trajectories showed that a Ag nanoparticle exposed to Au3+ makes an abrupt transition into a nanocage structure. The transition is limited by a critical structural event, which we identified by electron microscopy to comprise the formation of a nanosized void, similar to the pitting process commonly observed in the corrosion of metals. Trajectories also revealed a surprisingly strong nonlinearity of the reaction kinetics, which we explain by a model involving the critical coalescence of vacancies into a growing void. The critical void size for galvanic exchange to spontaneously proceed was found to be 20 atomic vacancies. In the future we hope to extend this approach to examine a wide variety of materials transformations and chemical reactions.

  19. Direct evidence for a substantive reaction between the Criegee intermediate, CH2OO, and the water vapour dimer.

    PubMed

    Lewis, Tom R; Blitz, Mark A; Heard, Dwayne E; Seakins, Paul W

    2015-02-21

    The C1 Criegee intermediate, CH2OO, reaction with water vapour has been studied. The removal rate constant shows a quadratic dependence on [H2O], implying reaction with the water dimer, (H2O)2. The rate constant, kCH2OO+(H2O)2 = (4.0 ± 1.2) × 10(-12) cm(3) molecule(-1) s(-1), is such that this is the major atmospheric sink for CH2OO.

  20. Furfuryl alcohol polymerization in H-Y confined spaces: reaction mechanism and structure of carbocationic intermediates.

    PubMed

    Bertarione, S; Bonino, F; Cesano, F; Damin, A; Scarano, D; Zecchina, A

    2008-03-06

    The acid-catalyzed polymerization and resinification, in the 300-673 K interval, of furfuryl alcohol adsorbed in the framework of a protonic Y zeolite is studied by means of FTIR, Raman, and UV-vis spectroscopies. The idea is that restricted spaces can impose a constraint to the growth of the oligomeric chains, therefore moderating the formation of conjugated sequences responsible for the color of the products and allowing their observation by means of spectroscopic techniques. The detailed study of the evolution of UV-vis, FTIR, and Raman spectra upon dosed amount, contact time, and temperature has allowed the spectroscopic features of some of the single species, either neutral and positively charged (carbocationic intermediates), to be singled out and assigned to understand the mechanism of initiation. The vibrational assignments have been confirmed by computer simulations on model compounds and compared with the results of the mechanistic description of the reaction mechanism made in the past (Choura, et al. Macromolecules 1996, 29, 3839-3850). The spectroscopic methods have been applied in a large temperature range in order to follow also the formation of more complex products into the pores, associated with longer conjugated sequences, gradually filling the open spaces of the zeolite. For samples contacted with furfuryl alcohol at 673 K, this methodology gives information also on the incipient carbonization process, leading to the formation of a carbonaceous replica phase inside the internal porosity of the zeolite.

  1. Photofragment imaging study of the CH2CCH2OH radical intermediate of the OH +allene reaction

    NASA Astrophysics Data System (ADS)

    Raman, Arjun S.; Justine Bell, M.; Lau, Kai-Chung; Butler, Laurie J.

    2007-10-01

    These velocity map imaging experiments characterize the photolytic generation of one of the two radical intermediates formed when OH reacts via an addition mechanism with allene. The CH2CCH2OH radical intermediate is generated photolytically from the photodissociation of 2-chloro-2-propen-1-ol at 193nm. Detecting the Cl atoms using [2+1] resonance-enhanced multiphoton ionization evidences an isotropic angular distribution for the Cl +CH2CCH2OH photofragments, a spin-orbit branching ratio for Cl(P1/22):Cl(P3/22) of 0.28, and a bimodal recoil kinetic energy distribution. Conservation of momentum and energy allows us to determine from this data the internal energy distribution of the nascent CH2CCH2OH radical cofragment. To assess the possible subsequent decomposition pathways of this highly vibrationally excited radical intermediate, we include electronic structure calculations at the G3//B3LYP level of theory. They predict the isomerization and dissociation transition states en route from the initial CH2CCH2OH radical intermediate to the three most important product channels for the OH +allene reaction expected from this radical intermediate: formaldehyde+C2H3, H +acrolein, and ethene+CHO. We also calculate the intermediates and transition states en route from the other radical adduct, formed by addition of the OH to the center carbon of allene, to the ketene+CH3 product channel. We compare our results to a previous theoretical study of the O +allyl reaction conducted at the CBS-QB3 level of theory, as the two reactions include several common intermediates.

  2. Spectroscopically identified intermediate age stars at 0.5-3 pc distance from Sagittarius A*

    NASA Astrophysics Data System (ADS)

    Nishiyama, Shogo; Schödel, Rainer; Yoshikawa, Tatsuhito; Nagata, Tetsuya; Minowa, Yosuke; Tamura, Motohide

    2016-04-01

    Context. Nuclear star clusters (NSCs) at the dynamical center of galaxies appear to have a complex star formation history. This suggests repeated star formation, even in the influence of the strong tidal field from supermassive black holes. Although the central region of our Galaxy is an ideal target for studies of the star formation history in the NSCs, most studies in the past have concentrated on a projected distance of RSgr A ∗ ~ 0.5 pc from the supermassive black hole Sgr A*. Aims: In our previous study, we detected 31 so far unknown early-type star candidates throughout the Galactic NSC (at RSgr A ∗ = 0.5-3 pc). They were found via near-infrared (NIR) imaging observations with narrow-band filters which are sensitive to CO absorption lines at ~2.3 μm, a prominent feature for old, late-type stars. The aim of this study is to confirm the spectral type for the early-type star candidates. Methods: We have carried out NIR spectroscopic observations of the early-type star candidates using Subaru/IRCS/AO188 and the laser guide star system. K-band spectra for 20 out of the 31 candidates and reference late-type stars were obtained. By determining an equivalent width, EW(CO), of the 12CO absorption feature at ≈2.294 μm, we have derived an effective temperature and a bolometric magnitude for each candidate and late-type star, and then constructed an HR diagram. Results: No young (~Myr) massive stars are included in the 20 candidates we observed; however, 13 candidates are most likely intermediate-age giants (50-500 Myr). Two other sources have ages of ~1 Gyr and the remaining five sources are old (>1 Gyr), late-type giants. Conclusions: Although none of the early-type star candidates from our previous narrow-band imaging observations can be confirmed as a young star, we find that the photometric technique can distinguish old, late-type giants from young and intermediate-age populations. From the 20 spectroscopically observed candidates, 65% of them are confirmed

  3. Identifying the Molecular Structures of Intermediates for Optimizing the Fabrication of High-Quality Perovskite Films.

    PubMed

    Cao, Jing; Jing, Xiaojing; Yan, Juanzhu; Hu, Chengyi; Chen, Ruihao; Yin, Jun; Li, Jing; Zheng, Nanfeng

    2016-08-10

    During the past two years, the introduction of DMSO has revolutionized the fabrication of high-quality pervoskite MAPbI3 (MA = CH3NH3) films for solar cell applications. In the developed DMSO process, the formation of (MA)2Pb3I8·2DMSO (shorted as Pb3I8) has well recognized as a critical factor to prepare high-quality pervoskite films and thus accomplish excellent performances in perovskite solar cells. However, Pb3I8 is an I-deficient intermediate and must further react with methylammonium iodide (MAI) to be fully converted into MAPbI3. By capturing and solving the molecular structures of several intermediates involved in the fabrication of perovskite films, we report in this work that the importance of DMSO is NOT due to the formation of Pb3I8. The use of different PbI2-DMSO ratios leads to two different structures of PbI2-DMSO precursors (PbI2·DMSO and PbI2·2DMSO), thus dramatically influencing the quality of fabricated perovskite films. However, such an influence can be minimized when the PbI2-DMSO precursor films are thermally treated to create mesoporous PbI2 films before reacting with MAI. Such a development makes the fabrication of high-quality pervoskite films highly reproducible without the need to precisely control the PbI2:DMSO ratio. Moreover, the formation of ionic compound (MA)4PbI6 is observed when excess MAI is used in the preparation of perovskite film. This I-rich phase heavily induces the hysteresis in PSCs, but is readily removed by isopropanol treatment. On the basis of all these findings, we develop a new effective protocol to fabricate high-performance PSCs. In the new protocol, high-quality perovskite films are prepared by simply treating the mesoporous PbI2 films (made from PbI2-DMSO precursors) with an isopropanol solution of MAI, followed by isopropanol washing. The best efficiency of fabricated MAPbI3 PSCs is up to 19.0%. As compared to the previously reported DMSO method, the devices fabricated by the method reported in this work

  4. Extremely rapid self-reaction of the simplest Criegee intermediate CH2OO and its implications in atmospheric chemistry.

    PubMed

    Su, Yu-Te; Lin, Hui-Yu; Putikam, Raghunath; Matsui, Hiroyuki; Lin, M C; Lee, Yuan-Pern

    2014-06-01

    Criegee intermediates, which are carbonyl oxides produced when ozone reacts with unsaturated hydrocarbons, play an important role in the formation of OH and organic acids in the atmosphere, but they have eluded direct detection until recently. Reactions that involve Criegee intermediates are not understood fully because data based on their direct observation are limited. We used transient infrared absorption spectroscopy to probe directly the decay kinetics of formaldehyde oxide (CH2OO) and found that it reacts with itself extremely rapidly. This fast self-reaction is a result of its zwitterionic character. According to our quantum-chemical calculations, a cyclic dimeric intermediate that has the terminal O atom of one CH2OO bonded to the C atom of the other CH2OO is formed with large exothermicity before further decomposition to 2H2CO + O2((1)Δg). We suggest that the inclusion of this previously overlooked rapid reaction in models may affect the interpretation of previous laboratory experiments that involve Criegee intermediates.

  5. Extremely rapid self-reaction of the simplest Criegee intermediate CH2OO and its implications in atmospheric chemistry

    NASA Astrophysics Data System (ADS)

    Su, Yu-Te; Lin, Hui-Yu; Putikam, Raghunath; Matsui, Hiroyuki; Lin, M. C.; Lee, Yuan-Pern

    2014-06-01

    Criegee intermediates, which are carbonyl oxides produced when ozone reacts with unsaturated hydrocarbons, play an important role in the formation of OH and organic acids in the atmosphere, but they have eluded direct detection until recently. Reactions that involve Criegee intermediates are not understood fully because data based on their direct observation are limited. We used transient infrared absorption spectroscopy to probe directly the decay kinetics of formaldehyde oxide (CH2OO) and found that it reacts with itself extremely rapidly. This fast self-reaction is a result of its zwitterionic character. According to our quantum-chemical calculations, a cyclic dimeric intermediate that has the terminal O atom of one CH2OO bonded to the C atom of the other CH2OO is formed with large exothermicity before further decomposition to 2H2CO + O2(1Δg). We suggest that the inclusion of this previously overlooked rapid reaction in models may affect the interpretation of previous laboratory experiments that involve Criegee intermediates.

  6. The GC-MS Observation of Intermediates in a Stepwise Grignard Addition Reaction

    ERIC Educational Resources Information Center

    Latimer, Devin

    2007-01-01

    Preparation of phenylmagnesium bromide described by Eckert, addition of three equivalents of Grignard reagent to diethyl carbonate to form triphenylmethanol and a series of GC-MS procedures that form intermediates. The analysis is consistent with a gas chromatogram and mass spectrum for each of the expected intermediates and final product of the…

  7. [NiFe]-hydrogenases: spectroscopic and electrochemical definition of reactions and intermediates.

    PubMed

    Armstrong, Fraser A; Albracht, Simon P J

    2005-04-15

    Production and usage of di-hydrogen, H2, in micro-organisms is catalysed by highly active, 'ancient' metalloenzymes known as hydrogenases. Based on the number and identity of metal atoms in their active sites, hydrogenases fall into three main classes, [NiFe]-, [FeFe]- and [Fe]-. All contain the unusual ligand CO (and in most cases CN- as well) making them intriguing examples of 'organometallic' cofactors. These ligands render the active sites superbly 'visible' using infrared spectroscopy, which complements the use of electron paramagnetic resonance spectroscopy in studying mechanisms and identifying intermediates. Hydrogenases are becoming a focus of attention for research into future energy technologies, not only H2 production but also H2 oxidation in fuel cells. Hydrogenases immobilized on electrodes exhibit high electrocatalytic activity, providing not only an important new technique for their investigation, but also a basis for novel fuel cells either using the enzyme itself, or inspired synthetic catalysts. Favourable comparisons have been made with platinum electrocatalysts, an advantage of enzymes being their specificity for H2 and tolerance of CO. A challenge for exploiting hydrogenases is their sensitivity to O2, but some organisms are known to produce enzymes that overcome this problem by subtle alterations of the active site and gas access channels.

  8. Identifying Predictors of Negative Psychological Reactions to Stalking Victimization

    ERIC Educational Resources Information Center

    Johnson, Matthew C.; Kercher, Glen A.

    2009-01-01

    Victims of stalking often experience a number of negative psychological problems including such things as fear, symptoms of depression, and anger. However, research on factors that lead to these outcomes is limited. The goal of this study was to first identify distinct subgroups of stalking victims based on measures of psychological problems…

  9. Identifying of meat species using polymerase chain reaction (PCR)

    SciTech Connect

    Foong, Chow Ming; Sani, Norrakiah Abdullah

    2013-11-27

    Meat has been widely consumed as an important protein source in daily life of human. Furthermore, with busy and intense urban lifestyle, processed food is now one of the main protein sources of one’s diet. Consumers rely on the food labeling to decide if the meat product purchased is safe and reliable. Therefore, it is important to ensure the food labeling is done in a correct manner to avoid consumer fraud. More consumers are now concern about the food quality and safety as compared to before. This study described the meat species identification and detection method using Polymerase Chain Reaction (PCR) in 8 types of meats (cattle, buffalo, goat, sheep, chicken, duck, pork and horse). The objective of this study is to decide on the specificity of oligonucleotide sequences obtained from previous study. There were 5 proposed oligonucleotide primer in this study. The main important finding in this work is the specificity of oligonucleotide primers to raw meats. It if found that the oligonucleotide primers proposed were not specific to the local raw meat species. Therefore, further study is needed to obtain a species-specific oligonucletide primers for PCR, in order to be applied in food product testing.

  10. Identifying of meat species using polymerase chain reaction (PCR)

    NASA Astrophysics Data System (ADS)

    Foong, Chow Ming; Sani, Norrakiah Abdullah

    2013-11-01

    Meat has been widely consumed as an important protein source in daily life of human. Furthermore, with busy and intense urban lifestyle, processed food is now one of the main protein sources of one's diet. Consumers rely on the food labeling to decide if the meat product purchased is safe and reliable. Therefore, it is important to ensure the food labeling is done in a correct manner to avoid consumer fraud. More consumers are now concern about the food quality and safety as compared to before. This study described the meat species identification and detection method using Polymerase Chain Reaction (PCR) in 8 types of meats (cattle, buffalo, goat, sheep, chicken, duck, pork and horse). The objective of this study is to decide on the specificity of oligonucleotide sequences obtained from previous study. There were 5 proposed oligonucleotide primer in this study. The main important finding in this work is the specificity of oligonucleotide primers to raw meats. It if found that the oligonucleotide primers proposed were not specific to the local raw meat species. Therefore, further study is needed to obtain a species-specific oligonucletide primers for PCR, in order to be applied in food product testing.

  11. Highly Active Nickel Catalysts for C-H Functionalization Identified through Analysis of Off-Cycle Intermediates.

    PubMed

    Nett, Alex J; Zhao, Wanxiang; Zimmerman, Paul M; Montgomery, John

    2015-06-24

    An inhibitory role of 1,5-cyclooctadiene (COD) in nickel-catalyzed C-H functionalization processes was identified and studied. The bound COD participates in C-H activation by capturing the hydride, leading to a stable off-cycle π-allyl complex that greatly diminished overall catalytic efficiency. Computational studies elucidated the origin of the effect and enabled identification of a 1,5-hexadiene-derived pre-catalyst that avoids the off-cycle intermediate and provides catalytic efficiencies that are superior to those of catalysts derived from Ni(COD)2.

  12. Light Charged Particles and Intermediate Mass Fragments from the Reactions 486, 550, 640, and 730 Mev KRYPTON-86 + COPPER-63

    NASA Astrophysics Data System (ADS)

    Boger, John Thomas

    1992-01-01

    A detailed study has been made of the reaction ^{86}Kr + ^ {63}Cu at incident energies of 486, 550, 640, and 730 MeV. Measurements include cross sections, angular distributions, and energy spectra for light charged particles (^{1,2,3}H and ^4He), intermediate mass fragments (IMF) (4 <= Z <= 17), and heavy fragments (Z >= 18). Coincidences between light charged particles and between particles and fragments have also been measured to obtain exclusive cross sections, energy spectra, and angular distributions. Statistical model analysis of the energy spectra for ^1 H and ^4He detected in coincidence with the fragments has allowed estimation of ^1 H and ^4He multiplicities associated with the evaporation residues, fragments, and composite nuclei prior to scission. In particular, the light charged particle multiplicities for the IMF's have allowed for the derivation of their primary masses. This in turn has permitted refined measurements of the kinetic energies of the primary IMF's. The ^{86}Kr bombarding energies were selected so that the excitation energies of the composite nuclei (^{149} Tb*) were matched to those of other entrance channel reactions that produce the same composite nuclei. A close comparison of cross sections, energy spectra, angular distributions, and particle multiplicities for these matched entrance channels has provided the means for a detailed test of the Bohr Independence Hypothesis. Results of this comparison indicate extensive shape and thermal equilibration of the composite nuclei over the excitation energy range of 128 to 231 MeV. This conclusion is reached even for nuclear systems whose decay lifetimes are expected to be similar to their relaxation times. For the 640 MeV ^{86} Kr + ^{63}Cu reaction, cross sections were measured for IMF's of 4 <= Z <= 17 in singles and in coincidence with heavy fragments. Three sources for IMF production have been identified: (1) asymmetric binary fission, (2) sequential binary fission, and (3) simultaneous

  13. NO3 radical production from the reaction between the Criegee intermediate CH2OO and NO2.

    PubMed

    Ouyang, Bin; McLeod, Matthew W; Jones, Roderic L; Bloss, William J

    2013-10-28

    Formation of the NO3 radical was observed following photolysis of the CH2I2 + O2 system at 248 nm under ambient atmospheric boundary layer conditions (~760 Torr and 297 K) in the presence of NO2. The Criegee intermediate (CI) CH2OO is believed to be responsible for the NO3 production. The potential of such reactions to enhance the rate of NO3 production in the atmosphere is discussed.

  14. Intermediate-energy inverse-kinematics one-proton pickup reactions on neutron-deficient fp-shell nuclei

    NASA Astrophysics Data System (ADS)

    McDaniel, S.; Gade, A.; Tostevin, J. A.; Baugher, T.; Bazin, D.; Brown, B. A.; Cook, J. M.; Glasmacher, T.; Grinyer, G. F.; Ratkiewicz, A.; Weisshaar, D.

    2012-01-01

    Background: Thick-target-induced nucleon-adding transfer reactions onto energetic rare-isotope beams are an emerging spectroscopic tool. Their sensitivity to single-particle structure complements one-nucleon removal reaction capabilities in the quest to reveal the evolution of nuclear shell structure in very exotic nuclei. Purpose: Our purpose is to add intermediate-energy, carbon-target-induced one-proton pickup reactions to the arsenal of γ-ray-tagged direct reactions applicable in the regime of low beam intensities and to apply these for the first time to fp-shell nuclei. Methods: Inclusive and partial cross sections were measured for the 12C(48Cr,49Mn+γ)X and 12C(50Fe,51Co+γ)X proton pickup reactions at 56.7 and 61.2 MeV/nucleon, respectively, using coincident particle-γ spectroscopy at the National Superconducting Cyclotron Laboratory. The results are compared to reaction theory calculations using fp-shell-model nuclear structure input. For comparison with our previous work, the same reactions were measured on 9Be targets. Results: The measured partial cross sections confirm the specific population pattern predicted by theory, with pickup into high-ℓ orbitals being strongly favored, driven by linear and angular momentum matching. Conclusion: Carbon-target-induced pickup reactions are well suited, in the regime of modest beam intensity, to study the evolution of nuclear structure, with specific sensitivities that are well described by theory.

  15. Modeling of catalytically active metal complex species and intermediates in reactions of organic halides electroreduction.

    PubMed

    Lytvynenko, Anton S; Kolotilov, Sergey V; Kiskin, Mikhail A; Eremenko, Igor L; Novotortsev, Vladimir M

    2015-02-28

    The results of quantum chemical modeling of organic and metal-containing intermediates that occur in electrocatalytic dehalogenation reactions of organic chlorides are presented. Modeling of processes that take place in successive steps of the electrochemical reduction of representative C1 and C2 chlorides - CHCl3 and Freon R113 (1,1,2-trifluoro-1,2,2-trichloroethane) - was carried out by density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2). It was found that taking solvation into account using an implicit solvent model (conductor-like screening model, COSMO) or considering explicit solvent molecules gave similar results. In addition to modeling of simple non-catalytic dehalogenation, processes with a number of complexes and their reduced forms, some of which were catalytically active, were investigated by DFT. Complexes M(L1)2 (M = Fe, Co, Ni, Cu, Zn, L1H = Schiff base from 2-pyridinecarbaldehyde and the hydrazide of 4-pyridinecarboxylic acid), Ni(L2) (H2L2 is the Schiff base from salicylaldehyde and 1,2-ethylenediamine, known as salen) and Co(L3)2Cl2, representing a fragment of a redox-active coordination polymer [Co(L3)Cl2]n (L3 is the dithioamide of 1,3-benzenedicarboxylic acid), were considered. Gradual changes in electronic structure in a series of compounds M(L1)2 were observed, and correlations between [M(L1)2](0) spin-up and spin-down LUMO energies and the relative energies of the corresponding high-spin and low-spin reduced forms, as well as the shape of the orbitals, were proposed. These results can be helpful for determination of the nature of redox-processes in similar systems by DFT. No specific covalent interactions between [M(L1)2](-) and the R113 molecule (M = Fe, Co, Ni, Zn) were found, which indicates that M(L1)2 electrocatalysts act rather like electron transfer mediators via outer-shell electron transfer. A relaxed surface scan of the adducts {M(L1)2·R113}(-) (M = Ni or Co) versus the distance between the

  16. Reactivity of TEMPO toward 16- and 17-electron organometallic reaction intermediates: a time-resolved IR study.

    PubMed

    Lomont, Justin P; Nguyen, Son C; Harris, Charles B

    2013-07-31

    The (2,2,6,6-tetramethylpiperidin-1-yl)oxyl radical (TEMPO) has been employed for an extensive range of chemical applications, ranging from organometallic catalysis to serving as a structural probe in biological systems. As a ligand in an organometallic complex, TEMPO can exhibit several distinct coordination modes. Here we use ultrafast time-resolved infrared spectroscopy to study the reactivity of TEMPO toward coordinatively unsaturated 16- and 17-electron organometallic reaction intermediates. TEMPO coordinates to the metal centers of the 16-electron species CpCo(CO) and Fe(CO)4, and to the 17-electron species CpFe(CO)2 and Mn(CO)5, via an associative mechanism with concomitant oxidation of the metal center. In these adducts, TEMPO thus behaves as an anionic ligand, characterized by a pyramidal geometry about the nitrogen center. Density functional theory calculations are used to facilitate interpretation of the spectra and to further explore the structures of the TEMPO adducts. To our knowledge, this study represents the first direct characterization of the mechanism of the reaction of TEMPO with coordinatively unsaturated organometallic complexes, providing valuable insight into its reactions with commonly encountered reaction intermediates. The similar reactivity of TEMPO toward each of the species studied suggests that these results can be considered representative of TEMPO's reactivity toward all low-valent transition metal complexes.

  17. Direct Measurements of Unimolecular and Bimolecular Reaction Kinetics of the Criegee Intermediate (CH3)2COO.

    PubMed

    Chhantyal-Pun, Rabi; Welz, Oliver; Savee, John D; Eskola, Arkke J; Lee, Edmond P F; Blacker, Lucy; Hill, Henry R; Ashcroft, Matilda; Khan, M Anwar H; Lloyd-Jones, Guy C; Evans, Louise; Rotavera, Brandon; Huang, Haifeng; Osborn, David L; Mok, Daniel K W; Dyke, John M; Shallcross, Dudley E; Percival, Carl J; Orr-Ewing, Andrew J; Taatjes, Craig A

    2017-01-12

    The Criegee intermediate acetone oxide, (CH3)2COO, is formed by laser photolysis of 2,2-diiodopropane in the presence of O2 and characterized by synchrotron photoionization mass spectrometry and by cavity ring-down ultraviolet absorption spectroscopy. The rate coefficient of the reaction of the Criegee intermediate with SO2 was measured using photoionization mass spectrometry and pseudo-first-order methods to be (7.3 ± 0.5) × 10(-11) cm(3) s(-1) at 298 K and 4 Torr and (1.5 ± 0.5) × 10(-10) cm(3) s(-1) at 298 K and 10 Torr (He buffer). These values are similar to directly measured rate coefficients of anti-CH3CHOO with SO2, and in good agreement with recent UV absorption measurements. The measurement of this reaction at 293 K and slightly higher pressures (between 10 and 100 Torr) in N2 from cavity ring-down decay of the ultraviolet absorption of (CH3)2COO yielded even larger rate coefficients, in the range (1.84 ± 0.12) × 10(-10) to (2.29 ± 0.08) × 10(-10) cm(3) s(-1). Photoionization mass spectrometry measurements with deuterated acetone oxide at 4 Torr show an inverse deuterium kinetic isotope effect, kH/kD = (0.53 ± 0.06), for reactions with SO2, which may be consistent with recent suggestions that the formation of an association complex affects the rate coefficient. The reaction of (CD3)2COO with NO2 has a rate coefficient at 298 K and 4 Torr of (2.1 ± 0.5) × 10(-12) cm(3) s(-1) (measured with photoionization mass spectrometry), again similar to rate for the reaction of anti-CH3CHOO with NO2. Cavity ring-down measurements of the acetone oxide removal without added reagents display a combination of first- and second-order decay kinetics, which can be deconvolved to derive values for both the self-reaction of (CH3)2COO and its unimolecular thermal decay. The inferred unimolecular decay rate coefficient at 293 K, (305 ± 70) s(-1), is similar to determinations from ozonolysis. The present measurements confirm the large rate coefficient for reaction of

  18. Production of Neutron-Unbound States in Intermediate - Fragments from Nitrogen + Silver Reactions at E/a = 35 Mev

    NASA Astrophysics Data System (ADS)

    Heilbronn, Lawrence Harvey

    The populations of neutron-unbound states and of bound states in intermediate-mass fragments have been measured at 15^circ, 31 ^circ, and 64^circ from the ^{14}N + Ag reaction at E/A = 35 MeV. The data are identified in terms of the reaction mechanism producing them, which is either a deep-inelastic mechanism or a quasielastic mechanism. In order to test the assumption that the deep -inelastic data are produced from a thermal source, the unbound-state/bound-state population ratios of deep-inelastic fragments are compared to the predictions of a thermal sequential decay model. Most, but not all, of the deep -inelastic population ratios are fitted with model calculations that assume a source temperature between 2.5 and 3.4 MeV. Three or more populations from the same isotope were measured for ^{13}C, ^ {12}B, and ^{10} Be. The deep-inelastic populations from ^{13}C and ^{10 }Be were fitted with a single temperature, while the deep-inelastic populations from ^ {12}B were not fitted. There is enough of the deep-inelastic data that is not fitted with the predictions of a thermal model that the assumption of a thermal source for the production of deep-inelastic fragments may be incorrect, or there may be other effects present which alter the thermal properties of the data. The dependence of the unbound-state/bound-state population ratio on the fragment kinetic energy shows a difference between the quasielastic and deep-inelastic data. For quasielastic fragments whose mass is near the mass of the beam, the ratio decreases towards zero as the fragment velocity approaches the beam velocity. In contrast, the ratio for half-beam mass quasielastic fragments is constant or only slightly decreasing as the kinetic energy increases. The ratio for deep-inelastic fragments is approximately constant as a function of kinetic energy, independent of fragment mass. The amount of feeding from several neutron-unbound channels into bound states is measured and compared to the sequential

  19. Reaction of a copper(II)-nitrosyl complex with hydrogen peroxide: phenol ring nitration through a putative peroxynitrite intermediate.

    PubMed

    Kalita, Apurba; Deka, Ramesh C; Mondal, Biplab

    2013-10-07

    Copper(II) complex, 1, with the histidine-derived ligand L (L = methyl 2-(2-hydroxybenzylamino)-3-(1H-imidazol-5-yl)propanoate) has been synthesized and characterized. Single-crystal structure determination reveals a diphenolato-bridged dicopper(II) core in 1. Addition of (•)NO to an acetonitrile solution of 1 affords the corresponding mononuclear copper(II)-nitrosyl complex, 2. In the presence of H2O2, 2 results in formation of the corresponding copper(I)-peroxynitrite. Formation of peroxynitrite ((-)OONO) intermediate is evident from its characteristic phenol ring nitration reaction which resembles the tyrosine nitration in biological systems. Further, isolation of nitrate (NO3(-)) as the decomposition product from 2 at room temperature also supports the involvement of (-)OONO intermediate.

  20. Detailed mechanism of the CH2I + O2 reaction: Yield and self-reaction of the simplest Criegee intermediate CH2OO

    NASA Astrophysics Data System (ADS)

    Ting, Wei-Lun; Chang, Chun-Hung; Lee, Yu-Fang; Matsui, Hiroyuki; Lee, Yuan-Pern; Lin, Jim-Min, Jr.

    2014-09-01

    The application of a new reaction scheme using CH2I + O2 to generate the simplest Criegee intermediate, CH2OO, has stimulated lively research; the Criegee intermediates are extremely important in atmospheric chemistry. The detailed mechanism of CH2I + O2 is hence important in understanding kinetics involving CH2OO. We employed ultraviolet absorption to probe simultaneously CH2I2, CH2OO, CH2I, and IO in the reaction system of CH2I + O2 upon photolysis at 248 nm of a flowing mixture of CH2I2, O2, and N2 (or SF6) in the pressure range 7.6-779 Torr to investigate the reaction kinetics. With a detailed mechanism to model the observed temporal profiles of CH2I, CH2OO, and IO, we found that various channels of the reaction CH2I + O2 and CH2OO + I play important roles; an additional decomposition channel of CH2I + O2 to form products other than CH2OO or ICH2OO becomes important at pressure less than 60 Torr. The pressure dependence of the derived rate coefficients of various channels of reactions of CH2I + O2 and CH2OO + I has been determined. We derived a rate coefficient also for the self-reaction of CH2OO as k = (8 ± 4) × 10-11 cm3 molecule-1 s-1 at 295 K. The yield of CH2OO from CH2I + O2 was found to have a pressure dependence on N2 and O2 smaller than in previous reports; for air under 1 atm, the yield of ˜30% is about twice of previous estimates.

  1. Detailed mechanism of the CH₂I + O₂ reaction: yield and self-reaction of the simplest Criegee intermediate CH₂OO.

    PubMed

    Ting, Wei-Lun; Chang, Chun-Hung; Lee, Yu-Fang; Matsui, Hiroyuki; Lee, Yuan-Pern; Lin, Jim Jr-Min

    2014-09-14

    The application of a new reaction scheme using CH2I + O2 to generate the simplest Criegee intermediate, CH2OO, has stimulated lively research; the Criegee intermediates are extremely important in atmospheric chemistry. The detailed mechanism of CH2I + O2 is hence important in understanding kinetics involving CH2OO. We employed ultraviolet absorption to probe simultaneously CH2I2, CH2OO, CH2I, and IO in the reaction system of CH2I + O2 upon photolysis at 248 nm of a flowing mixture of CH2I2, O2, and N2 (or SF6) in the pressure range 7.6-779 Torr to investigate the reaction kinetics. With a detailed mechanism to model the observed temporal profiles of CH2I, CH2OO, and IO, we found that various channels of the reaction CH2I + O2 and CH2OO + I play important roles; an additional decomposition channel of CH2I + O2 to form products other than CH2OO or ICH2OO becomes important at pressure less than 60 Torr. The pressure dependence of the derived rate coefficients of various channels of reactions of CH2I + O2 and CH2OO + I has been determined. We derived a rate coefficient also for the self-reaction of CH2OO as k = (8 ± 4) × 10(-11) cm(3) molecule(-1) s(-1) at 295 K. The yield of CH2OO from CH2I + O2 was found to have a pressure dependence on N2 and O2 smaller than in previous reports; for air under 1 atm, the yield of ~30% is about twice of previous estimates.

  2. NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity

    PubMed Central

    2016-01-01

    Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5′-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography—the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry—to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first-principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established. Most significantly, we find that a deprotonated pyridine nitrogen on PLP precludes formation of a true quinonoid species and that there is an equilibrium between the phenolic and protonated Schiff base tautomeric forms of this intermediate. Natural bond orbital analysis indicates that the latter builds up negative charge at the substrate Cα and positive charge at C4′ of the cofactor, consistent with its role as the catalytic tautomer. These findings support the hypothesis that the specificity for β-elimination/replacement versus transamination is dictated in part by the protonation states of ionizable groups on PLP and the reacting substrates and underscore the essential role that NMR crystallography can play in characterizing both chemical structure and dynamics within functioning enzyme active sites. PMID:27779384

  3. The reaction of indole with the aminoacrylate intermediate of Salmonella typhimurium tryptophan synthase: observation of a primary kinetic isotope effect with 3-[(2)H]indole.

    PubMed

    Cash, Michael T; Miles, Edith W; Phillips, Robert S

    2004-12-15

    The bacterial tryptophan synthase alpha(2)beta(2) complex catalyzes the final reactions in the biosynthesis of L-tryptophan. Indole is produced at the active site of the alpha-subunit and is transferred through a 25-30 A tunnel to the beta-active site, where it reacts with an aminoacrylate intermediate. Lane and Kirschner proposed a two-step nucleophilic addition-tautomerization mechanism for the reaction of indole with the aminoacrylate intermediate, based on the absence of an observed kinetic isotope effect (KIE) when 3-[(2)H]indole reacts with the aminoacrylate intermediate. We have now observed a KIE of 1.4-2.0 in the reaction of 3-[(2)H]indole with the aminoacrylate intermediate in the presence of monovalent cations, but not when an alpha-subunit ligand, disodium alpha-glycerophosphate (Na(2)GP), is present. Rapid-scanning stopped flow kinetic studies were performed of the reaction of indole and 3-[(2)H]indole with tryptophan synthase preincubated with L-serine, following the decay of the aminoacrylate intermediate at 350 nm, the formation of the quinonoid intermediate at 476 nm, and the formation of the L-Trp external aldimine at 423 nm. The addition of Na(2)GP dramatically slows the rate of reaction of indole with the alpha-aminoacrylate intermediate. A primary KIE is not observed in the reaction of 3-[(2)H]indole with the aminoacrylate complex of tryptophan synthase in the presence of Na(2)GP, suggesting binding of indole with tryptophan synthase is rate limiting under these conditions. The reaction of 2-methylindole does not show a KIE, either in the presence of Na(+) or Na(2)GP. These results support the previously proposed mechanism for the beta-reaction of tryptophan synthase, but suggest that the rate limiting step in quinonoid intermediate formation from indole and the aminoacrylate intermediate is deprotonation.

  4. Processes forming Gas, Tar, and Coke in Cellulose Gasification from Gas-Phase Reactions of Levoglucosan as Intermediate.

    PubMed

    Fukutome, Asuka; Kawamoto, Haruo; Saka, Shiro

    2015-07-08

    The gas-phase pyrolysis of levoglucosan (LG), the major intermediate species during cellulose gasification, was studied experimentally over the temperature range of 400-900 °C. Gaseous LG did not produce any dehydration products, which include coke, furans, and aromatic substances, although these are characteristic products of the pyrolysis of molten LG. Alternatively, at >500 °C, gaseous LG produced only fragmentation products, such as noncondensable gases and condensable C1 -C3 fragments, as intermediates during noncondensable gas formation. Therefore, it was determined that secondary reactions of gaseous LG can result in the clean (tar- and coke-free) gasification of cellulose. Cooling of the remaining LG in the gas phase caused coke formation by the transition of the LG to the molten state. The molecular mechanisms that govern the gas- and molten-phase reactions of LG are discussed in terms of the acid catalyst effect of intermolecular hydrogen bonding to promote the molten-phase dehydration reactions.

  5. Measuring Rate Constants for Reactions of the Simplest Criegee Intermediate CH_2OO by Monitoring the OH Radical

    NASA Astrophysics Data System (ADS)

    Liu, Yingdi; Bayes, Kyle D.; Sander, Stanley P.

    2014-06-01

    Criegee radicals are important atmospheric intermediates formed from ozonolysis of alkenes. It potentially contributes to the atmospheric oxidation cycle mainly by generating OH radicals through unimolecular decomposition. In this work, we focus on studying the unimolecular decomposition reaction of the smallest Criegee intermediate (CH2OO), which was generated by reacting CH2I with O2. While generating the CH2OO molecule by reacting CH2I with O2, significant amounts of the OH radical were observed by laser-induced fluorescence. The addition of molecules known to react with CH2OO increased the observed decay rates of the OH signal. Using the OH signals as a proxy for the CH2OO concentration, the rate constant for the reaction of hexafluoroacetone with CH2OO was determined. The rate constant for the reaction of SO2 with CH2OO showed no pressure dependence over the range of 50 to 200 Torr. This work provides the direct experimental evidence for the unimolecular decomposition of CH2OO, and possible mechanisms of CH2OO have been investigated by this multidimensional study.

  6. Electrochemically assisted photocatalysis. 2. The role of oxygen and reaction intermediates in the degradation of 4-chlorophenol on immobilized TiO[sub 2] particulate films

    SciTech Connect

    Vinodgopal, K. ); Stafford, U.; Gray, K.A.; Kamat, P.V. )

    1994-07-07

    The electrochemically-assisted photocatalytic degradation of 4-chlorophenol (4-CP) using immobilized TiO[sub 2] particulate films has been investigated by analyzing reaction intermediates under a variety of experimental conditions. The degradations were carried out in both nitrogen- and oxygen-saturated solutions to explore the role of reduced oxygen species and molecular oxygen in the formation of reaction intermediates and in the mineralization of 4-CP. The degradation rate can be greatly improved even in a nitrogen-saturated atmosphere by applying an anodic bias to the TiO[sub 2] film electrodes. 4-Chlorocatechol (4-CC) is the predominant intermediate observed in oxygen-saturated solutions, whereas hydroquinone (HQ) is the primary intermediate in nitrogen-saturated solutions. Molecular oxygen plays an important role in the enhancement of the electrochemically assisted photocatalytic decay rate of 4-CP and the subsequent degradation of reaction intermediates, viz., 4-CC and HQ. 37 refs., 7 figs., 1 tab.

  7. Does shoe heel design influence ground reaction forces and knee moments during maximum lunges in elite and intermediate badminton players?

    PubMed Central

    Cheung, Jason Tak-Man; Ryu, Jiseon

    2017-01-01

    Background Lunge is one frequently executed movement in badminton and involves a unique sagittal footstrike angle of more than 40 degrees at initial ground contact compared with other manoeuvres. This study examined if the shoe heel curvature design of a badminton shoe would influence shoe-ground kinematics, ground reaction forces, and knee moments during lunge. Methods Eleven elite and fifteen intermediate players performed five left-forward maximum lunge trials with Rounded Heel Shoe (RHS), Flattened Heel Shoe (FHS), and Standard Heel Shoes (SHS). Shoe-ground kinematics, ground reaction forces, and knee moments were measured by using synchronized force platform and motion analysis system. A 2 (Group) x 3 (Shoe) ANOVA with repeated measures was performed to determine the effects of different shoes and different playing levels, as well as the interaction of two factors on all variables. Results Shoe effect indicated that players demonstrated lower maximum vertical loading rate in RHS than the other two shoes (P < 0.05). Group effect revealed that elite players exhibited larger footstrike angle, faster approaching speed, lower peak horizontal force and horizontal loading rates but higher vertical loading rates and larger peak knee flexion and extension moments (P < 0.05). Analysis of Interactions of Group x Shoe for maximum and mean vertical loading rates (P < 0.05) indicated that elite players exhibited lower left maximum and mean vertical loading rates in RHS compared to FHS (P < 0.01), while the intermediate group did not show any Shoe effect on vertical loading rates. Conclusions These findings indicate that shoe heel curvature would play some role in altering ground reaction force impact during badminton lunge. The differences in impact loads and knee moments between elite and intermediate players may be useful in optimizing footwear design and training strategy to minimize the potential risks for impact related injuries in badminton. PMID:28334016

  8. Process for preparing transition metal nitrides and transition metal carbonitrides and their reaction intermediates

    DOEpatents

    Maya, Leon

    1988-05-24

    A process for making ammonolytic precursors to nitride and carbonitride ceramics. Extreme reaction conditions are not required and the precursor is a powder-like substance that produces ceramics of improved purity and morphology upon pyrolysis.

  9. Precursors in the preparation of transition metal nitrides and transition metal carbonitrides and their reaction intermediates

    DOEpatents

    Maya, Leon

    1991-01-01

    A process for making ammonolytic precursors to nitride and carbonitride ceramics. Extreme reaction conditions are not required and the precursor is a powder-like substance that produces ceramics of improved purity and morphology upon pyrolysis.

  10. Energy-loss cross sections for inclusive charge-exchange reactions at intermediate energies

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Townsend, Lawrence W.; Dubey, Rajendra R.

    1993-01-01

    Charge-exchange reactions for scattering to the continuum are considered in a high-energy multiple scattering model. Calculations for (p,n) and (He-3,H-3) reactions are made and compared with experimental results for C-12, O-16, and Al-27 targets. Coherent effects are shown to lead to an important role for inelastic multiple scattering terms when light projectiles are considered.

  11. A Rh(II)-catalyzed multicomponent reaction by trapping an α-amino enol intermediate in a traditional two-component reaction pathway

    PubMed Central

    Liu, Shunying; Yao, Wenfeng; Liu, Yuan; Wei, Qinghua; Chen, Jianghui; Wu, Xiang; Xia, Fei; Hu, Wenhao

    2017-01-01

    Multicomponent reactions (MCRs) represent an ideal organic synthesis tool for the rapid construction of complex molecules due to their step and atom economy. Compared to two-component reactions, the development of new MCRs has been greatly limited during the 170 years since the first MCR was reported. Theoretically, the trapping of an active intermediate generated from two components by a third component could change the traditional two-component reaction pathway, leading to the discovery of MCRs. We report an example of the trapping of α-imino enols generated in situ from 1-sulfonyl-1,2,3-triazoles via α-imino metal carbene species by vinylimine ions using C(2)-substituted indoles and paraformaldehyde as precursors in the presence of a rhodium(II) catalyst. The traditional enol-ketone transformation pathway was suspended by the trapping procedure and efficiently switched to an MCR pathway to produce α-amino-β-indole ketones in moderate to good yields. Unexpectedly, the resulting products and the theoretical density functional theory (DFT) calculation results indicated that the enolic carbon had a stronger nucleophilicity than the well-known traditional enamic carbon in the trapping process. The reaction mechanism was investigated using control experiments and detailed DFT calculations, and the synthetic application of the products was also illustrated. The developed strategy provides a mild and rapid access to α-amino-β-indole ketones and suggests a rationale for the discovery of MCRs by trapping an active intermediate with a third component in a traditional two-component reaction pathway. PMID:28345053

  12. Inverse Kinematics Studies of Intermediate-Energy Reactions Relevant for SEE and Medical Problems

    SciTech Connect

    Aichelin, J.; Bargholtz, Ch.; Geren, L.; Tegner, P.-E.; Zartova, I.; Blomgren, J.; Olsson, N.; Budzanowski, A.; Czech, B.; Skwirczynska, I.; Chubarov, M.; Lozhkin, O.; Murin, Yu.; Pljuschev, V.; Zubkov, M.; Ekstroem, C.; Kolozhvari, A.; Persson, H.; Westerberg, L.; Jakobsson, B.

    2005-05-24

    The lack of systematic experimental checks on the intermediate-energy nuclear model simulations of heavily ionizing recoils from nucleon-nucleus collisions -- critical inputs for the Single Event Effect analysis of microelectronics and dosimetry calculations including high-LET components in the cancer tumor radiation therapy -- has been a primary motivation for a new experiment planned at the CELSIUS nuclear storage ring of The Svedberg Laboratory, Uppsala, Sweden. Details of the experiment and the first results from a feasibility study are presented here.

  13. Direct experimental probing and theoretical analysis of the reaction between the simplest Criegee intermediate CH2OO and isoprene.

    PubMed

    Decker, Z C J; Au, K; Vereecken, L; Sheps, L

    2017-03-13

    Recent advances in the spectroscopy of Criegee intermediates (CI) have enabled direct kinetic studies of these highly reactive chemical species. The impact of CI chemistry is currently being incorporated into atmospheric models, including their reactions with trace organic and inorganic compounds. Isoprene, C5H8, is a doubly-unsaturated hydrocarbon that accounts for the largest share of all biogenic emissions around the globe and is also a building block of larger volatile organic compounds. We report direct measurements of the reaction of the simplest CI (CH2OO) with isoprene, using time-resolved cavity-enhanced UV absorption spectroscopy. We find the reaction to be pressure-independent between 15-100 Torr, with a rate coefficient that varies from (1.5 ± 0.1) × 10(-15) cm(3) molecule(-1) s(-1) at room temperature to (23 ± 2) × 10(-15) cm(3) molecule(-1) s(-1) at 540 K. Quantum chemical and transition-state theory calculations of 16 unique channels for CH2OO + isoprene somewhat underpredict the observed T-dependence of the total reaction rate coefficient, but are overall in good agreement with the experimental measurements. This reaction is broadly similar to those with smaller alkenes, proceeding by 1,3-dipolar cycloaddition to one of the two conjugated double bonds of isoprene.

  14. Direct experimental probing and theoretical analysis of the reaction between the simplest Criegee intermediate CH 2 OO and isoprene

    DOE PAGES

    Decker, Z. C. J.; Au, K.; Vereecken, L.; ...

    2017-01-01

    Recent advances in the spectroscopy of Criegee intermediates (CI) have enabled direct kinetic studies of these highly reactive chemical species. The impact of CI chemistry is currently being incorporated into atmospheric models, including their reactions with trace organic and inorganic compounds. Isoprene, C5H8, is a doubly-unsaturated hydrocarbon that accounts for the largest share of all biogenic emissions around the globe and is also a building block of larger volatile organic compounds. We report direct measurements of the reaction of the simplest CI (CH2OO) with isoprene, using time-resolved cavity-enhanced UV absorption spectroscopy. We find the reaction to be pressure-independent between 15–100more » Torr, with a rate coefficient that varies from (1.5 ± 0.1) × 10–15 cm3 molecule–1 s–1 at room temperature to (23 ± 2) × 10–15 cm3 molecule–1 s–1 at 540 K. Quantum chemical and transition-state theory calculations of 16 unique channels for CH2OO + isoprene somewhat underpredict the observed T-dependence of the total reaction rate coefficient, but are overall in good agreement with the experimental measurements. Finally, this reaction is broadly similar to those with smaller alkenes, proceeding by 1,3-dipolar cycloaddition to one of the two conjugated double bonds of isoprene.« less

  15. Direct experimental probing and theoretical analysis of the reaction between the simplest Criegee intermediate CH2OO and isoprene

    DOE PAGES

    Decker, Z. C. J.; Au, K.; Vereecken, L.; ...

    2017-03-07

    Recent advances in the spectroscopy of Criegee intermediates (CI) have enabled direct kinetic studies of these highly reactive chemical species. The impact of CI chemistry is currently being incorporated into atmospheric models, including their reactions with trace organic and inorganic compounds. Isoprene, C5H8, is a doubly-unsaturated hydrocarbon that accounts for the largest share of all biogenic emissions around the globe and is also a building block of larger volatile organic compounds. We report direct measurements of the reaction of the simplest CI (CH2OO) with isoprene, using time-resolved cavity-enhanced UV absorption spectroscopy. We find the reaction to be pressure-independent between 15–100more » Torr, with a rate coefficient that varies from (1.5 ± 0.1) × 10–15 cm3 molecule–1 s–1 at room temperature to (23 ± 2) × 10–15 cm3 molecule–1 s–1 at 540 K. Quantum chemical and transition-state theory calculations of 16 unique channels for CH2OO + isoprene somewhat underpredict the observed T-dependence of the total reaction rate coefficient, but are overall in good agreement with the experimental measurements. Finally, this reaction is broadly similar to those with smaller alkenes, proceeding by 1,3-dipolar cycloaddition to one of the two conjugated double bonds of isoprene.« less

  16. Oligomerization reaction of the Criegee intermediate leads to secondary organic aerosol formation in ethylene ozonolysis.

    PubMed

    Sakamoto, Yosuke; Inomata, Satoshi; Hirokawa, Jun

    2013-12-05

    Ethylene ozonolysis was investigated in laboratory experiments using a Teflon bag reactor. A negative ion chemical ionization mass spectrometer (NI-CIMS) using SO2Cl(-) and Cl(-) as reagent ions was used for product analysis. In addition to the expected gas-phase products, such as formic acid and hydroperoxymethyl formate, oligomeric hydroperoxides composed of the Criegee intermediate (CH2OO) as a chain unit were observed. Furthermore, we observed secondary organic aerosol (SOA) formation from the ethylene ozonolysis, and the particle-phase products were also analyzed by NI-CIMS. The CH2OO oligomers were also observed as particle-phase components, suggesting that the oligomeric hydroperoxides formed in the gas phase partition into the particle phase. By adding methanol as a stabilized Criegee intermediate scavenger, both the gas-phase oligomer formation and SOA formation were strongly suppressed. This indicates that CH2OO plays a critical role in the formation of oligomeric hydroperoxides followed by SOA formation in ethylene ozonolysis. A new formation mechanism for the oligomeric hydroperoxides, which includes sequential addition of CH2OO to hydroperoxides, is proposed.

  17. Understanding and Mitigating the Effects of Stable Dodecahydro- closo -dodecaborate Intermediates on Hydrogen-Storage Reactions

    DOE PAGES

    White, James L.; Newhouse, Rebecca J.; Zhang, Jin Z.; ...

    2016-10-25

    Alkali metal borohydrides can reversibly store hydrogen; however, the materials display poor cyclability, often times linked to occurrence of stable closo-polyborate intermediate species. In an effort to understand the role of such intermediates on the hydrogen storage properties of metal borohydrides, several alkali metal dodecahydro-closo-dodecaborate salts were isolated in anhydrous form and characterized by diffraction and spectroscopic techniques. Mixtures of Li2B12H12, Na2B12H12, and K2B12H12 with the corresponding alkali metal hydrides were subjected to hydrogenation conditions known to favor partial or full reversibility in metal borohydrides. The stoichiometric mixtures of MH and M2B12H12 salts form the corresponding metal borohydrides MBH4 (M=Li,more » Na, K) in almost quantitative yield at 100 MPa H2 and 500 °C. In addition, stoichiometric mixtures of Li2B12H12 and MgH2 were found to form MgB2 at 500 °C and above upon desorption in vacuum. The two destabilization strategies outlined above suggest that metal polyhydro-closo-polyborate species can be converted into the corresponding metal borohydrides or borides, albeit under rather harsh conditions of hydrogen pressure and temperature.« less

  18. Synthesis of Y1BaCu3O(x) superconducting powders by intermediate phase reactions

    NASA Technical Reports Server (NTRS)

    Moure, C.; Fernandez, J. F.; Tartaj, J.; Recio, P.; Duran, P.

    1991-01-01

    A procedure for synthesizing Y1Ba2Cu3O(x) by solid state reactions was developed. The method is based on the use of barium compounds, previously synthesized, as intermediate phases for the process. The reaction kinetics of this procedure were established between 860 C and 920 C. The crystal structure and the presence of second phases were studied by means of XRD. The sintering behavior and ceramic parameters were also determined. The orthorhombic type-I structure was obtained on the synthesized bodies after a cooling cycle in an air atmosphere. Superconducting transition took place at 91 K. Sintering densities higher than 95 percent D sub th were attained at temperatures below 940 C.

  19. Identification of intermediates and products in the reaction of porphyrin iron(III) alkyl complexes with dioxygen

    SciTech Connect

    Arasasingham, R.D.; Balch, A.L.; Latos-Grazynski, L.

    1987-09-16

    Unlike most PFe/sup III+/ (P is a porphyrin dianion) complexes, complexes of the type PFe/sup III/CH/sub 2/R (R = H or CH/sub 3/) are reactive toward dioxygen with the ubiquitous PFe/sup III/O-Fe/sup III/P as the only reported product. Here the authors report on /sup 1/H NMR studies of this reaction which focus on the detection of intermediates and the fate of the alkyl group. These results should be viewed in the context of extensive previous studies on model systems for dioxygen activation in biological systems (heme oxygenases) involving reaction of dioxygen with PFe/sup II/ and on the interaction of peracids and hydroperoxides with PFe/sup III/. Through these studies a number of reactive intermediates including the peroxobridge complex, PFe/sup III/-O-O-Fe/sup III/P, and the ferryl complexes, PFe/sup IV/ double bond O, (B)P-Fe/sup IV/ double bond O (B is an amine), and (P)Fe/sup IV/ double bond O/sup +/ (P is a porphyrin radical monoanion), have been detected.

  20. Photocatalytic decomposition of crotamiton over aqueous TiO(2) suspensions: determination of intermediates and the reaction pathway.

    PubMed

    Fukahori, Shuji; Fujiwara, Taku; Ito, Ryusei; Funamizu, Naoyuki

    2012-09-01

    The photocatalytic degradation of crotamiton in aqueous solution using TiO(2) was investigated. To investigate the effect of initial pH, the photodegradation behaviors of three types of pharmaceuticals were compared (crotamiton, clofibric acid, sulfamethoxazole). The degradation rates of crotamiton in the pH range 3-9 were nearly equal, but those of clofibric acid and sulfamethoxazole were affected by pH. At pH>6.5, TiO(2) particles, clofibric acid and sulfamethoxazole had negative charge, therefore, the repulsive force between TiO(2) particles and anionic pharmaceuticals occurred and a low reaction rate at high pH was observed. The effect of UV intensity and TiO(2) concentration on photodegradation efficiency was also investigated. Linear and logarithmical relationships between UV intensity, TiO(2) concentration and the reaction rate constant were confirmed. Furthermore, the structures of photodegradation intermediates formed concomitantly with the disappearance of crotamiton were estimated. Seven intermediates were characterized by LC/MS/MS analyses, and it was assumed that the photocatalytic degradation of crotamiton was initiated by the attack of electrophilic hydroxyl radicals on aromatic rings and alkyl chains.

  1. Fear load: The psychophysiological over-expression of fear as an intermediate phenotype associated with trauma reactions.

    PubMed

    Norrholm, Seth Davin; Glover, Ebony M; Stevens, Jennifer S; Fani, Negar; Galatzer-Levy, Isaac R; Bradley, Bekh; Ressler, Kerry J; Jovanovic, Tanja

    2015-11-01

    Psychophysiological measures of fear expression provide observable intermediate phenotypes of fear-related symptoms. Research Domain Criteria (RDoC) advocate using neurobiological intermediate phenotypes that provide dimensional correlates of psychopathology. Negative Valence Systems in the RDoC matrix include the construct of acute threat, which can be measured on a physiological level using potentiation of the acoustic startle reflex assessed via electromyography recordings of the orbicularis oculi muscle. Impairments in extinction of fear-potentiated startle due to high levels of fear (termed fear load) during the early phases of extinction have been observed in posttraumatic stress disorder (PTSD). The goals of the current work were to examine dimensional associations between fear-related symptoms of PTSD and fear load variables to test their validity as an intermediate phenotype. We examined extinction of fear-potentiated startle in a cohort (n=269) of individuals with a broad range of civilian trauma exposure (range 0-13 traumatic events per person, mean=3.5). Based on previously reported findings, we hypothesized that fear load would be significantly associated with intrusion and fear memories of an index traumatic event. The results indicated that early extinction was correlated with intrusive thoughts (p=0.0007) and intense physiological reactions to trauma reminders (p=0.036). Degree of adult or childhood trauma exposure, and depression severity were not associated with fear load. After controlling for age, sex, race, income, level of prior trauma, and level of fear conditioning, fear load during extinction was still significantly predictive of intrusive thoughts (p=0.004). The significance of these findings is that they support dimensional associations with symptom severity rather than diagnostic category and, as such, fear load may emerge as a transdiagnostic intermediate phenotype expressed across fear-related disorders (e.g., specific phobia, social

  2. Fear Load: The Psychophysiological Over-expression of Fear as an Intermediate Phenotype Associated with Trauma Reactions

    PubMed Central

    Norrholm, Seth Davin; Glover, Ebony M.; Stevens, Jennifer S.; Fani, Negar; Galatzer-Levy, Isaac R.; Bradley, Bekh; Ressler, Kerry J.; Jovanovic, Tanja

    2014-01-01

    Psychophysiological measures of fear expression provide observable intermediate phenotypes of fear-related symptoms. Research Domains Criteria (RDoC) advocate using neurobiological intermediate phenotypes that provide dimensional correlates of psychopathology. Negative Valence Systems in the RDoC matrix include the construct of acute threat, which can be measured on a physiological level using potentiation of the acoustic startle reflex assessed via electromyography recordings of the orbicularis oculi muscle. Impairments in extinction of fearpotentiated startle due to high levels of fear (termed fear load) during the early phases of extinction have been observed in posttraumatic stress disorder (PTSD). The goals of the current work were to examine dimensional associations between fear-related symptoms of PTSD and fear load variables to test their validity as an intermediate phenotype. We examined extinction of fear-potentiated startle in a cohort (n = 269) of individuals with a broad range of civilian trauma exposure (range 0–13 traumatic events per person, mean = 3.5). Based on previously reported findings, we hypothesized that fear load would be significantly associated with intrusion and fear memories of an index traumatic event. The results indicated that early extinction was correlated with intrusive thoughts (p = 0.0007) and intense physiological reactions to trauma reminders (p = 0.036). Degree of adult or childhood trauma exposure, and depression severity were not associated with fear load. After controlling for age, sex, race, income, level of prior trauma, and level of fear conditioning, fear load during extinction was still significantly predictive of intrusive thoughts (p = 0.004). The significance of these findings is that they support dimensional associations with symptom severity rather than diagnostic category and, as such, fear load may emerge as a transdiagnostic intermediate phenotype expressed across fear-related disorders (e.g., specific

  3. Can we identify patients at risk of life-threatening allergic reactions to food?

    PubMed

    Turner, P J; Baumert, J L; Beyer, K; Boyle, R J; Chan, C-H; Clark, A T; Crevel, R W R; DunnGalvin, A; Fernández-Rivas, M; Gowland, M H; Grabenhenrich, L; Hardy, S; Houben, G F; O'B Hourihane, J; Muraro, A; Poulsen, L K; Pyrz, K; Remington, B C; Schnadt, S; van Ree, R; Venter, C; Worm, M; Mills, E N C; Roberts, G; Ballmer-Weber, B K

    2016-09-01

    Anaphylaxis has been defined as a 'severe, life-threatening generalized or systemic hypersensitivity reaction'. However, data indicate that the vast majority of food-triggered anaphylactic reactions are not life-threatening. Nonetheless, severe life-threatening reactions do occur and are unpredictable. We discuss the concepts surrounding perceptions of severe, life-threatening allergic reactions to food by different stakeholders, with particular reference to the inclusion of clinical severity as a factor in allergy and allergen risk management. We review the evidence regarding factors that might be used to identify those at most risk of severe allergic reactions to food, and the consequences of misinformation in this regard. For example, a significant proportion of food-allergic children also have asthma, yet almost none will experience a fatal food-allergic reaction; asthma is not, in itself, a strong predictor for fatal anaphylaxis. The relationship between dose of allergen exposure and symptom severity is unclear. While dose appears to be a risk factor in at least a subgroup of patients, studies report that individuals with prior anaphylaxis do not have a lower eliciting dose than those reporting previous mild reactions. It is therefore important to consider severity and sensitivity as separate factors, as a highly sensitive individual will not necessarily experience severe symptoms during an allergic reaction. We identify the knowledge gaps that need to be addressed to improve our ability to better identify those most at risk of severe food-induced allergic reactions.

  4. Flow-injection determination of acetone with diazotized anthranilic acid through a fluorescent reaction intermediate.

    PubMed

    García de María, C; Hueso Domínguez, K B; Martín Garrido, N

    2007-09-26

    Acetone and diazotized anthranilic acid react in alkaline solution, giving a fluorescent intermediate that can be measured at excitation and emission wavelengths of 305 and 395 nm, respectively. Based on this, a fluorimetric flow-injection method is proposed for the determination of acetone in aqueous solution. Under the proposed conditions, acetone can be detected at concentrations higher than 8 x 10(-7)M, with a linear application range from 1 x 10(-6) to 2 x 10(-4)M and an R.S.D. of 2.7% (1.0 x 10(-5)M, n=10). A sampling frequency of 24h(-1) is achieved. Some potentially interfering species are investigated.

  5. Workshop on hadron structure from photo-reactions at intermediate energies: Proceedings

    SciTech Connect

    Nathan, A.M.; Sandorfi, A.M.

    1992-01-01

    This report contains papers on the following topics: The proton compton effect: Recent measurements of the electric and magnetic polorizabilities of the proton; experiments on the electric polarizability of the neutron; chiral symmetry and nucleon polarizabilities; chiral model predictions for electromagnetic polarizabilities of the nucleon, a consumer report; the polarizabilities of bound nucleons; nucleon polarizability in free space and in nuclear matter; mechanisms of photon scattering on nucleons at intermediate energies; pion polarizabilities in chiral perturbation theory; pion polarizabilities and the shielding of [sigma](700)-meson exchange in [gamma][gamma][yields][pi][pi] processes; pion and kaon polarizabilities in the quark confinement model; radiative pion photoproduction and pion polarizabilities; pion and sigma polarizabilities and radiative transitions; the quadrupole amplitude in the [gamma][Nu]-[Delta] transition; pion photoproduction and the [gamma][Nu]-[Delta] amplitudes; effective- lagrangians, Watson's theorem, and the E2/M1 mixing ratio in the excitation of the delta resonance; new measurements of the p([rvec [gamma

  6. Ligand intermediates in metal catalyzed reactions. Technical report: third budget year

    SciTech Connect

    Gladysz, J.A.

    1988-04-01

    A progress report is presented in which a new method for the activation of metal-bound methyl groups and the oxidative disproportionation of coordinated ethylene and methane are discussed. Also considered in the report is the divergent kinetic and thermodynamic acidity in organotransition metal hydride complexes and the synthesis, structure, and reactions of chiral rhenium vinylidene complexes.

  7. Fenton-like oxidation of small aromatic acids from biomass burning in atmospheric water and in the absence of light: Identification of intermediates and reaction pathways.

    PubMed

    Santos, Patrícia S M; Domingues, M Rosário M; Duarte, Armando C

    2016-07-01

    A previous work showed that the night period is important for the occurrence of Fenton-like oxidation of small aromatic acids from biomass burning in atmospheric waters, which originate new chromophoric compounds apparently more complex than the precursors, although the chemical transformations involved in the process are still unknown. In this work were identified by gas chromatography-mass spectrometry (GC-MS) and by electrospray mass spectrometry (ESI-MS) the organic intermediate compounds formed during the Fenton-like oxidation of three aromatic acids from biomass burning (benzoic, 4-hydroxybenzoic and 3,5-dihydroxybenzoic acids), the same compounds evaluated in the previous study, in water and in the absence of light, which in turns allows to disclose the chemical reaction pathways involved. The oxidation intermediate compounds found for benzoic acid were 2-hydroxybenzoic, 3-hydroxybenzoic, 4-hydroxybenzoic, 2,3-dihydroxybenzoic, 2,5-dihydroxybenzoic, 2,6-dihydroxybenzoic and 3,4-dihydroxybenzoic acids. The oxidation intermediates for 4-hydroxybenzoic acid were 3,4-hydroxybenzoic acid and hydroquinone, while for 3,5-dihydroxybenzoic acid were 2,4,6-trihydroxybenzoic and 3,4,5-trihydroxybenzoic acids, and tetrahydroxybenzene. The results suggested that the hydroxylation of the three small aromatic acids is the main step of Fenton-like oxidation in atmospheric waters during the night, and that the occurrence of decarboxylation is also an important step during the oxidation of the 4-dihydroxybenzoic and 3,5-dihydroxybenzoic acids. In addition, it is important to highlight that the compounds produced are also small aromatic compounds with potential adverse effects on the environment, besides becoming available for further chemical reactions in atmospheric waters.

  8. Intermediate-scale sodium-concrete reaction tests with basalt and limestone concrete

    SciTech Connect

    Hassberger, J.A.; Muhlestein, L.D.

    1981-01-01

    Ten tests were performed to investigate the chemical reactions and rate and extent of attack between sodium and basalt and limestone concretes. Test temperatures ranged from 510 to 870/sup 0/C (950 to 1600/sup 0/F) and test times from 2 to 24 hours. Sodium hydroxide was added to some of the tests to assess the impact of a sodium hydroxide-aided reaction on the overall penetration characteristics. Data suggest that the sodium penetration of concrete surfaces is limited. Penetration of basalt concrete in the presence of sodium hydroxide is shown to be less severe than attack by the metallic sodium alone. Presence of sodium hydroxide changes the characteristics of sodium penetration of limestone concrete, but no major differences in bulk penetration were observed as compared to penetration by metallic sodium.

  9. Direct measurements of unimolecular and bimolecular reaction kinetics of the Criegee intermediate (CH3)2COO

    DOE PAGES

    Chhantyal-Pun, Rabi; Welz, Oliver; Savee, John D.; ...

    2016-10-18

    Here, the Criegee intermediate acetone oxide, (CH3)2COO, is formed by laser photolysis of 2,2-diiodopropane in the presence of O2 and characterized by synchrotron photoionization mass spectrometry and by cavity ring-down ultraviolet absorption spectroscopy. The rate coefficient of the reaction of the Criegee intermediate with SO2 was measured using photoionization mass spectrometry and pseudo-first-order methods to be (7.3 ± 0.5) × 10–11 cm3 s–1 at 298 K and 4 Torr and (1.5 ± 0.5) × 10–10 cm3 s–1 at 298 K and 10 Torr (He buffer). These values are similar to directly measured rate coefficients of anti-CH3CHOO with SO2, and inmore » good agreement with recent UV absorption measurements. The measurement of this reaction at 293 K and slightly higher pressures (between 10 and 100 Torr) in N2 from cavity ring-down decay of the ultraviolet absorption of (CH3)2COO yielded even larger rate coefficients, in the range (1.84 ± 0.12) × 10–10 to (2.29 ± 0.08) × 10–10 cm3 s–1. Photoionization mass spectrometry measurements with deuterated acetone oxide at 4 Torr show an inverse deuterium kinetic isotope effect, kH/kD = (0.53 ± 0.06), for reactions with SO2, which may be consistent with recent suggestions that the formation of an association complex affects the rate coefficient. The reaction of (CD3)2COO with NO2 has a rate coefficient at 298 K and 4 Torr of (2.1 ± 0.5) × 10–12 cm3 s–1 (measured with photoionization mass spectrometry), again similar to rate for the reaction of anti-CH3CHOO with NO2. Cavity ring-down measurements of the acetone oxide removal without added reagents display a combination of first- and second-order decay kinetics, which can be deconvolved to derive values for both the self-reaction of (CH3)2COO and its unimolecular thermal decay. The inferred unimolecular decay rate coefficient at 293 K, (305 ± 70) s–1, is similar to determinations from ozonolysis. The present measurements confirm the large rate coefficient for

  10. Characterization of the low-temperature intermediates of the reaction of fully reduced soluble cytochrome oxidase with oxygen by electron-paramagnetic-resonance and optical spectroscopy.

    PubMed Central

    Clore, G M; Andréasson, L E; Karlsson, B; Aasa, R; Malmström, B G

    1980-01-01

    The reaction of fully reduced soluble bovine heart cytochrome oxidase with O2 at 173K was investigated by low-temperature optical and e.p.r. spectroscopy, and the kinetics of the reaction were analysed by non-linear optimization techniques. The only e.p.r. signals seen during the course of the reaction are those attributable to low-spin cytochrome a3+ and CuA2+. Quantitative analysis of e.p.r. signals shows that, at the end point of the reaction at 173K, nearly 100% of CuA is in the cupric state but only about 40% of cytochrome a is in the ferric low-spin state. The optical spectra recorded at this stage of the reaction show incomplete oxidation of haem and the absence of a 655 nm absorption band. The only reaction scheme that accounts for both the e.p.r. and optical data is a four-intermediate mechanism involving a branching pathway. The reaction is initiated when fully reduced cytochrome oxidase reacts with O2 to form intermediate I. This is then converted into either intermediate IIA or intermediate IIB. Of these, intermediate IIB is a stable end product at 173 K, but intermediate IIA is converted into intermediate III, which is the stable state at 173 K in this branch of the mechanism. The kinetic analysis of the e.p.r. data allows the unambiguous assignments of the valence states of cytochrome a and CuA in the intermediates. Intermediate I contains cytochrome a2+ and CuA+, intermediate IIA contains low-spin cytochroma a3+ and CuA+, intermediate IIB contains cytochrome a2+ and CuA2+, and intermediate III contains low-spin cytochrome a3+ and CuA2+. The electronic state of the O2-binding CuBa3 couple during the reoxidation of cytochrome oxidase is discussed in terms of an integrated structure containing CuB, cytochrome a3 and O2. PMID:6246874

  11. Ionotropic Receptors Identified within the Tentacle of the Freshwater Snail Biomphalaria glabrata, an Intermediate Host of Schistosoma mansoni

    PubMed Central

    Liang, Di; Wang, Tianfang; Rotgans, Bronwyn A.; McManus, Donald P.; Cummins, Scott F.

    2016-01-01

    Biomphalaria glabrata (B. glabrata) is an air-breathing aquatic mollusc found in freshwater habitats across the Western Hemisphere. It is most well-known for its recognized capacity to act as a major intermediate host for Schistosoma mansoni, the human blood fluke parasite. Ionotropic receptors (IRs), a variant family of the ionotropic glutamate receptors (iGluR), have an evolutionary ancient function in detecting odors to initiate chemosensory signaling. In this study, we applied an array of methods towards the goal of identifying IR-like family members in B. glabrata, ultimately revealing two types, the iGluR and IR. Sequence alignment showed that three ligand-binding residues are conserved in most Biomphalaria iGluR sequences, while the IRs did exhibit a variable pattern, lacking some or all known glutamate-interactingresidues, supporting their distinct classification from the iGluRs. We show that B. glabrata contains 7 putative IRs, some of which are expressed within its chemosensory organs. To further investigate a role for the more ancient IR25a type in chemoreception, we tested its spatial distribution pattern within the snail cephalic tentacle by in situ hybridization. The presence of IR25a within presumptive sensory neurons supports a role for this receptor in olfactory processing, contributing to our understanding of the molecular pathways that are involved in Biomphalaria olfactory processing. PMID:27253696

  12. Dynamics of Radical Intermediates in Prostaglandin H Synthase-1 Cyclooxygenase Reactions is Modulated by Multiple Factors.

    PubMed

    Wu, Gang; Tsai, Ah-Lim

    2016-01-01

    Prostaglandin H synthase (PGHS) catalyzes the biosynthesis of PGG2 and PGH2, the precursor of all prostanoids, from arachidonic acid (AA). PGHS exhibits two enzymatic activities following a branched-chain radical mechanism: 1) a peroxidase activity (POX) that utilizes hydroperoxide through heme redox cycles to generate the critical Tyr385 tyrosyl radical for coupling both enzyme activities; 2) the cyclooxygenase (COX) activity inserting two oxygen molecules into AA to generate endoperoxide/hydroperoxide PGG2 through a series of radical intermediates. Upon the generation of Tyr385 radical, COX catalysis is initiated, with C13 pro-S hydrogen abstraction from AA by Tyr385 radical to generate arachidonyl substrate radical. Oxygen provides a large driving force for the subsequent fast steps leading to the formation of PGG2, including radical redistributions, ring formations, and rearrangements. On the other hand, if the supply of oxygen is severed, equilibrium between arachidonyl radical and tyrosyl radical(s) biases largely towards the latter. In this study, we demonstrate that such equilibrium is shifted by many factors, including temperature, chemical structures of fatty acid substrates and limited supply of oxygen. We also, for the first time, reveal that this equilibrium is significantly affected by co-substrates of POX. The presence of efficient POX co-substrates, which reduces heme to its ferric state, apparently biases the equilibrium towards arachidonyl radical. Therefore a dynamic interplay exists between the two activities of PGHS.

  13. Exome Sequencing Identifies GNB4 Mutations as a Cause of Dominant Intermediate Charcot-Marie-Tooth Disease

    PubMed Central

    Soong, Bing-Wen; Huang, Yen-Hua; Tsai, Pei-Chien; Huang, Chien-Chang; Pan, Hung-Chuan; Lu, Yi-Chun; Chien, Hsin-Ju; Liu, Tze-Tze; Chang, Ming-Hong; Lin, Kon-Ping; Tu, Pang-Hsien; Kao, Lung-Sen; Lee, Yi-Chung

    2013-01-01

    Charcot-Marie-Tooth disease (CMT) is a heterogeneous group of inherited neuropathies. Mutations in approximately 45 genes have been identified as being associated with CMT. Nevertheless, the genetic etiologies of at least 30% of CMTs have yet to be elucidated. Using a genome-wide linkage study, we previously mapped a dominant intermediate CMT to chromosomal region 3q28–q29. Subsequent exome sequencing of two affected first cousins revealed heterozygous mutation c.158G>A (p.Gly53Asp) in GNB4, encoding guanine-nucleotide-binding protein subunit beta-4 (Gβ4), to cosegregate with the CMT phenotype in the family. Further analysis of GNB4 in an additional 88 unrelated CMT individuals uncovered another de novo mutation, c.265A>G (p.Lys89Glu), in this gene in one individual. Immunohistochemistry studies revealed that Gβ4 was abundant in the axons and Schwann cells of peripheral nerves and that expression of Gβ4 was significantly reduced in the sural nerve of the two individuals carrying the c.158G>A (p.Gly53Asp) mutation. In vitro studies demonstrated that both the p.Gly53Asp and p.Lys89Glu altered proteins impaired bradykinin-induced G-protein-coupled-receptor (GPCR) signaling, which was facilitated by the wild-type Gβ4. This study identifies GNB4 mutations as a cause of CMT and highlights the importance of Gβ4-related GPCR signaling in peripheral-nerve function in humans. PMID:23434117

  14. [Ligand intermediates in metal-catalyzed reactions]. Progress report, July 1, 1989--June 30, 1992

    SciTech Connect

    Not Available

    1992-08-01

    This report consists of sections on sigma bond complexes of alkenes, a new carbon-hydrogen bond activation reaction of alkene complexes, carbon-hydrogen bond migrations in alkylidene complexes, carbon- hydrogen bond migrations in alkyne complexes, synthesis, structure and reactivity of C{sub x} complexes, synthesis and reactivity of alcohol and ether complexes, new catalysts for the epimerization of secondary alcohols; carbon-hydrogen bond activation in alkoxide complexes, pi/sigma equilibria in metal/O=CXX` complexes, and other hydrocarbon ligands; miscellaneous.(WET)

  15. Laboratory detection of the D3h isomer of carbon trioxide (CO3): Potential intermediate in the CO2 + O reaction in atmospheres

    NASA Astrophysics Data System (ADS)

    Jamieson, C.; Mebel, A.; Kaiser, R.

    Radiation induced degradation of oxygen-bearing molecules like ozone or carbon dioxide can liberate oxygen atoms that are electronically excited 1 D state and or superthermal high kinetic energy and may subsequently react with carbon dioxide in the atmospheres of Venus Mars or the Earth In this reaction the carbon trioxide CO 3 intermediate was found to form and has been subsequently included in many reaction models to explain the heavy isotope enrichment of stratospheric carbon dioxide on Earth and the regeneration of carbon dioxide on Mars both in the upper atmosphere and catalyzed in solid CO 2 surfaces Studies of the O 1 D CO 2 reaction show a nearly statistical rate of isotope exchange suggesting that the CO 3 intermediate may possess a high degree of symmetry From theoretical calculations and matrix isolation studies we know that the lowest energy CO 3 isomer has C 2v symmetry however the D 3h isomer lies only 0 1 kcal mol -1 higher in energy than the C 2v structure with an isomerization barrier of 4 4 kcal mol -1 thus interconversion of these two structures should readily occur To date the C 2v structure has been the only isomer that has been experimentally detected and therefore inclusion of the symmetric D 3h isomer in the isotope exchange models is only theoretical Here we present the first experimental detection of the D 3h isomer of carbon trioxide which was identified by two fundamental vibrational frequencies nu 1 and nu 5 using infrared

  16. Using first principles calculations to identify new destabilized metal hydride reactions for reversible hydrogen storage.

    PubMed

    Alapati, Sudhakar V; Karl Johnson, J; Sholl, David S

    2007-03-28

    Hydrides of period 2 and 3 elements are promising candidates for hydrogen storage, but typically have heats of reaction that are too high to be of use for fuel cell vehicles. Recent experimental work has focused on destabilizing metal hydrides through mixing metal hydrides with other compounds. A very large number of possible destabilized metal hydride reaction schemes exist, but the thermodynamic data required to assess the enthalpies of these reactions are not available in many cases. We have used density functional theory calculations to predict the reaction enthalpies for more than 300 destabilization reactions that have not previously been reported. The large majority of these reactions are predicted not to be useful for reversible hydrogen storage, having calculated reaction enthalpies that are either too high or too low, and hence these reactions need not be investigated experimentally. Our calculations also identify multiple promising reactions that have large enough hydrogen storage capacities to be useful in practical applications and have reaction thermodynamics that appear to be suitable for use in fuel cell vehicles and are therefore promising candidates for experimental work.

  17. Chlorobenzene degradation by electro-heterogeneous catalysis in aqueous solution: intermediates and reaction mechanism.

    PubMed

    Wang, Jiade; Mei, Yu; Liu, Chenliang; Chen, Jianmeng

    2008-01-01

    This study was performed to investigate the variables that influence chlorobenzene (CB) degradation in aqueous solution by electro-heterogeneous catalysis. The effects of current density, pH, and electrolyte concentration on CB degradation were determined. The degradation efficiency of CB was almost 100% with an initial CB concentration of 50 mg/L, current density 15 mA/cm2, initial pH 10, electrolyte concentration 0.1 mol/L, and temperature 25 degrees C after 90 min of reaction. Under the same conditions, the degradation efficiency of CB was only 51% by electrochemical (EC) process, which showed that electro-heterogeneous catalysis was more efficient than EC alone. The analysis results of Purge-and-Trap chromatography-mass spectrometry (P&T/GC/MS) and ion chromatography (IC) indicated that in the reaction process, the initial *OH attack could occur at the C-Cl bond of CB, yielding phenol and biphenyl with the release of Cl-. Further oxidation of phenol and biphenyl produced p-Vinylbenzoic acid and hydroquinol. Finally, the compounds were oxidized to butenedioic acid and other small-molecule acids.

  18. Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA

    DOE PAGES

    Hashimoto, Hideharu; Pais, June E.; Dai, Nan; ...

    2015-08-31

    The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and α-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solvedmore » NgTet1–5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH2-) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH2 towards the metal-ligand water molecule, where a dioxygen O2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably due to the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate.« less

  19. Isolation of bis(copper) key intermediates in Cu-catalyzed azide-alkyne "click reaction".

    PubMed

    Jin, Liqun; Tolentino, Daniel R; Melaimi, Mohand; Bertrand, Guy

    2015-06-01

    The copper-catalyzed 1,3-dipolar cycloaddition of an azide to a terminal alkyne (CuAAC) is one of the most popular chemical transformations, with applications ranging from material to life sciences. However, despite many mechanistic studies, direct observation of key components of the catalytic cycle is still missing. Initially, mononuclear species were thought to be the active catalysts, but later on, dinuclear complexes came to the front. We report the isolation of both a previously postulated π,σ-bis(copper) acetylide and a hitherto never-mentioned bis(metallated) triazole complex. We also demonstrate that although mono- and bis-copper complexes promote the CuAAC reaction, the dinuclear species are involved in the kinetically favored pathway.

  20. Reactivity and reaction intermediates for acetic acid adsorbed on CeO2(111)

    SciTech Connect

    Calaza, Florencia C.; Chen, Tsung -Liang; Mullins, David R.; Xu, Ye; Steven H. Overbury

    2015-05-02

    Adsorption and reaction of acetic acid on a CeO2(1 1 1) surface was studied by a combination of ultra-highvacuum based methods including temperature desorption spectroscopy (TPD), soft X-ray photoelectronspectroscopy (sXPS), near edge X-ray absorption spectroscopy (NEXAFS) and reflection absorption IRspectroscopy (RAIRS), together with density functional theory (DFT) calculations. TPD shows that thedesorption products are strongly dependent upon the initial oxidation state of the CeO2 surface, includingselectivity between acetone and acetaldehyde products. The combination of sXPS and NEXAFS demon-strate that acetate forms upon adsorption at low temperature and is stable to above 500 K, above whichpoint ketene, acetone and acetic acid desorb. Furthermore, DFT and RAIRS show that below 500 K, bridge bondedacetate coexists with a moiety formed by adsorption of an acetate at an oxygen vacancy, formed bywater desorption.

  1. Reactivity and reaction intermediates for acetic acid adsorbed on CeO2(111)

    DOE PAGES

    Calaza, Florencia C.; Chen, Tsung -Liang; Mullins, David R.; ...

    2015-05-02

    Adsorption and reaction of acetic acid on a CeO2(1 1 1) surface was studied by a combination of ultra-highvacuum based methods including temperature desorption spectroscopy (TPD), soft X-ray photoelectronspectroscopy (sXPS), near edge X-ray absorption spectroscopy (NEXAFS) and reflection absorption IRspectroscopy (RAIRS), together with density functional theory (DFT) calculations. TPD shows that thedesorption products are strongly dependent upon the initial oxidation state of the CeO2 surface, includingselectivity between acetone and acetaldehyde products. The combination of sXPS and NEXAFS demon-strate that acetate forms upon adsorption at low temperature and is stable to above 500 K, above whichpoint ketene, acetone and acetic acidmore » desorb. Furthermore, DFT and RAIRS show that below 500 K, bridge bondedacetate coexists with a moiety formed by adsorption of an acetate at an oxygen vacancy, formed bywater desorption.« less

  2. Modeling stopped-flow data for nucleic acid duplex formation reactions: the importance of off-path intermediates.

    PubMed

    Sikora, Jacqueline R; Rauzan, Brittany; Stegemann, Rachel; Deckert, Alice

    2013-08-01

    Evidence for unexpected off-path intermediates to DNA duplex formation is presented. These off-path intermediates are shown to involve unimolecular and, in one case, bimolecular structure in one of the single strands of complementary DNA. Three models are developed to account for the observed single-stranded structures that are formed in parallel with duplex formation. These models are applied to the analysis of stopped-flow data for eight different nonself-complementary duplex formation reactions in order to extract the elementary rate constant for formation of the duplex from the complementary random coil single-stranded DNA. The free energy of activation (at 25 °C) for the denaturation of each duplex is calculated from these data and is shown to have a linear correlation to the overall standard free energy for duplex formation (also at 25 °C). Duplexes that contain mismatches obey a parallel linear free-energy (LFE) relationship with a y-intercept that is greater than that of duplexes without mismatches. Slopes near unity for the LFE relationships indicate that all duplexes go through an early, unstructured transition state.

  3. Investigation of the O+allyl addition/elimination reaction pathways from the OCH{sub 2}CHCH{sub 2} radical intermediate

    SciTech Connect

    FitzPatrick, Benjamin L.; Lau, K.-C.; Butler, Laurie J.; Lee, S.-H.; Lin, Jim Jr-Min

    2008-08-28

    These experiments study the preparation of and product channels resulting from OCH{sub 2}CHCH{sub 2}, a key radical intermediate in the O+allyl bimolecular reaction. The data include velocity map imaging and molecular beam scattering results to probe the photolytic generation of the radical intermediate and the subsequent pathways by which the radicals access the energetically allowed product channels of the bimolecular reaction. The photodissociation of epichlorohydrin at 193.3 nm produces chlorine atoms and c-OCH{sub 2}CHCH{sub 2} radicals; these undergo a facile ring opening to the OCH{sub 2}CHCH{sub 2} radical intermediate. State-selective resonance-enhanced multiphoton ionization (REMPI) detection resolves the velocity distributions of ground and spin-orbit excited state chlorine independently, allowing for a more accurate determination of the internal energy distribution of the nascent radicals. We obtain good agreement detecting the velocity distributions of the Cl atoms with REMPI, vacuum ultraviolet (VUV) photoionization at 13.8 eV, and electron bombardment ionization; all show a bimodal distribution of recoil kinetic energies. The dominant high recoil kinetic energy feature peaks near 33 kcal/mol. To elucidate the product channels resulting from the OCH{sub 2}CHCH{sub 2} radical intermediate, the crossed laser-molecular beam experiment uses VUV photoionization and detects the velocity distribution of the possible products. The data identify the three dominant product channels as C{sub 3}H{sub 4}O (acrolein)+H, C{sub 2}H{sub 4}+HCO (formyl radical), and H{sub 2}CO (formaldehyde)+C{sub 2}H{sub 3}. A small signal from C{sub 2}H{sub 2}O (ketene) product is also detected. The measured velocity distributions and relative signal intensities at m/e=27, 28, and 29 at two photoionization energies show that the most exothermic product channel, C{sub 2}H{sub 5}+CO, does not contribute significantly to the product branching. The higher internal energy onset of the

  4. Characterization of the folding and unfolding reactions of single-chain monellin: evidence for multiple intermediates and competing pathways.

    PubMed

    Patra, Ashish K; Udgaonkar, Jayant B

    2007-10-23

    folding process could be determined quantitatively by an unfolding assay, indicated that the fast phase of fluorescence change corresponds to the accumulation of two intermediates of differing stabilities on competing folding pathways. They also indicated that the very slow kinetic phase of refolding, identified by ANS binding, corresponds to the formation of native protein. Kinetic experiments in which the unfolding of native protein in GdnHCl was monitored by the change in intrinsic tryptophan fluorescence indicated that this change occurs in two kinetic phases. Double-jump, interrupted-unfolding experiments, in which the accumulation of unfolding intermediates and native protein during the unfolding process could be determined quantitatively by a refolding assay, indicated that the fast unfolding phase corresponds to the formation of fully unfolded protein via one unfolding pathway and that the slow unfolding phase corresponds to a separate unfolding pathway populated by partially unfolded intermediates. It is shown that the unfolded form produced by the fast unfolding pathway is the one which gives rise to the very fast folding pathway and that the unfolded form produced by the slower unfolding pathway is the one which gives rise to the slow and fast folding pathways.

  5. 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.

  6. Single turnover kinetics of tryptophan hydroxylase: evidence for a new intermediate in the reaction of the aromatic amino acid hydroxylases.

    PubMed

    Pavon, Jorge Alex; Eser, Bekir; Huynh, Michaela T; Fitzpatrick, Paul F

    2010-09-07

    Tryptophan hydroxylase (TrpH) uses a non-heme mononuclear iron center to catalyze the tetrahydropterin-dependent hydroxylation of tryptophan to 5-hydroxytryptophan. The reactions of the TrpH.Fe(II), TrpH.Fe(II).tryptophan, TrpH.Fe(II).6MePH(4).tryptophan, and TrpH.Fe(II).6MePH(4).phenylalanine complexes with O(2) were monitored by stopped-flow absorbance spectroscopy and rapid quench methods. The second-order rate constant for the oxidation of TrpH.Fe(II) has a value of 104 M(-1) s(-1) irrespective of the presence of tryptophan. Stopped-flow absorbance analyses of the reaction of the TrpH.Fe(II).6MePH(4).tryptophan complex with oxygen are consistent with the initial step being reversible binding of oxygen, followed by the formation with a rate constant of 65 s(-1) of an intermediate I that has maximal absorbance at 420 nm. The rate constant for decay of I, 4.4 s(-1), matches that for formation of the 4a-hydroxypterin product monitored at 248 nm. Chemical-quench analyses show that 5-hydroxytryptophan forms with a rate constant of 1.3 s(-1) and that overall turnover is limited by a subsequent slow step, presumably product release, with a rate constant of 0.2 s(-1). All of the data with tryptophan as substrate can be described by a five-step mechanism. In contrast, with phenylalanine as substrate, the reaction can be described by three steps: a second-order reaction with oxygen to form I, decay of I as tyrosine forms, and slow product release.

  7. Isomer production in intermediate-energy deuteron-induced reactions on a gold target

    NASA Astrophysics Data System (ADS)

    Balabekyan, A. R.; Karapetyan, G. S.; Demekhina, N. A.; Drnoyan, D. R.; Zhemenik, V. I.; Adam, J.; Zavorka, L.; Solnyshkin, A. A.; Tsoupko-Sitnikov, V. M.; Guimarães, V.; Deppman, A.

    2016-05-01

    Residual nuclei formed at ground and isomeric states from the interaction of 4.4 GeV deuteron with a gold target have been measured and investigated by the induced-activity method. Eight isomeric and ground-state pairs of target residues in the mass range of 44 identified by off-line γ -spectroscopy analysis and their isomer ratios were obtained from the cross-section production. From the isomer ratio data of the formed 196Au and 197Hg nuclei, the average intrinsic angular momentum of the composite system was estimated by means of a simple statistical model based on the formalism developed by Huizenga and Vandenbosch.

  8. Two progressive substrates of the M-intermediate can be identified in glucose-embedded, wild-type bacteriorhodopsin.

    PubMed Central

    Vonck, J; Han, B G; Burkard, F; Perkins, G A; Glaeser, R M

    1994-01-01

    Glucose-embedded bacteriorhodopsin shows M-intermediates with different Amide I infrared bands when samples are illuminated at 240 or 260 K, in contrast with fully hydrated samples where a single M-intermediate is formed at all temperatures. In hydrated, but not in glucose-embedded specimens, the N intermediate is formed together with M at 260 K. Both Fourier transform infrared and electron diffraction data from glucose-embedded bacteriorhodopsin suggest that at 260 K a mixture is formed of the M-state that is trapped at 240 K, and a different M-intermediate (MN) that is also formed by mutant forms of bacteriorhodopsin that lack a carboxyl group at the 96 position, necessary for the M to N transition. The fact that an MN species is trapped in glucose-embedded, wild-type bacteriorhodopsin suggests that the glucose samples lack functionally important water molecules that are needed for the proton transfer aspartate 96 to the Schiff base (and, thus, to form the N-intermediate); thus, aspartate 96 is rendered ineffective as a proton donor. PMID:7811930

  9. A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

    NASA Astrophysics Data System (ADS)

    Nguyen, Trong-Nghia; Putikam, Raghunath; Lin, M. C.

    2015-03-01

    We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH2OO and anti/syn-CH3C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH2OO and anti-CH3C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH3C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C-H bonds. For syn-CH3C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH3 group by the terminal O atom producing CH2C(H)O-OH. At 298 K, the intramolecular insertion process in CH2OO was found to be 600 times faster than the commonly assumed ring-closing reaction.

  10. Reactions of connective tissue to amalgam, intermediate restorative material, mineral trioxide aggregate, and mineral trioxide aggregate mixed with chlorhexidine.

    PubMed

    Sumer, Mahmut; Muglali, Mehtap; Bodrumlu, Emre; Guvenc, Tolga

    2006-11-01

    The aim of this study was to histopathologically examine the biocompatibility of the high-copper amalgam, intermediate restorative material (IRM), mineral trioxide aggregate (MTA), and MTA mixed with chlorhexidine (CHX). This study was conducted to observe the rat subcutaneous connective tissue reaction to the implanted tubes filled with amalgam, IRM, MTA, and MTA mixed with CHX. The animals were sacrificed 15, 30, and 60 days after the implantation procedure. The implant sites were excised and prepared for histological evaluation. Sections of 5 to 6 microm thickness were cut by a microtome and stained with hemotoxylin eosin and examined under a light microscope. The inflammatory reactions were categorized as weak (none or few inflammatory cells < or =25 cells), moderate (>25 cells), and severe (a lot of inflammatory cells not to be counted, giant cells, and granulation tissue). Thickness of fibrous capsules measured five different areas by the digital imaging and the mean values were scored. Amalgam, IRM, and MTA mixed with CHX caused a weak inflammatory response on days 15, 30, and 60. MTA provoked an initial severe inflammatory response that subsided at the 30 and 60 day study period. A clear fibrous capsule was observed beginning from the 15 days in all of the groups. Within the limits of this study, amalgam, IRM, MTA, and MTA mixed with CHX materials were surrounded by fibrous connective tissue indicated that they were well tolerated by the tissues, therefore, MTA/CHX seemed to be biocompatible.

  11. A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

    SciTech Connect

    Nguyen, Trong-Nghia; Putikam, Raghunath; Lin, M. C.

    2015-03-28

    We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH{sub 2}OO and anti/syn-CH{sub 3}C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH{sub 2}OO and anti-CH{sub 3}C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH{sub 3}C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C–H bonds. For syn-CH{sub 3}C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH{sub 3} group by the terminal O atom producing CH{sub 2}C(H)O–OH. At 298 K, the intramolecular insertion process in CH{sub 2}OO was found to be 600 times faster than the commonly assumed ring-closing reaction.

  12. Understanding the reaction mechanism and intermediate stabilization in mammalian serine racemase using multiscale quantum-classical simulations.

    PubMed

    Nitoker, Neta; Major, Dan Thomas

    2015-01-20

    Serine racemase (SerR) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme catalyzing the racemization of l-Ser to d-Ser. In mammals, d-Ser is an endogenous coagonist required for the activation of N-methyl-d-aspartate receptors (NMDARs), thus making SerR a promising pharmaceutical target. However, mechanistic studies of SerR are scarce, and the details of the enzymatic racemization reaction are not fully understood. In the current study we elucidate the catalytic mechanism in SerR by employing combined multiscale classical/quantum simulations. The free energy profile of a model SerR racemization reaction is first calculated in the gas phase and in aqueous solution. To obtain the free energy profile for the enzymatic reaction, hybrid quantum mechanics/molecular mechanics molecular dynamics simulations in conjunction with umbrella sampling are performed. The results suggest that in SerR, similarly to the related enzyme alanine racemase, the unprotonated PLP-substrate intermediate is stabilized mostly due to solvation effects contributed by water molecules and active-site residues, as well as long-range electrostatic interactions with the enzyme environment. In addition to a deeper understanding of the racemization mechanism in SerR, based on our simulations we propose specific mutations, which might shift the SerR equilibrium in favor of either l-Ser or d-Ser. Finally, the current studies have produced catalytically competent forms of the rat and human enzymes, which may serve as targets for future docking studies and drug design.

  13. Oxo iron(IV) as an oxidative active intermediate of p-chlorophenol in the Fenton reaction: a DFT study.

    PubMed

    Mignon, Pierre; Pera-Titus, Marc; Chermette, Henry

    2012-03-21

    Debate continues over which active species plays the role of oxidative agent during the Fenton reaction-the HO˙ radical or oxo iron [Fe(IV)O](2+). In this context, the present study investigates the oxidation of p-chlorophenol by [Fe(IV)O(H(2)O)(5)](2+) using DFT calculations, within gas-phase and micro-solvated models, in order to explore the possible role of oxo iron as a reactant. The results show that the chlorine atom substitution of p-chlorophenol by oxo iron is a highly stabilising step (ΔH = -83 kcal mol(-1)) with a free energy barrier of 5.8 kcal mol(-1) in the micro-solvated model. This illustrates the high oxidising power of the [Fe(IV)O(H(2)O)(5)](2+) complex. On the other hand, the breaking of the Fe-O bond, leading to the formation of hydroquinone, is observed to be the rate-determining step of the reaction. The rather large free energy barrier corresponding to this bond cleavage amounts to 10.2 and 9.3 kcal mol(-1) in the gas-phase and micro-solvated models, respectively. Elsewhere, the lifetime of the HO˙ radical has previously been shown to be extremely small. These facts, combined with observations of oxo iron under certain experimental conditions, suggest that oxo iron is a highly plausible oxidative species of the reaction. In addition, a trigonal bipyramidal iron complex, coordinated either by hydroxyl groups and/or by water molecules, has been found in all described mechanisms. This structure appears to be a stable intermediate; and to our knowledge, it has not been characterised by previous studies.

  14. Synthesis of Y1Ba2Cu3O(sub x) superconducting powders by intermediate phase reaction

    NASA Technical Reports Server (NTRS)

    Moore, C.; Fernandez, J. F.; Recio, P.; Duran, P.

    1990-01-01

    One of the more striking problems for the synthesis of the Y1Ba2Cu3Ox compound is the high-temperature decomposition of the BaCO3. This compound is present as raw material or as an intermediate compound in chemical processes such as amorphous citrate, coprecipitation oxalate, sol-gel process, acetate pyrolisis, etc. This fact makes difficult the total formation reaction of the Y1Ba2Cu3Ox phase and leads to the presence of undesirable phases such as the BaCuO2 phase, the 'green phase', Y2BaCuO5 and others. Here, a new procedure to overcome this difficulty is studied. The barium cation is previously combined with yttrium and/or copper to form intermediate compounds which can react between them to give Y1Ba2Cu3Ox. BaY2O4 and BaCu2O3 react according to the equation BaY2O4+3BaCu2O3 yields 2Y1Ba2Cu3Ox. BaY2O4 is a stable compound of the Y2O3-BaO system; BaCu2O3 is an intimate mixture of BaCuO2 and uncombined CuO. The reaction kinetics of these phases have been established between 860 and 920 C. The phase evolution has been determined. The crystal structure of the Y1Ba2Cu3Ox obtained powder was studied. According to the results obtained from the kinetics study the Y1Ba2Cu3Ox the synthesis was performed at temperatures of 910 to 920 C for short treatment times (1 to 2 hours). Pure Y1Ba2Cu3Ox was prepared, which develops orthorombic type I structure despite of the cooling cycle. Superconducting transition took place at 91 K. The sintering behavior and the superconducting properties of sintered samples were studied. Density, microstructure and electrical conductivity were measured. Sintering densities higher than 95 percent D(sub th) were attained at temperatures below 940 C. Relatively fine grained microstructure was observed, and little or no-liquid phase was detected.

  15. Atmospheric isoprene ozonolysis: impacts of stabilized Criegee intermediate reactions with SO2, H2O and dimethyl sulfide

    NASA Astrophysics Data System (ADS)

    Newland, M. J.; Rickard, A. R.; Vereecken, L.; Muñoz, A.; Ródenas, M.; Bloss, W. J.

    2015-03-01

    Isoprene is the dominant global biogenic volatile organic compound (VOC) emission. Reactions of isoprene with ozone are known to form stabilised Criegee intermediates (SCIs), which have recently been shown to be potentially important oxidants for SO2 and NO2 in the atmosphere; however the significance of this chemistry for SO2 processing (affecting sulfate aerosol) and NO2 processing (affecting NOx levels) depends critically upon the fate of the SCI with respect to reaction with water and decomposition. Here, we have investigated the removal of SO2 in the presence of isoprene and ozone, as a function of humidity, under atmospheric boundary layer conditions. The SO2 removal displays a clear dependence on relative humidity, confirming a significant reaction for isoprene derived SCI with H2O. Under excess SO2 conditions, the total isoprene ozonolysis SCI yield was calculated to be 0.56 (±0.03). The observed SO2 removal kinetics are consistent with a relative rate constant, k(SCI + H2O)/k(SCI + SO2), of 5.4 (±0.8) × 10-5 for isoprene derived SCI. The relative rate constant for k(SCI decomposition)/k(SCI + SO2) is 8.4 (±5.0) × 1010 cm-3. Uncertainties are ±2σ and represent combined systematic and precision components. These kinetic parameters are based on the simplification that a single SCI species is formed in isoprene ozonolysis, an approximation which describes the results well across the full range of experimental conditions. Our data indicate that isoprene-derived SCIs are unlikely to make a substantial contribution to gas-phase SO2 oxidation in the troposphere. We also present results from an analogous set of experiments, which show a clear dependence of SO2 removal in the isoprene-ozone system as a function of dimethyl sulfide concentration. We propose that this behaviour arises from a rapid reaction between isoprene-derived SCI and DMS; the observed SO2 removal kinetics are consistent with a relative rate constant, k(SCI + DMS)/k(SCI + SO2), of 4.1 (±2

  16. Atmospheric isoprene ozonolysis: impacts of stabilised Criegee intermediate reactions with SO2, H2O and dimethyl sulfide

    NASA Astrophysics Data System (ADS)

    Newland, M. J.; Rickard, A. R.; Vereecken, L.; Muñoz, A.; Ródenas, M.; Bloss, W. J.

    2015-08-01

    Isoprene is the dominant global biogenic volatile organic compound (VOC) emission. Reactions of isoprene with ozone are known to form stabilised Criegee intermediates (SCIs), which have recently been shown to be potentially important oxidants for SO2 and NO2 in the atmosphere; however the significance of this chemistry for SO2 processing (affecting sulfate aerosol) and NO2 processing (affecting NOx levels) depends critically upon the fate of the SCIs with respect to reaction with water and decomposition. Here, we have investigated the removal of SO2 in the presence of isoprene and ozone, as a function of humidity, under atmospheric boundary layer conditions. The SO2 removal displays a clear dependence on relative humidity, confirming a significant reaction for isoprene-derived SCIs with H2O. Under excess SO2 conditions, the total isoprene ozonolysis SCI yield was calculated to be 0.56 (±0.03). The observed SO2 removal kinetics are consistent with a relative rate constant, k(SCI + H2O) / k(SCI + SO2), of 3.1 (±0.5) × 10-5 for isoprene-derived SCIs. The relative rate constant for k(SCI decomposition) / k(SCI+SO2) is 3.0 (±3.2) × 1011 cm-3. Uncertainties are ±2σ and represent combined systematic and precision components. These kinetic parameters are based on the simplification that a single SCI species is formed in isoprene ozonolysis, an approximation which describes the results well across the full range of experimental conditions. Our data indicate that isoprene-derived SCIs are unlikely to make a substantial contribution to gas-phase SO2 oxidation in the troposphere. We also present results from an analogous set of experiments, which show a clear dependence of SO2 removal in the isoprene-ozone system as a function of dimethyl sulfide concentration. We propose that this behaviour arises from a rapid reaction between isoprene-derived SCIs and dimethyl sulfide (DMS); the observed SO2 removal kinetics are consistent with a relative rate constant, k(SCI + DMS

  17. Mixed Anhydride Intermediates in the Reaction of 5(4H)‐Oxazolones with Phosphate Esters and Nucleotides

    PubMed Central

    Liu, Ziwei; Rigger, Lukas; Rossi, Jean‐Christophe; Sutherland, John D.

    2016-01-01

    Abstract 5(4H)‐Oxazolones can be formed through the activation of acylated α‐amino acids or of peptide C termini. They constitute potentially activated intermediates in the abiotic chemistry of peptides that preceded the origin of life or early stages of biology and are capable of yielding mixed carboxylic‐phosphoric anhydrides upon reaction with phosphate esters and nucleotides. Here, we present the results of a study aimed at investigating the chemistry that can be built through this interaction. As a matter of fact, the formation of mixed anhydrides with mononucleotides and nucleic acid models is shown to take place at positions involving a mono‐substituted phosphate group at the 3’‐ or 5’‐terminus but not at the internal phosphodiester linkages. In addition to the formation of mixed anhydrides, the subsequent intramolecular acyl or phosphoryl transfers taking place at the 3’‐terminus are considered to be particularly relevant to the common prebiotic chemistry of α‐amino acids and nucleotides. PMID:27534830

  18. Transition Metal Donor-Peptide-Acceptor Complexes: From Intramolecular Electron Transfer Reactions to the Study of Reactive Intermediates

    SciTech Connect

    Isied, Stephan S.

    2003-03-11

    The trans-polyproline (PII) oligomers (Figure 1) are unusually rigid peptide structures which have been extensively studied by our group for peptide mediated intramolecular electron transfer (ET) at long distances. We have previously studied ET across a series of metal ion donor (D) acceptor (A) oligoproline peptides with different distances, driving forces and reorganizational energies. The majority of these experiments involve generating the ET intermediate using pulse radiolysis methods, although more recently photochemical methods are also used. Results of these studies showed that ET across peptides can vary by more than twelve orders of magnitude. Using ruthenium bipyridine donors, ET reaction rate constants across several proline residues (n = 4 - 9) occurred in the millisecond (ms) to {micro}s timescale, thus limiting the proline peptide conformational motions to only minor changes (far smaller than the large changes that occur on the ms to sec timescale, such as trans to cis proline isomerization). The present report describes our large data base of experimental results for D-peptide-A complexes in terms of a model where the involvement of both superexchange and hopping (hole and electron) mechanisms account for the long range ET rate constants observed. Our data shows that the change from superexchange to hopping mechanisms occurs at different distances depending on the type of D and A and their interactions with the peptides. Our model is also consistent with generalized models for superexchange and hopping which have been put forward by a number of theoretical groups to account for long range ET phenomena.

  19. Photochemical reactions of fac-[Mn(CO)3(phen)imidazole]+: evidence for long-lived radical species intermediates.

    PubMed

    de Aguiar, Inara; Inglez, Simone D; Lima, Francisco C A; Daniel, Juliana F S; McGarvey, Bruce R; Tedesco, Antônio C; Carlos, Rose M

    2008-12-15

    The electronic absorption spectrum of fac-[Mn(CO)(3)(phen)imH](+), fac-1 in CH(2)Cl(2) is characterized by a strong absorption band at 378 nm (epsilon(max) = 3200 mol(-1) L cm(-1)). On the basis of quantum mechanical calculations, the visible absorption band has been assigned to ligand-to-ligand charge-transfer (LLCT, im-->phen) and metal-to-ligand charge-transfer (MLCT, Mn-->phen) charge transfer transition. When fac-1 in CH(2)Cl(2) is irradiated with 350 nm continuous light, the absorption features are gradually shifted to represent those of the meridional complex mer-[Mn(CO)(3)(phen)imH](+), mer-1 (lambda(max) = 556 nm). The net photoreaction under these conditions is a photoisomerization, although, the presence of the long-lived radical species was also detected by (1)H NMR and FTIR spectroscopy. 355 nm continuous photolysis of fac-1 in CH(3)CN solution also gives the long-lived intermediate which is readily trapped by metylviologen (MV(2+)) giving rise to the formation of the one-electron reduced methyl viologen (MV(*+)). The UV-vis spectra monitored during the slow (45 min) thermal back reaction exhibited isosbestic conversion at 426 nm. On the basis of spectroscopic techniques and quantum mechanical calculations, the role of the radicals produced is analyzed.

  20. Mixed Anhydride Intermediates in the Reaction of 5(4H)-Oxazolones with Phosphate Esters and Nucleotides.

    PubMed

    Liu, Ziwei; Rigger, Lukas; Rossi, Jean-Christophe; Sutherland, John D; Pascal, Robert

    2016-10-10

    5(4H)-Oxazolones can be formed through the activation of acylated α-amino acids or of peptide C termini. They constitute potentially activated intermediates in the abiotic chemistry of peptides that preceded the origin of life or early stages of biology and are capable of yielding mixed carboxylic-phosphoric anhydrides upon reaction with phosphate esters and nucleotides. Here, we present the results of a study aimed at investigating the chemistry that can be built through this interaction. As a matter of fact, the formation of mixed anhydrides with mononucleotides and nucleic acid models is shown to take place at positions involving a mono-substituted phosphate group at the 3'- or 5'-terminus but not at the internal phosphodiester linkages. In addition to the formation of mixed anhydrides, the subsequent intramolecular acyl or phosphoryl transfers taking place at the 3'-terminus are considered to be particularly relevant to the common prebiotic chemistry of α-amino acids and nucleotides.

  1. 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

  2. Identifying genomic and developmental causes of adverse drug reactions in children

    PubMed Central

    Becker, Mara L; Leeder, J Steven

    2011-01-01

    Adverse drug reactions are a concern for all clinicians who utilize medications to treat adults and children; however, the frequency of adult and pediatric adverse drug reactions is likely to be under-reported. In this age of genomics and personalized medicine, identifying genetic variation that results in differences in drug biotransformation and response has contributed to significant advances in the utilization of several commonly used medications in adults. In order to better understand the variability of drug response in children however, we must not only consider differences in genotype, but also variation in gene expression during growth and development, namely ontogeny. In this article, recommendations for systematically approaching pharmacogenomic studies in children are discussed, and several examples of studies that investigate the genomic and developmental contribution to adverse drug reactions in children are reviewed. PMID:21121777

  3. A Computational Study of a Recreated G Protein-GEF Reaction Intermediate Competent for Nucleotide Exchange: Fate of the Mg Ion

    PubMed Central

    Ben Hamida-Rebaï, Mériam; Robert, Charles H.

    2010-01-01

    Small G-proteins of the superfamily Ras function as molecular switches, interacting with different cellular partners according to their activation state. G-protein activation involves the dissociation of bound GDP and its replacement by GTP, in an exchange reaction that is accelerated and regulated in the cell by guanine-nucleotide exchange factors (GEFs). Large conformational changes accompany the exchange reaction, and our understanding of the mechanism is correspondingly incomplete. However, much knowledge has been derived from structural studies of blocked or inactive mutant GEFs, which presumably closely represent intermediates in the exchange reaction and yet which are by design incompetent for carrying out the nucleotide exchange reaction. In this study we have used comparative modelling to recreate an exchange-competent form of a late, pre-GDP-ejection intermediate species in Arf1, a well-characterized small G-protein. We extensively characterized three distinct models of this intermediate using molecular dynamics simulations, allowing us to address ambiguities related to the mutant structural studies. We observed in particular the unfavorable nature of Mg associated forms of the complex and the establishment of closer Arf1-GEF contacts in its absence. The results of this study shed light on GEF-mediated activation of this small G protein and on predicting the fate of the Mg ion at a critical point in the exchange reaction. The structural models themselves furnish additional targets for interfacial inhibitor design, a promising direction for exploring potentially druggable targets with high biological specificity. PMID:20174625

  4. A confirmation of the quench-cryoannealing relaxation protocol for identifying reduction states of freeze-trapped nitrogenase intermediates.

    PubMed

    Lukoyanov, Dmitriy; Yang, Zhi-Yong; Duval, Simon; Danyal, Karamatullah; Dean, Dennis R; Seefeldt, Lance C; Hoffman, Brian M

    2014-04-07

    We have advanced a mechanism for nitrogenase catalysis that rests on the identification of a low-spin EPR signal (S = 1/2) trapped during turnover of a MoFe protein as the E4 state, which has accumulated four reducing equivalents as two [Fe-H-Fe] bridging hydrides. Because electrons are delivered to the MoFe protein one at a time, with the rate-limiting step being the off-rate of oxidized Fe protein, it is difficult to directly control, or know, the degree of reduction, n, of a trapped intermediate, denoted En, n = 1-8. To overcome this previously intractable problem, we introduced a quench-cryoannealing relaxation protocol for determining n of an EPR-active trapped En turnover state. The trapped "hydride" state was allowed to relax to the resting E0 state in frozen medium, which prevents additional accumulation of reducing equivalents; binding of reduced Fe protein and release of oxidized protein from the MoFe protein both are abolished in a frozen solid. Relaxation of En was monitored by periodic EPR analysis at cryogenic temperature. The protocol rests on the hypothesis that an intermediate trapped in the frozen solid can relax toward the resting state only by the release of a stable reduction product from FeMo-co. In turnover under Ar, the only product that can be released is H2, which carries two reducing equivalents. This hypothesis implicitly predicts that states that have accumulated an odd number of electrons/protons (n = 1, 3) during turnover under Ar cannot relax to E0: E3 can relax to E1, but E1 cannot relax to E0 in the frozen state. The present experiments confirm this prediction and, thus, the quench-cryoannealing protocol and our assignment of E4, the foundation of the proposed mechanism for nitrogenase catalysis. This study further gives insights into the identity of the En intermediates with high-spin EPR signals, 1b and 1c, trapped under high electron flux.

  5. Spectroscopic investigations of intermediates in the reaction of cytochrome P450(BM3)-F87G with surrogate oxygen atom donors.

    PubMed

    Raner, Gregory M; Thompson, Jonathan I; Haddy, Alice; Tangham, Valary; Bynum, Nicole; Ramachandra Reddy, G; Ballou, David P; Dawson, John H

    2006-12-01

    Rapid mixing of substrate-free ferric cytochrome P450(BM3)-F87G with m-chloroperoxybenzoic acid (mCPBA) resulted in the sequential formation of two high-valent intermediates. The first was spectrally similar to compound I species reported previously for P450(CAM) and CYP 119 using mCPBA as an oxidant, and it featured a low intensity Soret absorption band characterized by shoulder at 370nm. This is the first direct observation of a P450 compound I intermediate in a type II P450 enzyme. The second intermediate, which was much more stable at pH values below 7.0, was characterized by an intense Soret absorption peak at 406nm, similar to that seen with P450(CAM) [T. Spolitak, J.H. Dawson, D.P. Ballou, J. Biol. Chem. 280 (2005) 20300-20309]. Double mixing experiments in which NADPH was added to the transient 406nm-absorbing intermediate resulted in rapid regeneration of the resting ferric state, with the flavins of the flavoprotein domain in their reduced state. EPR results were consistent with this stable intermediate species being a cytochrome c peroxidase compound ES-like species containing a protein-based radical, likely localized on a nearby Trp or Tyr residue in the active site. Iodosobenzene, peracetic acid, and sodium m-periodate also generated the intermediate at 406nm, but not the 370nm intermediate, indicating a probable kinetic barrier to accumulating compound I in reactions with these oxidants. The P450 ES intermediate has not been previously reported using iodosobenzene or m-periodate as the oxygen donor.

  6. Preverbal infants identify emotional reactions that are incongruent with goal outcomes.

    PubMed

    Skerry, Amy E; Spelke, Elizabeth S

    2014-02-01

    Identifying the goal of another agent's action allows an observer to make inferences not only about the outcomes the agent will pursue in the future and the means to be deployed in a given context, but also about the emotional consequences of goal-related outcomes. While numerous studies have characterized the former abilities in infancy, expectations about emotions have gone relatively unexplored. Using a violation of expectation paradigm, we present infants with an agent who attains or fails to attain a demonstrated goal, and reacts with positive or negative affect. Across several studies, we find that infants' attention to a given emotional display differs depending on whether that reaction is congruent with the preceding goal outcome. Specifically, infants look longer at a negative emotional display when it follows a completed goal compared to when it follows a failed goal. The present results suggest that infants' goal representations support expectations not only about future actions but also about emotional reactions, and that infants in the first year of life can relate different emotional reactions to conditions that elicit them.

  7. Online Quantification of Criegee Intermediates of α-Pinene Ozonolysis by Stabilization with Spin Traps and Proton-Transfer Reaction Mass Spectrometry Detection.

    PubMed

    Giorio, Chiara; Campbell, Steven J; Bruschi, Maurizio; Tampieri, Francesco; Barbon, Antonio; Toffoletti, Antonio; Tapparo, Andrea; Paijens, Claudia; Wedlake, Andrew J; Grice, Peter; Howe, Duncan J; Kalberer, Markus

    2017-03-07

    Biogenic alkenes, which are among the most abundant volatile organic compounds in the atmosphere, are readily oxidized by ozone. Characterizing the reactivity and kinetics of the first-generation products of these reactions, carbonyl oxides (often named Criegee intermediates), is essential in defining the oxidation pathways of organic compounds in the atmosphere but is highly challenging due to the short lifetime of these zwitterions. Here, we report the development of a novel online method to quantify atmospherically relevant Criegee intermediates (CIs) in the gas phase by stabilization with spin traps and analysis with proton-transfer reaction mass spectrometry. Ozonolysis of α-pinene has been chosen as a proof-of-principle model system. To determine unambiguously the structure of the spin trap adducts with α-pinene CIs, the reaction was tested in solution, and reaction products were characterized with high-resolution mass spectrometry, electron paramagnetic resonance, and nuclear magnetic resonance spectroscopy. DFT calculations show that addition of the Criegee intermediate to the DMPO spin trap, leading to the formation of a six-membered ring adduct, occurs through a very favorable pathway and that the product is significantly more stable than the reactants, supporting the experimental characterization. A flow tube set up has been used to generate spin trap adducts with α-pinene CIs in the gas phase. We demonstrate that spin trap adducts with α-pinene CIs also form in the gas phase and that they are stable enough to be detected with online mass spectrometry. This new technique offers for the first time a method to characterize highly reactive and atmospherically relevant radical intermediates in situ.

  8. Spectroscopic and Kinetic Characterization of Peroxidase-Like π-Cation Radical Pinch-Porphyrin-Iron(III) Reaction Intermediate Models of Peroxidase Enzymes.

    PubMed

    Hernández Anzaldo, Samuel; Arroyo Abad, Uriel; León García, Armando; Ramírez Rosales, Daniel; Zamorano Ulloa, Rafael; Reyes Ortega, Yasmi

    2016-06-27

    The spectroscopic and kinetic characterization of two intermediates from the H₂O₂ oxidation of three dimethyl ester [(proto), (meso), (deuteroporphyrinato) (picdien)]Fe(III) complexes ([FePPPic], [FeMPPic] and [FeDPPic], respectively) pinch-porphyrin peroxidase enzyme models, with s = 5/2 and 3/2 Fe(III) quantum mixed spin (qms) ground states is described herein. The kinetic study by UV/Vis at λmax = 465 nm showed two different types of kinetics during the oxidation process in the guaiacol test for peroxidases (1-3 + guaiacol + H₂O₂ → oxidation guaiacol products). The first intermediate was observed during the first 24 s of the reaction. When the reaction conditions were changed to higher concentration of pinch-porphyrins and hydrogen peroxide only one type of kinetics was observed. Next, the reaction was performed only between pinch-porphyrins-Fe(III) and H₂O₂, resulting in only two types of kinetics that were developed during the first 0-4 s. After this time a self-oxidation process was observed. Our hypotheses state that the formation of the π-cation radicals, reaction intermediates of the pinch-porphyrin-Fe(III) family with the ligand picdien [N,N'-bis-pyridin-2-ylmethyl-propane-1,3-diamine], occurred with unique kinetics that are different from the overall process and was involved in the oxidation pathway. UV-Vis, ¹H-NMR and ESR spectra confirmed the formation of such intermediates. The results in this paper highlight the link between different spectroscopic techniques that positively depict the kinetic traits of artificial compounds with enzyme-like activity.

  9. Heptad repeat 2-based peptides inhibit avian sarcoma and leukosis virus subgroup a infection and identify a fusion intermediate.

    PubMed

    Netter, Robert C; Amberg, Sean M; Balliet, John W; Biscone, Mark J; Vermeulen, Arwen; Earp, Laurie J; White, Judith M; Bates, Paul

    2004-12-01

    Fusion proteins of enveloped viruses categorized as class I are typified by two distinct heptad repeat domains within the transmembrane subunit. These repeats are important structural elements that assemble into the six-helix bundles characteristic of the fusion-activated envelope trimer. Peptides derived from these domains can be potent and specific inhibitors of membrane fusion and virus infection. To facilitate our understanding of retroviral entry, peptides corresponding to the two heptad repeat domains of the avian sarcoma and leukosis virus subgroup A (ASLV-A) TM subunit of the envelope protein were characterized. Two peptides corresponding to the C-terminal heptad repeat (HR2), offset from one another by three residues, were effective inhibitors of infection, while two overlapping peptides derived from the N-terminal heptad repeat (HR1) were not. Analysis of envelope mutants containing substitutions within the HR1 domain revealed that a single amino acid change, L62A, significantly reduced sensitivity to peptide inhibition. Virus bound to cells at 4 degrees C became sensitive to peptide within the first 5 min of elevating the temperature to 37 degrees C and lost sensitivity to peptide after 15 to 30 min, consistent with a transient intermediate in which the peptide binding site is exposed. In cell-cell fusion experiments, peptide inhibitor sensitivity occurred prior to a fusion-enhancing low-pH pulse. Soluble receptor for ASLV-A induces a lipophilic character in the envelope which can be measured by stable liposome binding, and this activation was found to be unaffected by inhibitory HR2 peptide. Finally, receptor-triggered conformational changes in the TM subunit were also found to be unaffected by inhibitory peptide. These changes are marked by a dramatic shift in mobility on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, from a subunit of 37 kDa to a complex of about 80 kDa. Biotinylated HR2 peptide bound specifically to the 80-kDa complex

  10. P-Cadherin Linking Breast Cancer Stem Cells and Invasion: A Promising Marker to Identify an "Intermediate/Metastable" EMT State.

    PubMed

    Ribeiro, Ana Sofia; Paredes, Joana

    2014-01-01

    Epithelial-mesenchymal transition (also known as EMT) is a fundamental mechanism occurring during embryonic development and tissue differentiation, being also crucial for cancer progression. Actually, the EMT program contributes to the dissemination of cancer cells from solid tumors and to the formation of micro-metastasis that subsequently develop into clinically detectable metastases. Besides being a process that is defined by the progressive loss of epithelial cell characteristics and the acquisition of mesenchymal features, EMT has also been implicated in therapy resistance, immune escape, and maintenance of cancer stem cell properties, such as self-renewal capacity. However, the majority of the studies usually neglect the progressive alterations occurring during intermediate EMT states, which imply a range of phenotypic cellular heterogeneity that can potentially generate more metastable and plastic tumor cells. In fact, few studies have tried to identify these transitory states, partly due to the current lack of a detailed understanding of EMT, as well as of reliable readouts for its progression. Herein, a brief review of evidences is presented, showing that P-cadherin expression, which has been already identified as a breast cancer stem cell marker and invasive promoter, is probably able to identify an intermediate EMT state associated with a metastable phenotype. This hypothesis is based on our own work, as well as on the results described by others, which suggest the use of P-cadherin as a promising EMT marker, clearly functioning as an important clinical prognostic factor and putative therapeutic target in breast carcinogenesis.

  11. Interaction of CO with OH on Au(111): HCOO, CO3, and HOCO as Key Intermediates in the Water-Gas Shift Reaction

    SciTech Connect

    Senanayake, S.; Stacchiola, D; Liu, P; Mullins, C; Hrbek, J; Rodriguez, J

    2009-01-01

    We have investigated the role of formate (HCOO), carbonate (CO{sub 3}), and carboxyl (HOCO) species as possible intermediates in the OH{sub ads} + CO{sub gas} {yields} CO{sub 2,gas} + 0.5H{sub 2,gas} reaction on Au(111) using synchrotron-based core level photoemission, near-edge X-ray absorption fine structure (NEXAFS), and infrared absorption spectroscopy (IR). Adsorbed HCOO, CO{sub 3}, and OH species were prepared by adsorbing formic acid, carbon dioxide, and water on a Au(111) surface precovered with 0.2 ML of atomic oxygen, respectively. HCOOH interacts weakly with Au(111), but on O/Au(111) it dissociates its acidic H to yield adsorbed formate. The results of NEXAFS, IR, and density-functional calculations indicate that the formate adopts a bidentate configuration on Au(111). Since the HCOO groups are stable on Au(111) up to temperatures near 350 K, it is not likely that formate is a key intermediate for the OH{sub ads} + CO{sub gas} {yields} CO{sub 2,gas} + 0.5H{sub 2,gas} reaction at low temperatures. In fact, the formation of this species could lead eventually to surface poisoning. When compared to a formate species, a carbonate species formed by the reaction of CO{sub 2} with O/Au(111) has low stability, decomposing at temperatures between 100 and 125 K, and should not poison the gold surface. Neither HCOO nor CO{sub 3} was detected during the reaction of CO with OH on Au(111) at 90-120 K. The results of photoemission and IR spectroscopy point to HO {leftrightarrow} CO interactions, consistent with the formation of an unstable HOCO intermediate which has a very short lifetime on the gold surface. The possible mechanism for the low-temperature water-gas shift on gold catalysts is discussed in light of these results.

  12. Forward scattering due to slow-down of the intermediate in the H + HD --> D + H2 reaction

    NASA Astrophysics Data System (ADS)

    Harich, Steven A.; Dai, Dongxu; Wang, Chia C.; Yang, Xueming; Chao, Sheng Der; Skodje, Rex T.

    2002-09-01

    Quantum dynamical processes near the energy barrier that separates reactants from products influence the detailed mechanism by which elementary chemical reactions occur. In fact, these processes can change the product scattering behaviour from that expected from simple collision considerations, as seen in the two classical reactions F + H2 --> HF + H and H + H2 --> H2 + H and their isotopic variants. In the case of the F + HD reaction, the role of a quantized trapped Feshbach resonance state had been directly determined, confirming previous conclusions that Feshbach resonances cause state-specific forward scattering of product molecules. Forward scattering has also been observed in the H + D2 --> HD + D reaction and attributed to a time-delayed mechanism. But despite extensive experimental and theoretical investigations, the details of the mechanism remain unclear. Here we present crossed-beam scattering experiments and quantum calculations on the H + HD --> H2 + D reaction. We find that the motion of the system along the reaction coordinate slows down as it approaches the top of the reaction barrier, thereby allowing vibrations perpendicular to the reaction coordinate and forward scattering. The reaction thus proceeds, as previously suggested, through a well-defined `quantized bottleneck state' different from the trapped Feshbach resonance states observed before.

  13. Reaction of chromium(VI) with glutathione or with hydrogen peroxide: Identification of reactive intermediates and their role in chromium(VI)-induced DNA damage

    SciTech Connect

    Aiyar, J.; Berkovits, H.J.; Wetterhahn, K.E. ); Floyd, R.A. )

    1991-05-01

    The types of reactive intermediates generated upon reduction of chromium (VI) by glutathione or hydrogen peroxide and the resulting DNA damage have been determined. In vitro, reaction of chromium (VI) with glutathione led to formation of two chromium (V) complexes and the glutathione thiyl radical. When chromium (VI) was reacted with DNA in the presence of glutathione, chromium-DNA adducts were obtained, with no DNA strand breakage. The level of chromium-DNA adduct formation correlated with chromium (V) formation. Reaction of chromium (VI) with hydrogen peroxide led to formation of hydroxyl radical. No chromium (V) was detectable at 24 C (297 K); however, low levels of the tetraperoxochromium (V) complex were detected at 77 K. Reaction of chromium (VI) with DNA in the presence of hydrogen peroxide produced significant DNA strand breakage and the 8-hydroxydeoxyguanosine adduct, whose formation correlated with hydroxyl radical production. No significant chromium-DNA adduct formation was detected. Thus, the nature of chromium (VI)-induced DNA damage appears to be dependent on the reactive intermediates, i.e., chromium (V) or hydroxyl radical, produced during the reduction of chromium (VI).

  14. Kinetics of the Reaction of beta-Methoxy-alpha-nitrostilbene with Cyanamide in 50 DMSO-50 Water. Failure to Detect the S(N)V Intermediate.

    PubMed

    Bernasconi, Claude F.; Leyes, Aquiles E.; Rappoport, Zvi

    1999-04-16

    A kinetic study of the reaction of beta-methoxy-alpha-nitrostilbene (1-OMe) with cyanamide (CNA) over a pH range from 8.5 to 12.4 shows that it is the anion (CNA(-), pK(a) = 11.38) rather than the neutral amine that is the reactive species. Attempts at monitoring the reaction with the neutral CNA at low pH were unsuccessful because of competing hydrolysis. It is shown that the nucleophilic reactivity of CNA is abnormally low, probably because of a resonance effect, and that the reactivity of CNA(-) is high, higher than that of strongly basic oxyanion because of relatively weak solvation. The high reactivity of both 1-OMe and CNA(-) appeared to constitute favorable conditions conducive to the detection of the S(N)V intermediate, as has been the case in the reactions of 1-OMe with thiolate ions, alkoxide ions, and some amines. However, no intermediate was observed. Reasons for this failure are discussed.

  15. Characterisation of Criegee intermediates in the gas phase by stabilisation with a spin trap and analysis by proton transfer reaction mass spectrometry (PTR-MS)

    NASA Astrophysics Data System (ADS)

    Giorio, Chiara; Tapparo, Andrea; Barbon, Antonio; Toffoletti, Antonio; Kalberer, Markus

    2014-05-01

    Biogenic and anthropogenic volatile organic compounds (VOCs) can react with o xidants present in the atmosphere to form less volatile compounds which could partition in the condensed phase and contribute to organic aerosol mass. One of the most important and efficient reaction for the formation of secondary organic aerosol (SOA) is the ozonolysis of alkenes. This process occurs with a generally accepted mechanism, proposed for the first time by Rudolf Criegee (Criegee, 1975). According to the Criegee mechanism, ozone coordinates to the double bond of alkenes forming a primary ozonide, which promptly decomposes to form biradical intermediates called Criegee intermediates (CIs). CIs further react quickly to form first generation oxidation products. The analysis of Criegee intermediates represent an analytical challenge due to their characteristic high reactivity and low concentrations. Their role in the formation of SOA remains highly uncertain because of uncertainty in the kinetic of their reaction with different atmospheric compounds. Up to date, only a few studies have been able to detect the CIs directly (Welz et al., 2012) or indirectly (Mauldin et al., 2012). The aim of this study is the development of a method for the on-line measurement of CIs by stabilization with a spin trap (5,5-dimethyl-pyrroline N-oxide, DMPO) and detection via proton transfer reaction mass spectrometry (PTR-MS). The novel method is used to study the ozonolysis of α-pinene in a flow tube, one of the most important precursors in the formation of SOA, often used as a proxy in global aerosol models to study the effects of biogenic organic aerosols on climate change. Criegee R., 1975. Angewandte Chemie 14, 745-752. Welz O., et al., 2012. Science 335, 204 207. Mauldin R. L., et al., 2012. Nature 488, 193-196.

  16. Kinetic and product studies of Criegee intermediate reactions with halogenated and non-halogenated carboxylic acids and their implications in the troposphere

    NASA Astrophysics Data System (ADS)

    Chhantyal-Pun, Rabi; Rotavera, Brandon; Eskola, Arkke; Taatjes, Craig; Percival, Carl; Shallcross, Dudley; Orr-Ewing, Andrew

    2016-04-01

    Criegee intermediates are important species formed during the ozonolysis of alkenes. Direct measurement and modelling studies have shown that reactions of stabilized Criegee intermediates with species like SO2 and NO2 may have a significant effect in tropospheric chemistry.[1, 2] Reaction rates of Criegee intermediates with simple carboxylic acids like HCOOH and CH3COOH have been shown to be near the collision limit and may be a significant sink for these otherwise stable species in the atmosphere.[3, 4] Results obtained from our time-resolved Cavity Ring-Down Spectroscopy (CRDS) apparatus[5] for reactions of the Criegee intermediates, CH2OO and (CH3)2COO with various halogenated (CF3COOH, CF3CF2COOH, CClF2COOH and CHCl2COOH) and non-halogenated (HCOOH and CH3COOH) carboxylic acids will be presented, together with Structure Activity Relationship (SAR) based on these observations. Structure characterization of the products from these reactions using the Multiplexed PhotoIonization Mass Spectrometry (MPIMS) apparatus[1,3] as well as implications for Secondary Organic Aerosol (SOA) formation, assessed using the global atmospheric model STOCHEM, will also be discussed. Bibliography 1. O. Welz, J. D. Savee, D. L. Osborn, S. S. Vasu, C. J. Percival, D. E. Shallcross and C. A. Taatjes, Science, 2012, 335, 204-207. 2. C. J. Percival, O. Welz, A. J. Eskola, J. D. Savee, D. L. Osborn, D. O. Topping, D. Lowe, S. R. Utembe, A. Bacak, G. McFiggans, M. C. Cooke, P. Xiao, A. T. Archibald, M. E. Jenkin, R. G. Derwent, I. Riipinen, D. W. K. Mok, E. P. F. Lee, J. M. Dyke, C. A. Taatjes and D. E. Shallcross, Faraday Discuss., 2013, 165, 45-73. 3. O. Welz, A. J. Eskola, L. Sheps, B. Rotavera, J. D. Savee, A. M. Scheer, D. L. Osborn, D. Lowe, A. M. Booth, P. Xiao, M. A. H. Khan, C. J. Percival, D. E. Shallcross and C. A. Taatjes, Angew. Chem. Int. Ed., 2014, 53, 4547-4550. 4. M. D. Hurley, M. P. S. Andersen, T. J. Wallington, D. A. Ellis, J. W. Martin and S. A. Mabury, J. Phys. Chem. A

  17. Model for particle production in nuclear reactions at intermediate energies: Application to C-C collisions at 95 MeV/nucleon

    NASA Astrophysics Data System (ADS)

    Dudouet, J.; Durand, D.

    2016-07-01

    A model describing nuclear collisions at intermediate energies is presented and the results are compared with recently measured double differential cross sections in C-C reactions at 95 MeV/nucleon. Results show the key role played by geometrical effects and the memory of the entrance channel, in particular the momentum distributions of the two incoming nuclei. Special attention is paid to the description of processes occurring at midrapidity. To this end, a random particle production mechanism by means of a coalescence process in velocity space is considered in the overlap region of the two interacting nuclei.

  18. Identifying Enclosed Chemical Reaction and Dynamics at the Molecular Level Using Shell-Isolated Miniaturized Plasmonic Liquid Marble.

    PubMed

    Han, Xuemei; Lee, Hiang Kwee; Lee, Yih Hong; Hao, Wei; Liu, Yejing; Phang, In Yee; Li, Shuzhou; Ling, Xing Yi

    2016-04-21

    Current microscale tracking of chemical kinetics is limited to destructive ex situ methods. Here we utilize Ag nanocube-based plasmonic liquid marble (PLM) microreactor for in situ molecular-level identification of reaction dynamics. We exploit the ultrasensitive surface-enhanced Raman scattering (SERS) capability imparted by the plasmonic shell to unravel the mechanism and kinetics of aryl-diazonium surface grafting reaction in situ, using just a 2-μL reaction droplet. This reaction is a robust approach to generate covalently functionalized metallic surfaces, yet its kinetics remain unknown to date. Experiments and simulations jointly uncover a two-step sequential grafting process. An initial Langmuir chemisorption of sulfonicbenzene diazonium (dSB) salt onto Ag surfaces forms an intermediate sulfonicbenzene monolayer (Ag-SB), followed by subsequent autocatalytic multilayer growth of Ag-SB3. Kinetic rate constants reveal 19-fold faster chemisorption than multilayer growth. Our ability to precisely decipher molecular-level reaction dynamics creates opportunities to develop more efficient processes in synthetic chemistry and nanotechnology.

  19. Probing the neutron-skin thickness by photon production from reactions induced by intermediate-energy protons

    NASA Astrophysics Data System (ADS)

    Wei, Gao-Feng

    2015-07-01

    The photon from neutron-proton bremsstrahlung in p +Pb reactions is examined as a potential probe of the neutron-skin thickness in different centralities and at different proton incident energies. It is shown that the best choice of reaction environment is about 140 MeV for the incident proton and the 95%-100% centrality for the reaction system since the incident proton mainly interacts with neutrons inside the skin of the target and thus leads to different photon production to a maximal extent. Moreover, considering two main uncertainties from both photon production probability and nucleon-nucleon cross section in the reaction, I propose to use the ratio of photon production from two reactions to measure the neutron-skin thickness because of its cancellation effects on these uncertainties simultaneously, but preserved about 13%-15% sensitivities on the varied neutron-skin thickness from 0.1 to 0.3 fm within the current experimental uncertainty range of the neutron-skin size in 208Pb.

  20. Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions.

    PubMed

    Lambrecht, Jennifer A; Flynn, Jeffrey M; Downs, Diana M

    2012-01-27

    The YjgF/YER057c/UK114 family of proteins is conserved in all domains of life, suggesting that the role of these proteins arose early and was maintained throughout evolution. Metabolic consequences of lacking this protein in Salmonella enterica and other organisms have been described, but the biochemical function of YjgF remained unknown. This work provides the first description of a conserved biochemical activity for the YjgF protein family. Our data support the conclusion that YjgF proteins have enamine/imine deaminase activity and accelerate the release of ammonia from reactive enamine/imine intermediates of the pyridoxal 5'-phosphate-dependent threonine dehydratase (IlvA). Results from structure-guided mutagenesis experiments suggest that YjgF lacks a catalytic residue and that it facilitates ammonia release by positioning a critical water molecule in the active site. YjgF is renamed RidA (reactive intermediate/imine deaminase A) to reflect the conserved activity of the protein family described here. This study, combined with previous physiological studies on yjgF mutants, suggests that intermediates of pyridoxal 5'-phosphate-mediated reactions may have metabolic consequences in vivo that were previously unappreciated. The conservation of the RidA/YjgF family suggests that reactive enamine/imine metabolites are of concern to all organisms.

  1. Hydroxyacetone production from C3 Criegee intermediates

    DOE PAGES

    Taatjes, Craig A.; Liu, Fang; Rotavera, Brandon; ...

    2016-12-21

    Hydroxyacetone (CH3C(O)CH2OH) is observed as a stable end product from reactions of the (CH3)2COO Criegee intermediate, acetone oxide, in a flow tube coupled with multiplexed photoionization mass spectrometer detection. In the experiment, the isomers at m/z = 74 are distinguished by their different photoionization spectra and reaction times. Hydroxyacetone is observed as a persistent signal at longer reaction times at a higher photoionization threshold of ca. 9.7 eV than Criegee intermediate and definitively identified by comparison with the known photoionization spectrum. Complementary electronic structure calculations reveal multiple possible reaction pathways for hydroxyacetone formation, including unimolecular isomerization via hydrogen atom transfermore » and –OH group migration as well as self-reaction of Criegee intermediates. Varying the concentration of Criegee intermediates suggests contributions from both unimolecular and self-reaction pathways to hydroxyacetone. As a result, the hydroxyacetone end product can provide an effective, stable marker for the production of transient Criegee intermediates in future studies of alkene ozonolysis.« less

  2. Hydroxyacetone Production From C3 Criegee Intermediates.

    PubMed

    Taatjes, Craig A; Liu, Fang; Rotavera, Brandon; Kumar, Manoj; Caravan, Rebecca; Osborn, David L; Thompson, Ward H; Lester, Marsha I

    2017-01-12

    Hydroxyacetone (CH3C(O)CH2OH) is observed as a stable end product from reactions of the (CH3)2COO Criegee intermediate, acetone oxide, in a flow tube coupled with multiplexed photoionization mass spectrometer detection. In the experiment, the isomers at m/z = 74 are distinguished by their different photoionization spectra and reaction times. Hydroxyacetone is observed as a persistent signal at longer reaction times at a higher photoionization threshold of ca. 9.7 eV than Criegee intermediate and definitively identified by comparison with the known photoionization spectrum. Complementary electronic structure calculations reveal multiple possible reaction pathways for hydroxyacetone formation, including unimolecular isomerization via hydrogen atom transfer and -OH group migration as well as self-reaction of Criegee intermediates. Varying the concentration of Criegee intermediates suggests contributions from both unimolecular and self-reaction pathways to hydroxyacetone. The hydroxyacetone end product can provide an effective, stable marker for the production of transient Criegee intermediates in future studies of alkene ozonolysis.

  3. Superstructure in the Metastable Intermediate-Phase Li2/3 FePO4 Accelerating the Lithium Battery Cathode Reaction.

    PubMed

    Nishimura, Shin-ichi; Natsui, Ryuichi; Yamada, Atsuo

    2015-07-27

    LiFePO4 is an important cathode material for lithium-ion batteries. Regardless of the biphasic reaction between the insulating end members, Lix FePO4 , x≈0 and x≈1, optimization of the nanostructured architecture has substantially improved the power density of positive LiFePO4 electrode. The charge transport that occurs in the interphase region across the biphasic boundary is the primary stage of solid-state electrochemical reactions in which the Li concentrations and the valence state of Fe deviate significantly from the equilibrium end members. Complex interactions among Li ions and charges at the Fe sites have made understanding stability and transport properties of the intermediate domains difficult. Long-range ordering at metastable intermediate eutectic composition of Li2/3 FePO4 has now been discovered and its superstructure determined, which reflected predominant polaron crystallization at the Fe sites followed by Li(+) redistribution to optimize the Li-Fe interactions.

  4. Origin of product selectivity in a prenyl transfer reaction from the same intermediate: exploration of multiple FtmPT1-catalyzed prenyl transfer pathways.

    PubMed

    Pan, Li-Li; Yang, Yue; Merz, Kenneth M

    2014-09-30

    FtmPT1 is a fungal indole prenyltransferase that catalyzes the reaction of tryptophan derivatives with dimethylallyl pyrophosphate to form various biologically active compounds. Herein, we describe detailed studies of FtmPT1 catalysis involving dimethylallyl pyrophosphate and Brevianamide F following the native pathway (yielding Tryprostatin B) and an alternate pathway observed in the Gly115Thr mutant of FtmPT1 yielding a novel cyclized product. Importantly, these two products arise from the same intermediate state, meaning that a step other than the cleavage of the dimethylallyl pyrophosphate (DMAPP; C-O) bond is differentiating between the two product reaction channels. From detailed potential of mean force (PMF) and two-dimensional PMF analyses, we conclude that the rate-limiting step is the cleavage of the C-O bond in DMAPP, while the deprotonation/cyclization step determines the final product distribution. Hence, in the case of FtmPT1, the optimization of the necessary catalytic machinery guides the generation of the final product after formation of the intermediate carbocation.

  5. Identifying plausible adverse drug reactions using knowledge extracted from the literature

    PubMed Central

    Shang, Ning; Xu, Hua; Rindflesch, Thomas C.; Cohen, Trevor

    2014-01-01

    Pharmacovigilance involves continually monitoring drug safety after drugs are put to market. To aid this process; algorithms for the identification of strongly correlated drug/adverse drug reaction (ADR) pairs from data sources such as adverse event reporting systems or Electronic Health Records have been developed. These methods are generally statistical in nature, and do not draw upon the large volumes of knowledge embedded in the biomedical literature. In this paper, we investigate the ability of scalable Literature Based Discovery (LBD) methods to identify side effects of pharmaceutical agents. The advantage of LBD methods is that they can provide evidence from the literature to support the plausibility of a drug/ ADR association, thereby assisting human review to validate the signal, which is an essential component of pharmacovigilance. To do so, we draw upon vast repositories of knowledge that has been extracted from the biomedical literature by two Natural Language Processing tools, MetaMap and SemRep. We evaluate two LBD methods that scale comfortably to the volume of knowledge available in these repositories. Specifically, we evaluate Reflective Random Indexing (RRI), a model based on concept-level co-occurrence, and Predication-based Semantic Indexing (PSI), a model that encodes the nature of the relationship between concepts to support reasoning analogically about drug-effect relationships. An evaluation set was constructed from the Side Effect Resource 2 (SIDER2), which contains known drug/ADR relations, and models were evaluated for their ability to “rediscover” these relations. In this paper, we demonstrate that both RRI and PSI can recover known drug-adverse event associations. However, PSI performed better overall, and has the additional advantage of being able to recover the literature underlying the reasoning pathways it used to make its predictions. PMID:25046831

  6. Identifying the Structure of the Intermediate, Li2/3CoPO4, Formed during Electrochemical Cycling of LiCoPO4

    PubMed Central

    2014-01-01

    In situ synchrotron diffraction measurements and subsequent Rietveld refinements are used to show that the high energy density cathode material LiCoPO4 (space group Pnma) undergoes two distinct two-phase reactions upon charge and discharge, both occurring via an intermediate Li2/3(Co2+)2/3(Co3+)1/3PO4 phase. Two resonances are observed for Li2/3CoPO4 with intensity ratios of 2:1 and 1:1 in the 31P and 7Li NMR spectra, respectively. An ordering of Co2+/Co3+ oxidation states is proposed within a (a × 3b × c) supercell, and Li+/vacancy ordering is investigated using experimental NMR data in combination with first-principles solid-state DFT calculations. In the lowest energy configuration, both the Co3+ ions and Li vacancies are found to order along the b-axis. Two other low energy Li+/vacancy ordering schemes are found only 5 meV per formula unit higher in energy. All three configurations lie below the LiCoPO4–CoPO4 convex hull and they may be readily interconverted by Li+ hops along the b-direction. PMID:25960604

  7. Studies on the inhibition of sphingosine-1-phosphate lyase by stabilized reaction intermediates and stereodefined azido phosphates.

    PubMed

    Sanllehí, Pol; Abad, José-Luís; Bujons, Jordi; Casas, Josefina; Delgado, Antonio

    2016-11-10

    Two kinds of inhibitors of the PLP-dependent enzyme sphingosine-1-phosphate lyase have been designed and tested on the bacterial (StS1PL) and the human (hS1PL) enzymes. Amino phosphates 1, 12, and 32, mimicking the intermediate aldimines of the catalytic process, were weak inhibitors on both enzyme sources. On the other hand, a series of stereodefined azido phosphates, resulting from the replacement of the amino group of the natural substrates with an azido group, afforded competitive inhibitors in the low micromolar range on both enzyme sources. This similar behavior represents an experimental evidence of the reported structural similarities for both enzymes at their active site level. Interestingly, the anti-isomers of the non-natural enantiomeric series where the most potent inhibitors on hS1PL.

  8. Highly Enantioselective Dearomatizing Formal [3+3]-Cycloaddition Reactions of N-Acyliminopyridinium Ylides with Electrophilic Enolcarbene Intermediates

    PubMed Central

    Xu, Xinfang; Zavalij, Peter Y.; Doyle, Michael P.

    2013-01-01

    A effective dearomatizing formal [3+3]-cycloaddition reaction triggered by Rh(II)-catalyzed dinitrogen extrusion of enoldiazoacetates followed by vinylogous addition of metal enolcarbenes to N-acyliminopyridinium ylides that produces highly substituted 1,2,3,6-tetrahydropyridazines in up to 98% ee and in high yield has been developed. PMID:24123489

  9. Understanding and Mitigating the Effects of Stable Dodecahydro- closo -dodecaborate Intermediates on Hydrogen-Storage Reactions

    SciTech Connect

    White, James L.; Newhouse, Rebecca J.; Zhang, Jin Z.; Udovic, Terrence J.; Stavila, Vitalie

    2016-10-25

    Alkali metal borohydrides can reversibly store hydrogen; however, the materials display poor cyclability, often times linked to occurrence of stable closo-polyborate intermediate species. In an effort to understand the role of such intermediates on the hydrogen storage properties of metal borohydrides, several alkali metal dodecahydro-closo-dodecaborate salts were isolated in anhydrous form and characterized by diffraction and spectroscopic techniques. Mixtures of Li2B12H12, Na2B12H12, and K2B12H12 with the corresponding alkali metal hydrides were subjected to hydrogenation conditions known to favor partial or full reversibility in metal borohydrides. The stoichiometric mixtures of MH and M2B12H12 salts form the corresponding metal borohydrides MBH4 (M=Li, Na, K) in almost quantitative yield at 100 MPa H2 and 500 °C. In addition, stoichiometric mixtures of Li2B12H12 and MgH2 were found to form MgB2 at 500 °C and above upon desorption in vacuum. The two destabilization strategies outlined above suggest that metal polyhydro-closo-polyborate species can be converted into the corresponding metal borohydrides or borides, albeit under rather harsh conditions of hydrogen pressure and temperature.

  10. Perspective: Spectroscopy and kinetics of small gaseous Criegee intermediates.

    PubMed

    Lee, Yuan-Pern

    2015-07-14

    The Criegee intermediates, carbonyl oxides proposed by Criegee in 1949 as key intermediates in the ozonolysis of alkenes, play important roles in many aspects of atmospheric chemistry. Because direct detection of these gaseous intermediates was unavailable until recently, previous understanding of their reactions, derived from indirect experimental evidence, had great uncertainties. Recent laboratory detection of the simplest Criegee intermediate CH2OO and some larger members, produced from ultraviolet irradiation of corresponding diiodoalkanes in O2, with various methods such as photoionization, ultraviolet absorption, infrared absorption, and microwave spectroscopy opens a new door to improved understanding of the roles of these Criegee intermediates. Their structures and spectral parameters have been characterized; their significant zwitterionic nature is hence confirmed. CH2OO, along with other products, has also been detected directly with microwave spectroscopy in gaseous ozonolysis reactions of ethene. The detailed kinetics of the source reaction, CH2I + O2, which is critical to laboratory studies of CH2OO, are now understood satisfactorily. The kinetic investigations using direct detection identified some important atmospheric reactions, including reactions with NO2, SO2, water dimer, carboxylic acids, and carbonyl compounds. Efforts toward the characterization of larger Criegee intermediates and the investigation of related reactions are in progress. Some reactions of CH3CHOO are found to depend on conformation. This perspective examines progress toward the direct spectral characterization of Criegee intermediates and investigations of the associated reaction kinetics, and indicates some unresolved problems and prospective challenges for this exciting field of research.

  11. Perspective: Spectroscopy and kinetics of small gaseous Criegee intermediates

    NASA Astrophysics Data System (ADS)

    Lee, Yuan-Pern

    2015-07-01

    The Criegee intermediates, carbonyl oxides proposed by Criegee in 1949 as key intermediates in the ozonolysis of alkenes, play important roles in many aspects of atmospheric chemistry. Because direct detection of these gaseous intermediates was unavailable until recently, previous understanding of their reactions, derived from indirect experimental evidence, had great uncertainties. Recent laboratory detection of the simplest Criegee intermediate CH2OO and some larger members, produced from ultraviolet irradiation of corresponding diiodoalkanes in O2, with various methods such as photoionization, ultraviolet absorption, infrared absorption, and microwave spectroscopy opens a new door to improved understanding of the roles of these Criegee intermediates. Their structures and spectral parameters have been characterized; their significant zwitterionic nature is hence confirmed. CH2OO, along with other products, has also been detected directly with microwave spectroscopy in gaseous ozonolysis reactions of ethene. The detailed kinetics of the source reaction, CH2I + O2, which is critical to laboratory studies of CH2OO, are now understood satisfactorily. The kinetic investigations using direct detection identified some important atmospheric reactions, including reactions with NO2, SO2, water dimer, carboxylic acids, and carbonyl compounds. Efforts toward the characterization of larger Criegee intermediates and the investigation of related reactions are in progress. Some reactions of CH3CHOO are found to depend on conformation. This perspective examines progress toward the direct spectral characterization of Criegee intermediates and investigations of the associated reaction kinetics, and indicates some unresolved problems and prospective challenges for this exciting field of research.

  12. Delayed hemolytic transfusion reaction with multiple alloantibody (Anti S, N, K) and a monospecific autoanti-JK(b) in intermediate β-thalassemia patient in Tabriz.

    PubMed

    Dolatkhah, Roya; Esfahani, Ali; Torabi, Seyed Esmaeil; Kermani, Iraj Asvadi; Sanaat, Zohreh; Ziaei, Jamal Eivazei; Nikanfar, Alireza; Chavoshi, Seyed Hadi; Ghoreishi, Zohreh; Kermani, Atabak Asvadi

    2013-07-01

    It appears that delayed hemolytic transfusion reactions may occur several days after the administration of donor red cells is true even though they have been shown to be compatible in cross match tests by the antiglobulin technique. A specific case was observed in our center, which confirms the fact. The patient was a 37-year-old male suffering from intermediate β-thalassemia. He had a history of two previous transfusions, with unknown transfusion reaction. In the last transfusion, laboratory data showed: Hb 7.8 g/dL and Hematocrit (Hct) 24.2%. The patient received two units of cross matched, compatible concentrated red blood cells (RBCs). After eight days a severe reaction was observed with clinical evidence of tachycardia, fatigue, fever, back pain, chest discomfort, jaundice, nausea and anorexia. Accordingly delayed hemolytic transfusion reaction was suspected, and anti-RBC antibodies were tested. Laboratory tests revealed the presence of three alloantibodies: Anti-N, anti-S, anti-K, and a monospecific autoanti-JK(b).

  13. Study of a reaction between 2,3-dichloro-1,4-naphthoquinone and N,N'-diphenyl thiourea involving an EDA adduct as intermediate.

    PubMed

    Datta, Kakali; Mukherjee, Asok K

    2004-06-01

    The reaction between 2,3-dichloro-1,4-naphthoquinone and N,N'-diphenyl thiourea in acetonitrile medium, which yields the product, 2,3-(N,N'-diphenylthioureylene)-naphtho-1,4-quinone has been found to take place in two ways--thermal and photochemical. The thermal (dark) reaction occurs through an electron donor-acceptor (EDA) adduct as intermediate with evolution of HCl and kinetic data fit into the scheme A + B<==>AB(fast)-->product(slow) Formation constant of the EDA adduct and the rate constant of the slow process have been determined at four different temperatures from which the enthalpy of formation of AB has been determined. The photochemical reaction has been studied with 360 nm ordinary light and also with 365 and 370 nm laser beams. Use of laser causes about 10(3)-fold increase in the rate of the reaction but does not affect the quantum yield. The final product has been isolated and characterised by elemental analysis, 1H and 13C NMR, IR spectroscopy and mass spectrometry.

  14. H2SO4 formation from the gas-phase reaction of stabilized Criegee Intermediates with SO2: Influence of water vapour content and temperature

    NASA Astrophysics Data System (ADS)

    Berndt, Torsten; Jokinen, Tuija; Sipilä, Mikko; Mauldin, Roy L.; Herrmann, Hartmut; Stratmann, Frank; Junninen, Heikki; Kulmala, Markku

    2014-06-01

    The importance of gas-phase products from alkene ozonolysis other than OH radicals, most likely stabilized Criegee Intermediates (sCI), for the process of atmospheric SO2 oxidation to H2SO4 has been recently discovered. Subjects of this work are investigations on H2SO4 formation as a function of water vapour content (RH = 2-65%) and temperature (278-343 K) starting from the ozonolysis of trans-2-butene and 2,3-dimethyl-2-butene (TME). H2SO4 production other than via the OH radical reaction was attributed to the reaction of SO2 with sCI, i.e. acetaldehyde oxide arising from trans-2-butene ozonolysis and acetone oxide from TME. Measurements have been conducted in an atmospheric pressure flow tube using NO3--CI-APi-TOF mass spectrometry for H2SO4 detection. The sCI yields derived from H2SO4 measurements at 293 K were 0.49 ± 0.22 for acetaldehyde oxide and 0.45 ± 0.20 for acetone oxide. Our findings indicate a H2SO4 yield from sCI + SO2 of unity or close to unity. The deduced rate coefficient ratio for the reaction of sCI with H2O and SO2, k(sCI + H2O)/k(sCI + SO2), was found to be strongly dependent on the structure of the Criegee Intermediate, for acetaldehyde oxide at 293 K: (8.8 ± 0.4)·10-5 (syn- and anti-conformer in total) and for acetone oxide: <4·10-6. H2SO4 formation from sCI was pushed back with rising temperature in both reaction systems most probably due to an enhancement of sCI decomposition. The ratio k(dec)/k(sCI + SO2) increased by a factor of 34 (acetone oxide) increasing the temperature from 278 to 343 K. In the case of acetaldehyde oxide the temperature effect is less pronounced. The relevance of atmospheric H2SO4 formation via sCI + SO2 is discussed in view of its dependence on the structure of the Criegee Intermediate.

  15. An important difference between "exposed" and "photodistributed" underscores the importance of identifying common reactions.

    PubMed

    Jacob, Sharon E; Breithaupt, Andrew D

    2009-09-01

    This article presents the case of a patient with rheumatoid arthritis who was referred to dermatology for what was suspected to be a photosensitivity reaction to hydroxychloroquine, a common culprit in photodrug reactions. Despite the patient's insistence to the contrary, the cause of her eruption was an airborne allergic contact dermatitis to chemicals she was exposed to during her longtime hobby of soap-making. This case serves as an important illustration of the anatomical differences between eruptions occurring in exposed and photodistributed areas. This article also discusses the causes of dermatitis that may mimic photodrug reactions.

  16. The nature of the intermediates in the reactions of Fe(III)- and Mn(III)-microperoxidase-8 with H(2)O(2): a rapid kinetics study.

    PubMed

    Primus, Jean-Louis; Grunenwald, Sylvie; Hagedoorn, Peter-Leon; Albrecht-Gary, Anne-Marie; Mandon, Dominique; Veeger, Cees

    2002-02-20

    Kinetic studies were performed with microperoxidase-8 (Fe(III)MP-8), the proteolytic breakdown product of horse heart cytochrome c containing an octapeptide linked to an iron protoporphyrin IX. Mn(III) was substituted for Fe(III) in Mn(III)MP-8. The mechanism of formation of the reactive metal-oxo and metal-hydroperoxo intermediates of M(III)MP-8 upon reaction of H(2)O(2) with Fe(III)MP-8 and Mn(III)MP-8 was investigated by rapid-scan stopped-flow spectroscopy and transient EPR. Two steps (k(obs1) and k(obs2)) were observed and analyzed for the reaction of hydrogen peroxide with both catalysts. The plots of k(obs1) as function of [H(2)O(2)] at pH 8.0 and pH 9.1 for Fe(III)MP-8, and at pH 10.2 and pH 10.9 for Mn(III)MP-8, exhibit saturation kinetics, which reveal the accumulation of an intermediate. Double reciprocal plots of 1/k(obs1) as function of 1/[H(2)O(2)] at different pH values reveal a competitive effect of protons in the oxidation of M(III)MP-8. This effect of protons is confirmed by the linear dependence of 1/k(obs1) on [H(+)] showing that k(obs1) increases with the pH. The UV-visible spectra of the intermediates formed at the end of the first step (k(obs1)) exhibit a spectrum characteristic of a high-valent metal-oxo intermediate for both catalysts. Transient EPR of Mn(III)MP-8 incubated with an excess of H(2)O(2), at pH 11.5, shows the detection of a free radical signal at g approximately equal to 2 and of a resonance at g approximately equal to 4 characteristic of a Mn(IV) (S = 3/2) species. On the basis of these results, the following mechanism is proposed: (i) M(III)MP-8-OH(2) is deprotonated to M(III)MP-8-OH in a rapid preequilibrium step, with a pK(a) = 9.2 +/- 0.9 for Fe(III)MP-8 and a pK(a) = 11.2 +/- 0.3 for Mn(III)MP-8; (ii) M(III)MP-8-OH reacts with H(2)O(2) to form Compound 0, M(III)MP8-OOH, with a second-order rate constant k(1) = (1.3 +/- 0.6) x 10(6) M(-1) x s(-1) for Fe(III)MP-8 and k(1) = (1.6 +/- 0.9) x 10(5) M(-1) x s(-1) for Mn

  17. Measuring rate constants for reactions of the simplest Criegee intermediate (CH2OO) by monitoring the OH radical.

    PubMed

    Liu, Yingdi; Bayes, Kyle D; Sander, Stanley P

    2014-01-30

    While generating the CH2OO molecule by reacting CH2I with O2, significant amounts of the OH radical were observed by laser-induced fluorescence. At least two different processes formed OH. A fast process was probably initiated by a reaction of vibrationally hot CH2I radicals. The second process appeared to be associated with the decay of the CH2OO molecule. The addition of molecules known to react with CH2OO increased the observed decay rates of the OH signal. Using the OH signals as a proxy for the CH2OO concentration, the rate constant for the reaction of hexafluoroacetone with CH2OO was determined to be (3.33 ± 0.27) × 10(-11) cm(3) molecule(-1) s(-1), in good agreement with the value measured by Taatjes et al.1 The rate constant for the reaction of SO2 with CH2OO, (3.53 ± 0.29) × 10(-11) cm(3) molecule(-1) s(-1), showed no pressure dependence over the range of 50-200 Torr and was in agreement with the value at 4 Torr reported by Welz et al.

  18. Direct measurements of unimolecular and bimolecular reaction kinetics of the Criegee intermediate (CH3)2COO

    SciTech Connect

    Chhantyal-Pun, Rabi; Welz, Oliver; Savee, John D.; Eskola, Arkke J.; Lee, Edmond P. F.; Blacker, Lucy; Hill, Henry R.; Ashcroft, Matilda; Khan, M. Anwar H.; Lloyd-Jones, Guy C.; Evans, Louise; Rotavera, Brandon; Huang, Haifeng; Osborn, David L.; Mok, Daniel K. W.; Dyke, John M.; Shallcross, Dudley E.; Percival, Carl J.; Orr-Ewing, Andrew J.; Taatjes, Craig A.

    2016-10-18

    Here, the Criegee intermediate acetone oxide, (CH3)2COO, is formed by laser photolysis of 2,2-diiodopropane in the presence of O2 and characterized by synchrotron photoionization mass spectrometry and by cavity ring-down ultraviolet absorption spectroscopy. The rate coefficient of the reaction of the Criegee intermediate with SO2 was measured using photoionization mass spectrometry and pseudo-first-order methods to be (7.3 ± 0.5) × 10–11 cm3 s–1 at 298 K and 4 Torr and (1.5 ± 0.5) × 10–10 cm3 s–1 at 298 K and 10 Torr (He buffer). These values are similar to directly measured rate coefficients of anti-CH3CHOO with SO2, and in good agreement with recent UV absorption measurements. The measurement of this reaction at 293 K and slightly higher pressures (between 10 and 100 Torr) in N2 from cavity ring-down decay of the ultraviolet absorption of (CH3)2COO yielded even larger rate coefficients, in the range (1.84 ± 0.12) × 10–10 to (2.29 ± 0.08) × 10–10 cm3 s–1. Photoionization mass spectrometry measurements with deuterated acetone oxide at 4 Torr show an inverse deuterium kinetic isotope effect, kH/kD = (0.53 ± 0.06), for reactions with SO2, which may be consistent with recent suggestions that the formation of an association complex affects the rate coefficient. The reaction of (CD3)2COO with NO2 has a rate coefficient at 298 K and 4 Torr of (2.1 ± 0.5) × 10–12 cm3 s–1 (measured with photoionization mass spectrometry), again similar to rate for the reaction of anti-CH3CHOO with NO2. Cavity ring-down measurements of the acetone oxide removal without added reagents display a combination of first- and second-order decay kinetics

  19. Photodegradation of imidacloprid insecticide by Ag-deposited titanate nanotubes: a study of intermediates and their reaction pathways.

    PubMed

    Grover, Inderpreet Singh; Singh, Satnam; Pal, Bonamali

    2014-12-31

    The present work demonstrates the influence of Ag-loading (0.2-1.0 wt %) onto sodium titanate nanotubes (TNT) for complete photomineralization of the neurotoxic imidacloprid (IMI) insecticide under UV light illumination. It has been observed that degradation of IMI follows pseudo-first-order kinetics, where 0.5 wt % Ag-loaded TNT exhibited highest apparent rate constant (2.2 × 10(-2) min(-1)) and corresponding least half-life (t1/2) of 31 min for IMI relative to bare P25-TiO2 (3.4 × 10(-3) min(-1), t1/2 = 230 min). The mineralization of IMI intermediates to CO2 during its photooxidation has been described by time course GC-MS and GC analysis and has been correlated with the kinetic analysis. The investigation for the role and quantitative estimation of the fate of heteroatoms (N, O, and Cl) present in IMI revealed an increase in the amount of nitrate, nitrite, and chloride ions with time during its photooxidation. On the basis of these results a mechanistic pathway for photomineralization of IMI is proposed.

  20. Apparent anti-Woodward-Hoffmann addition to a nickel bis(dithiolene) complex: the reaction mechanism involves reduced, dimetallic intermediates.

    PubMed

    Dang, Li; Shibl, Mohamed F; Yang, Xinzheng; Harrison, Daniel J; Alak, Aiman; Lough, Alan J; Fekl, Ulrich; Brothers, Edward N; Hall, Michael B

    2013-04-01

    Nickel dithiolene complexes have been proposed as electrocatalysts for alkene purification. Recent studies of the ligand-based reactions of Ni(tfd)2 (tfd = S2C2(CF3)2) and its anion [Ni(tfd)2](-) with alkenes (ethylene and 1-hexene) showed that in the absence of the anion, the reaction proceeds most rapidly to form the intraligand adduct, which decomposes by releasing a substituted dihydrodithiin. However, the presence of the anion increases the rate of formation of the stable cis-interligand adduct, and decreases the rate of dihydrodithiin formation and decomposition. In spite of both computational and experimental studies, the mechanism, especially the role of the anion, remained somewhat elusive. We are now providing a combined experimental and computational study that addresses the mechanism and explains the role of the anion. A kinetic study (global analysis) for the reaction of 1-hexene is reported, which supports the following mechanism: (1) reversible intraligand addition, (2) oxidation of the intraligand addition product prior to decomposition, and (3) interligand adduct formation catalyzed by Ni(tfd)2(-). Density functional theory (DFT) calculations were performed on the Ni(tfd)2/Ni(tfd)2(-)/ethylene system to shed light on the selectivity of adduct formation in the absence of anion and on the mechanism in which Ni(tfd)2(-) shifts the reaction from intraligand addition to interligand addition. Computational results show that in the neutral system the free energy of activation for intraligand addition is lower than that for interligand addition, in agreement with the experimental results. The computations predict that the anion enhances the rate of the cis-interligand adduct formation by forming a dimetallic complex with the neutral complex. The [(Ni(tfd)2)2](-) dimetallic complex then coordinates ethylene and isomerizes to form a Ni,S-bound ethylene complex, which then rapidly isomerizes to the stable interligand adduct but not to the intraligand adduct

  1. Kinetic reaction modeling framework for identifying and quantifying reductant reactivity in heterogeneous aquifer sediments.

    PubMed

    Descourvieres, Carlos; Prommer, Henning; Oldham, Carolyn; Greskowiak, Janek; Hartog, Niels

    2010-09-01

    Water-sediment interactions triggered by the injection of oxidized aqueous solutions into anoxic groundwater systems usually modify both the aquifer matrix and control the final aqueous composition. The identification and quantification of these reactions in complex heterogeneous systems remains a challenge for the analysis and prediction of water quality changes. Driven by the proposed injection of large quantities of oxic water into a deep anoxic heterogeneous pyritic aquifer; this study was undertaken to quantify the reactivity of aquifer sediments with respect to oxidant consumption and to characterize the variability of the reaction rates across different lithological units. A total of 53 samples were incubated for periods of 14, 37, and 50 days, during which the gas-phase was continuously monitored and the aqueous composition analyzed. A geochemical modeling framework was developed that incorporated a mixed set of equilibrium and kinetic reactions and supported the interpretation and quantification of the geochemical controls. The good agreement between simulated and experimental results of O2 consumption, CO2 production, pH, major ions, and trace metals suggests that the framework was able to successfully quantify reaction rates of competing redox and buffering reactions for the different lithological aquifer material.

  2. EPR and pulsed ENDOR study of intermediates from reactions of aromatic azides with group 13 metal trichlorides

    PubMed Central

    Bencivenni, Giorgio; Cesari, Riccardo; Nanni, Daniele; El Mkami, Hassane

    2010-01-01

    Summary The reactions of group 13 metal trichlorides with aromatic azides were examined by CW EPR and pulsed ENDOR spectroscopies. Complex EPR spectra were obtained from reactions of aluminium, gallium and indium trichlorides with phenyl azides containing a variety of substituents. Analysis of the spectra showed that 4-methoxy-, 3-methoxy- and 2-methoxyphenyl azides all gave ‘dimer’ radical cations [ArNHC6H4NH2]+• and trimers [ArNHC6H4NHC6H4NH2]+• followed by polymers. 4-Azidobenzonitrile, with its electron-withdrawing substituent, did not react. In general the aromatic azides appeared to react most rapidly with AlCl3 but this reagent tended to generate much polymer. InCl3 was the least reactive group 13 halide. DFT computations of the radical cations provided corroborating evidence and suggested that the unpaired electrons were accommodated in extensive π-delocalised orbitals. A mechanism to account for the reductive conversion of aromatic azides to the corresponding anilines and thence to the dimers and trimers is proposed. PMID:21049080

  3. Direct experimental probing and theoretical analysis of the reaction between the simplest Criegee intermediate CH 2 OO and isoprene

    SciTech Connect

    Decker, Z. C. J.; Au, K.; Vereecken, L.; Sheps, L.

    2017-01-01

    Recent advances in the spectroscopy of Criegee intermediates (CI) have enabled direct kinetic studies of these highly reactive chemical species. The impact of CI chemistry is currently being incorporated into atmospheric models, including their reactions with trace organic and inorganic compounds. Isoprene, C5H8, is a doubly-unsaturated hydrocarbon that accounts for the largest share of all biogenic emissions around the globe and is also a building block of larger volatile organic compounds. We report direct measurements of the reaction of the simplest CI (CH2OO) with isoprene, using time-resolved cavity-enhanced UV absorption spectroscopy. We find the reaction to be pressure-independent between 15–100 Torr, with a rate coefficient that varies from (1.5 ± 0.1) × 10–15 cm3 molecule–1 s–1 at room temperature to (23 ± 2) × 10–15 cm3 molecule–1 s–1 at 540 K. Quantum chemical and transition-state theory calculations of 16 unique channels for CH2OO + isoprene somewhat underpredict the observed T-dependence of the total reaction rate coefficient, but are overall in good agreement with the experimental measurements. Finally, this reaction is broadly similar to those with smaller alkenes, proceeding by 1,3-dipolar cycloaddition to one of the two conjugated double bonds of isoprene.

  4. Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA

    SciTech Connect

    Hashimoto, Hideharu; Pais, June E.; Dai, Nan; Corrêa, Jr., Ivan R.; Zhang, Xing; Zheng, Yu; Cheng, Xiaodong

    2015-08-31

    The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and α-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solved NgTet1–5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH2-) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH2 towards the metal-ligand water molecule, where a dioxygen O2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably due to the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate.

  5. Rate coefficients of C(1) and C(2) Criegee intermediate reactions with formic and acetic Acid near the collision limit: direct kinetics measurements and atmospheric implications.

    PubMed

    Welz, Oliver; Eskola, Arkke J; Sheps, Leonid; Rotavera, Brandon; Savee, John D; Scheer, Adam M; Osborn, David L; Lowe, Douglas; Murray Booth, A; Xiao, Ping; Anwar H Khan, M; Percival, Carl J; Shallcross, Dudley E; Taatjes, Craig A

    2014-04-25

    Rate coefficients are directly determined for the reactions of the Criegee intermediates (CI) CH2 OO and CH3 CHOO with the two simplest carboxylic acids, formic acid (HCOOH) and acetic acid (CH3 COOH), employing two complementary techniques: multiplexed photoionization mass spectrometry and cavity-enhanced broadband ultraviolet absorption spectroscopy. The measured rate coefficients are in excess of 1×10(-10)  cm(3)  s(-1) , several orders of magnitude larger than those suggested from many previous alkene ozonolysis experiments and assumed in atmospheric modeling studies. These results suggest that the reaction with carboxylic acids is a substantially more important loss process for CIs than is presently assumed. Implementing these rate coefficients in global atmospheric models shows that reactions between CI and organic acids make a substantial contribution to removal of these acids in terrestrial equatorial areas and in other regions where high CI concentrations occur such as high northern latitudes, and implies that sources of acids in these areas are larger than previously recognized.

  6. Rate Coefficients of C1 and C2 Criegee Intermediate Reactions with Formic and Acetic Acid Near the Collision Limit: Direct Kinetics Measurements and Atmospheric Implications**

    PubMed Central

    Welz, Oliver; Eskola, Arkke J; Sheps, Leonid; Rotavera, Brandon; Savee, John D; Scheer, Adam M; Osborn, David L; Lowe, Douglas; Murray Booth, A; Xiao, Ping; Anwar H Khan, M; Percival, Carl J; Shallcross, Dudley E; Taatjes, Craig A

    2014-01-01

    Rate coefficients are directly determined for the reactions of the Criegee intermediates (CI) CH2OO and CH3CHOO with the two simplest carboxylic acids, formic acid (HCOOH) and acetic acid (CH3COOH), employing two complementary techniques: multiplexed photoionization mass spectrometry and cavity-enhanced broadband ultraviolet absorption spectroscopy. The measured rate coefficients are in excess of 1×10−10 cm3 s−1, several orders of magnitude larger than those suggested from many previous alkene ozonolysis experiments and assumed in atmospheric modeling studies. These results suggest that the reaction with carboxylic acids is a substantially more important loss process for CIs than is presently assumed. Implementing these rate coefficients in global atmospheric models shows that reactions between CI and organic acids make a substantial contribution to removal of these acids in terrestrial equatorial areas and in other regions where high CI concentrations occur such as high northern latitudes, and implies that sources of acids in these areas are larger than previously recognized. PMID:24668781

  7. A model for the compositions of non-stoichiometric intermediate phases formed by diffusion reactions, and its application to Nb3Sn superconductors.

    PubMed

    Xu, X; Sumption, M D

    2016-01-12

    In this work we explore the compositions of non-stoichiometric intermediate phases formed by diffusion reactions: a mathematical framework is developed and tested against the specific case of Nb3Sn superconductors. In the first part, the governing equations for the bulk diffusion and inter-phase interface reactions during the growth of a compound are derived, numerical solutions to which give both the composition profile and growth rate of the compound layer. The analytic solutions are obtained with certain approximations made. In the second part, we explain an effect that the composition characteristics of compounds can be quite different depending on whether it is the bulk diffusion or grain boundary diffusion that dominates in the compounds, and that "frozen" bulk diffusion leads to unique composition characteristics that the bulk composition of a compound layer remains unchanged after its initial formation instead of varying with the diffusion reaction system; here the model is modified for the case of grain boundary diffusion. Finally, we apply this model to the Nb3Sn superconductors and propose approaches to control their compositions.

  8. A model for the compositions of non-stoichiometric intermediate phases formed by diffusion reactions, and its application to Nb3Sn superconductors

    SciTech Connect

    Xu, X.; Sumption, M. D.

    2016-01-12

    In this work we explore the compositions of non-stoichiometric intermediate phases formed by diffusion reactions: a mathematical framework is developed and tested against the specific case of Nb3Sn superconductors. In the first part, the governing equations for the bulk diffusion and interphase interface reactions during the growth of a compound are derived, numerical solutions to which give both the composition profile and growth rate of the compound layer. The analytic solutions are obtained with certain approximations made. In the second part, we explain an effect that the composition characteristics of compounds can be quite different depending on whether it is the bulk diffusion or grain boundary diffusion that dominates in the compounds, and that “frozen” bulk diffusion leads to unique composition characteristics that the bulk composition of a compound layer remains unchanged after its initial formation instead of varying with the diffusion reaction system; here the model is modified for the case of grain boundary diffusion. Lastly, we apply this model to the Nb3Sn superconductors and propose approaches to control their compositions.

  9. A model for the compositions of non-stoichiometric intermediate phases formed by diffusion reactions, and its application to Nb3Sn superconductors

    DOE PAGES

    Xu, X.; Sumption, M. D.

    2016-01-12

    In this work we explore the compositions of non-stoichiometric intermediate phases formed by diffusion reactions: a mathematical framework is developed and tested against the specific case of Nb3Sn superconductors. In the first part, the governing equations for the bulk diffusion and interphase interface reactions during the growth of a compound are derived, numerical solutions to which give both the composition profile and growth rate of the compound layer. The analytic solutions are obtained with certain approximations made. In the second part, we explain an effect that the composition characteristics of compounds can be quite different depending on whether it ismore » the bulk diffusion or grain boundary diffusion that dominates in the compounds, and that “frozen” bulk diffusion leads to unique composition characteristics that the bulk composition of a compound layer remains unchanged after its initial formation instead of varying with the diffusion reaction system; here the model is modified for the case of grain boundary diffusion. Lastly, we apply this model to the Nb3Sn superconductors and propose approaches to control their compositions.« less

  10. Cutting the Gordian Knot: Identifiability of anaplerotic reactions in Corynebacterium glutamicum by means of (13) C-metabolic flux analysis.

    PubMed

    Kappelmann, Jannick; Wiechert, Wolfgang; Noack, Stephan

    2016-03-01

    Corynebacterium glutamicum is the major workhorse for the microbial production of several amino and organic acids. As long as these derive from tricarboxylic acid cycle intermediates, the activity of anaplerotic reactions is pivotal for a high biosynthetic yield. To determine single anaplerotic activities (13) C-Metabolic Flux Analysis ((13) C-MFA) has been extensively used for C. glutamicum, however with different network topologies, inconsistent or poorly determined anaplerotic reaction rates. Therefore, in this study we set out to investigate whether a focused isotopomer model of the anaplerotic node can at all admit a unique solution for all fluxes. By analyzing different scenarios of active anaplerotic reactions, we show in full generality that for C. glutamicum only certain anaplerotic deletion mutants allow to uniquely determine the anaplerotic fluxes from (13) C-isotopomer data. We stress that the result of this analysis for different assumptions on active enzymes is directly transferable to other compartment-free organisms. Our results demonstrate that there exist biologically relevant metabolic network topologies for which the flux distribution cannot be inferred by classical (13) C-MFA.

  11. An integrated approach to identify distribution of Oncomelania hupensis, the intermediate host of Schistosoma japonicum, in a mountainous region in China.

    PubMed

    Yang, Kun; Wang, Xian-Hong; Yang, Guo-Jing; Wu, Xiao-Hua; Qi, Yun-Liang; Li, Hong-Jun; Zhou, Xiao-Nong

    2008-07-01

    The aim of this study is to better understand ecological variability related to the distribution of Oncomelania hupensis, the snail intermediate host of Schistosoma japonicum, and predict the spatial distribution of O. hupensis at the local scale in order to develop a more effective control strategy for schistosomiasis in the hilly and mountainous regions of China. A two-pronged approach was applied in this study consisting of a landscape pattern analysis complemented with Bayesian spatial modelling. The parasitological data were collected by cross-sectional surveys carried out in 11 villages in 2006 and mapped based on global positioning system (GPS) coordinates. Environmental surrogates and landscape metrics were derived from remotely-sensed images and land-cover/land-use classification data. Bayesian non-spatial and spatial models were applied to investigate the variation of snail density in relation to environmental surrogates and landscape metrics at the local scale. A Bayesian spatial model, validated by the deviance information criterion (DIC), was found to be the best-fitting model. The mean shape index (MSI) and Shannon's evenness indexes (SEI) were significantly associated with snail density. These findings suggest that decreasing the heterogeneity of the landscape can reduce snail density. A prediction maps were generated by the Bayesian model together with environmental surrogates and landscape metrics. In conclusion, the risk areas of snail distribution at the local scale can be identified using an integrated approach with landscape pattern analysis supported by remote sensing and GIS technologies, as well as Bayesian modelling.

  12. Stabilization and Characterization of a Heme-Oxy Reaction Intermediate in Inducible Nitric-oxide Synthase*S⃞

    PubMed Central

    Tejero, Jesús; Biswas, Ashis; Wang, Zhi-Qiang; Page, Richard C.; Haque, Mohammad Mahfuzul; Hemann, Craig; Zweier, Jay L.; Misra, Saurav; Stuehr, Dennis J.

    2008-01-01

    Nitric-oxide synthases (NOS) are heme-thiolate enzymes that N-hydroxylate l-arginine (l-Arg) to make NO. NOS contain a unique Trp residue whose side chain stacks with the heme and hydrogen bonds with the heme thiolate. To understand its importance we substituted His for Trp188 in the inducible NOS oxygenase domain (iNOSoxy) and characterized enzyme spectral, thermodynamic, structural, kinetic, and catalytic properties. The W188H mutation had relatively small effects on l-Arg binding and on enzyme heme-CO and heme-NO absorbance spectra, but increased the heme midpoint potential by 88 mV relative to wild-type iNOSoxy, indicating it decreased heme-thiolate electronegativity. The protein crystal structure showed that the His188 imidazole still stacked with the heme and was positioned to hydrogen bond with the heme thiolate. Analysis of a single turnover l-Arg hydroxylation reaction revealed that a new heme species formed during the reaction. Its build up coincided kinetically with the disappearance of the enzyme heme-dioxy species and with the formation of a tetrahydrobiopterin (H4B) radical in the enzyme, whereas its subsequent disappearance coincided with the rate of l-Arg hydroxylation and formation of ferric enzyme. We conclude: (i) W188H iNOSoxy stabilizes a heme-oxy species that forms upon reduction of the heme-dioxy species by H4B. (ii) The W188H mutation hinders either the processing or reactivity of the heme-oxy species and makes these steps become rate-limiting for l-Arg hydroxylation. Thus, the conserved Trp residue in NOS may facilitate formation and/or reactivity of the ultimate hydroxylating species by tuning heme-thiolate electronegativity. PMID:18815130

  13. Detection of alkylperoxo and ferryl, (Fe sup IV = O) sup 2+ , intermediates during the reaction of tert-butyl hydroperoxide with iron porphyrins in toluene solution

    SciTech Connect

    Arasasingham, R.D.; Cornman, C.R.; Balch, A.L. )

    1989-11-27

    PFe{sup II} and PFe{sup III}OH (P is a porphyrin dianion) catalyze the decomposition of tert-butyl hydroperoxide in toluene solution without appreciable attack on the porphyrin ligand. {sup 1}H NMR spectroscopic studies at low temperature ({minus}70{degree}C) give evidence for the formation of a high-spin, five-coordinate intermediate, PFe{sup III}OOC(CH{sub 3}){sub 3}. Organic products formed from this reaction are tert-butyl alcohol, di-tert-butyl peroxide, benzaldehyde, acetone, and benzyl-tert-butyl peroxide, which arise largely from a radical chain process initiated by the iron porphyrin but continuing without its intervention.

  14. Atmospheric Reaction Systems as Null-Models to Identify Structural Traces of Evolution in Metabolism

    PubMed Central

    Holme, Petter; Huss, Mikael; Lee, Sang Hoon

    2011-01-01

    The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic machinery that is subject to evolution. In this paper, we explore the possibility that reaction systems of planetary atmospheres can serve as a null-model against which we can define metabolic structure and trace the influence of evolution. We find that the two types of data can be distinguished by their respective degree distributions. This is especially clear when looking at the degree distribution of the reaction network (of reaction connected to each other if they involve the same molecular species). For the Earth's atmospheric network and the human metabolic network, we look into more detail for an underlying explanation of this deviation. However, we cannot pinpoint a single cause of the difference, rather there are several concurrent factors. By examining quantities relating to the modular-functional organization of the metabolism, we confirm that metabolic networks have a more complex modular organization than the atmospheric networks, but not much more. We interpret the more variegated modular arrangement of metabolism as a trace of evolved functionality. On the other hand, it is quite remarkable how similar the structures of these two types of networks are, which emphasizes that the constraints from the chemical properties of the molecules has a larger influence in shaping the reaction system than does natural selection. PMID:21573072

  15. Kinetic and spectroscopic characterization of intermediates and component interactions in reactions of methane monooxygenase from methylococcus capsulatus (Bath)

    SciTech Connect

    Liu, K.E.; Valentine, A.M.; Salifoglou, A.; Lippard, S.J.; Wang, D.; Huynh, B.H.; Edmondson, D.E.

    1995-10-18

    We describe mechanistic studies of the soluble methane monooxygenase (sMMO) enzyme system from Methylococcus capsulatus (Bath). Interactions among the three sMMO components, the hydroxylase (H), reductase (R), and protein B (B), were investigated by monitoring conversion of nitrobenzene to nitrophenol under both single turnover and catalytic conditions. During catalytic turnover, hydroxylation occurs to afford 3-nitrophenol (43%) and 4-nitrophenol (57%), whereas hydroxylation takes place exclusively (> 95%) to give 4-nitrophenol under single turnover conditions in the absence of reductase. Protein B exerts a strong influence on single turnover reactions of nitrobenzene, with optimal rate constants and yields obtained by using 1.5-2 equiv of protein R per equivalent of hydroxylase. The temperature dependence of these kinetic values was determined. Changes in dioxygen concentration and pH, as well as exchange of solvent accessible protons with D{sub 2}O, did not significantly affect the rate constants for either of these processes, the implications of which for the kinetic mechanism are discussed. From the present and related evidence, structures for H{sub peroxo} and Q are proposed. 54 refs., 11 figs., 4 tabs.

  16. Novel approach for identifying key residues in enzymatic reactions: proton abstraction in ketosteroid isomerase.

    PubMed

    Ito, Mika; Brinck, Tore

    2014-11-20

    We propose a computationally efficient approach for evaluating the individual contributions of many different residues to the catalytic efficiency of an enzymatic reaction. This approach is based on the fragment molecular orbital (FMO) method, and it defines the energy of a deletion form, i.e., the energy of the system when a particular residue is deleted. Using this approach, we found that, among 10 investigated residues, three, Tyr14, Asp99, and Tyr55, in this order, significantly reduce the activation energy of the proton abstraction from a substrate, cyclopent-2-enone, catalyzed by ketosteroid isomerase (KSI). The relative activation energies estimated in this study are in good agreement with available previous experimental and theoretical data obtained for the similar proton abstraction with a native substrate and substitution mutants of KSI. It was thus indicated that the new approach is efficient for rationally evaluating the catalytic effects of multiple residues on an enzymatic reaction.

  17. Characterization of Metastable Intermediates Formed in the Reaction Between a Mn(II) Complex and Dioxygen, Including a Crystallographic Structure of a Binuclear Mn(III)-Peroxo Species

    PubMed Central

    Coggins, Michael K.; Sun, Xianru; Kwak, Yeonju; Solomon, Edward I.; Rybak-Akimova, Elena; Kovacs, Julie A.

    2013-01-01

    Transition-metal peroxos have been implicated as key intermediates in a variety of critical biological processes involving O2. Due to their highly reactive nature, very few metal-peroxos have been characterized. The dioxygen chemistry of manganese remains largely unexplored despite the proposed involvement of a binuclear Mn-peroxo, either as a precursor to O2, or derived from O2, in both photosynthetic H2O oxidation and DNA biosynthesis, arguably two of the most fundamental processes of life. Neither of these biological intermediates has been observed. Herein we describe the dioxygen chemistry of coordinatively unsaturated [MnII(SMe2N4(6-MeDPEN))] +(1), and the characterization of intermediates formed en route to a binuclear mono-oxo bridged Mn(III) product {[MnIII(SMe2N4(6-MeDPEN)]2-(μ-O)}2+ (2), the oxo atom of which is derived from 18O2. At low-temperatures, a dioxygen intermediate, [Mn(SMe2N4(6-MeDPEN))(O2)]+ (4), is observed (by stopped-flow) to rapidly and irreversibly form in this reaction (k1(−10 °C)= 3780±180M−1s−1, ΔH1‡ = 26.4±1.7 kJ mol−1, ΔS1‡ = − 75.6±6.8 J mol−1K−1), and then convert more slowly (k2(−10 °C)= 417±3.2 M−1s−1, ΔH2‡ = 47.1±1.4 kJ mol−1, ΔS2‡ = − 15.0±5.7 J mol−1K−1) to a species 3 with isotopically sensitive stretches at νo-o (Δ18O) = 819(47) cm−1, kO–O= 3.02 mdyn/Å, and νMn-O(Δ18O) = 611(25) cm−1 consistent with a peroxo. Intermediate 3 releases approximately 0.5 equiv of H2O2 per Mn ion upon protonation, and the rate of conversion of 4 to 3 is dependent on [Mn(II)] concentration, consistent with the formation of a binuclear Mn-peroxo. This was verified by X-ray crystallography, where the peroxo of {[MnIII(SMe2N4(6-Me-DPEN)]2(trans–μ–1,2–O2)}2+ (3) is shown to be bridging between two Mn(III) ions in an end-on trans-μ-1,2-fashion. This represents the first characterized example of a binuclear Mn(III)-peroxo, and a rare case in which more than one intermediate is observed

  18. Modeling of S-Nitrosothiol-Thiol Reactions of Biological Significance: HNO Production by S-Thiolation Requires a Proton Shuttle and Stabilization of Polar Intermediates.

    PubMed

    Ivanova, Lena V; Cibich, Daniel; Deye, Gregory; Talipov, Marat R; Timerghazin, Qadir K

    2017-02-07

    Nitroxyl (HNO), a reduced form of the important gasotransmitter nitric oxide, exhibits its own unique biological activity. A possible biological pathway of HNO formation is the S-thiolation reaction between thiols and S-nitrosothiols (RSNOs). Our density functional theory (DFT) calculations suggested that S-thiolation proceeds through a proton transfer from the thiol to the RSNO nitrogen atom, which increases electrophilicity of the RSNO sulfur, followed by nucleophilic attack by thiol, yielding a charge-separated zwitterionic intermediate structure RSS(+) (R)N(H)O(-) (Zi), which decomposes to yield HNO and disulfide RSSR. In the gas phase, the proton transfer and the S-S bond formation are asynchronous, resulting in a high activation barrier (>40 kcal mol(-1) ), making the reaction infeasible. However, the barrier can decrease below the S-N bond dissociation energy in RSNOs (≈30 kcal mol(-1) ) upon transition into an aqueous environment that stabilizes Zi and provides a proton shuttle to synchronize the proton transfer and the S-S bond formation. These mechanistic features suggest that S-thiolation can easily lend itself to enzymatic catalysis and thus can be a possible route of endogenous HNO production.

  19. The formation of free radical intermediates in the reactions of gaseous NO 2 with solid NaCl and NaBr—Atmospheric and toxicological implications

    NASA Astrophysics Data System (ADS)

    Wan, J. K. S.; Pitts, J. N.; Beichert, P.; Finlayson-Pitts, B. J.

    The reaction of gaseous NO 2 with alkali halides is of significant interest for its potential to occur in polluted marine atmospheres ((Finlayson-Pitts, 1993), Res. Chem. Int.19, 235-249). We report here a new paramagnetic signal in NaBr and NaCl formed upon reaction with gaseous NO 2 and assigned to a radical anion intermediate of the type [X… NO 2] - where X = Br, Cl. This is a new type of V k center (Castner and Känzig, 1957, J. Phys. Chem. Solids3, 178-195; Fowler, 1968; Seidel, 1969, in Magnetic Resonance and Radiofrequency Spectroscopy (edited by Averbuch P.), North Holland, Amsterdam, pp. 141-156), which is remarkably stable. Indeed, with NaCl it can be observed for several days following the reaction after handling the sample in room light and ambient air. This intermediate may be responsible at least in part for synergistic effects observed in the deep lung in rats exposed simultaneously to gaseous NO 2 and NaCl aerosol (Last and Warren, 1987, Toxicol. Appl. Pharmacol.90, 34-42). While the gaseous product ClNO was suggested earlier as the causative agent (Last and Warren, 1987, Toxicol. Appl. Pharmacol.90, 34-42), it is highly reactive with liquid water and will be removed largely in the upper respiratory tract, while small particles are able to penetrate into the deep lung. Given the ubiquitous occurrence (Finlayson-Pitts and Pitts, 1986, Atmospheric Chemistry: Fundamentals and Experimental Techniques, Wiley, New York), of NO 2 and airborne salt particles, which occur not only in marine areas but also significant distances inland (Shaw, 1991, J. geophys. Res.96, 22,369-22,372) as well as in the plumes from oil well burning (Lowenthal et al., 1993, Geophys. Res. Lett.20, 691-693; Stevens et al., 1993, Wat. Sci. Technol.27, 223-233; Sheridan et al., 1992, Geophys. Res. Lett.19, 389-392; Parungo et al., 1992, J. geophys. Res. 97, 15,867-15,882; Cahill et al., 1992, J. geophys. Res.97, 14,513-14,520) this radical anion could provide a vehicle for delivery

  20. Utilization of Microwave Spectroscopy to Identify and Probe Reaction Dynamics of Hsno, a Crucial Biological Signaling Molecule

    NASA Astrophysics Data System (ADS)

    Nava, Matthew; Martin-Drumel, Marie-Aline; Stanton, John F.; Cummins, Christopher; McCarthy, Michael C.

    2016-06-01

    Thionitrous acid (HSNO), a potential key intermediate in biological signaling pathways, has been proposed to link NO and H2S biochemistries. Its existence and stability in vivo, however, remain controversial. By means of Fourier-transform microwave spectroscopy, we establish that HSNO is spontaneously formed in high concentration when NO and H2S gases are simply mixed at room temperature in the presence of metallic surfaces. Our measurements reveal that HSNO is formed with high efficiency by the reaction H2S and N2O3 to produce HSNO and HNO2, where N2O3 is a product of NO disproportionation. These studies also suggest that further reaction of HSNO with H2S may form HNO and HSSH. The length of the S--N bond has been derived to high precision from isotopic studies, and is found to be unusually long, 1.84 Å -- the longest S--N bond reported to date for an SNO compound. The present structural and reactivity investigations of this elusive molecule provide a firm fundation to better understand its physiological chemistry and propensity to undergo S--N bond homolysis in vivo.

  1. Negative ion photoelectron spectra of ISO3-, IS2O3-, and IS2O4- intermediates formed in interfacial reactions of ozone and iodide/sulfite aqueous microdroplets

    NASA Astrophysics Data System (ADS)

    Qin, Zhengbo; Hou, Gao-Lei; Yang, Zheng; Valiev, Marat; Wang, Xue-Bin

    2016-12-01

    Three short-lived, anionic intermediates, ISO3-, IS2O3-, and IS2O4-, are detected during reactions between ozone and aqueous iodine/sulfur oxide microdroplets. These species may play an important role in ozone-driven inorganic aerosol formation; however their chemical properties remain largely unknown. This is the issue addressed in this work using negative ion photoelectron spectroscopy (NIPES) and ab initio modeling. The NIPE spectra reveal that all of the three anionic species are characterized by high adiabatic detachment energies (ADEs) - 4.62 ± 0.10, 4.52 ± 0.10, and 4.60 ± 0.10 eV for ISO3-, IS2O3-, and IS2O4-, respectively. Vibrational progressions with frequencies assigned to the S-O symmetric stretching modes are discernable in the ground state transition features. Density functional theory calculations show the presence of several low-lying isomers involving different bonding scenarios. Further analysis based on high level CCSD(T) calculations reveal that the lowest energy structures are characterized by the formation of I-S and S-S bonds and can be structurally viewed as SO3 linked with I, IS, and ISO for ISO3-, IS2O3-, and IS2O4-, respectively. The calculated ADEs and vertical detachment energies are in excellent agreement with the experimental results, further supporting the identified minimum energy structures. The obtained intrinsic molecular properties of these anionic intermediates and neutral radicals should be useful to help understand their photochemical reactions in the atmosphere.

  2. A Novel Tool for Studying Auxin-Metabolism: The Inhibition of Grapevine Indole-3-Acetic Acid-Amido Synthetases by a Reaction Intermediate Analogue

    PubMed Central

    Böttcher, Christine; Dennis, Eric G.; Booker, Grant W.; Polyak, Steven W.; Boss, Paul K.; Davies, Christopher

    2012-01-01

    An important process for the regulation of auxin levels in plants is the inactivation of indole-3-acetic acid (IAA) by conjugation to amino acids. The conjugation reaction is catalysed by IAA-amido synthetases belonging to the family of GH3 proteins. Genetic approaches to study the biological significance of these enzymes have been hampered by large gene numbers and a high degree of functional redundancy. To overcome these difficulties a chemical approach based on the reaction mechanism of GH3 proteins was employed to design a small molecule inhibitor of IAA-amido synthetase activity. Adenosine-5′-[2-(1H-indol-3-yl)ethyl]phosphate (AIEP) mimics the adenylated intermediate of the IAA-conjugation reaction and was therefore proposed to compete with the binding of MgATP and IAA in the initial stages of catalysis. Two grapevine IAA-amido synthetases with different catalytic properties were chosen to test the inhibitory effects of AIEP in vitro. GH3-1 has previously been implicated in the grape berry ripening process and is restricted to two amino acid substrates, whereas GH3-6 conjugated IAA to 13 amino acids. AIEP is the most potent inhibitor of GH3 enzymes so far described and was shown to be competitive against MgATP and IAA binding to both enzymes with Ki-values 17-68-fold lower than the respective Km-values. AIEP also exhibited in vivo activity in an ex planta test system using young grape berries. Exposure to 5–20 µM of the inhibitor led to decreased levels of the common conjugate IAA-Asp and reduced the accumulation of the corresponding Asp-conjugate upon treatment with a synthetic auxin. AIEP therefore represents a novel chemical probe with which to study IAA-amido synthetase function. PMID:22649546

  3. Students' Understanding on Newton's Third Law in Identifying the Reaction Force in Gravity Interactions

    ERIC Educational Resources Information Center

    Zhou, Shaona; Zhang, Chunbin; Xiao, Hua

    2015-01-01

    In the past three decades, previous researches showed that students had various misconceptions of Newton's Third Law. The present study focused on students' difficulties in identifying the third-law force pair in gravity interaction situations. An instrument involving contexts with gravity and non-gravity associated interactions was designed and…

  4. Identification of a higher-order organozincate intermediate involved in Negishi cross-coupling reactions by mass spectrometry and NMR spectroscopy.

    PubMed

    Hunter, Howard N; Hadei, Niloufar; Blagojevic, Voislav; Patschinski, Pascal; Achonduh, George T; Avola, Stephanie; Bohme, Diethard K; Organ, Michael G

    2011-07-04

    Negishi cross-coupling reactions were analyzed in solution by mass spectrometry and NMR spectroscopy to identify both the effect of LiBr as an additive as well as the purpose of 3-dimethyl-2-imidazolidinone (DMI) as a co-solvent. The results suggest that the main role of DMI is to facilitate a higher order bromozincate formation during the addition of LiBr.

  5. Quantification of intermediate-abundance proteins in serum by multiple reaction monitoring mass spectrometry in a single-quadrupole ion trap.

    PubMed

    Lin, Shanhua; Shaler, Thomas A; Becker, Christopher H

    2006-08-15

    A method is presented to quantify intermediate-abundance proteins in human serum using a single-quadrupole linear ion trap mass spectrometer-in contrast, for example, to a triple-quadrupole mass spectrometer. Stable-isotope-labeled (tryptic) peptides are spiked into digested protein samples as internal standards, aligned with the traditional isotope dilution approach. As a proof-of-concept experiment, four proteins of intermediate abundance were selected, coagulation factor V, adiponectin, C-reactive protein (CRP), and thyroxine binding globulin. Stable-isotope-labeled peptides were synthesized with one tryptic sequence from each of these proteins. The normal human serum concentration ranges of these proteins are from 1 to 30 microg/mL (or 20 to 650 pmol/mL). These labeled peptides and their endogenous counterparts were analyzed by LC-MS/MS using multiple reaction monitoring, a multiplexed form of the selected reaction monitoring technique. For these experiments, only one chromatographic dimension (on-line reversed-phase capillary column) was used. Improved limits of detection will result with multidimensional chromatographic methods utilizing more material per sample. Standard curves of the spiked calibrants were generated with concentrations ranging from 3 to 700 pmol/mL using both neat solutions and peptides spiked into the complex matrix of digested serum protein solution where ion suppression effects and interferences are common. Endogenous protein concentrations were determined by comparing MS/MS peak areas of the endogenous peptides to the isotopically labeled internal calibrants. The derived concentrations from a normal human serum pool (neglecting loss of material during sample processing) were 9.2, 110, 120, and 246 pmol/mL for coagulation factor V, adiponectin, CRP, and thyroxine binding globulin, respectively. These concentrations generally agree with the reported normal ranges for these proteins. As a measure of analytical reproducibility of this

  6. Systems Biology Approaches for Identifying Adverse Drug Reactions and Elucidating Their Underlying Biological Mechanisms

    PubMed Central

    Boland, Mary Regina; Jacunski, Alexandra; Lorberbaum, Tal; Romano, Joseph; Moskovitch, Robert; Tatonetti, Nicholas P.

    2015-01-01

    Small molecules are indispensable to modern medical therapy. However, their use may lead to unintended, negative medical outcomes commonly referred to as adverse drug reactions (ADRs). These effects vary widely in mechanism, severity, and populations affected, making ADR prediction and identification important public health concerns. Current methods rely on clinical trials and post-market surveillance programs to find novel ADRs; however, clinical trials are limited by small sample size, while post-market surveillance methods may be biased and inherently leave patients at risk until sufficient clinical evidence has been gathered. Systems pharmacology, an emerging interdisciplinary field combining network and chemical biology, provides important tools to uncover and understand ADRs and may mitigate the drawbacks of traditional methods. In particular, network analysis allows researchers to integrate heterogeneous data sources and quantify the interactions between biological and chemical entities. Recent work in this area has combined chemical, biological, and large-scale observational health data to predict ADRs in both individual patients and global populations. In this review, we explore the rapid expansion of systems pharmacology in the study of ADRs. We enumerate the existing methods and strategies and illustrate progress in the field with a model framework that incorporates crucial data elements, such as diet and comorbidities, known to modulate ADR risk. Using this framework, we highlight avenues of research that may currently be underexplored, representing opportunities for future work. PMID:26559926

  7. Volatile Reaction Products From Silicon-Based Ceramics in Combustion Environments Identified

    NASA Technical Reports Server (NTRS)

    Opila, Elizabeth J.

    1997-01-01

    Silicon-based ceramics and composites are prime candidates for use as components in the hot sections of advanced aircraft engines. These materials must have long-term durability in the combustion environment. Because water vapor is always present as a major product of combustion in the engine environment, its effect on the durability of silicon-based ceramics must be understood. In combustion environments, silicon-based ceramics react with water vapor to form a surface silica (SiO2) scale. This SiO2 scale, in turn, has been found to react with water vapor to form volatile hydroxides. Studies to date have focused on how water vapor reacts with high-purity silicon carbide (SiC) and SiO2 in model combustion environments. Because the combustion environment in advanced aircraft engines is expected to contain about 10-percent water vapor at 10-atm total pressure, the durability of SiC and SiO2 in gas mixtures containing 0.1- to 1-atm water vapor is of interest. The reactions of SiC and SiO2 with water vapor were monitored by measuring weight changes of sample coupons in a 0.5-atm water vapor/0.5-atm oxygen gas mixture with thermogravimetric analysis.

  8. Systems biology approaches for identifying adverse drug reactions and elucidating their underlying biological mechanisms.

    PubMed

    Boland, Mary Regina; Jacunski, Alexandra; Lorberbaum, Tal; Romano, Joseph D; Moskovitch, Robert; Tatonetti, Nicholas P

    2016-01-01

    Small molecules are indispensable to modern medical therapy. However, their use may lead to unintended, negative medical outcomes commonly referred to as adverse drug reactions (ADRs). These effects vary widely in mechanism, severity, and populations affected, making ADR prediction and identification important public health concerns. Current methods rely on clinical trials and postmarket surveillance programs to find novel ADRs; however, clinical trials are limited by small sample size, whereas postmarket surveillance methods may be biased and inherently leave patients at risk until sufficient clinical evidence has been gathered. Systems pharmacology, an emerging interdisciplinary field combining network and chemical biology, provides important tools to uncover and understand ADRs and may mitigate the drawbacks of traditional methods. In particular, network analysis allows researchers to integrate heterogeneous data sources and quantify the interactions between biological and chemical entities. Recent work in this area has combined chemical, biological, and large-scale observational health data to predict ADRs in both individual patients and global populations. In this review, we explore the rapid expansion of systems pharmacology in the study of ADRs. We enumerate the existing methods and strategies and illustrate progress in the field with a model framework that incorporates crucial data elements, such as diet and comorbidities, known to modulate ADR risk. Using this framework, we highlight avenues of research that may currently be underexplored, representing opportunities for future work.

  9. Method for identifying biochemical and chemical reactions and micromechanical processes using nanomechanical and electronic signal identification

    DOEpatents

    Holzrichter, J.F.; Siekhaus, W.J.

    1997-04-15

    A scanning probe microscope, such as an atomic force microscope (AFM) or a scanning tunneling microscope (STM), is operated in a stationary mode on a site where an activity of interest occurs to measure and identify characteristic time-varying micromotions caused by biological, chemical, mechanical, electrical, optical, or physical processes. The tip and cantilever assembly of an AFM is used as a micromechanical detector of characteristic micromotions transmitted either directly by a site of interest or indirectly through the surrounding medium. Alternatively, the exponential dependence of the tunneling current on the size of the gap in the STM is used to detect micromechanical movement. The stationary mode of operation can be used to observe dynamic biological processes in real time and in a natural environment, such as polymerase processing of DNA for determining the sequence of a DNA molecule. 6 figs.

  10. Method for identifying biochemical and chemical reactions and micromechanical processes using nanomechanical and electronic signal identification

    DOEpatents

    Holzrichter, John F.; Siekhaus, Wigbert J.

    1997-01-01

    A scanning probe microscope, such as an atomic force microscope (AFM) or a scanning tunneling microscope (STM), is operated in a stationary mode on a site where an activity of interest occurs to measure and identify characteristic time-varying micromotions caused by biological, chemical, mechanical, electrical, optical, or physical processes. The tip and cantilever assembly of an AFM is used as a micromechanical detector of characteristic micromotions transmitted either directly by a site of interest or indirectly through the surrounding medium. Alternatively, the exponential dependence of the tunneling current on the size of the gap in the STM is used to detect micromechanical movement. The stationary mode of operation can be used to observe dynamic biological processes in real time and in a natural environment, such as polymerase processing of DNA for determining the sequence of a DNA molecule.

  11. Ethene insertion into vanadium hydride intermediates formed via vanadium atom reaction with water or ethene: a matrix isolation infrared spectroscopic study.

    PubMed

    Thompson, Matthew G K; Parnis, J Mark

    2008-05-19

    The reaction of V atoms with H2O and various concentrations of C2D4 in argon has been investigated by matrix isolation infrared (IR) spectroscopy. Both C2D6 and CD2H-CD2H are observed as the major products of a set of parallel processes involving hydrogenation of ethene where the formal source of hydrogen is either C2D4 or H2O. Portions of the IR spectrum of CD2H-CD2H isolated in an argon matrix are observed for the first time. For experiments involving low concentrations of C2D4, irradiation of the matrix with light of wavelengths >455 nm results in VH2 formation, with limited observation of ethene hydrogenation. The source of H2 is believed to be due to photoelimination of molecular hydrogen from HO-V-H species, during matrix deposition, with OV as an additional product. Recombination of OV with available H2 in the matrix is proposed as the source of OVH2 under low ethene conditions. No evidence for VD2 formation is observed under our conditions. At higher C2D4 concentrations, VH2 formation is suppressed, while products of ethene hydrogenation are maximized. A second process competing with H2 elimination in which HO-V-H reacts with C2D4 is proposed. Parallel reaction schemes involving V atom insertion into the O-H bonds of water or the photoinduced insertion of V atoms into the C-D bonds of C2D4 are proposed to account for the observed hydrogenation products. In each mechanism, insertion of C2D4 into the V-H or V-D bonds of transient intermediates is followed by photoinduced elimination of the associated ethane isotopomer.

  12. Antibodies to intermediate filament proteins as molecular markers in clinical tumor pathology. Differentiation of carcinomas by their reaction with different cytokeratin antibodies.

    PubMed

    Krepler, R; Denk, H; Artlieb, U; Fichtinger, E; Davidovits, A

    1982-01-01

    Antibodies to human and bovine epidermal prekeratin and antibodies to mouse liver cytokeratin component D (Mr 49 000) have been applied in indirect immunofluorescence microscopy on sections of human tumors of mammary gland and liver. In non-neoplastic mammary gland all epithelial cells were stained with these antibodies. In pre-invasive and invasive ductal and lobular carcinomas a cell population was observed which was not significantly stained with antibodies to epidermal prekeratin but did strongly react with antibodies to liver cytokeratin D. In the liver, the antibodies to epidermal prekeratin as well as those directed against liver cytokeratin D strongly decorated bile duct epithelia. In contrast, significant staining of the hepatocytes was only achieved with antibodies to liver cytokeratin D. This different staining reaction was maintained in liver tumors of hepatocellular and cholangiocellular origin. Antibodies to vimentin stained mesenchymal cells and tumors of mesenchymal derivation but reacted not significantly with any of the epithelial and carcinoma cells examined. The difference is of practical importance for the discrimination between anaplastic carcinomas and sarcomas of unknown origin. Cytokeratin could also be detected by antibody staining using the peroxidase-antiperoxidase (PAP) technique in formaldehyde-fixed and paraffin-embedded material of skin, gastrointestinal, respiratory, urinary and genital tract as well as various glands, liver and kidney. Examples of positive reactions were shown in a squamous cell carcinoma, a basalioma and a pleomorphic adenoma of the parotis. It is concluded that the immunohistochemical analysis of intermediate filament proteins has diagnostic potential in clinical pathology and may help to elucidate histogenesis and differentiation of tumors and possibly also prognosis of tumor growth. It is further suggested to use antibodies recognizing different subsets of proteins of the cytokeratin family in order to

  13. Identification of in vivo processing intermediates and of splice junctions of tRNAs from maize chloroplasts by amplification with the polymerase chain reaction.

    PubMed Central

    Delp, G; Igloi, G L; Kössel, H

    1991-01-01

    Total RNA from chloroplasts of maize seedlings was used for polymerase chain reaction (PCR) mediated amplification of tRNA precursors and of mature tRNAs encoded by the two split tRNA genes of the ribosomal spacer (tRNA(lle)GAU and tRNA(Ala)UGC) and the single intron-containing tRNA(Gly)UCC gene. Sequence analysis of DNAs amplified from the mature tRNAs by combinations of exon specific primers allows unambiguous identification of the respective splice junctions. Primer combinations in which 5'- or 3'-flanking precursor tRNA sequences are included, leads to the amplification of processing intermediates in which 5'-terminal extensions are still present, whereas no PCR products corresponding to 3'-terminal extensions could be detected. From this it is concluded that in chloroplasts the 5'-terminal endonucleolytic cleavage by RNase P occurs as one of the final steps in the tRNA processing pathway of which the endonucleolytic cleavage at the 3' side probably occurs prior to the splicing of the intron sequences. Images PMID:2017358

  14. Kinetics of the E. coli replication factor DnaC protein-nucleotide interactions. II. Fluorescence anisotropy and transient, dynamic quenching stopped-flow studies of the reaction intermediates.

    PubMed

    Galletto, Roberto; Bujalowski, Wlodzimierz

    2002-07-16

    The nature of the intermediates in the binding of MANT-ATP and MANT-ADP to the E. coli replicative factor DnaC protein (accompanying paper) has been examined using the fluorescence intensity, anisotropy, and transient dynamic quenching stopped-flow techniques. Using molar fluorescence intensities of individual intermediates of the reaction, we derived the Stern-Volmer equation that provides a direct method to quantitatively address the quenching of the fluorescence of a transient intermediate by an external, neutral quencher. The data indicate that in the first intermediate, (C)(1), the solvent has full access to the MANT group. Thus, the nucleotide-binding site is located on the surface of the protein, fully open to the solvent. Moreover, formation of the first intermediate does not affect the structure of the binding site. On the other hand, in the second intermediate, (C)(2), the entire binding site changes its conformation, resulting in diminished access of the solvent to the bound nucleotide. The time course of the fluorescence anisotropy in the reaction provides direct, unique insight into the mobility of bound nucleotides in each intermediate. The analysis is facilitated by the fact that the anisotropy can be expressed as a function of the relative molar intensities and steady-state anisotropies of the individual intermediates. The major decrease of the nucleotide mobility occurs in the formation of the first intermediate and reflects the fact that the MANT group is immobilized to a similar extent as the ribose region of the bound nucleotides. Transition to the second intermediate and closing of the binding site leads to only a moderate, additional decrease of nucleotide mobility. The temperature effect on the studied interactions indicates that the formation of individual intermediates is accompanied by very different enthalpy and entropy changes predominantly generated from the structural changes of the protein. Analysis of the salt effect indicates that

  15. Chromophoric spin-labeled beta-lactam antibiotics for ENDOR structural characterization of reaction intermediates of class A and class C beta-lactamases.

    PubMed

    Mustafi, Devkumar; Hofer, Jennifer E; Huang, Wanzhi; Palzkill, Timothy; Makinen, Marvin W

    2004-05-01

    The chromophoric spin-label substrate 6-N-[3-(2,2,5,5-tetramethyl-1-oxypyrrolin-3-yl)-propen-2-oyl]penicillanic acid (SLPPEN) was synthesized by acylation of 6-aminopenicillanic acid with the acid chloride of 3-(2,2,5,5-tetramethyl-1-oxypyrrolinyl)-2-propenoic acid and characterized by physical methods. By application of angle-selected electron nuclear double resonance (ENDOR), we have determined the molecular structure of SLPPEN in solution. SLPPEN exhibited UV absorption properties that allowed accurate monitoring of the kinetics of its enzyme-catalyzed hydrolysis. The maximum value of the (substrate-product) difference extinction coefficient was 2824 M(-1) cm(-1) at 275 nm compared to 670 M(-1) cm(-1) at 232 nm for SLPEN [J. Am. Chem. Soc. 117 (1995) 6739]. For SLPPEN, the steady-state kinetic parameters kcat and kcat/KM, determined under initial velocity conditions, were 637 +/- 36 s(-1) and 13.8 +/- 1.4 x 10(6) M(-1) s(-1), respectively, for hydrolysis catalyzed by TEM-1 beta-lactamase of E. coli, and 0.5 +/- 0.04 s(-1) and 3.9 +/- 0.4 x 10(4) M(-1) s(-1) for hydrolysis catalyzed by the beta-lactamase of Enterobacter cloacae P99. We have also observed "burst kinetics" for the hydrolysis of SLPPEN with P99 beta-lactamase, indicative of formation of an acylenzyme reaction intermediate. In DMSO:H2O (30:70, v:v) cryosolvent mixtures buffered to pH* 7.0, the half-life of the acylenzyme intermediate formed with the P99 enzyme at -5 degrees C was > or = 3 min, suitable for optical characterization. The observation of burst kinetics in the hydrolysis of SLPPEN catalyzed by P99 beta-lactamase suggests that this chromophoric spin-labeled substrate is differentially sensitive to active site interactions underlying the cephalosporinase and penicillinase reactivity of this class C enzyme.

  16. Metabolism-dependent mutagenicity of a compound containing a piperazinyl indazole motif: Role of a novel p450-mediated metabolic reaction involving a putative oxaziridine intermediate.

    PubMed

    Chen, Hao; Murray, Joel; Kornberg, Brian; Dethloff, Lloyd; Rock, David; Nikam, Sham; Mutlib, Abdul E

    2006-10-01

    Compound 1a (6-chloro-5-{3-[4-(1H-indazol-3-yl)-piperazin-1-yl]-propyl}-3,3-dimethyl-1,3-dihydro-indol-2-one) was mutagenic to Salmonella typhimurium TA98 in the presence of rat liver S9 subcellular fraction. The metabolism of 1a in rat liver S9 or microsomes demonstrated that it underwent a P450-mediated N-deindazolation (loss of indazole ring) as a predominant metabolic pathway. To investigate a possible link between metabolism and mutagenicity, a structural analogue 1b (6-chloro-5-{3-[4-(1H-indazol-3-yl)-piperidin-1-yl]-propyl}-3,3-dimethyl-1,3-dihydro-indol-2-one), the cleaved product 2a (6-chloro-3,3-dimethyl-5-(3-piperazin-1-yl-propyl)-1,3-dihydro-indol-2-one), and the core motif 3a (3-piperazinyl indazole) were evaluated in the Ames assay. It was found that 1b was not mutagenic to Salmonella typhimurium TA98 in the absence or presence of a metabolic activating system. In contrast to 1a, 1b did not undergo the metabolic cleavage (loss of indazole ring). Marginal mutagenicity of 2a to TA98 was observed with rat liver S9, whereas 3a was shown to be a promutagen. It was further demonstrated that 1a inactivated P450 3A, the principle enzyme catalyzing the N-deindazolation reaction, in an NADPH-, time-, and concentration-dependent manner. The kinetics of inactivation was characterized by a K(I) of 8.1 microM and k(inact) of 0.114 min(-1). The differences in mutagenicity between 1a and 1b suggest that a chemical bond extending from the 3-position of the indazole to a heteroatom (as part of another cyclic ring) is a prerequisite for the toxicity. The metabolic process leading to the elimination of the indazole from the rest of the molecule apparently plays a key role in causing mutagenicity. It is postulated that the N-deindazolation of 1a proceeds via an oxaziridine intermediate, the formation of which is indirectly inferred from the presence of benzoic acid in microsomal incubations. Benzoic acid is thought to be derived from the hydrolysis of 3-indazolone, an

  17. The Validity of Claims-Based Algorithms to Identify Serious Hypersensitivity Reactions and Osteonecrosis of the Jaw.

    PubMed

    Wright, Nicole C; Curtis, Jeffrey R; Arora, Tarun; Smith, Wilson K; Kilgore, Meredith L; Saag, Kenneth G; Safford, Monika M; Delzell, Elizabeth S

    2015-01-01

    Validation of claims-based algorithms to identify serious hypersensitivity reactions and osteonecrosis of the jaw has not been performed in large osteoporosis populations. The objective of this project is to estimate the positive predictive value of the claims-based algorithms in older women with osteoporosis enrolled in Medicare. Using the 2006-2008 Medicare 5% sample data, we identified potential hypersensitivity and osteonecrosis of the jaw cases based on ICD-9 diagnosis codes. Potential hypersensitivity cases had a 995.0, 995.2, or 995.3 diagnosis code on emergency department or inpatient claims. Potential osteonecrosis of the jaw cases had ≥1 inpatient or outpatient physician claim with a 522.7, 526.4, 526.5, or 733.45 diagnosis code or ≥2 claims of any type with a 526.9 diagnosis code. All retrieved records were redacted and reviewed by experts to determine case status: confirmed, not confirmed, or insufficient information. We calculated the positive predictive value as the number of confirmed cases divided by the total number of retrieved records with sufficient information. We requested 412 potential hypersensitivity and 304 potential osteonecrosis of the jaw records and received 174 (42%) and 84 (28%) records respectively. Of 84 potential osteonecrosis of the jaw cases, 6 were confirmed, resulting in a positive predictive value (95% CI) of 7.1% (2.7, 14.9). Of 174 retrieved potential hypersensitivity records, 95 were confirmed. After exclusion of 25 records with insufficient information for case determination, the overall positive predictive value (95% CI) for hypersensitivity reactions was 76.0% (67.5, 83.2). In a random sample of Medicare data, a claim-based algorithm to identify serious hypersensitivity reactions performed well. An algorithm for osteonecrosis of the jaw did not, partly due to the inclusion of diagnosis codes that are not specific for osteoporosis of the jaw.

  18. Crystal structures of the substrate free-enzyme, and reaction intermediate of the HAD superfamily member, haloacid dehalogenase DehIVa from Burkholderia cepacia MBA4.

    PubMed

    Schmidberger, Jason W; Wilce, Jackie A; Tsang, Jimmy S H; Wilce, Matthew C J

    2007-05-04

    DehIVa is a haloacid dehalogenase (EC 3.8.1.2) from the soil and water borne bacterium Burkholderia cepacia MBA4, which belongs to the functionally variable haloacid dehalogenase (HAD) superfamily of enzymes. The haloacid dehalogenases catalyse the removal of halides from haloacids resulting in a hydroxlated product. These enzymes are of interest for their potential to degrade recalcitrant halogenated environmental pollutants and their use in the synthesis of industrial chemicals. The haloacid dehalogenases utilise a nucleophilic attack on the substrate by an aspartic acid residue to form an enzyme-substrate ester bond and concomitantly cleaving of the carbon-halide bond and release of a hydroxylated product following ester hydrolysis. We present the crystal structures of both the substrate-free DehIVa refined to 1.93 A resolution and DehIVa covalently bound to l-2-monochloropropanoate trapped as a reaction intermediate, refined to 2.7 A resolution. Electron density consistent with a previously unidentified yet anticipated water molecule in the active site poised to donate its hydroxyl group to the product and its proton to the catalytic Asp11 is evident. It has been unclear how substrate enters the active site of this and related enzymes. The results of normal mode analysis (NMA) are presented and suggest a means whereby the predicted global dynamics of the enzyme allow for entry of the substrate into the active site. In the context of these results, the possible role of Arg42 and Asn178 in a "lock down" mechanism affecting active site access is discussed. In silico substrate docking of enantiomeric substrates has been examined in order to evaluate the enzymes enantioselectivity.

  19. Crystal structure of activated tobacco rubisco complexed with the reaction-intermediate analogue 2-carboxy-arabinitol 1,5-bisphosphate.

    PubMed Central

    Schreuder, H. A.; Knight, S.; Curmi, P. M.; Andersson, I.; Cascio, D.; Sweet, R. M.; Brändén, C. I.; Eisenberg, D.

    1993-01-01

    The crystal structure of activated tobacco rubisco, complexed with the reaction-intermediate analogue 2-carboxy-arabinitol 1,5-bisphosphate (CABP) has been determined by molecular replacement, using the structure of activated spinach rubisco (Knight, S., Andersson, I., & Brändén, C.-I., 1990, J. Mol. Biol. 215, 113-160) as a model. The R-factor after refinement is 21.0% for 57,855 reflections between 9.0 and 2.7 A resolution. The local fourfold axis of the rubisco hexadecamer coincides with a crystallographic twofold axis. The result is that the asymmetric unit of the crystals contains half of the L8S8 complex (molecular mass 280 kDa in the asymmetric unit). The activated form of tobacco rubisco is very similar to the activated form of spinach rubisco. The root mean square difference is 0.4 A for 587 equivalent C alpha atoms. Analysis of mutations between tobacco and spinach rubisco revealed that the vast majority of mutations concerned exposed residues. Only 7 buried residues were found to be mutated versus 54 residues at or near the surface of the protein. The crystal structure suggests that the Cys 247-Cys 247 and Cys 449-Cys 459 pairs are linked via disulfide bridges. This pattern of disulfide links differ from the pattern of disulfide links observed in crystals of unactivated tobacco rubisco (Curmi, P.M.G., et al., 1992, J. Biol. Chem. 267, 16980-16989) and is similar to the pattern observed for activated spinach tobacco. PMID:8358296

  20. Ultrastructural characteristics of novel epithelial cell types identified in human pathologic liver specimens with chronic ductular reaction.

    PubMed

    De Vos, R; Desmet, V

    1992-06-01

    Previous immunohistochemical studies on human liver biopsies with chronic ductular reaction revealed the presence of "small cells" with bile-duct type cytokeratin profile in the periportal area. This study identified similar cells by electron microscopy. The authors studied 13 human liver specimens with various liver diseases, but all characterized by chronic ductular reaction. In all specimens, variable numbers of "small cells" with common epithelial characteristics were identified in the periportal area. They could be classified into three types. Type I cells showed an oval cell shape and oval nucleus, early or established formation of junctional complexes with adjacent cells, a full assortment of cytoplasmic organelles, and bundles of tonofilaments. Type II cells showed features of bile-duct cell differentiation, including lateral interdigitations, apical microvilli, basal pinocytotic vacuoles, and basement membrane formation. In contrast, type III cells displayed additional features indicating hepatocellular differentiation, such as a more prominent nucleus, formation of a hemicanaliculus, and glycogen rosettes. It is concluded that these small cells of epithelial nature display variable differentiation characteristics of either bile-duct type cells or hepatocytes. These findings support the existence of bipotential progenitor epithelial cells in human liver. They may have implications for liver regeneration and carcinogenesis.

  1. Formation of diphenylphosphanylbutadienyl complexes by insertion of two P-coordinated alkynylphosphanes into a PtbondC6F5 bond: detection of intermediate and reaction products.

    PubMed

    Ara, Irene; Forniés, Juan; García, Ana; Gómez, Julio; Lalinde, Elena; Moreno, M Teresa

    2002-08-16

    The reactions between cis-[M(C(6)F(5))(2)(PPh(2)CtriplebondCR)(2)] (M=Pt, Pd; R=Ph, tBu, Tol 2, 3) or cis-[Pt(C(6)F(5))(2)(PPh(2)CtriplebondCR)(PPh(2)CtriplebondCtBu)] (R=Ph 4, Tol 5) and cis-[Pt(C(6)F(5))(2)(thf)(2)] 1 have been investigated. Whereas [M](PPh(2)CtriplebondCtBu)(2) ([M]=cis-M(C(6)F(5))(2)) is inert towards 1, the analogous reactions starting from [M](PPh(2)CtriplebondCR)(2) or [Pt](PPh(2)CtriplebondCR)(PPh(2)CtriplebondCtBu) (R=Ph, Tol) afford unusual binuclear species [Pt(C(6)F(5))(S)mu-[C(R')dbondC(PPh(2))C(PPh(2))doublebondC(R)(C(6)F(5))]M(C(6)F(5))(2)] (R=R'=Ph, Tol, M=Pt 6 a,c, M=Pd 7 a,c; M=Pt, R'=tBu, R=Ph 8, Tol 9) containing a bis(diphenylphosphanyl)butadienyl bridging ligand formed by an unprecedented sequential insertion reaction of two P-coordinated PPh(2)CtriplebondCR ligands into a PtbondC(6)F(5) bond. Although in solution the presence of coordinated solvent S (S=(thf)(x)(H(2)O)(y)) in 6, 7 is suggested by NMR spectroscopy, X-ray diffraction analyses of different crystals of the mixed complex [Pt(C(6)F(5))mu-[C(tBu)doublebondC(PPh(2))C(PPh(2))doublebondC(Tol)(C(6)F(5))]Pt(C(6)F(5))(2)] 9 unequivocally establish that in the solid state the steric crowding of the new diphenylbutadienyl ligand formed stabilizes an unusual coordinatively unsaturated T-shaped 3-coordinated platinum(II) center. Structure determinations of the mononuclear precursors cis-[Pt(C(6)F(5))(2)(PPh(2)CtriplebondCR)(2)] (R=Ph, tBu, Tol) have been carried out to evaluate the factors affecting the insertion processes. The reactions of the platinum complexes 6 towards neutral ligands (L=CO, py, PPh(2)H, CNtBu) in a 1:1 molar ratio afford related diplatinum derivatives 10-13, whereas treatment with CNtBu (1:2 molar ratio) or 2,2'-bipy (1:1 molar ratio) results in the opening of the chelating ring to give cis,cis-[Pt(C(6)F(5))(L)(2)mu-[1-kappaC(1):2-kappaPP'-C(R)doublebondC(PPh(2))C(PPh(2))doublebondC(R)(C(6)F(5))]Pt(C(6)F(5))(2)] (14, 15). The unsaturated or solvento

  2. Multicomponent reactions of phosphines, diynedioates, and aryl aldehydes generated furans appending reactive phosphorus ylides through cumulated trienoates as key intermediates: a phosphine α-addition-δ-evolvement of an anion pathway.

    PubMed

    Deng, Jie-Cheng; Chuang, Shih-Ching

    2014-11-07

    Multicomponent reactions of phosphines, diynedioates, and aryl aldehydes have been demonstrated, providing trisubstituted furans appending reactive phosphorus ylides, through cumulated trienoates as key intermediates. The proposed trienoate intermediates, 1,5-dipolar species formed via nucleophilic α-attack of phosphines toward diynedioates (α-addition-δ-evolvement of an anion, abbreviated αAδE), undergo addition to aryl aldehydes followed by 5-endo-dig cyclization, proton transfer, and resonance to give trisubstituted furans. Furthermore, the phosphorus ylides are oxidized to α-keto ester furans and utilized as Wittig reagents.

  3. Perspective: Spectroscopy and kinetics of small gaseous Criegee intermediates

    SciTech Connect

    Lee, Yuan-Pern

    2015-07-14

    The Criegee intermediates, carbonyl oxides proposed by Criegee in 1949 as key intermediates in the ozonolysis of alkenes, play important roles in many aspects of atmospheric chemistry. Because direct detection of these gaseous intermediates was unavailable until recently, previous understanding of their reactions, derived from indirect experimental evidence, had great uncertainties. Recent laboratory detection of the simplest Criegee intermediate CH{sub 2}OO and some larger members, produced from ultraviolet irradiation of corresponding diiodoalkanes in O{sub 2}, with various methods such as photoionization, ultraviolet absorption, infrared absorption, and microwave spectroscopy opens a new door to improved understanding of the roles of these Criegee intermediates. Their structures and spectral parameters have been characterized; their significant zwitterionic nature is hence confirmed. CH{sub 2}OO, along with other products, has also been detected directly with microwave spectroscopy in gaseous ozonolysis reactions of ethene. The detailed kinetics of the source reaction, CH{sub 2}I + O{sub 2}, which is critical to laboratory studies of CH{sub 2}OO, are now understood satisfactorily. The kinetic investigations using direct detection identified some important atmospheric reactions, including reactions with NO{sub 2}, SO{sub 2}, water dimer, carboxylic acids, and carbonyl compounds. Efforts toward the characterization of larger Criegee intermediates and the investigation of related reactions are in progress. Some reactions of CH{sub 3}CHOO are found to depend on conformation. This perspective examines progress toward the direct spectral characterization of Criegee intermediates and investigations of the associated reaction kinetics, and indicates some unresolved problems and prospective challenges for this exciting field of research.

  4. Linking chemical electron-proton transfer to proton pumping in cytochrome c oxidase: broken-symmetry DFT exploration of intermediates along the catalytic reaction pathway of the iron-copper dinuclear complex.

    PubMed

    Noodleman, Louis; Han Du, Wen-Ge; Fee, James A; Götz, Andreas W; Walker, Ross C

    2014-07-07

    After a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear Fe-a3-CuB reaction center in this enzyme. A specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. A larger family of tautomers/protonation states is generated compared to our earlier work, and a new lowest-energy pathway is proposed. The entire reaction cycle is calculated for the new smaller model (about 185-190 atoms), and two selected arcs of the wheel are chosen for calculations using a larger model (about 205 atoms). We compare the structural and redox energetics and protonation calculations with available experimental data. The reaction cycle map that we have built is positioned for further improvement and testing against experiment.

  5. EPR and optical spectroscopic properties of the electron carrier intermediate between the reaction center bacteriochlorophylls and the primary acceptor in Chromatium vinosum.

    PubMed

    Tiede, D M; Prince, R C; Dutton, P L

    1976-12-06

    1. A reaction center-cytochrome c complex has been isolated from Chromatium vinosum which is capable of normal photochemistry and light-activated rapid cytochrome c553 and c555 oxidation, but which has no antenna bacteriochlorophyll. As is found in whole cells, ferrocytochrome c553 is oxidized irreversibly in milliseconds by light at 7 K. 2. Room temperature redox potentiometry in combination with EPR analysis at 7 K, of cytochrome c553 and the reaction center bacteriochlorophyll dimer (BChl)2 absorbing at 883 nm yields identical results to those previously reported using optical analytical techniques at 77 K. It shows directly that two cytochrome c553 hemes are equivalent with respect to the light induced (BChl)2+. At 7 K, only one heme can be rapidly oxidized in the light, commensurate with the electron capacity of the primary acceptor (quinone-iron) being unity. 3. Prior chemical reduction of the quinone-iron followed by illumination at 200K, however, leads to the slow (t1/2 approximately equal to 30 s) oxidation of one cytochrome c553 heme, with what appears to be concommitant reduction of one of the two bacteriophytins (BPh) of the reaction center as shown by bleaching of the 760 nm band, a broad absorbance increase at approx. 650 nm and a bleaching at 543 nm. The 800 nm absorbing bacteriochlorophyll is also involved since there is also bleaching at 595 and 800 nm; at the latter wave-length the remaining unbleached band appears to shift significantly to the blue. No redox changes in the 883 absorbing bacteriochlorophyll dimer are seen during or after illumination under these conditions. The reduced part of the state represents what is considered to be the reduced form of the electron carrier (I) which acts as an intermediate between the bacteriochlorophyll dimer and quinone-iron. The state (oxidized c553/reduced I) relaxes in the dark at 200K in t1/2 approx. 20 min but below 77 K it is trapped on a days time scale. 4. EPR analysis of the state trapped as

  6. Hydroxyacetone production from C3 Criegee intermediates

    SciTech Connect

    Taatjes, Craig A.; Liu, Fang; Rotavera, Brandon; Kumar, Manoj; Caravan, Rebecca; Osborn, David L.; Thompson, Ward H.; Lester, Marsha I.

    2016-12-21

    Hydroxyacetone (CH3C(O)CH2OH) is observed as a stable end product from reactions of the (CH3)2COO Criegee intermediate, acetone oxide, in a flow tube coupled with multiplexed photoionization mass spectrometer detection. In the experiment, the isomers at m/z = 74 are distinguished by their different photoionization spectra and reaction times. Hydroxyacetone is observed as a persistent signal at longer reaction times at a higher photoionization threshold of ca. 9.7 eV than Criegee intermediate and definitively identified by comparison with the known photoionization spectrum. Complementary electronic structure calculations reveal multiple possible reaction pathways for hydroxyacetone formation, including unimolecular isomerization via hydrogen atom transfer and –OH group migration as well as self-reaction of Criegee intermediates. Varying the concentration of Criegee intermediates suggests contributions from both unimolecular and self-reaction pathways to hydroxyacetone. As a result, the hydroxyacetone end product can provide an effective, stable marker for the production of transient Criegee intermediates in future studies of alkene ozonolysis.

  7. Comment on “A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states” [J. Chem. Phys. 142, 124312 (2015)

    SciTech Connect

    Harding, Lawrence B.; Klippenstein, Stephen J.

    2015-10-28

    We discuss the recent report of a roaming type mechanism for the decomposition of the Criegee intermediate. We show that the predicted barrier height for this new pathway is too low by ∼30 kcal/mol owing to an inconsistent use of spin-restricted and spin-unrestricted calculations. As a result, this new pathway is not expected to compete significantly with the well-known dioxirane pathways for the decomposition of the Criegee intermediate.

  8. Comment on "A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states" [J. Chem. Phys. 142, 124312 (2015)

    NASA Astrophysics Data System (ADS)

    Harding, Lawrence B.; Klippenstein, Stephen J.

    2015-10-01

    We discuss the recent report of a roaming type mechanism for the decomposition of the Criegee intermediate. We show that the predicted barrier height for this new pathway is too low by ˜30 kcal/mol owing to an inconsistent use of spin-restricted and spin-unrestricted calculations. As a result, this new pathway is not expected to compete significantly with the well-known dioxirane pathways for the decomposition of the Criegee intermediate.

  9. Comment on "A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states" [J. Chem. Phys. 142, 124312 (2015)].

    PubMed

    Harding, Lawrence B; Klippenstein, Stephen J

    2015-10-28

    We discuss the recent report of a roaming type mechanism for the decomposition of the Criegee intermediate. We show that the predicted barrier height for this new pathway is too low by ∼30 kcal/mol owing to an inconsistent use of spin-restricted and spin-unrestricted calculations. As a result, this new pathway is not expected to compete significantly with the well-known dioxirane pathways for the decomposition of the Criegee intermediate.

  10. Role of the reaction intermediates in determining PHIP (parahydrogen induced polarization) effect in the hydrogenation of acetylene dicarboxylic acid with the complex [Rh (dppb)]{sup +} (dppb: 1,4-bis(diphenylphosphino)butane)

    SciTech Connect

    Reineri, F.; Aime, S.; Gobetto, R.; Nervi, C.

    2014-03-07

    This study deals with the parahydrogenation of the symmetric substrate acetylene dicarboxylic acid catalyzed by a Rh(I) complex bearing the chelating diphosphine dppb (1,4-bis(diphenylphosphino)butane). The two magnetically equivalent protons of the product yield a hyperpolarized emission signal in the {sup 1}H-NMR spectrum. Their polarization intensity varies upon changing the reaction solvent from methanol to acetone. A detailed analysis of the hydrogenation pathway is carried out by means of density functional theory calculations to assess the structure of hydrogenation intermediates and their stability in the two solvents. The observed polarization effects have been accounted on the basis of the obtained structures. Insights into the lifetime of a short-lived reaction intermediate are also obtained.

  11. Role of the reaction intermediates in determining PHIP (parahydrogen induced polarization) effect in the hydrogenation of acetylene dicarboxylic acid with the complex [Rh (dppb)]+ (dppb: 1,4-bis(diphenylphosphino)butane).

    PubMed

    Reineri, F; Aime, S; Gobetto, R; Nervi, C

    2014-03-07

    This study deals with the parahydrogenation of the symmetric substrate acetylene dicarboxylic acid catalyzed by a Rh(I) complex bearing the chelating diphosphine dppb (1,4-bis(diphenylphosphino)butane). The two magnetically equivalent protons of the product yield a hyperpolarized emission signal in the (1)H-NMR spectrum. Their polarization intensity varies upon changing the reaction solvent from methanol to acetone. A detailed analysis of the hydrogenation pathway is carried out by means of density functional theory calculations to assess the structure of hydrogenation intermediates and their stability in the two solvents. The observed polarization effects have been accounted on the basis of the obtained structures. Insights into the lifetime of a short-lived reaction intermediate are also obtained.

  12. Pathways of the North Pacific Intermediate Water identified through the tangent linear and adjoint models of an ocean general circulation model

    NASA Astrophysics Data System (ADS)

    Fujii, Y.; Nakano, T.; Usui, N.; Matsumoto, S.; Tsujino, H.; Kamachi, M.

    2014-12-01

    This study develops a strategy for tracing a target water mass, and applies it to analyzing the pathway of the North Pacific Intermediate Water (NPIW) from the subarctic gyre to the northwestern part of the subtropical gyre south of Japan in a simulation of an ocean general circulation model. This strategy estimates the pathway of the water mass that travels from an origin to a destination area during a specific period using a conservation property concerning tangent linear and adjoint models. In our analysis, a large fraction of the low salinity origin water mass of NPIW initially comes from the Okhotsk or Bering Sea, flows through the southeastern side of the Kuril Islands, and is advected to the Mixed Water Region (MWR) by the Oyashio current. It then enters the Kuroshio Extension (KE) at the first KE ridge, and is advected eastward by the KE current. However, it deviates southward from the KE axis around 158°E over the Shatsky Rise, or around 170ºE on the western side of the Emperor Seamount Chain, and enters the subtropical gyre. It is finally transported westward by the recirculation flow. This pathway corresponds well to the shortcut route of NPIW from MWR to the region south of Japan inferred from analysis of the long-term freshening trend of NPIW observation.

  13. Pathways of the North Pacific Intermediate Water identified through the tangent linear and adjoint models of an ocean general circulation model

    NASA Astrophysics Data System (ADS)

    Fujii, Yosuke; Nakano, Toshiya; Usui, Norihisa; Matsumoto, Satoshi; Tsujino, Hiroyuki; Kamachi, Masafumi

    2013-04-01

    This study develops a strategy for tracing a target water mass, and applies it to analyzing the pathway of the North Pacific Intermediate Water (NPIW) from the subarctic gyre to the northwestern part of the subtropical gyre south of Japan in a simulation of an ocean general circulation model. This strategy estimates the pathway of the water mass that travels from an origin to a destination area during a specific period using a conservation property concerning tangent linear and adjoint models. In our analysis, a large fraction of the low salinity origin water mass of NPIW initially comes from the Okhotsk or Bering Sea, flows through the southeastern side of the Kuril Islands, and is advected to the Mixed Water Region (MWR) by the Oyashio current. It then enters the Kuroshio Extension (KE) at the first KE ridge, and is advected eastward by the KE current. However, it deviates southward from the KE axis around 158°E over the Shatsky Rise, or around 170°E on the western side of the Emperor Seamount Chain, and enters the subtropical gyre. It is finally transported westward by the recirculation flow. This pathway corresponds well to the shortcut route of NPIW from MWR to the region south of Japan inferred from analysis of the long-term freshening trend of NPIW observation. Copyright 2013 John Wiley & Sons, Ltd.

  14. Simultaneous infrared detection of the ICH2OO radical and Criegee intermediate CH2OO: the pressure dependence of the yield of CH2OO in the reaction CH2I + O2.

    PubMed

    Huang, Yu-Hsuan; Chen, Li-Wei; Lee, Yuan-Pern

    2015-11-19

    The simplest Criegee intermediate CH2OO, important in atmospheric reactions, has been recently produced from the reaction of CH2I + O2 and detected with various methods. In this reaction, the yield of CH2OO decreases with increasing pressure because of the stabilization of the adduct ICH2OO, but no definitive spectral identification of ICH2OO has been reported. We recorded the infrared spectrum of ICH2OO using the same reaction under high pressure; the spectrum agrees with that simulated according to theoretical predictions. With direct detection of both CH2OO and ICH2OO, we determined the pressure dependence of the yield of CH2OO. The yield of CH2OO near 1 atm is greater than previously reported values, which might have significant consequences in atmospheric chemistry.

  15. New mechanistic insight into the oxygen reduction reaction on Ruddlesden-Popper cathodes for intermediate-temperature solid oxide fuel cells.

    PubMed

    Li, Wenyuan; Guan, Bo; Zhang, Xinxin; Yan, Jianhua; Zhou, Yue; Liu, Xingbo

    2016-03-28

    Ruddlesden-Popper (R-P) phase materials have been investigated widely as cathode candidates for IT-SOFCs. However, widespread application of R-P phase cathodes demands further improvement in electrode activity whose progress is hindered by the limited information in the oxygen reduction reaction (ORR). The ORR mechanism for the R-P phase is therefore investigated in this paper using (LaSr)2NiO(4±δ) as an example. Accurate characterization of the surface oxygen exchange process is realized by developing thin and dense polycrystalline LSNO layers via a versatile spray-modified pressing method we invented before to avoid perceptible bulk diffusion contribution, surface enrichment and geometry complication. The governing factors of the ORR are identified as oxygen adsorption and incorporation based on the findings in reaction orders from electrochemical impedance spectroscopy (EIS), stoichiometry-related chemical capacitance and intrinsic anisotropic properties. The incorporation rate is proven to drastically depend on the amount of interstitial oxygen (O(i)"). Since the unfilled interstitial sites(V(i)(×)) in the R-P phase serve to accommodate the adsorbed oxygen during incorporation, like vacancies in the perovskite structure (V(O)(••)), more O(i)" would seem to suppress the kinetics of this process. In regards to this, for the first time, a physical model is proposed to reconcile the discrepancy between the experimental results and intuitive reasoning. Based on supporting evidence, this model illustrates a possibility of how O(i)" works to regulate the exchange rate, and how the contradiction between V(O)(••) and O(i)" is harmonized so that the latter in the R-P structure also positively promotes the incorporation rate in the ORR.

  16. Bacterial contamination of blood components: Norwegian strategies in identifying donors with higher risk of inducing septic transfusion reactions in recipients.

    PubMed

    Klausen, Sofie Strand; Hervig, Tor; Seghatchian, Jerard; Reikvam, Håkon

    2014-10-01

    Bacterial contamination of blood and its cellular components remains the most common microbiological cause of transfusion associated morbidity and mortality, even in developed countries. This yet unresolved complication is seen more often in platelet transfusions, as platelet concentrates are stored at room temperature, in gas permeable containers with constant agitation, which support bacterial proliferation from relatively low undetectable levels, at the beginning of storage time, to relatively high virulent bacteria titers and endotoxin generation, at the end of shelf life. Accordingly, several combined strategies are introduced and implemented to at least reduce the potential risk of bacterial contaminated products for transfusion. These embody: improved donors arms cleaning; bacterial avoidance by diversion of the first portion of collection; reducing bacterial growth through development of newer storage media for longer platelet shelf life; bacterial load reduction by leucoreduction/viral inactivation, in some countries and eliminating the use potentially contaminated units through screening, through current available testing procedures, though none are not yet fully secure. We have not seen the same reduction in bacterial associated transfusion infections as we have observed for the sharp drop in transfusion associated transmission rates of HIV and hepatitis B and C. This great viral reduction is not only caused by the introduction of newer and more sensitive and specific detection methods for different viruses, but also the identification of donor risk groups through questionnaires and personal interviews. While search for more efficient methods for identifying potential blood donors with asymptomatic bacteremia, as well as a better way for detecting bacteria in stored blood components will be continuing, it is necessary to establish more standardized guidelines for the recognition the adverse reactions in recipients of potentially contaminated units

  17. Measurements of activation reaction rates in transverse shielding concrete exposed to the secondary particle field produced by intermediate energy heavy ions on an iron target

    NASA Astrophysics Data System (ADS)

    Ogawa, T.; Morev, M. N.; Iimoto, T.; Kosako, T.

    2012-01-01

    Reaction rate distributions were measured inside a 60-cm thick concrete pile placed at the lateral position of a thick (stopping length) iron target that was bombarded with heavy ions, 400 MeV/u C and 800 MeV/u Si. Foils of aluminum and gold, as well as gold, tungsten and manganese covered with cadmium were inserted at various locations in the concrete pile to serve as activation detectors. Features of reaction rate distribution, such as the shape of the reaction rate profile, contribution of the neutrons from intra-nuclear cascade and that from evaporation to the activation reactions are determined by the analysis of measured reaction rates. The measured reaction rates were compared with those calculated with radiation transport simulation codes, FLUKA and PHITS, to verify their capability to predict induced activity. The simulated reaction rates agree with the experimental results within a factor of three in general. However, systematic discrepancies between simulated reaction rates and measured reaction rates attributed to the neutron source terms are observed.

  18. Polymerase chain reaction-based screening method applicable universally to environmental haloarchaea and halobacteria for identifying polyhydroxyalkanoate producers among them.

    PubMed

    Mahansaria, Riddhi; Choudhury, Jayanta Debabrata; Mukherjee, Joydeep

    2015-09-01

    The existing techniques for detection of polyhydroxyalkanoates (PHA) in halophilic archaea/bacteria are either imprecise or require prior PHA production before screening. The proposed method involves amplification of the approximately 280-300 bp conserved region of Class III PHA synthase (phaC) gene of halophiles using the primers codehopCF and codehopCR (Han et al. Appl Environ Microb 76:7811-7819, 2010). In this study, the best reaction condition was ascertained after repeated trials. This developed method was tested on nine haloarchaeal and halobacterial type strains and 28 environmental halophilic archaea and bacteria isolated from the salt pans of the east and west coasts of India. 29 strains were found to be phaC-positive, while eight were found to be phaC-negative although they appeared PHA positive through conventional Nile Red staining. 16S rRNA-based phylogenetic analysis identified 9 haloarchaeal and 9 halobacterial species as novel PHA producers. Multiple sequence alignment of the phaC gene-derived amino acid sequences showed that only 7 amino acid residues were conserved within all four classes of phaC enzymes, whereas 61 amino acids were identical among the phaC enzyme specific to the haloarchaeal and halobacterial strains presently investigated. All phaC-positive strains produced PHA in standard nutrient deficient medium, whereas the phaC-negative strains did not accumulate any PHA as detected by gas chromatography and nuclear magnetic resonance analyses, thus proving the precision of the developed method and elimination of false positives seen with the traditional Nile Red staining procedure.

  19. The Chemoselective Reduction of Isoxazoline γ-Lactams Through Iminium Aza-Diels-Alder Reactions: A Short-Cut Synthesis of Aminols as Valuable Intermediates towards Nucleoside Derivatives

    PubMed Central

    Memeo, Misal Giuseppe; Mella, Mariella; Quadrelli, Paolo

    2012-01-01

    Isoxazoline γ-lactams are prepared starting from the regioisomeric cycloadducts of benzonitrile oxide to the N-alkyl 2-azanorbornenes taking advantage of the efficient catalytic oxidation by RuO4. The reduction of the amide groups is easily conducted in the presence of LiAlH4 under mild conditions, which allowed for the chemoselective reduction of the amide moiety followed by ring opening to afford the desired conformationally locked isoxazoline-carbocyclic aminols, as valuable intermediates for nucleoside synthesis. PMID:22629174

  20. Enantioselective Reactions of 2-Sulfonylalkyl Phenols with Allenic Esters: Dynamic Kinetic Resolution and [4+2] Cycloaddition Involving ortho-Quinone Methide Intermediates.

    PubMed

    Chen, Ping; Wang, Kai; Guo, Wengang; Liu, Xianghui; Liu, Yan; Li, Can

    2017-03-20

    We report herein a dynamic kinetic resolution (DKR) involving ortho-quinone methide (o-QM) intermediates. In the presence of Et3 N and the cinchonine-derived nucleophilic catalyst D, the DKR of 2-sulfonylalkyl phenols with allenic esters afforded chiral benzylic sulfones in 57-79 % yield with good to excellent enantioselectivity (85-95 % ee). Furthermore, with 2-(tosylmethyl)sesamols or 2-(tosylmethyl)naphthols, from which stable o-QM substrates can be generated, a formal [4+2] cycloaddition delivered 4-aryl- or alkyl-substituted chromans with excellent enantioselectivity (88-97 % ee).

  1. Linking Chemical Electron–Proton Transfer to Proton Pumping in Cytochrome c Oxidase: Broken-Symmetry DFT Exploration of Intermediates along the Catalytic Reaction Pathway of the Iron–Copper Dinuclear Complex

    PubMed Central

    2015-01-01

    After a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear Fe-a3–CuB reaction center in this enzyme. A specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. A larger family of tautomers/protonation states is generated compared to our earlier work, and a new lowest-energy pathway is proposed. The entire reaction cycle is calculated for the new smaller model (about 185–190 atoms), and two selected arcs of the wheel are chosen for calculations using a larger model (about 205 atoms). We compare the structural and redox energetics and protonation calculations with available experimental data. The reaction cycle map that we have built is positioned for further improvement and testing against experiment. PMID:24960612

  2. Identified Light and Strange Hadron Spectra at √{sNN} = 14.5 GeV and Systematic Study of Baryon/Meson Effect at Intermediate Transverse Momentum with STAR at RHIC BES I

    NASA Astrophysics Data System (ADS)

    Brandenburg, James D.

    2016-12-01

    With the recently measured Au+Au collisions at √{sNN} = 14.5 GeV, STAR completed its first phase of the Beam Energy Scan (BES) program at RHIC. The main motivation of the BES program is the study of the QCD phase diagram and the search for a conjectured critical point. Amongst the various collision energies of 7.7, 11.5, 19.6, 27, and 39 GeV, that have been previously presented by STAR, collisions at 14.5 GeV will provide data set in the relatively large chemical potential gap between the 11.5 and 19.6 GeV center-of-mass energies. In this contribution, we report new STAR measurements of Au+Au at √{sNN} = 14.5 GeV that include identified light particle RCP and spectra, as well as measurements of the strange hadrons (Ks0, Λ , Ξ , Ω, and ϕ). The spectra from both light and strange particles cover a significant range of the intermediate transverse momentum (2 intermediate pT from BES Phase I. We will discuss its physics implications and whether hadronic interactions at late stage dominate the collision dynamics.

  3. PAH Intermediates: Links between the Atmosphere and Biological Systems

    PubMed Central

    SIMONICH, STACI L. MASSEY; MOTORYKIN, OLEKSII; JARIYASOPIT, NARUMOL

    2010-01-01

    China is now the world's largest emitter of polycyclic aromatic hydrocarbons (PAHs). In addition, PAHs, and their reactive intermediates, undergo trans-Pacific atmospheric transport to the Western U.S. The objectives of our research are to predict, identify and quantify novel PAH intermediates in the atmosphere and biological systems, using computational methods, as well as laboratory and field experiments. Gaussian is used to predict the thermodynamic properties of parent structure PAHs, as well as the associated nitro-, oxy-, and hydroxy- PAH intermediates. Based on these predictions, state-of-the-art analytical chemistry techniques are used to identify and quantify these potential intermediates on Asian particulate matter before and after reaction in a continuous flow photochemical reactor. These same techniques are used to identify the relative proportion of PAH intermediates in PAH source regions (such as Beijing, China) and during long-range atmospheric transport to the Western U.S. PAH personal exposure studies in China and the Confederated Tribes of the Umatilla Indian Reservation in Oregon will be used to assess the similarities and differences in the PAH intermediates in biological systems relative to the atmosphere. PMID:20849837

  4. Study of the CH2I + O2 Reaction with a Step-Scan Fourier-Transform Infrared Absorption Spectrometer: Spectra of the Criegee Intermediate CH2OO and DIOXIRANE(?)

    NASA Astrophysics Data System (ADS)

    Huang, Yu-Hsuan; Lee, Yuan-Pern

    2014-06-01

    The Criegee intermediates are carbonyl oxides that play key roles in ozonolysis of unsaturated organic compounds. This mechanism was first proposed by Criegee in 1949, but the first direct observation of the simplest Criegee intermediate CH2OO in the gaseous phase has been reported only recently using photoionization mass spectrometry. Our group has reported the low-resolution IR spectra of CH2OO, produced from the reaction of CH2I + O2, with a second-generation step-scan Fourier-transfom IR absorption spectrometer. The spectral assignments were based on comparison of observed vibrational wavenumbers and rotational contours with theoretical predictions. Here, we report the IR absorption spectra of CH2OO at a resolution of 0.32 wn, showing partially rotationally-resolved structures. The origins of the νb{3}, νb{4}, νb{6}, and νb{8} vibrational modes of CH2OO are determined to be 1434.1, 1285.7, 909.2, and 847.3 wn, respectively. With the analysis of the vibration-rotational spectra, we provide a definitive assignment of these bands to CH2OO. The observed vibrational wavenumbers indicate a zwitterionic contribution to this singlet biradical showing a strengthened C-O bond and a weakened O-O bond. This zwitterionic character results to an extremely rapid self reaction via a cyclic dimer to form 2H2CO + O2 (1Δg). Another group of weak transient IR bands centered at 1231.5, 1213.3, and 899.8 wn are also observed. These bands might be contributed from dioxirane, which was postulated to be another important intermediate that might be isomerized from the Criegee intermediate in the reaction of O3 with 1-alkenes. O. Welz, J. D. Savee, D. L. Osborn, S. S.Vasu, C. J. Percival, D. E. Shallcross, and C. A. Taatjes, Science 335, 204 (2012). Y.-T. Su, Y.-H. Huang, H. A.Witek, and Y.-P. Lee, Science 340, 174 (2013).

  5. Caffeoylquinic acid derived free radicals identified during antioxidant reactions of bitter tea (Ilex latifolia and Ilex kudincha).

    PubMed

    Pirker, Katharina Franziska; Goodman, Bernard Albert

    2010-12-01

    In order to provide some insight into the chemical basis for the antioxidant behaviour of bitter tea, the Chinese medicinal beverage derived from leaves of Ilex kudincha or Ilex latifolia, free radicals generated during the oxidation of aqueous extracts of dried leaves have been investigated by electron paramagnetic resonance (EPR) spectroscopy. With both beverages, the major components in the EPR spectra after accelerated autoxidation under alkaline conditions or oxidation with the superoxide anion radical were comparable to those derived from reactions of caffeoylquinic acids. Thus these reaction products have sufficient stability for biological activity, and the present results suggest that such molecules contribute appreciably to the antioxidant chemistry of these beverages.

  6. Shedding new light on ZnCl2-mediated addition reactions of Grignard reagents to ketones: structural authentication of key intermediates and diffusion-ordered NMR studies.

    PubMed

    Armstrong, David R; Clegg, William; García-Alvarez, Pablo; McCall, Matthew D; Nuttall, Lorraine; Kennedy, Alan R; Russo, Luca; Hevia, Eva

    2011-04-11

    Building on recent advances in synthesis showing that the addition of inorganic salts to Grignard reagents can greatly enhance their performance in alkylation reactions to ketones, this study explores the reactions of EtMgCl with benzophenone in the presence of stoichiometric or catalytic amounts of ZnCl(2) with the aim of furthering the understanding of the role and constitution of the organometallic species involved in these transformations. Investigations into the metathesis reactions of three molar equivalents of EtMgCl with ZnCl(2) led to the isolation and characterisation (X-ray crystallography and (1)H and (13)C NMR spectroscopy) of novel magnesium "zinc-rich" zincate [{(THF)(6)Mg(2)Cl(3)}(+){Zn(2)Et(5)}(-)] (1), whose complicated constitution in THF solutions was assessed by variable-temperature (1)H DOSY NMR studies. Compound 1 reacted with one equivalent of benzophenone to yield magnesium magnesiate [{(THF)(6)Mg(2)Cl(3)}(+){Mg(2)(OC(Et)Ph(2))(2)Cl(3)(THF)}(-)] (3), whose structure was determined by X-ray crystallography. (1)H NMR monitoring of this reaction showed two equivalents of ZnEt(2) formed as a co-product, which together with the "magnesium only constitution" of 3 provides experimental insights into how zinc can be efficiently recycled in these reactions, and therefore used catalytically. The chemoselectivity of this reaction can be rationalised in terms of the synergic effect of magnesium and zinc and contrasts with the results obtained when benzophenone was allowed to react with EtMgCl in the absence of ZnCl(2), where the reduction of the ketone takes place preferentially. The reduction product [{(THF)(5)Mg(3)Cl(4){OC(H)Ph(CF(3))}(2)] (4) obtained from the reaction of EtMgCl with 2,2,2-trifluoroacetophenone was established by X-ray crystallography and multinuclear ((1)H, (13)C and (19)F) NMR spectroscopy. Compounds 3 and 4 exhibit new structural motifs in magnesium chemistry having MgCl(2) integrated within their constitution, which highlights

  7. Synthesized TiO2/ZSM-5 composites used for the photocatalytic degradation of azo dye: Intermediates, reaction pathway, mechanism and bio-toxicity

    NASA Astrophysics Data System (ADS)

    Zhou, Kefu; Hu, Xin-Yan; Chen, Bor-Yann; Hsueh, Chung-Chuan; Zhang, Qian; Wang, Jiajie; Lin, Yu-Jung; Chang, Chang-Tang

    2016-10-01

    In this study, a one-step solid dispersion method was used to synthesize titanium dioxide (TiO2)/Zeolite Socony Mobil-5 (ZSM-5) composites with substantially reduced time and energy consumption. A degradation efficiency of more than 95% was achieved within 10 min using 50% PTZ (synthesized TiO2/ZSM-5 composites with TiO2 contents of 50 wt% loaded on ZSM-5) at pH 7 and 25 °C. The possible degradation pathway of azo-dye Reactive Black 5 (RB5) was investigated using gas chromatography-mass spectrometry and ion chromatography (IC). The bonds between the N atoms and naphthalene groups are likely attacked first and cleaved by hydroxyl radicals, ultimately resulting in the decolorization and mineralization of the azo dye. A comparative assessment of the characteristics of abiotic and biotic dye decolorization was completed. In addition, the toxicity effects of the degradation intermediates of azo-dye RB5 on cellular respiratory activity were analyzed. The bio-toxicity results showed that the decay rate constants of CO2 production from the azo-dye RB5 samples at different degradation times increased initially and subsequently decreased, indicating that intermediates of higher toxicity could adhere to the catalyst surface and gradually destroyed by further photocatalytic oxidation. Additionally, EDTA (hole scavengers) and t-BuOH (radical scavengers) were used to detect the main active oxidative species in the system. The results showed that the hydroxyl radicals are the main oxidation species in the photocatalytic process.

  8. Synchrotron photoionization mass spectrometry study of intermediates in fuel-rich 1,2-dimethoxyethane flame

    SciTech Connect

    Lin, Z. K.; Han, D. L.; Li, S. F.; Li, Y. Y.; Yuan, T.

    2009-04-21

    Intermediates in a fuel-rich premixed laminar 1,2-dimethoxyethane (DME) flame are studied by molecular beam mass spectrometry combined with tunable synchrotron vacuum ultraviolet photoionization. About 30 intermediate species are identified in the present work, and their mole fraction profiles are evaluated. The experimental results show that the formations of intermediates, both hydrocarbons and oxygenated hydrocarbons, are closely linked to the structure of fuel, which is consistent with the previous reports. Species produced from H atom abstraction and beta scission of DME usually have much higher concentrations than others. The oxygen atoms in DME are considered to act as partitions of the primary intermediates; therefore farther reactions among these primary intermediates are difficult to occur, resulting in absence of most large intermediate species.

  9. Synchrotron photoionization mass spectrometry study of intermediates in fuel-rich 1,2-dimethoxyethane flame

    NASA Astrophysics Data System (ADS)

    Lin, Z. K.; Han, D. L.; Li, S. F.; Li, Y. Y.; Yuan, T.

    2009-04-01

    Intermediates in a fuel-rich premixed laminar 1,2-dimethoxyethane (DME) flame are studied by molecular beam mass spectrometry combined with tunable synchrotron vacuum ultraviolet photoionization. About 30 intermediate species are identified in the present work, and their mole fraction profiles are evaluated. The experimental results show that the formations of intermediates, both hydrocarbons and oxygenated hydrocarbons, are closely linked to the structure of fuel, which is consistent with the previous reports. Species produced from H atom abstraction and beta scission of DME usually have much higher concentrations than others. The oxygen atoms in DME are considered to act as partitions of the primary intermediates; therefore farther reactions among these primary intermediates are difficult to occur, resulting in absence of most large intermediate species.

  10. Synthesis of heterocyclic analogues of epibatidine via 7-azabicyclo[2.2.1]hept-2-yl radical intermediates. 1. Intermolecular reactions.

    PubMed

    Gómez-Sánchez, Elena; Soriano, Elena; Marco-Contelles, José

    2008-09-05

    The synthesis and reactivity of the 7-azabicyclo[2.2.1]hept-2-yl radical has been extensively investigated in inter- and intramolecular reaction processes for the first time. In this work we will present the preparation of the radical and its successful intermolecular reaction with radical acceptors such as tert-butylisocyanide and acrylonitrile. Computational analyses have been carried out to show and explain the mechanisms and stereochemical outcome of these transformations. Overall and from the chemical point of view, a new and convenient synthetic approach has been developed for the synthesis of exo-2-(cyano)alkyl substituted 7-azabicyclo[2.2.1]heptane derivatives, a series of compounds of wide interest for the synthesis of heterocyclic analogues of epibatidine. As a result, we describe here the synthesis of the tetrazoloepibatidines (8 and 15) and the oxadiazoloepibatidine (10).

  11. The role of carbonate as a catalyst of Fenton-like reactions in AOP processes: CO3˙(-) as the active intermediate.

    PubMed

    Burg, Ariela; Shamir, Dror; Shusterman, Inna; Kornweitz, Haya; Meyerstein, Dan

    2014-11-07

    Kinetic and DFT results for the carbonate catalysed Co(H2O)6(2+) + H2O2 Fenton-like reaction suggest a mechanism involving the formation of a cyclic transient, cyclic-(CO4)Co(II)(OOH)(H2O)2(-) that decomposes into Co(II)(H2O)(OOH)(OH)2 + CO3˙(-), i.e. no OH˙ radicals are involved. Plausible biological implications are pointed out.

  12. Identifying environmental variables explaining genotype-by-environment interaction for body weight of rainbow trout (Onchorynchus mykiss): reaction norm and factor analytic models

    PubMed Central

    2014-01-01

    Background Identifying the relevant environmental variables that cause GxE interaction is often difficult when they cannot be experimentally manipulated. Two statistical approaches can be applied to address this question. When data on candidate environmental variables are available, GxE interaction can be quantified as a function of specific environmental variables using a reaction norm model. Alternatively, a factor analytic model can be used to identify the latent common factor that explains GxE interaction. This factor can be correlated with known environmental variables to identify those that are relevant. Previously, we reported a significant GxE interaction for body weight at harvest in rainbow trout reared on three continents. Here we explore their possible causes. Methods Reaction norm and factor analytic models were used to identify which environmental variables (age at harvest, water temperature, oxygen, and photoperiod) may have caused the observed GxE interaction. Data on body weight at harvest was recorded on 8976 offspring reared in various locations: (1) a breeding environment in the USA (nucleus), (2) a recirculating aquaculture system in the Freshwater Institute in West Virginia, USA, (3) a high-altitude farm in Peru, and (4) a low-water temperature farm in Germany. Akaike and Bayesian information criteria were used to compare models. Results The combination of days to harvest multiplied with daily temperature (Day*Degree) and photoperiod were identified by the reaction norm model as the environmental variables responsible for the GxE interaction. The latent common factor that was identified by the factor analytic model showed the highest correlation with Day*Degree. Day*Degree and photoperiod were the environmental variables that differed most between Peru and other environments. Akaike and Bayesian information criteria indicated that the factor analytical model was more parsimonious than the reaction norm model. Conclusions Day*Degree and

  13. Identifying and managing an adverse food reaction in a polar bear (Ursus maritimus) by an elimination diet trial.

    PubMed

    Monson, Sara; Minter, Larry J; Krouse, Marissa; De Voe, Ryan S

    2014-06-01

    A 16-yr-old polar bear (Ursus maritimus) presented with severe diarrhea shortly following transfer to the North Carolina Zoological Park. Multiple diagnostic procedures were performed over several months and the cause of the chronic diarrhea was inconclusive. Histologically, colonic mucosal biopsies were consistent with severe chronic eosinophilic and lymphoplasmacytic colitis with no evidence of etiologic agents present. A dietary elimination trial was conducted and an adverse food reaction to the dog chow in the diet was confirmed.

  14. Isoporphyrin Intermediate in Heme Oxygenase Catalysis

    PubMed Central

    Evans, John P.; Niemevz, Fernando; Buldain, Graciela; de Montellano, Paul Ortiz

    2008-01-01

    Human heme oxygenase-1 (hHO-1) catalyzes the O2- and NADPH-dependent oxidation of heme to biliverdin, CO, and free iron. The first step involves regiospecific insertion of an oxygen atom at the α-meso carbon by a ferric hydroperoxide and is predicted to proceed via an isoporphyrin π-cation intermediate. Here we report spectroscopic detection of a transient intermediate during oxidation by hHO-1 of α-meso-phenylheme-IX, α-meso-(p-methylphenyl)-mesoheme-III, and α-meso-(p-trifluoromethylphenyl)-mesoheme-III. In agreement with previous experiments (Wang, J., Niemevz, F., Lad, L., Huang, L., Alvarez, D. E., Buldain, G., Poulos, T. L., and Ortiz de Montellano, P. R. (2004) J. Biol. Chem. 279, 42593–42604), only the α-biliverdin isomer is produced with concomitant formation of the corresponding benzoic acid. The transient intermediate observed in the NADPH-P450 reductase-catalyzed reaction accumulated when the reaction was supported by H2O2 and exhibited the absorption maxima at 435 and 930 nm characteristic of an isoporphyrin. Product analysis by reversed phase high performance liquid chromatography and liquid chromatography electrospray ionization mass spectrometry of the product generated with H2O2 identified it as an isoporphyrin that, on quenching, decayed to benzoylbiliverdin. In the presence of H218O2, one labeled oxygen atom was incorporated into these products. The hHO-1-isoporphyrin complexes were found to have half-lives of 1.7 and 2.4 h for the p-trifluoromethyl- and p-methyl-substituted phenylhemes, respectively. The addition of NADPH-P450 reductase to the H2O2-generated hHO-1-isoporphyrin complex produced α-biliverdin, confirming its role as a reaction intermediate. Identification of an isoporphyrin intermediate in the catalytic sequence of hHO-1, the first such intermediate observed in hemoprotein catalysis, completes our understanding of the critical first step of heme oxidation. PMID:18487208

  15. Intermediate Nuclear Structure for 2v 2{beta} Decay of {sup 48}Ca Studied by (p, n) and (n, p) Reactions at 300 MeV

    SciTech Connect

    Sakai, H.; Yako, K.

    2009-08-26

    Angular distributions of the double differential cross sections for the {sup 48}Ca(p,n) and the {sup 48}Ti(n,p) reactions were measured at 300 MeV. A multipole decomposition technique was applied to the spectra to extract the Gamow-Teller (GT) transition strengths. In the (n, p) spectrum beyond 8 MeV excitation energy extra B(GT{sup +}) strengths which are not predicted by the shell model calculation. This extra B(GT{sup +}) strengths significantly contribute to the nuclear matrix element of the 2v2{beta}-decay.

  16. High-Valent Oxo, Methoxorhenium Complexes: Models for Intermediates and Transition States in Proton-Coupled Multi-Electron Transfer Reactions

    DTIC Science & Technology

    1993-05-30

    useful as redox catalysts .ŗ On the other hand, we have found them to be remarkably versatile model reactants for systematic Atudies of interfacial (i.e...context of possible mechanisms for trans-dioxorhenium-based oxidativeŗ and reductive" electrocatalytic reactions, respectively. Experimental Section...3.26; N, 5.64. Caled: C, 33.52; H, 3.49; N, 6.26. ’H-NMR (acetone-d,)(ppm): 8.52(d,8H), 7.77(d,8H), 4.27(s,3H), 2.79(s, 12H). Metathesis of selected

  17. Thermally-generated reactive intermediates: Trapping of the parent ferrocene-based o-quinodimethane and reactions of diradicals generated by hydrogen-atom transfers

    SciTech Connect

    Ferguson, John Michael

    1993-09-01

    Ferrocenocyclobutene is prepared by flash vacuum pyrolysis (FVP) of the N-amino-2-phenylaziridine hydrazone of 2-methylferrocenealdehyde. In the second section of this dissertation, a series of hydrocarbon rearrangements were observed. FVP of o-allyltoluene at 0.1 Torr (700--900 C) gives 2-methylindan and indene, accompanied by o-propenyltoluene. FVP of 2-methyl-2`-vinylbiphenyl gives 9-methyl-9,10-dihydrophenanthrene, which fits the proposed mechanism. However, FVP of 2-(o-methylbenzyl)styrene gives mainly anthracene and 1-methylanthracene. This cyclization reaction was also successful with o-allylphenol and o-(2-methylallyl)phenol.

  18. Intermediate inputs and economic productivity.

    PubMed

    Baptist, Simon; Hepburn, Cameron

    2013-03-13

    Many models of economic growth exclude materials, energy and other intermediate inputs from the production function. Growing environmental pressures and resource prices suggest that this may be increasingly inappropriate. This paper explores the relationship between intermediate input intensity, productivity and national accounts using a panel dataset of manufacturing subsectors in the USA over 47 years. The first contribution is to identify sectoral production functions that incorporate intermediate inputs, while allowing for heterogeneity in both technology and productivity. The second contribution is that the paper finds a negative correlation between intermediate input intensity and total factor productivity (TFP)--sectors that are less intensive in their use of intermediate inputs have higher productivity. This finding is replicated at the firm level. We propose tentative hypotheses to explain this association, but testing and further disaggregation of intermediate inputs is left for further work. Further work could also explore more directly the relationship between material inputs and economic growth--given the high proportion of materials in intermediate inputs, the results in this paper are suggestive of further work on material efficiency. Depending upon the nature of the mechanism linking a reduction in intermediate input intensity to an increase in TFP, the implications could be significant. A third contribution is to suggest that an empirical bias in productivity, as measured in national accounts, may arise due to the exclusion of intermediate inputs. Current conventions of measuring productivity in national accounts may overstate the productivity of resource-intensive sectors relative to other sectors.

  19. Effect of radial flow on two particle correlations with identified triggers at intermediate pT in p-Pb collisions at √{sNN} = 5.02 TeV

    NASA Astrophysics Data System (ADS)

    Sarkar, Debojit; Choudhury, Subikash; Chattopadhyay, Subhasis

    2016-09-01

    Results from two-particle correlation between identified triggers (pions (π±), protons (p / p bar)) and un-identified charged particles at intermediate transverse momentum (pT) in p-Pb collisions at √{sNN} = 5.02 TeV have been presented. The events generated from a hybrid Monte-Carlo event generator, EPOS 3.107 that implements a flux-tube initial conditions followed by event by event 3+1D viscous hydrodynamical evolution, have been analyzed to calculate two-dimensional correlation functions in Δη- Δϕ. The strength of angular correlations at small relative angles (jet-like correlations), quantified in terms of near-side jet-like per-trigger yield has been calculated as a function of the event multiplicity. The yield associated with pion triggers exhibit negligible multiplicity dependence, while the proton-triggered yield shows a gradual suppression from low to high multiplicity events. In small collision systems like p-Pb where jet modification is expected to be less dominant, the observed suppression may be associated with the hydrodynamical evolution of the bulk system that generates an outward radial flow. Analogous measurements in Au-Au collisions at RHIC energy have shown a hint of dilution in proton-triggered correlation at its highest multiplicity suggesting that the soft physics processes in p-Pb and heavy ion collisions may have qualitative similarity.

  20. Extensional flow convecting a reactant undergoing a first order homogeneous reaction and diffusional mass transfer from a sphere at low to intermediate Peclet and Damkohler numbers

    NASA Technical Reports Server (NTRS)

    Shah, N. Y.; Reed, X. B., Jr.

    1995-01-01

    Forced convective diffusion-reaction is considered for viscous axisymmetric extensional convecting velocity in the neighborhood of a sphere. For Peclet numbers in the range 0.1 less than or equal to Pe less than or equal to 500 and for Damkohler numbers increasing with increasing Pe but in the overall range 0.02 less than or equal to Da less than or equal to 10, average and local Sherwood numbers have been computed. By introducing the eigenfunction expansion c(r, Theta) = Sum of c(n)(r)P(n)(cos Theta) into the forced convective diffusion equation for the concentration of a chemical species undergoing a first order homogeneous reaction and by using properties of the Legendre functions Pn(cos Theta), the variable coefficient PDE can be reduced to a system of N + 1 second order ODEs for the radial functions c(sub n)(r), n = 0, 1, 2,..., N. The adaptive grid algorithm of Pereyra and Lentini can be used to solve the corresponding 2(N + 1) first order differential equations as a two-point boundary value problem on 1 less than or equal to r less than or equal to r(sub infinity). Convergence of the expansion for a specific value of N can thus be established and provides 'spectral' behavior as well as the full concentration field c(r, Theta).

  1. Genes that encode botulism neurotoxins A, B, E and F in neotropical bee honey identified with the polymerase chain reaction.

    PubMed

    Fournier, Ana Teresa; Gamboa, María del Mar; Arias, María Laura

    2006-03-01

    Honey can be used for the treatment of wounds, sores and skin bums, but it might be contaminated with Clostridium botulinum spores. In order to evaluate Costa Rican raw honey samples, the detection of neurotoxin gene sequences (corresponding to the bacterium) C. botulinum A, B, E and F was done with the polymerase chain reaction. A total of 64 raw honey samples, coming from different Costa Rican sites were analyzed. Reference C. botulinum strains type A (ATCC 19397), type B (ATCC 7949), type E (ATCC 17786) and type F (ATCC 25764) were used as templates for testing the effectivity of the method. The process consisted in culturing the honey samples in prereduced triptose-peptone-glucose-yeast extract media (TGPY) for 5 days. After this, the bacteria lysate obtained was used for PCR. The amplicons, product of the reaction, were visualized using agarose gel 2%. From the 64 honey samples analyzed, none produced positive results in the PCR, since no amplicons were obtained. Even though, all the reference C. botulinum strains used as controls were visualized and showed the effectivity of the extraction method and of the PCR used. The results obtained show promising therapeutic uses for honey from Costa Rica, but further evaluations shall be done in order to be sure of the safety of the product.

  2. Switchable Synthesis of Pyrroles and Pyrazines via Rh(II)-Catalyzed Reaction of 1,2,3-Triazoles with Isoxazoles: Experimental and DFT Evidence for the 1,4-Diazahexatriene Intermediate.

    PubMed

    Rostovskii, Nikolai V; Ruvinskaya, Julia O; Novikov, Mikhail S; Khlebnikov, Alexander F; Smetanin, Ilia A; Agafonova, Anastasiya V

    2017-01-06

    4-Aminopyrrole-3-carboxylates and pyrazine-2-carboxylates were synthesized from 5-alkoxyisoxazoles and 1-sulfonyl-1,2,3-triazoles by tuning the Rh(II) catalyst and the reaction conditions. The reaction in chloroform at 100 °C under Rh2(OAc)4 catalysis provides 4-aminopyrrole-3-carboxylates in good yields. The use of Rh2(Piv)4 in refluxing toluene results in the formation of 1,2-dihydropyrazine-2-carboxylates as the main products, which can be converted by a one-pot procedure to pyrazine-2-carboxylates by heating with catalytic amounts of TsOH. According to the NMR and DFT investigations of the reaction mechanism, pyrroles and dihydropyrazines are formed, respectively, via 1,5- and 1,6-cyclization of common (5Z)-1,4-diazahexa-1,3,5-triene intermediates. The influence of the nature of the catalyst on the product distribution is rationalized in terms of the Rh-catalyzed isomerization of a pyrrolin-2-ylium-3-aminide zwitterion, the primary product of 1,4-diazahexatriene 1,5-cyclization.

  3. Theoretical vibrational spectroscopy of intermediates and the reaction mechanism of the guanosine triphosphate hydrolysis by the protein complex Ras-GAP

    NASA Astrophysics Data System (ADS)

    Khrenova, Maria G.; Grigorenko, Bella L.; Nemukhin, Alexander V.

    2016-09-01

    The structures and vibrational spectra of the reacting species upon guanosine triphosphate (GTP) hydrolysis to guanosine diphosphate and inorganic phosphate (Pi) trapped inside the protein complex Ras-GAP were analyzed following the results of QM/MM simulations. The frequencies of the phosphate vibrations referring to the reactants and to Pi were compared to those observed in the experimental FTIR studies. A good correlation between the theoretical and experimental vibrational data provides a strong support to the reaction mechanism of GTP hydrolysis by the Ras-GAP enzyme system revealed by the recent QM/MM modeling. Evolution of the vibrational bands associated with the inorganic phosphate Pi during the elementary stages of GTP hydrolysis is predicted.

  4. THE EFFECT OF THE {sup 14}N(p, {gamma}){sup 15}O REACTION ON THE BLUE LOOPS IN INTERMEDIATE-MASS STARS

    SciTech Connect

    Halabi, Ghina M.; El Eid, Mounib F.; Champagne, Arthur

    2012-12-10

    We present stellar evolutionary sequences of stars in the mass range 5-12 M{sub Sun }, having solar-like initial composition. The stellar models are obtained using updated input physics, including recent rates of thermonuclear reactions. We investigate the effects of a modification of the {sup 14}N(p, {gamma}){sup 15}O reaction rate, as suggested by recent evaluations, on the formation and extension of the blue loops encountered during the evolution of the stars in the above mass range. We find that a reduced {sup 14}N(p, {gamma}){sup 15}O rate, as described in the text, has a striking impact on the physical conditions of burning and mixing during shell hydrogen burning when the blue loops are formed. In particular, we find that the efficiency of shell hydrogen burning is crucial for the formation of an extended blue loop. We show that a significantly reduced {sup 14}N(p, {gamma}){sup 15}O rate affects severely the extension of the blue loops and the time spent by the star in the blue part of the Hertzsprung-Russell diagram in the mass range 5-7 M{sub Sun} if the treatment of convection is based on the Schwarzschild criterion only. In this case, envelope overshooting helps to restore well-extended blue loops as supported by the observations of the Cepheid stars. If core overshooting is included during the core hydrogen and core helium burning phases, the loop formation and its properties depend on how this overshooting is treated for a given stellar mass range, as well as on its efficiency.

  5. An Artificial Enzyme Made by Covalent Grafting of an Fe(II) Complex into β-Lactoglobulin: Molecular Chemistry, Oxidation Catalysis, and Reaction-Intermediate Monitoring in a Protein.

    PubMed

    Buron, Charlotte; Sénéchal-David, Katell; Ricoux, Rémy; Le Caër, Jean-Pierre; Guérineau, Vincent; Méjanelle, Philippe; Guillot, Régis; Herrero, Christian; Mahy, Jean-Pierre; Banse, Frédéric

    2015-08-17

    An artificial metalloenzyme based on the covalent grafting of a nonheme Fe(II) polyazadentate complex into bovine β-lactoglobulin has been prepared and characterized by using various spectroscopic techniques. Attachment of the Fe(II) catalyst to the protein scaffold is shown to occur specifically at Cys121. In addition, spectrophotometric titration with cyanide ions based on the spin-state conversion of the initial high spin (S=2) Fe(II) complex into a low spin (S=0) one allows qualitative and quantitative characterization of the metal center's first coordination sphere. This biohybrid catalyst activates hydrogen peroxide to oxidize thioanisole into phenylmethylsulfoxide as the sole product with an enantiomeric excess of up to 20 %. Investigation of the reaction between the biohybrid system and H2 O2 reveals the generation of a high spin (S=5/2) Fe(III) (η(2) -O2 ) intermediate, which is proposed to be responsible for the catalytic sulfoxidation of the substrate.

  6. Impetigo-like tinea faciei around the nostrils caused by Arthroderma vanbreuseghemii identified using polymerase chain reaction-based sequencing of crusts.

    PubMed

    Kang, Daoxian; Ran, Yuping; Li, Conghui; Dai, Yaling; Lama, Jebina

    2013-01-01

    We report a case of Arthroderma vanbreuseghemii (a teleomorph of Trichophyton interdigitale) infection around the nostrils in a 3-year-old girl. The culture was negative, so the pathogenic agent was identified using polymerase chain reaction-based sequencing of the crusts taken from the lesion on the nostril. Treatment with oral itraconazole and topical 1% naftifine/0.25% ketoconazole cream after a topical wash with ketoconazole shampoo was effective.

  7. Study of intermediates from transition metal excited-state electron-transfer reactions. Final report, August 4, 1986--August 31, 1997

    SciTech Connect

    Hoffman, M.Z.

    1997-12-31

    The techniques of continuous photolysis and pulsed laser flash photolysis, continuous and pulse radiolysis, fast-scan cyclic voltammetry, and time-resolved fluorimetry have been used to examine intramolecular electron transfer within the solvent quenching cage, photodynamics of quenching of the excited states of transition-metal photosensitizers, the properties of excites states and one-electron reduced forms, ground- and excited-state interactions with solutes, and photoinduced oxidations of organic solutes in aqueous solution. The following specific areas were examined: (1) the parameters that govern the yields of redox products from excited-state electron-transfer quenching reactions; (2) the mediation of the properties of excited states and one-electron reduced forms by the ligands and the solution medium; (3) the effect of the interactions between the ground state of the complex and the solution components on the behavior of the excited state; (4) the yields of singlet oxygen from excited-state energy-transfer quenching by O{sub 2}; and (5) the oxidations of solutes by singlet oxygen, excited-state electron-transfer quenching, and free radicals. This report contains the abstracts of 50 publications describing the studies.

  8. Chemical vapour deposition: a matrix isolation study of precursor compounds and reaction intermediates in the formation of cadmium telluride and gallium nitride

    NASA Astrophysics Data System (ADS)

    Almond, Matthew J.; Jenkins, Carolyn E.; Rice, David A.; Yates, Carol A.

    1990-05-01

    Infrared spectra for the matrix-isolated species R 2Te, R 2Cd (R=Me or Et), Me 3N·GaH 3, Me 3N·GaMe 3 and Me 2NH·GaMe 3 are reported for the first time. Evidence is also presented for the formation of the weakly bound adducts Me 2Cd·(TeEt 2) x and Et 2Cd·(TeMe 2) t x ( x = 1 or 2) in a gaseous mixture before trapping in Ar matrices at 14 K. The strength of bonding in Et 2Cd·(TeMe 2) x is similar to that in the adduct Et 2Cd·(SEt 2) x and it has a non-linear CCdC unit. Thermal decomposition (60°C) of gaseous Me 3N·GaH 3 in a glass tube yields Me 3N and a Ga mirror — an observation which suggests that the primary step of the reaction is GaN bond rupture. By contrast, the two gaseous adducts Me 3N·GaMe 3 and Me 2NH·GaMe 3 decompose thermally and photochemically to yield inter alia methane, a result which implies that the GaN bond remains intact in the primary decomposition step.

  9. Stochastic-convective transport with nonlinear reaction and mixing: application to intermediate-scale experiments in aerobic biodegradation in saturated porous media.

    PubMed

    Ginn, T R; Murphy, E M; Chilakapati, A; Seeboonruang, U

    2001-03-01

    Aerobic biodegradation of benzoate by Pseudomonas cepacia sp. in a saturated heterogeneous porous medium was simulated using the stochastic-convective reaction (SCR) approach. A laboratory flow cell was randomly packed with low permeability silt-size inclusions in a high permeability sand matrix. In the SCR upscaling approach, the characteristics of the flow field are determined by the breakthrough of a conservative tracer. Spatial information on the actual location of the heterogeneities is not used. The mass balance equations governing the nonlinear and multicomponent reactive transport are recast in terms of reactive transports in each of a finite number of discrete streamtubes. The streamtube ensemble members represent transport via a steady constant average velocity per streamtube and a conventional Fickian dispersion term, and their contributions to the observed breakthroughs are determined by flux-averaging the streamtube solute concentrations. The resulting simulations were compared to those from a high-resolution deterministic simulation of the reactive transport, and to alternative ensemble representations involving (i) effective Fickian travel time distribution function, (ii) purely convective streamtube transport, and (iii) streamtube ensemble subset simulations. The results of the SCR simulation compare favorably to that of a sophisticated high-resolution deterministic approach.

  10. Stochastic-convective transport with nonlinear reaction and mixing: application to intermediate-scale experiments in aerobic biodegradation in saturated porous media

    NASA Astrophysics Data System (ADS)

    Ginn, T. R.; Murphy, E. M.; Chilakapati, A.; Seeboonruang, U.

    2001-03-01

    Aerobic biodegradation of benzoate by Pseudomonas cepacia sp. in a saturated heterogeneous porous medium was simulated using the stochastic-convective reaction (SCR) approach. A laboratory flow cell was randomly packed with low permeability silt-size inclusions in a high permeability sand matrix. In the SCR upscaling approach, the characteristics of the flow field are determined by the breakthrough of a conservative tracer. Spatial information on the actual location of the heterogeneities is not used. The mass balance equations governing the nonlinear and multicomponent reactive transport are recast in terms of reactive transports in each of a finite number of discrete streamtubes. The streamtube ensemble members represent transport via a steady constant average velocity per streamtube and a conventional Fickian dispersion term, and their contributions to the observed breakthroughs are determined by flux-averaging the streamtube solute concentrations. The resulting simulations were compared to those from a high-resolution deterministic simulation of the reactive transport, and to alternative ensemble representations involving (i) effective Fickian travel time distribution function, (ii) purely convective streamtube transport, and (iii) streamtube ensemble subset simulations. The results of the SCR simulation compare favorably to that of a sophisticated high-resolution deterministic approach.

  11. LiCuS, an intermediate phase in the electrochemical conversion reaction of CuS with Li: A potential environment-friendly battery and solar cell material

    NASA Astrophysics Data System (ADS)

    Beleanu, Andreea; Kiss, Janos; Baenitz, Michael; Majumder, Mayukh; Senyshyn, Anatoliy; Kreiner, Guido; Felser, Claudia

    2016-05-01

    The crystal structure of a ternary sulfide with the approximate composition LiCuS, which is a promising candidate for environment-friendly battery and solar cell materials is reported. The crystal structure was solved by a combination of neutron and X-ray powder diffraction data, and 7Li solid-state NMR analysis. A yellow powder, Li1.1Cu0.9S, was obtained by the reaction of CuS with a slight excess of Li metal. The compound crystallizes in the Na3AgO2 structure type in the space group Ibam. An idealized crystal structure of Li1.1Cu0.9S can be derived from the cubic Li2S structure by moving a part of the Li along the c axis so that these Li atoms become linearly coordinated by S. All the metal sites are occupied by randomly mixed Li and Cu atoms; however, there is a strong preference for linear coordination by Cu. The density functional theory calculations show that Li1.1Cu0.9S is a direct band-gap semiconductor with an energy gap of 1.95 eV in agreement with experimental data.

  12. Degradation mechanisms of geosmin and 2-MIB during UV photolysis and UV/chlorine reactions.

    PubMed

    Kim, Tae-Kyoung; Moon, Bo-Ram; Kim, Taeyeon; Kim, Moon-Kyung; Zoh, Kyung-Duk

    2016-11-01

    We conducted chlorination, UV photolysis, and UV/chlorin reactions to investigate the intermediate formation and degradation mechanisms of geosmin and 2-methylisoborneol (2-MIB) in water. Chlorination hardly removed geosmin and 2-MIB, while the UV/chlorine reaction at 254 nm completely removed geosmin and 2-MIB within 40 min and 1 h, respectively, with lesser removals of both compounds during UV photolysis. The kinetics during both UV photolysis and UV/chlorine reactions followed a pseudo first-order reaction. Chloroform was found as a chlorinated intermediate during the UV/chlorine reaction of both geosmin and 2-MIB. The pH affected both the degradation and chloroform production during the UV/chlorine reaction. The open ring and dehydration intermediates identified during UV/chlorine reactions were 1,4-dimethyl-adamantane, and 1,3-dimethyl-adamantane from geosmin, 2-methylenebornane, and 2-methyl-2-bornene from 2-MIB, respectively. Additionally, 2-methyl-3-pentanol, 2,4-dimethyl-1-heptene, 4-methyl-2-heptanone, and 1,1-dichloro-2,4-dimethyl-1-heptane were newly identified intermediates from UV/chlorine reactions of both geosmin and 2-MIB. These intermediates were degraded as the reaction progressed. We proposed possible degradation pathways during the UV photolysis and UV/chlorine reactions of both compounds using the identified intermediates.

  13. Improving the Production of L-Phenylalanine by Identifying Key Enzymes Through Multi-Enzyme Reaction System in Vitro

    PubMed Central

    Ding, Dongqin; Liu, Yongfei; Xu, Yiran; Zheng, Ping; Li, Haixing; Zhang, Dawei; Sun, Jibin

    2016-01-01

    L-Phenylalanine (L-Phe) is an important amino acid used in both food and medicinal applications. We developed an in vitro system that allowed a direct, quantitative investigation of phenylalanine biosynthesis in E. coli. Here, the absolute concentrations of six enzymes (AroK, AroL, AroA, AroC, PheA and TyrB) involved in the shikimate (SHIK) pathway were determined by a quantitative proteomics approach and in vitro enzyme titration experiments. The reconstitution of an in vitro reaction system for these six enzymes was established and their effects on the phenylalanine production were tested. The results showed that the yield of phenylalanine increased 3.0 and 2.1 times when the concentrations of shikimate kinase (AroL) and 5-enolpyruvoyl shikimate 3-phosphate (EPSP) synthase (AroA) were increased 2.5 times. Consistent results were obtained from in vivo via the overexpression of AroA in a phenylalanine-producing strain, and the titer of phenylalanine reached 62.47 g/l after 48 h cultivation in a 5-liter jar fermentor. Our quantitative findings provide a practical method to detect the potential bottleneck in a specific metabolic pathway to determine which gene products should be targeted to improve the yield of the desired product. PMID:27558633

  14. Browning inhibition mechanisms by cysteine, ascorbic acid and citric acid, and identifying PPO-catechol-cysteine reaction products.

    PubMed

    Ali, Hussein M; El-Gizawy, Ahmed M; El-Bassiouny, Rawia E I; Saleh, Mahmoud A

    2015-06-01

    The titled compounds were examined as PPO inhibitors and antibrowning agents; their various mechanisms were investigated and discussed. All compounds reduced significantly both the browning process and PPO activity. Browning index gave strong correlation with PPO activity (r(2) = 0.96, n = 19) indicating that the browning process is mainly enzymatic. Ascorbic acid could reduce the formed quinone instantly to the original substrate (catechol) at high concentration (>1.5 %) while at lower concentrations acted as competitive inhibitor (KI = 0.256 ± 0.067 mM). Cysteine, at higher concentrations (≥1.0 %), reacted with the resulted quinone to give a colorless products while at the low concentrations, cysteine worked as competitive inhibitor (KI = 1.113 ± 0.176 mM). Citric acid acted only as PPO non-competitive inhibitor with KI = 2.074 ± 0.363 mM. The products of PPO-catechole-cysteine reaction could be separation and identification by LC-ESI-MS. Results indicated that the product of the enzymatic oxidation of catechol, quinone, undergoes two successive nucleophilic attacks by cysteine thiol group. Cysteine was condensed with the resulted mono and dithiocatechols to form peptide side chains.

  15. Identifying, by first-principles simulations, Cu[amyloid-β] species making Fenton-type reactions in Alzheimer's disease.

    PubMed

    La Penna, Giovanni; Hureau, Christelle; Andreussi, Oliviero; Faller, Peter

    2013-12-27

    According to the amyloid cascade hypothesis, amyloid-β peptides (Aβ) play a causative role in Alzheimer's disease (AD), of which oligomeric forms are proposed to be the most neurotoxic by provoking oxidative stress. Copper ions seem to play an important role as they are bound to Aβ in amyloid plaques, a hallmark of AD. Moreover, Cu-Aβ complexes are able to catalyze the production of hydrogen peroxide and hydroxyl radicals, and oligomeric Cu-Aβ was reported to be more reactive. The flexibility of the unstructured Aβ peptide leads to the formation of a multitude of different forms of both Cu(I) and Cu(II) complexes. This raised the question of the structure-function relationship. We address this question for the biologically relevant Fenton-type reaction. Computational models for the Cu-Aβ complex in monomeric and dimeric forms were built, and their redox behavior was analyzed together with their reactivity with peroxide. A set of 16 configurations of Cu-Aβ was studied and the configurations were classified into 3 groups: (A) configurations that evolve into a linearly bound and nonreactive Cu(I) coordination; (B) reactive configurations without large reorganization between the two Cu redox states; and (C) reactive configurations with an open structure in the Cu(I)-Aβ coordination, which have high water accessibility to Cu. All the structures that showed high reactivity with H2O2 (to form HO(•)) fall into class C. This means that within all the possible configurations, only some pools are able to produce efficiently the deleterious HO(•), while the other pools are more inert. The characteristics of highly reactive configurations consist of a N-Cu(I)-N coordination with an angle far from 180° and high water crowding at the open side. This allows the side-on entrance of H2O2 and its cleavage to form a hydroxyl radical. Interestingly, the reactive Cu(I)-Aβ states originated mostly from the dimeric starting models, in agreement with the higher reactivity of

  16. The deterioration of intermediate moisture foods

    NASA Technical Reports Server (NTRS)

    Labruza, T. P.

    1971-01-01

    Deteriorative reactions are low and food quality high if intermediate moisture content of a food is held at a water activity of 0.6 to 0.75. Information is of interest to food processing and packaging industry.

  17. Effect of a chemical modification on the hydrated adenosine intermediate produced by adenosine deaminase and a model reaction for a potential mechanism of action of 5-aminoimidazole ribonucleotide carboxylase.

    PubMed

    Groziak, M P; Huan, Z W; Ding, H; Meng, Z; Stevens, W C; Robinson, P D

    1997-10-10

    Using the hydrated adenosine intermediate (6R)-6-amino-1, 6-dihydro-6-hydroxy-9-(beta-D-ribofuranosyl)purine (2) produced by adenosine deaminase (ADA, EC 3.5.4.4) as a starting point, the active site probe and inhibitor platform 5-(formylamino)imidazole riboside (FAIRs, 4) was designed by removal of the-C6(OH)(NH2)-molecular fragment of 2 generated by the early events of the enzyme-catalyzed hydrolysis. FAIRs was synthesized directly from the sodium salt of 5-amino-1-(beta-D-ribofuranosyl)imidazole-4-carboxylic acid (CAIR) along a reaction sequence involving a tandem N-formylation/decarboxylation that may have a mechanistic connection to the Escherichia coli purE-catalyzed constitutional isomerization of N5-CAIR to CAIR. The physical and spectral properties of FAIRs were elucidated, its X-ray crystal and NMR solution structures were determined, and its interaction with ADA was investigated. Crystalline FAIRs exists solely as the Z-formamide rotamer and exhibits many of the same intramolecular hydrogen bonding events known to contribute to the association of Ado to ADA. In water and various organic solvents, however, FAIRs exists as NMR-distinct, slowly interconverting Z and E rotamers. This truncated enzymatic tetrahedral intermediate analog was determined to be a competitive inhibitor of ADA with an apparent Ki binding constant of 40 microM, a value quite close to that (33 microM) of the natural substrate's K(m). The actual species selected for binding by ADA, though, is likely the minor hydroxyimino prototropic form of Z-FAIRs possessing a far lower true Ki value. As the structural features of FAIRs appear well-suited to support its use as a template for constructing active site probes of both ADA and AIR carboxylases, a variety of carbohydrate-protected versions of FAIRs suitable for facile aglycon elaborations were synthesized. The N3-alkylation, N3-borane complexation, and C4-iodination of some of these were investigated in order to assess physicochemical

  18. Mechanism of HDS/HDN reactions

    SciTech Connect

    Mullins, D.R.; Lyman, P.F.

    1993-06-01

    One method for exploring the mechanisms involved in HDS/HDN reactions is to study the elementary reaction steps that occur for model systems using UHV surface science techniques. Our approach has been to examine reactions involving a prototypical organosulfur molecule, methanethiol, adsorbed on different clean and modified metal surfaces. In general, as the surface is heated, this molecule follows two principle reaction pathways on most transition metal surfaces. At low coverages, the molecule undergoes total decomposition producing adsorbed atomic sulfur and carbon and gaseous H{sub 2}. At higher coverages a competing pathway results in adsorbed sulfur and gaseous methane. In order to understand these reactions, the different chemical intermediates are identified, and the differences in reactivity for these intermediates are studied as a function of adsorbate coverage, surface composition and sample temperature. Several analytical techniques are employed in these experiments. Temperature programmed desorption, TPD, is used to identify the desorbed reaction products, their desorption temperature and the branching ratio as the system is modified. Auger electron spectroscopy, AES, is used to determine the amount of adsorbed atomic species that result from the reaction. The reaction intermediates are studied by high resolution soft x-ray photoelectron spectroscopy.

  19. Mechanism of HDS/HDN reactions

    SciTech Connect

    Mullins, D.R.; Lyman, P.F.

    1993-01-01

    One method for exploring the mechanisms involved in HDS/HDN reactions is to study the elementary reaction steps that occur for model systems using UHV surface science techniques. Our approach has been to examine reactions involving a prototypical organosulfur molecule, methanethiol, adsorbed on different clean and modified metal surfaces. In general, as the surface is heated, this molecule follows two principle reaction pathways on most transition metal surfaces. At low coverages, the molecule undergoes total decomposition producing adsorbed atomic sulfur and carbon and gaseous H[sub 2]. At higher coverages a competing pathway results in adsorbed sulfur and gaseous methane. In order to understand these reactions, the different chemical intermediates are identified, and the differences in reactivity for these intermediates are studied as a function of adsorbate coverage, surface composition and sample temperature. Several analytical techniques are employed in these experiments. Temperature programmed desorption, TPD, is used to identify the desorbed reaction products, their desorption temperature and the branching ratio as the system is modified. Auger electron spectroscopy, AES, is used to determine the amount of adsorbed atomic species that result from the reaction. The reaction intermediates are studied by high resolution soft x-ray photoelectron spectroscopy.

  20. The serum D-xylose test as a useful tool to identify malabsorption in rats with antigen specific gut inflammatory reaction

    PubMed Central

    Antunes, Danielle Mota Fontes; da Costa, Janilda Pacheco; Campos, Sylvia Maria Nicolau; Paschoal, Patrícia Olaya; Garrido, Valéria; Siqueira, Munique; Teixeira, Gerlinde Agate Platais Brasil; Cardoso, Gilberto Perez

    2009-01-01

    The inappropriate immune response to foods, such as peanut, wheat and milk may be the basis in the pathogenesis of enteropathies like coeliac and Crohn disease, which present small intestinal malabsorption. A number of recent studies have utilized d-xylose absorption as an investigative tool to study small intestinal function in a variety of clinical settings. Thus, the aim of this experimental study was to evaluate the intestinal absorption of d-xylose in an antigen-specific gut inflammatory reaction rat model. Animals of the experimental group were inoculated with peanut protein extract before their exposure to a challenge diet containing exclusively peanut seeds to induce the gut inflammatory reaction caused by peanut allergy. Our results show that systemic inoculation with peanut protein extract renders significantly higher antibody titres (5.085 ± 0.126 units) (P < 0.0001) than control rats (0.905 ± 0.053 units) and that the antibody titres correlate positively to an inflammatory alteration of the gut morphology (P < 0.0001). Animals pertaining to the experimental group showed an intestinal absorption of d-xylose lower than control rats (P < 0.0001). We also observed that d-xylose absorption correlates negatively with IgG titres and positively with morphometric parameters (Pearson correlation). In conclusion, the use of serum d-xylose test was useful to identify the presence of small intestinal malabsorption in our antigen specific gut inflammatory reaction rat model. PMID:19335552

  1. Ligand intermediates in metal-catalyzed reactions

    SciTech Connect

    Gladysz, J.A.

    1991-09-06

    This report consists of six sections, which cover pi/sigma equilibria in aldehyde and ketone complexes, abstraction of vinylic protons from alkene complexes, mechanism of rearrangement of alkylidene to alkene complexes, rearrangement of terminal acetylene to vinylidene complexes, synthesis and reactivity of lithiocarbide complexes, and new catalysts for the epimerization of secondary alcohols; carbon-hydrogen bond activation in alkoxide complexes. (WET)

  2. Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.

    PubMed

    Barabás, Orsolya; Németh, Veronika; Bodor, Andrea; Perczel, András; Rosta, Edina; Kele, Zoltán; Zagyva, Imre; Szabadka, Zoltán; Grolmusz, Vince I; Wilmanns, Matthias; Vértessy, Beáta G

    2013-12-01

    Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason-Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the α-phosphate site. Phosphorus-31 NMR spectroscopy ((31)P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue α,β-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme-product complex structure.

  3. Detection of the Sn(III) intermediate and the mechanism of the Sn(IV)/Sn(II) electroreduction reaction in bromide media by cyclic voltammetry and scanning electrochemical microscopy.

    PubMed

    Chang, Jinho; Bard, Allen J

    2014-01-08

    Fast-scan cyclic voltammetry (CV) and scanning electrochemical microscopy (SECM) were used to investigate the reduction of Sn(IV) as the hexabromo complex ion in a 2 M HBr-4 M NaBr medium. CV at scan rates to 100 V/s and SECM indicated the reaction pathway involves ligand-coupled electron transfer via an ECEC-DISP process: (1) one-electron reduction of Sn(IV)Br6(2-) to Sn(III)Br6(3-); (2) bromide dissociation of the reduced Sn(III)Br6(3-) to Sn(III)Br5(2-); (3) disproportionation of the reduced 2Sn(III)Br5(2-) to Sn(IV)Br5(-) and Sn(II)Br5(3-); (4) one-electron reduction of Sn(III)Br5(2-) to Sn(II)Br5(3-); (5) bromide dissociation from Sn(II)Br5 to Sn(II)Br4(2-). The intermediate Sn(III) species was confirmed by SECM(3-), where the Sn(III) generated at the Au tip was collected on a Au substrate in the tip generation/substrate collection mode when the distance between the tip and substrate was a few hundred nanometers.

  4. Eleven new heaviest isotopes of elements Z=105 to Z=117 identified among the products of {sup 249}Bk+{sup 48}Ca reactions

    SciTech Connect

    Oganessian, Yu. Ts.; Abdullin, F. Sh.; Dmitriev, S. N.; Itkis, M. G.; Lobanov, Yu. V.; Mezentsev, A. N.; Polyakov, A. N.; Sagaidak, R. N.; Shirokovsky, I. V.; Subbotin, V. G.; Sukhov, A. M.; Tsyganov, Yu. S.; Utyonkov, V. K.; Voinov, A. A.; Vostokin, G. K.; Bailey, P. D.; Benker, D. E.; Ezold, J. G.; Porter, C. E.; Riley, F. D.

    2011-05-15

    The heaviest isotopes of elements Z=117 to Z=105, {sup 294}117, {sup 293}117, {sup 290}115, {sup 289}115, {sup 286}113, {sup 285}113, {sup 282}Rg, {sup 281}Rg, {sup 278}Mt, {sup 274}Bh, and {sup 270}Db, were identified by means of the Dubna gas-filled recoil separator among the products of the {sup 249}Bk + {sup 48}Ca reaction. The details of the observed six decay chains, indicating the production and decay of isotopes {sup 293}117 and {sup 294}117, are presented and discussed. The decay energies and resulting half-lives of these new nuclei show a strong rise of stability with increasing neutron number, validating the concept of the island of enhanced stability for superheavy nuclei [Oganessian et al., Phys. Rev. Lett. 104, 142502 (2010)].

  5. Functionalization of the corrole ring: the role of isocorrole intermediates.

    PubMed

    Tortora, Luca; Nardis, Sara; Fronczek, Frank R; Smith, Kevin M; Paolesse, Roberto

    2011-04-14

    Bromination of 3-nitro-5,10,15-triarylcorrole selectively provides two regioisomers, depending on the reaction pathway. An isocorrole species is the key intermediate to drive the reaction towards the 2-Br-17-nitro regioisomer.

  6. Negative ion photoelectron spectra of ISO3, IS2O3, and IS2O4 intermediates formed in interfacial reactions of ozone and iodide/sulfite aqueous microdroplets

    SciTech Connect

    Qin, Zhengbo; Hou, Gao-Lei; Yang, Zheng; Valiev, Marat; Wang, Xue-Bin

    2016-12-07

    Three short-lived, anionic intermediates, ISO3, IS2O3, and IS2O4, are detected during reactions between ozone and aqueous iodine/sulfur oxides microdroplets. These species may play an important role in ozone-driven inorganic aerosol formation; however their chemical properties remain largely unknown. This is the issue addressed in this work using negative ion photoelectron spectroscopy (NIPES) and ab-initio modeling. The NIPE spectra reveal that all of the three anionic species are characterized by high adiabatic detachment energies (ADEs) - 4.62 ± 0.10, 4.52 ± 0.10, and 4.60 ± 0.10 eV for ISO3, IS2O3, and IS2O4, respectively. Vibrational progressions with frequencies assigned to the S–O symmetric stretching modes are also discernable in the ground state transition features. Density functional theory (DFT) calculations show the presence of several low-lying isomers involving different bonding scenarios. Further analysis based on high level CCSD(T) calculations reveal that the lowest energy structures are characterized by formation of I–S and S–S bonds and can be structurally viewed as SO3 linked with I, IS, and ISO for ISO3, IS2O3, and IS2O4, respectively. The calculated ADEs and vertical detachment energies (VDEs) are in excellent agreement with the experimental results, further supporting the identified minimum energy structures. The obtained intrinsic molecular properties of these anionic intermediates and neutral radicals should be useful to help understand their photochemical reactions in the atmosphere.

  7. Metamorphosis-like photochemical growth route for silver nanoprisms synthesis via the unrevealed key intermediates of nanorods and nanotrapezoids

    NASA Astrophysics Data System (ADS)

    Zhu, Yingming; Yang, Shaobo; Cai, Jinmeng; Yu, Yifu; Meng, Ming; Li, Xingfei

    2014-10-01

    Photochemical synthesis is a promising strategy for the control of both the size and shape of silver nanoprisms; however, the mechanism of nanoprism formation under irradiation still remains as a mystery. Intermediates, which often contain abundant information about the reaction process, are significant to the understanding of reaction mechanisms. Unfortunately, intermediates are usually hard to be acquired due to the fast reaction rate. Herein, we successfully slow down the conversion rate of the photochemical reactions by enlarging the solution volume and removing morphology-directing agent bis(p-sulfonatophe-nyl) phenylphosphine dihydrate dipotassium. Nanorods and nanotrapezoids were found to be the key intermediates for the photoinduced formation of silver nanoprisms with 100 nm edge length, especially the nanorods which have never identified as the intermediates for silver nanoprism formation. Characterization methods including time-dependent ultraviolet-visible spectroscopy, high resolution transmission electron microscopy (TEM and HRTEM), and selected area electron diffraction were employed to characterize these intermediates. Based upon the revealed evidences, a plausible metamorphosis-like photochemical growth route for the formation of Ag nanoprisms via the intermediates of nanorods and nanotrapezoid is proposed.

  8. Some Intermediate-Level Violin Concertos.

    ERIC Educational Resources Information Center

    Abramson, Michael

    1997-01-01

    Contends that many violin students attempt difficult concertos before they are technically or musically prepared. Identifies a variety of concertos at the intermediate and advanced intermediate-level for students to study and master before attempting the advanced works by Bach and Mozart. Includes concertos by Vivaldi, Leclair, Viotti, Haydn,…

  9. Data requirements for intermediate energy nuclear applications

    SciTech Connect

    Pearlstein, S.

    1990-01-01

    Several applications that include spallation neutron sources, space radiation effects, biomedical isotope production, accelerator shielding and radiation therapy make use of intermediate energy nuclear data extending to several GeV. The overlapping data needs of these applications are discussed in terms of what projectiles, targets and reactions are of interest. Included is a discussion of what is generally known about these data and what is needed to facilitate their use in intermediate energy applications. 40 refs., 2 figs., 2 tabs.

  10. Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds

    PubMed Central

    Alves, Vinicius M.; Muratov, Eugene; Fourches, Denis; Strickland, Judy; Kleinstreuer, Nicole; Andrade, Carolina H.; Tropsha, Alexander

    2015-01-01

    Repetitive exposure to a chemical agent can induce an immune reaction in inherently susceptible individuals that leads to skin sensitization. Although many chemicals have been reported as skin sensitizers, there have been very few rigorously validated QSAR models with defined applicability domains (AD) that were developed using a large group of chemically diverse compounds. In this study, we have aimed to compile, curate, and integrate the largest publicly available dataset related to chemically-induced skin sensitization, use this data to generate rigorously validated and QSAR models for skin sensitization, and employ these models as a virtual screening tool for identifying putative sensitizers among environmental chemicals. We followed best practices for model building and validation implemented with our predictive QSAR workflow using random forest modeling technique in combination with SiRMS and Dragon descriptors. The Correct Classification Rate (CCR) for QSAR models discriminating sensitizers from non-sensitizers were 71–88% when evaluated on several external validation sets, within a broad AD, with positive (for sensitizers) and negative (for non-sensitizers) predicted rates of 85% and 79% respectively. When compared to the skin sensitization module included in the OECD QSAR toolbox as well as to the skin sensitization model in publicly available VEGA software, our models showed a significantly higher prediction accuracy for the same sets of external compounds as evaluated by Positive Predicted Rate, Negative Predicted Rate, and CCR. These models were applied to identify putative chemical hazards in the ScoreCard database of possible skin or sense organ toxicants as primary candidates for experimental validation. PMID:25560674

  11. Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds

    SciTech Connect

    Alves, Vinicius M.; Muratov, Eugene; Fourches, Denis; Strickland, Judy; Kleinstreuer, Nicole; Tropsha, Alexander

    2015-04-15

    Repetitive exposure to a chemical agent can induce an immune reaction in inherently susceptible individuals that leads to skin sensitization. Although many chemicals have been reported as skin sensitizers, there have been very few rigorously validated QSAR models with defined applicability domains (AD) that were developed using a large group of chemically diverse compounds. In this study, we have aimed to compile, curate, and integrate the largest publicly available dataset related to chemically-induced skin sensitization, use this data to generate rigorously validated and QSAR models for skin sensitization, and employ these models as a virtual screening tool for identifying putative sensitizers among environmental chemicals. We followed best practices for model building and validation implemented with our predictive QSAR workflow using Random Forest modeling technique in combination with SiRMS and Dragon descriptors. The Correct Classification Rate (CCR) for QSAR models discriminating sensitizers from non-sensitizers was 71–88% when evaluated on several external validation sets, within a broad AD, with positive (for sensitizers) and negative (for non-sensitizers) predicted rates of 85% and 79% respectively. When compared to the skin sensitization module included in the OECD QSAR Toolbox as well as to the skin sensitization model in publicly available VEGA software, our models showed a significantly higher prediction accuracy for the same sets of external compounds as evaluated by Positive Predicted Rate, Negative Predicted Rate, and CCR. These models were applied to identify putative chemical hazards in the Scorecard database of possible skin or sense organ toxicants as primary candidates for experimental validation. - Highlights: • It was compiled the largest publicly-available skin sensitization dataset. • Predictive QSAR models were developed for skin sensitization. • Developed models have higher prediction accuracy than OECD QSAR Toolbox. • Putative

  12. Degradation of methyl bromide and methyl chloride in soil microcosms: Use of stable C isotope fractionation and stable isotope probing to identify reactions and the responsible microorganisms

    USGS Publications Warehouse

    Miller, L.G.; Warner, K.L.; Baesman, S.M.; Oremland, R.S.; McDonald, I.R.; Radajewski, S.; Murrell, J.C.

    2004-01-01

    Bacteria in soil microcosm experiments oxidized elevated levels of methyl chloride (MeCl) and methyl bromide (MeBr), the former compound more rapidly than the latter. MeBr was also removed by chemical reactions while MeCl was not. Chemical degradation dominated the early removal of MeBr and accounted for more than half of its total loss. Fractionation of stable carbon isotopes during chemical degradation of MeBr resulted in a kinetic isotope effect (KIE) of 59 ?? 7???. Soil bacterial oxidation dominated the later removal of MeBr and MeCl and was characterized by different KIEs for each compound. The KIE for MeBr oxidation was 69 ?? 9??? and the KIE for MeCl oxidation was 49 ?? 3???. Stable isotope probing revealed that different populations of soil bacteria assimilated added 13C-labeled MeBr and MeCl. The identity of the active MeBr and MeCl degrading bacteria in soil was determined by analysis of 16S rRNA gene sequences amplified from 13C-DNA fractions, which identified a number of sequences from organisms not previously thought to be involved in methyl halide degradation. These included Burkholderia , the major clone type in the 13C-MeBr fraction, and Rhodobacter, Lysobacter and Nocardioides the major clone types in the 13C-MeCl fraction. None of the 16S rRNA gene sequences for methyl halide oxidizing bacteria currently in culture (including Aminobacter strain IMB-1 isolated from fumigated soil) were identified. Functional gene clone types closely related to Aminobacter spp. were identified in libraries containing the sequences for the cmuA gene, which codes for the enzyme known to catalyze the initial step in the oxidation of MeBr and MeCl. The cmuA gene was limited to members of the alpha-Proteobacteria whereas the greater diversity demonstrated by the 16S rRNA gene may indicate that other enzymes catalyze methyl halide oxidation in different groups of bacteria. Copyright ?? 2004 Elsevier Ltd.

  13. Water-Shale interactions in bench-top and high pressure/high temperature autoclave experiments: Identifying geochemical reaction controlling flow back water chemistry

    NASA Astrophysics Data System (ADS)

    Molnar, I. L.; O'Carroll, D. M.; Willson, C. S.; Gerhard, J.

    2011-12-01

    increase in alkalinity during the experiment. Molar comparisons between Na-Cl and Ca-SO4 suggest Ca is preferentially removed from solution and Na is added to solution through interactions with clay minerals. Cation exchange and desorption during clay hydration likely has a secondary effect on the observed geochemical trend. Ca is sorbed and Na is released preferentially resulting in a Ca depletion seen on the Ca vs. SO4 plot and a Na excess seen in the Na vs. Cl plot. Although this study does not consider mixing of HF-water with formation brines, the identified water-rock reactions may provide insights into observed flow-back water chemistry.

  14. Water-Shale interactions in bench-top and high pressure/high temperature autoclave experiments: Identifying geochemical reaction controlling flow back water chemistry

    NASA Astrophysics Data System (ADS)

    Mickler, P. J.; Lu, J.; Nicot, J.

    2013-12-01

    increase in alkalinity during the experiment. Molar comparisons between Na-Cl and Ca-SO4 suggest Ca is preferentially removed from solution and Na is added to solution through interactions with clay minerals. Cation exchange and desorption during clay hydration likely has a secondary effect on the observed geochemical trend. Ca is sorbed and Na is released preferentially resulting in a Ca depletion seen on the Ca vs. SO4 plot and a Na excess seen in the Na vs. Cl plot. Although this study does not consider mixing of HF-water with formation brines, the identified water-rock reactions may provide insights into observed flow-back water chemistry.

  15. Intermediate-energy nuclear chemistry workshop

    SciTech Connect

    Butler, G.W.; Giesler, G.C.; Liu, L.C.; Dropesky, B.J.; Knight, J.D.; Lucero, F.; Orth, C.J.

    1981-05-01

    This report contains the proceedings of the LAMPF Intermediate-Energy Nuclear Chemistry Workshop held in Los Alamos, New Mexico, June 23-27, 1980. The first two days of the Workshop were devoted to invited review talks highlighting current experimental and theoretical research activities in intermediate-energy nuclear chemistry and physics. Working panels representing major topic areas carried out indepth appraisals of present research and formulated recommendations for future research directions. The major topic areas were Pion-Nucleus Reactions, Nucleon-Nucleus Reactions and Nuclei Far from Stability, Mesonic Atoms, Exotic Interactions, New Theoretical Approaches, and New Experimental Techniques and New Nuclear Chemistry Facilities.

  16. A comparative study of nitrite reduction by synthetic and biogenic Fe(II-III) hydroxysalts green rusts: Evidence for hydroxyl-nitrite green rust formation as an intermediate reaction product.

    NASA Astrophysics Data System (ADS)

    Ona-Nguema, G.; Guerbois, D.; Morin, G.; Zhang, Y.; Noel, V.; Brest, J.

    2013-12-01

    -GR(Cl) led to the reduction of nitrite ions to ammonium, and that the production of ammonium depended on their Fe(II) content. XRD patterns indicated that both synthetic green rusts were fully oxidized into magnetite during the reaction with nitrite. For biogenic green rusts, the study revealed that both bio-GR(CO3)F and bio-GR(CO3)L were capable of reducing nitrite ions without ammonium production, suggesting the conversion of nitrite ions to nitrogen gas. Moreover, we provided evidence for the first time that the interactions of bio-GR(CO3)F with nitrite led to the formation of an hydroxy-nitrite green rust as a result of the incorporation of nitrite in the interlayer region of bio-GR(CO3)F; such an intercalation of nitrite ions was not observed in experiments with bio-GR(CO3)L. XRD analysis indicated that GR(NO2) was formed as an intermediate reaction product prior to the fully oxidation of GR to ferric oxyhydroxides. [1] Philips S., Laanbroek H. J. and Verstraete W. (2002). Rev. Environ. Sci. Biotechnol. 1, 115-141.

  17. Phase 2 study of (99m)Tc-trofolastat SPECT/CT to identify and localize prostate cancer in intermediate- and high-risk patients undergoing radical prostatectomy and extended pelvic lymph node dissection.

    PubMed

    Goffin, Karolien E; Joniau, Steven; Tenke, Peter; Slawin, Kevin; Klein, Eric A; Stambler, Nancy; Strack, Thomas; Babich, John; Armor, Thomas; Wong, Vivien

    2017-03-16

    Rationale:(99m)Tc-trofolastat ((99m)Tc-MIP-1404), a small-molecule inhibitor of prostate-specific membrane antigen (PSMA), shows high potential to detect prostate cancer (PCa) non-invasively using single-photon-emission-computed-tomography (SPECT). We therefore wanted to assess the performance of (99m)Tc-trofolastat SPECT/CT in a phase 2 multi-center, multi-reader prospective study in patients with intermediate- and high-grade PCa, prior to radical prostatectomy and extended pelvic lymph node dissection, with histopathology as gold standard. Methods: 105 PCa patients with an increased risk of lymph node involvement (LNI) received a pelvic (99m)Tc-trofolastat SPECT/CT prior to radical prostatectomy with extended pelvic lymph node dissection. Sensitivity of (99m)Tc-trofolastat for detection of PCa on a patient- and lobe-basis, using visual and semi-quantitative (tumor-to-background ratio, TBR) scores and of LNI was evaluated as well as correlation of uptake within the gland to Gleason scores (GS) and assessment of the predictive potential of (99m)Tc-trofolastat-uptake for LNI. Results: PCa was detected in 98 patients (94%) with acceptable variability between readers. There was a significantly higher visual score and TBR in positive lobes compared to tumor-negative lobes. ROC analysis showed that visual scores more accurately discriminated lobes with GS ≤3+3 from ≥3+4, while TBRs discriminated high-grade disease from normal lobes better. Visual scores and TBRs correlated significantly with GS. (99m)Tc-trofolastat SPECT/CT detected LNI with sensitivity of 50%, and specificity of 87% and TBR values significantly predicted LNI with a sensitivity of 90%. Conclusion:(99m)Tc-trofolastat SPECT/CT detects PCa with high sensitivity in patients with intermediate- and high-risk PCa compared to histology. It has potential to be used as surrogate marker for Gleason scores and predict LNI.

  18. Variant translocation partners of the anaplastic lymphoma kinase (ALK) gene in two cases of anaplastic large cell lymphoma, identified by inverse cDNA polymerase chain reaction.

    PubMed

    Takeoka, Kayo; Okumura, Atsuko; Honjo, Gen; Ohno, Hitoshi

    2014-01-01

    In anaplastic large cell lymphoma (ALCL), the anaplastic lymphoma kinase (ALK) gene is rearranged with diverse partners due to variant translocations/inversions. Case 1 was a 39-year-old man who developed multiple tumors in the mediastinum, psoas muscle, lung, and lymph nodes. A biopsy specimen of the inguinal node was effaced by large tumor cells expressing CD30, epithelial membrane antigen, and cytoplasmic ALK, which led to a diagnosis of ALK(+) ALCL. Case 2 was a 51-year-old man who was initially diagnosed with undifferentiated carcinoma. He developed multiple skin tumors eight years after his initial presentation, and was finally diagnosed with ALK(+) ALCL. He died of therapy-related acute myeloid leukemia. G-banding and fluorescence in situ hybridization using an ALK break-apart probe revealed the rearrangement of ALK and suggested variant translocation in both cases. We applied an inverse cDNA polymerase chain reaction (PCR) strategy to identify the partner of ALK. Nucleotide sequencing of the PCR products and a database search revealed that the sequences of ATIC in case 1 and TRAF1 in case 2 appeared to follow those of ALK. We subsequently confirmed ATIC-ALK and TRAF1-ALK fusions by reverse transcriptase PCR and nucleotide sequencing. We successfully determined the partner gene of ALK in two cases of ALK(+) ALCL. ATIC is the second most common partner of variant ALK rearrangements, while the TRAF1-ALK fusion gene was first reported in 2013, and this is the second reported case of ALK(+) ALCL carrying TRAF1-ALK.

  19. A common intermediate for N2 formation in enzymes and zeolites: side-on Cu-nitrosyl complexes

    SciTech Connect

    Kwak, Ja Hun; Lee, Jong H.; Burton, Sarah D.; Lipton, Andrew S.; Peden, Charles HF; Szanyi, Janos

    2013-09-16

    Understanding the mechanisms of catalytic processes requires the identification of reaction centers and key intermediates, both of which are often achieved by the use of spectroscopic characterization tools. Due to the heterogeneity of active centers in heterogeneous catalysts, it is frequently difficult to identify the specific sites that are responsible for the overall activity. Furthermore, the simultaneous presence of a large number of surface species on the catalyst surface often poses a great challenge for the unambiguous determination of the relevant species in the reaction mechanism. In contrast, enzymes possess catalytically active centers with precisely defined coordination environments that are only able to accommodate intermediates relevant to the specific catalytic process. Here we show that side-on Cu+-NO+ complexes characterized by high magnetic field solid state magic angle spinning nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR) spectroscopies are the key intermediates in the selective catalytic reduction of NO over Cu-SSZ-13 zeolite catalysts. Analogous intermediates have been observed and characterized in nitrite reductase enzymes, and shown to be the critical intermediates in the formation of N2 for anaerobic ammonium oxidation reactions.[1] The identification of this key reaction intermediate, combined with the results of our prior kinetic studies, allows us to propose a new reaction mechanism for the selective catalytic reduction of NO with NH3 under oxygen-rich environments over Cu-SSZ-13 zeolites, a key reaction in automotive emission control. The authors acknowledge the US Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy/Vehicle Technologies Program for the support of this work. The research described in this paper was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental

  20. Pulsed-EPR evidence of a manganese(II) hydroxycarbonyl intermediate in the electrocatalytic reduction of carbon dioxide by a manganese bipyridyl derivative.

    PubMed

    Bourrez, Marc; Orio, Maylis; Molton, Florian; Vezin, Hervé; Duboc, Carole; Deronzier, Alain; Chardon-Noblat, Sylvie

    2014-01-03

    A key intermediate in the electroconversion of carbon dioxide to carbon monoxide, catalyzed by a manganese tris(carbonyl) complex, is characterized. Different catalytic pathways and their potential reaction mechanisms are investigated using a large range of experimental and computational techniques. Sophisticated spectroscopic methods including UV/Vis absorption and pulsed-EPR techniques (2P-ESEEM and HYSCORE) were combined together with DFT calculations to successfully identify a key intermediate in the catalytic cycle of CO2 reduction. The results directly show the formation of a metal-carboxylic acid-CO2 adduct after oxidative addition of CO2 and H(+) to a Mn(0) carbonyl dimer, an unexpected intermediate.

  1. The aromatic ene reaction

    PubMed Central

    Niu, Dawen; Hoye, Thomas R.

    2014-01-01

    The ene reaction is a pericyclic process in which an alkene having an allylic hydrogen atom (the ene donor) reacts with a second unsaturated species (the enophile) to form a new product with a transposed π-bond. The aromatic ene reaction, in which the alkene component is embedded in an aromatic ring, has only been reported in a few (four) instances and has proceeded in low yield (≤6%). Here we show efficient aromatic ene reactions in which a thermally generated aryne engages a pendant m-alkylarene substituent to produce a dearomatized isotoluene, itself another versatile but rare reactive intermediate. Our experiments were guided by computational studies that revealed structural features conducive to the aromatic ene process. We proceeded to identify a cascade comprising three reactions: (i) hexadehydro-Diels-Alder (for aryne generation), (ii) intramolecular aromatic ene, and (iii) bimolecular Alder ene. The power of this cascade is evident from the structural complexity of the final products, the considerable scope, and the overall efficiency of these multi-stage, reagent- and byproduct-free, single-pot transformations. PMID:24345944

  2. Separation of intermediates of iron-catalyzed dopamine oxidation reactions using reversed-phase ion-pairing chromatography coupled in tandem with UV-visible and ESI-MS detections.

    PubMed

    Zhang, Lin; Yagnik, Gargey; Jiang, Dianlu; Shi, Shuyun; Chang, Peter; Zhou, Feimeng

    2012-12-12

    Reversed-phase ion-pairing chromatography (RP-IPC) is coupled on-line with electrospray ionization-mass spectrometry (ESI-MS) through an interface comprising a four-way switch valve and an anion exchange column. Regeneration of the anion exchange column can be accomplished on-line by switching the four-way switch valve to interconnect the column to a regeneration solution. Positioning the anion exchange column between the RP-IPC and ESI-MS instruments allows the ion-pairing reagent (IPR) sodium octane sulfonate to be removed. The IPC-ESI-MS method enabled us to separate and detect four intermediates of the Fe(III)-catalyzed dopamine oxidation. In particular, 6-hydroxydopamine, which is short-lived and highly neurotoxic, was detected and quantified. Together with the separation of other intermediates, gaining insight into the mechanism and kinetics of the Fe(III)-catalyzed dopamine oxidation becomes possible.

  3. Branching of keratin intermediate filaments.

    PubMed

    Nafeey, Soufi; Martin, Ines; Felder, Tatiana; Walther, Paul; Felder, Edward

    2016-06-01

    Keratin intermediate filaments (IFs) are crucial to maintain mechanical stability in epithelial cells. Since little is known about the network architecture that provides this stiffness and especially about branching properties of filaments, we addressed this question with different electron microscopic (EM) methods. Using EM tomography of high pressure frozen keratinocytes, we investigated the course of several filaments in a branching of a filament bundle. Moreover we found several putative bifurcations in individual filaments. To verify our observation we also visualized the keratin network in detergent extracted keratinocytes with scanning EM. Here bifurcations of individual filaments could unambiguously be identified additionally to bundle branchings. Interestingly, identical filament bifurcations were also found in purified keratin 8/18 filaments expressed in Escherichia coli which were reassembled in vitro. This excludes that an accessory protein contributes to the branch formation. Measurements of the filament cross sectional areas showed various ratios between the three bifurcation arms. This demonstrates that intermediate filament furcation is very different from actin furcation where an entire new filament is attached to an existing filament. Instead, the architecture of intermediate filament bifurcations is less predetermined and hence consistent with the general concept of IF formation.

  4. The physical chemistry of Criegee intermediates in the gas phase

    DOE PAGES

    Osborn, David L.; Taatjes, Craig A.

    2015-07-24

    Here, carbonyl oxides, also known as Criegee intermediates, are key intermediates in both gas phase ozonolysis of unsaturated hydrocarbons in the troposphere and solution phase organic synthesis via ozonolysis. Although the study of Criegee intermediates in both arenas has a long history, direct studies in the gas phase have only recently become possible through new methods of generating stabilised Criegee intermediates in sufficient quantities. This advance has catalysed a large number of new experimental and theoretical investigations of Criegee intermediate chemistry. In this article we review the physical chemistry of Criegee intermediates, focusing on their molecular structure, spectroscopy, unimolecular andmore » bimolecular reactions. These recent results have overturned conclusions from some previous studies, while confirming others, and have clarified areas of investigation that will be critical targets for future studies. In addition to expanding our fundamental understanding of Criegee intermediates, the rapidly expanding knowledge base will support increasingly predictive models of their impacts on society.« less

  5. The physical chemistry of Criegee intermediates in the gas phase

    SciTech Connect

    Osborn, David L.; Taatjes, Craig A.

    2015-07-24

    Here, carbonyl oxides, also known as Criegee intermediates, are key intermediates in both gas phase ozonolysis of unsaturated hydrocarbons in the troposphere and solution phase organic synthesis via ozonolysis. Although the study of Criegee intermediates in both arenas has a long history, direct studies in the gas phase have only recently become possible through new methods of generating stabilised Criegee intermediates in sufficient quantities. This advance has catalysed a large number of new experimental and theoretical investigations of Criegee intermediate chemistry. In this article we review the physical chemistry of Criegee intermediates, focusing on their molecular structure, spectroscopy, unimolecular and bimolecular reactions. These recent results have overturned conclusions from some previous studies, while confirming others, and have clarified areas of investigation that will be critical targets for future studies. In addition to expanding our fundamental understanding of Criegee intermediates, the rapidly expanding knowledge base will support increasingly predictive models of their impacts on society.

  6. Discovery-Oriented Approach To Organic Synthesis: Tandem Aldol Condensation-Michael Addition Reactions. Identifying Diastereotopic Hydrogens in an Achiral Molecule by NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wachter-Jurcsak, Nanette; Reddin, Kendra

    2001-09-01

    We have found a beautiful example of anisochrony of diastereotopic acyclic methylene hydrogens in a symmetric diketone, synthesized by techniques traditionally performed in an introductory organic laboratory course. Synthesis of the diketone is high-yielding and easy to carry out, and the products can be directly isolated with a good degree of purity with no need of further manipulation. The reaction can be accomplished in a single laboratory session.

  7. A unified intermediate and mechanism for soot combustion on potassium-supported oxides

    PubMed Central

    Li, Qian; Wang, Xiao; Xin, Ying; Zhang, Zhaoliang; Zhang, Yexin; Hao, Ce; Meng, Ming; Zheng, Lirong; Zheng, Lei

    2014-01-01

    The soot combustion mechanism over potassium-supported oxides (MgO, CeO2 and ZrO2) was studied to clarify the active sites and discover unified reaction intermediates in this typical gas-solid-solid catalytic reaction. The catalytically active sites were identified as free K+ rather than K2CO3, which can activate gaseous oxygen. The active oxygen spills over to soot and forms a common intermediate, ketene, before it was further oxidized into the end product CO2. The existence of ketene species was confirmed by density functional theory (DFT) calculations. The oxygen spillover mechanism is proposed, which is explained as an electron transfer from soot to gaseous oxygen through the active K+ sites. The latter mechanism is confirmed for the first time since it was put forward in 1950, not only by ultraviolet photoelectron spectroscopy (UPS) results but also by semi-empirical theoretical calculations. PMID:24740213

  8. Laser Cavity Ringdown Studies of Peroxy Radical Intermediates in the Oxidation of Volatile Organic Compounds

    NASA Astrophysics Data System (ADS)

    Okumura, M.; Takematsu, K.; Eddingsaas, N. C.; Dodson, L. G.; Voss, M.; Nishimura, A.

    2012-12-01

    The detection of reactive intermediates in laboratory kinetics experiments provides a powerful method for determining reaction pathways in the oxidation of Volatile Organic Compounds (VOCs). Many Biogenic VOCs (BVOCs) such as isoprene are unsaturated, and their oxidation can proceed through initial addition of an OH, Cl or NO3 radicals, followed by addition of O2 to form peroxy radicals. We have used cavity ringdown spectroscopy to directly detect substituted peroxy radical intermediates formed in the initial oxidation of a number of unsaturated species, including ethene, propene, butene, butadiene, MBO-232, and MPAN. These experiments have allowed us to identify specific pathways in the oxidation of the parent unsaturated VOC species and to begin studying the rates of subsequent peroxy radical reactions. These studies shed light on the possible pathways for OVOC formation and likely impact on secondary aerosol formation.

  9. A unified intermediate and mechanism for soot combustion on potassium-supported oxides

    NASA Astrophysics Data System (ADS)

    Li, Qian; Wang, Xiao; Xin, Ying; Zhang, Zhaoliang; Zhang, Yexin; Hao, Ce; Meng, Ming; Zheng, Lirong; Zheng, Lei

    2014-04-01

    The soot combustion mechanism over potassium-supported oxides (MgO, CeO2 and ZrO2) was studied to clarify the active sites and discover unified reaction intermediates in this typical gas-solid-solid catalytic reaction. The catalytically active sites were identified as free K+ rather than K2CO3, which can activate gaseous oxygen. The active oxygen spills over to soot and forms a common intermediate, ketene, before it was further oxidized into the end product CO2. The existence of ketene species was confirmed by density functional theory (DFT) calculations. The oxygen spillover mechanism is proposed, which is explained as an electron transfer from soot to gaseous oxygen through the active K+ sites. The latter mechanism is confirmed for the first time since it was put forward in 1950, not only by ultraviolet photoelectron spectroscopy (UPS) results but also by semi-empirical theoretical calculations.

  10. A unified intermediate and mechanism for soot combustion on potassium-supported oxides.

    PubMed

    Li, Qian; Wang, Xiao; Xin, Ying; Zhang, Zhaoliang; Zhang, Yexin; Hao, Ce; Meng, Ming; Zheng, Lirong; Zheng, Lei

    2014-04-17

    The soot combustion mechanism over potassium-supported oxides (MgO, CeO2 and ZrO2) was studied to clarify the active sites and discover unified reaction intermediates in this typical gas-solid-solid catalytic reaction. The catalytically active sites were identified as free K(+) rather than K2CO3, which can activate gaseous oxygen. The active oxygen spills over to soot and forms a common intermediate, ketene, before it was further oxidized into the end product CO2. The existence of ketene species was confirmed by density functional theory (DFT) calculations. The oxygen spillover mechanism is proposed, which is explained as an electron transfer from soot to gaseous oxygen through the active K(+) sites. The latter mechanism is confirmed for the first time since it was put forward in 1950, not only by ultraviolet photoelectron spectroscopy (UPS) results but also by semi-empirical theoretical calculations.

  11. Intermediates and kinetics for phenol gasification in supercritical water.

    PubMed

    Huelsman, Chad M; Savage, Phillip E

    2012-02-28

    We processed phenol with supercritical water in a series of experiments, which systematically varied the temperature, water density, reactant concentration, and reaction time. Both the gas and liquid phases were analyzed post-reaction using gas chromatographic techniques, which identified and quantified the reaction intermediates and products, including H(2), CO, CH(4), and CO(2) in the gas phase and twenty different compounds--mainly polycyclic aromatic hydrocarbons--in the liquid phase. Many of these liquid phase compounds were identified for the first time and could pose environmental risks. Higher temperatures promoted gasification and resulted in a product gas rich in H(2) and CH(4) (33% and 29%, respectively, at 700 °C), but char yields increased as well. We implicated dibenzofuran and other identified phenolic dimers as precursor molecules for char formation pathways, which can be driven by free radical polymerization at high temperatures. Examination of the trends in conversion as a function of initial water and phenol concentrations revealed competing effects, and these informed the kinetic modeling of phenol disappearance. Two different reaction pathways emerged from the kinetic modeling: one in which rate ∝ [phenol](1.73)[water](-16.60) and the other in which rate ∝ [phenol](0.92)[water](1.39). These pathways may correspond to pyrolysis, which dominates when there is abundant phenol and little water, and hydrothermal reactions, which dominate in excess water. This result confirms that supercritical water gasification of phenol does not simply follow first-order kinetics, as previous efforts to model phenol disappearance had assumed.

  12. MATERIALS FOR INTERMEDIATE TELUGU.

    ERIC Educational Resources Information Center

    KELLEY, GERALD B.

    ONE OF THE FOUR DRAVIDIAN LANGUAGES RECOGNIZED BY THE INDIAN CONSTITUTION OF 1950 AS OFFICIAL LANGUAGES OF THE COUNTRY, TELUGU IS SPOKEN BY 42 MILLION PEOPLE IN ANDHRA PRADESH. THESE INSTRUCTIONAL MATERIALS ARE DESIGNED FOR THE INTERMEDIATE STUDENT OF TELUGU AND ARE DIVIDED INTO NEWSPAPER READINGS AND DIALOGUES OF EVERYDAY CONVERSATION. SUBJECTS…

  13. Intermediate Pashto. Textbook.

    ERIC Educational Resources Information Center

    Tegey, Habibullah; Robson, Barbara

    The textbook for intermediate level Pashto instruction consists of 14 units (15-28) on a variety of cultural topics and linguistic structures. Cultural topics include engagement and marriage, children's education, agriculture and related subjects, the family, Pashtun history, genealogies of major Pashtun tribes, the Pashtun code of behavior,…

  14. Sara Intermediate Course.

    ERIC Educational Resources Information Center

    Thayer, James E.; Maraby, Julien

    This volume consists of an intermediate course in Sara, a language of the Chad Republic of Africa. It is designed for native speakers of English and includes forty reading selections in Sara and an English translation of each selection. The readings are followed by a corresponding set of dialogues in Sara, accompanied by an English translation.…

  15. SPACE: Intermediate Level Modules.

    ERIC Educational Resources Information Center

    Indiana State Dept. of Education, Indianapolis. Center for School Improvement and Performance.

    These modules were developed to assist teachers at the intermediate level to move away from extensive skill practice and toward more meaningful interdisciplinary learning. This packet, to be used by teachers in the summer Extended Learning Program, provides detailed thematic lesson plans matched to the Indiana Curriculum Proficiency Guide. The…

  16. Hispanic American Heritage, Intermediate.

    ERIC Educational Resources Information Center

    Shepherd, Mike

    This resource book features the cultural heritage of Hispanics living within the United States and includes ideas, materials, and activities to be used with students in the intermediate grades and middle school. This book explores the definition of the term "Hispanic Americans" and suggests a multilayered population with a variety of cultural…

  17. Criegee intermediates in the indoor environment. New insights

    DOE PAGES

    Shallcross, D. E.; Taatjes, C. A.; Percival, C. J.

    2014-03-25

    Criegee intermediates are formed in the ozonolysis of alkenes and play an important role in indoor chemistry, notably as a source of OH radicals. Recent studies have shown that these Criegee intermediates react very quickly with NO2, SO2, and carbonyls, and in this study, steady-state calculations are used to inspect the potential impact of these data on indoor chemistry. It is shown that these reactions could accelerate NO3 formation and SO2 removal in the indoor environment significantly. In addition, reaction between Criegee intermediates and halogenated carbonyls could provide a significant loss process indoors, where currently one does not exist.

  18. The Intermediate Neutrino Program

    SciTech Connect

    Adams, C.; et al.

    2015-03-23

    The US neutrino community gathered at the Workshop on the Intermediate Neutrino Program (WINP) at Brookhaven National Laboratory February 4-6, 2015 to explore opportunities in neutrino physics over the next five to ten years. Scientists from particle, astroparticle and nuclear physics participated in the workshop. The workshop examined promising opportunities for neutrino physics in the intermediate term, including possible new small to mid-scale experiments, US contributions to large experiments, upgrades to existing experiments, R&D plans and theory. The workshop was organized into two sets of parallel working group sessions, divided by physics topics and technology. Physics working groups covered topics on Sterile Neutrinos, Neutrino Mixing, Neutrino Interactions, Neutrino Properties and Astrophysical Neutrinos. Technology sessions were organized into Theory, Short-Baseline Accelerator Neutrinos, Reactor Neutrinos, Detector R&D and Source, Cyclotron and Meson Decay at Rest sessions.This report summarizes discussion and conclusions from the workshop.

  19. Intermediate water recovery system

    NASA Technical Reports Server (NTRS)

    Deckman, G.; Anderson, A. R. (Editor)

    1973-01-01

    A water recovery system for collecting, storing, and processing urine, wash water, and humidity condensates from a crew of three aboard a spacecraft is described. The results of a 30-day test performed on a breadboard system are presented. The intermediate water recovery system produced clear, sterile, water with a 96.4 percent recovery rate from the processed urine. Recommendations for improving the system are included.

  20. Modeling DNA Replication Intermediates

    SciTech Connect

    Broyde, S.; Roy, D.; Shapiro, R.

    1997-06-01

    While there is now available a great deal of information on double stranded DNA from X-ray crystallography, high resolution NMR and computer modeling, very little is known about structures that are representative of the DNA core of replication intermediates. DNA replication occurs at a single strand/double strand junction and bulged out intermediates near the junction can lead to frameshift mutations. The single stranded domains are particularly challenging. Our interest is focused on strategies for modeling the DNA of these types of replication intermediates. Modeling such structures presents special problems in addressing the multiple minimum problem and in treating the electrostatic component of the force field. We are testing a number of search strategies for locating low energy structures of these types and we are also investigating two different distance dependent dielectric functions in the coulombic term of the force field. We are studying both unmodified DNA and DNA damaged by aromatic amines, carcinogens present in the environment in tobacco smoke, barbecued meats and automobile exhaust. The nature of the structure adopted by the carcinogen modified DNA at the replication fork plays a key role in determining whether the carcinogen will cause a mutation during replication that can initiate the carcinogenic process. In the present work results are presented for unmodified DNA.

  1. Substrate Activation by Iron Superoxo Intermediates

    PubMed Central

    van der Donk, Wilfred A.; Krebs, Carsten; Bollinger, J. Martin

    2010-01-01

    A growing number of non-heme-iron oxygenases and oxidases catalyze reactions for which the well-established mechanistic paradigm involving a single C-H-bond cleaving intermediate of the Fe(IV)-oxo (ferryl) type [1] is insufficient to explain the chemistry. It is becoming clear that, in several of these cases, Fe(III)-superoxide complexes formed by simple addition of O2 to the reduced [Fe(II)] cofactor initiate substrate oxidation by abstracting hydrogen [2]. This substrate-oxidizing entry route into high-valent-iron intermediates makes possible an array of complex and elegant oxidation reactions without consumption of valuable reducing equivalents. Examples of this novel mechanistic strategy are discussed with the goal of bringing forth unifying principles. PMID:20951572

  2. Radicals: Reactive Intermediates with Translational Potential

    PubMed Central

    2016-01-01

    This Perspective illustrates the defining characteristics of free radical chemistry, beginning with its rich and storied history. Studies from our laboratory are discussed along with recent developments emanating from others in this burgeoning area. The practicality and chemoselectivity of radical reactions enable rapid access to molecules of relevance to drug discovery, agrochemistry, material science, and other disciplines. Thus, these reactive intermediates possess inherent translational potential, as they can be widely used to expedite scientific endeavors for the betterment of humankind. PMID:27631602

  3. Identifying the major bacteria causing intramammary infections in individual milk samples of sheep and goats using traditional bacteria culturing and real-time polymerase chain reaction.

    PubMed

    Rovai, M; Caja, G; Salama, A A K; Jubert, A; Lázaro, B; Lázaro, M; Leitner, G

    2014-09-01

    Use of DNA-based methods, such as real-time PCR, has increased the sensitivity and shortened the time for bacterial identification, compared with traditional bacteriology; however, results should be interpreted carefully because a positive PCR result does not necessarily mean that an infection exists. One hundred eight lactating dairy ewes (56 Manchega and 52 Lacaune) and 24 Murciano-Granadina dairy goats were used for identifying the main bacteria causing intramammary infections (IMI) using traditional bacterial culturing and real-time PCR and their effects on milk performance. Udder-half milk samples were taken for bacterial culturing and somatic cell count (SCC) 3 times throughout lactation. Intramammary infections were assessed based on bacteria isolated in ≥2 samplings accompanied by increased SCC. Prevalence of subclinical IMI was 42.9% in Manchega and 50.0% in Lacaune ewes and 41.7% in goats, with the estimated milk yield loss being 13.1, 17.9, and 18.0%, respectively. According to bacteriology results, 87% of the identified single bacteria species (with more than 3 colonies/plate) or culture-negative growth were identical throughout samplings, which agreed 98.9% with the PCR results. Nevertheless, the study emphasized that 1 sampling may not be sufficient to determine IMI and, therefore, other inflammatory responses such as increased SCC should be monitored to identify true infections. Moreover, when PCR methodology is used, aseptic and precise milk sampling procedures are key for avoiding false-positive amplifications. In conclusion, both PCR and bacterial culture methods proved to have similar accuracy for identifying infective bacteria in sheep and goats. The final choice will depend on their response time and cost analysis, according to the requirements and farm management strategy.

  4. Development of a Qualitative Quantitative Polymerase Chain Reaction Test to Identify Patients Failing First-Line Therapy to Non-Nucleotide Reverse Transcriptase Inhibitor.

    PubMed

    L Machado, Sergio; Gonçalves, Gabriel S; Dudley, Dawn; O'Connor, David; Keiko Toma, Helena; Couto Fernandes, José Carlos; Tanuri, Amilcar

    2017-01-11

    Antiretroviral therapy (ART) can be compromised by selection of drug resistance strains, which can be promoted by lack of adherence during therapy and drug tolerance, and some of these drug-resistant strains can persist for years as minority populations. The K103N drug resistance mutation is selected by the use of non-nucleotide reverse transcriptase inhibitors, including nevirapine or efavirenz (EFV), used in low-income countries. Here we describe the use of a less expensive qualitative point mutation polymerase chain reaction (PMqPCRK103N) targeting K103N mutation. To validate the use of this methodology, we tested previously sequenced samples from patients treated with highly active ART with viral loads above 2,000 copies/ml and compared the results of our assay with Illumina deep sequencing. Due to its low cost and high specificity, this test is particularly suitable for low-income countries to screen for pretreatment resistance in patients either initiating ART or failing first-line regimens containing EFV.

  5. Epidemiology of imported cutaneous leishmaniasis at the Hospital for Tropical Diseases, London, United Kingdom: use of polymerase chain reaction to identify the species.

    PubMed

    Wall, Emma C; Watson, Julie; Armstrong, Margaret; Chiodini, Peter L; Lockwood, Diana N

    2012-01-01

    This study reviewed all patients diagnosed with imported cutaneous leishmaniasis (CL) at the Hospital for Tropical Diseases in London, United Kingdom, over an 11-year period. Diagnostic and epidemiologic information was collected prospectively for all patients with imported CL to this hospital during 1998-2009. A total of 223 patients were given a diagnosis of CL. Ninety patients were diagnosed with Old World CL, which was caused most commonly by Leishmania donovani complex (n = 20). A total of 71% were tourists to the Mediterranean region, 36% were migrants or visiting friends and relatives, and 17% were soldiers. One hundred thirty-three patients were given a diagnosis of New World CL. The Leishmania subgenus Viannia caused 97 of these cases; 44% of these were in backpackers and 29% were in soldiers. Polymerase chain reaction was more sensitive and faster for detecting Leishmania DNA (86% for Old World CL and 96% for New World CL) than culture. This is the largest study of imported leishmaniasis, and demonstrates that tourists to the Mediterranean and backpackers in Central and South America are at risk for this disease.

  6. Myosin proteins identified from masseter muscle using quantitative reverse transcriptase-polymerase chain reaction--a pilot study of the relevance to orthodontics.

    PubMed

    Suchak, Archna; Hunt, Nigel P; Shah, Rishma; Sinanan, Andrea C M; Lloyd, Tim; Lewis, Mark P

    2009-04-01

    There is a clearly established relationship between masticatory muscle structure and facial form. Human studies in this area, however, have been limited, especially in consideration of the myosin heavy chain (MyHC) family of contractile proteins. The aim of this pilot study was to assess if differences were detectable between genotype with respect to MyHC isoforms and the vertical facial phenotype in a sample of nine Caucasian female patients, age range 18-49 years, using a novel rapid technique. Masseter muscle biopsies were taken from patients with a range of vertical facial form. The levels of expression of the MyHC isoform genes MYH 1, 2, 3, 6, 7, and 8 were compared with the expression in a female calibrator patient aged 23 years with normal vertical facial form, using quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) analysis. Statistical analysis was undertaken using Pearson correlation coefficient. The results showed that there were distinct differences in gene expression between patients with a wide range of variation although changes in MYH1 were consistent with one cephalometric variable, the maxillo-mandibular angle. The full procedure, from start to finish, can be completed within half a day. Rapid genotyping of patients in this way could reveal important information of relevance to treatment. This technology has potential as a diagnostic and prognostic aid when considering correction of certain malocclusions.

  7. Statistical properties of multistep enzyme-mediated reactions

    SciTech Connect

    Nemenman, Ilya; Sinitsyn, Nikolai A; De Ronde, Wiet H; Daniels, Bryan C; Mugler, Andrew

    2008-01-01

    Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In this paper, we address this problem by solving the chemical master equations for various enzymatic reactions. We devise a perturbation theory analogous to that used in quantum mechanics that allows us to determine the first () and the second (variance) cumulants of the distribution of created product molecules as a function of the substrate concentration and the kinetic rates of the intermediate processes. The mean product flux V=d/dt (or 'dose-response' curve) and the Fano factor F=variance/ are both realistically measurable quantities, and while the mean flux can often appear the same for different reaction types, the Fano factor can be quite different. This suggests both qualitative and quantitative ways to discriminate between different reaction schemes, and we explore this possibility in the context of four sample multistep enzymatic reactions. We argue that measuring both the mean flux and the Fano factor can not only discriminate between reaction types, but can also provide some detailed information about the internal, unobserved kinetic rates, and this can be done without measuring single-molecule transition events.

  8. Oxidation of sulfoxides and arsenic(III) in corrosion of nanoscale zero valent iron by oxygen: evidence against ferryl ions (Fe(IV)) as active intermediates in Fenton reaction.

    PubMed

    Pang, Su-Yan; Jiang, Jin; Ma, Jun

    2011-01-01

    Previous studies have shown that the corrosion of zerovalent iron (ZVI) by oxygen (O(2)) via the Fenton reaction can lead to the oxidation of various organic and inorganic compounds. However, the nature of the oxidants involved (i.e., ferryl ion (Fe(IV)) versus hydroxyl radical (HO(•))) is still a controversial issue. In this work, we reevaluated the relative importance of these oxidants and their role in As(III) oxidation during the corrosion of nanoscale ZVI (nZVI) in air-saturated water. It was shown that Fe(IV) species could react with sulfoxides (e.g., dimethyl sulfoxide, methyl phenyl sulfoxide, and methyl p-tolyl sulfoxide) through a 2-electron transfer step producing corresponding sulfones, which markedly differed from their HO(•)-involved products. When using these sulfoxides as probe compounds, the formation of oxidation products indicative of HO(•) but no generation of sulfone products supporting Fe(IV) participation were observed in the nZVI/O(2) system over a wide pH range. As(III) could be completely or partially oxidized by nZVI in air-saturated water. Addition of scavengers for solution-phase HO(•) and/or Fe(IV) quenched As(III) oxidation at acidic pH but had little effect as solution pH increased, highlighting the importance of the heterogeneous iron surface reactions for As(III) oxidation at circumneutral pH.

  9. Impact of sulfur dioxide oxidation by Stabilized Criegee Intermediate on sulfate

    EPA Science Inventory

    We revise the Carbon Bond chemical mechanism to explicitly represent three Stabilized Criegee Intermediates (SCIs) and their subsequent reactions with sulfur dioxide, water monomer, and water dimer, and incorporate the reactions into the Community Multiscale Air Quality model. Th...

  10. Synthetic mononuclear nonheme iron-oxygen intermediates.

    PubMed

    Nam, Wonwoo

    2015-08-18

    Mononuclear nonheme iron-oxygen species, such as iron-superoxo, -peroxo, -hydroperoxo, and -oxo, are key intermediates involved in dioxygen activation and oxidation reactions catalyzed by nonheme iron enzymes. Because these iron-oxygen intermediates are short-lived due to their thermal instability and high reactivity, it is challenging to investigate their structural and spectroscopic properties and reactivity in the catalytic cycles of the enzymatic reactions themselves. One way to approach such problems is to synthesize biomimetic iron-oxygen complexes and to tune their geometric and electronic structures for structural characterization and reactivity studies. Indeed, a number of biologically important iron-oxygen species, such as mononuclear nonheme iron(III)-superoxo, iron(III)-peroxo, iron(III)-hydroperoxo, iron(IV)-oxo, and iron(V)-oxo complexes, were synthesized recently, and the first X-ray crystal structures of iron(III)-superoxo, iron(III)-peroxo, and iron(IV)-oxo complexes in nonheme iron models were successfully obtained. Thus, our understanding of iron-oxygen intermediates in biological reactions has been aided greatly from the studies of the structural and spectroscopic properties and the reactivities of the synthetic biomimetic analogues. In this Account, we describe our recent results on the synthesis and characterization of mononuclear nonheme iron-oxygen complexes bearing simple macrocyclic ligands, such as N-tetramethylated cyclam ligand (TMC) and tetraamido macrocyclic ligand (TAML). In the case of iron-superoxo complexes, an iron(III)-superoxo complex, [(TAML)Fe(III)(O2)](2-), is described, including its crystal structure and reactivities in electrophilic and nucleophilic oxidative reactions, and its properties are compared with those of a chromium(III)-superoxo complex, [(TMC)Cr(III)(O2)(Cl)](+), with respect to its reactivities in hydrogen atom transfer (HAT) and oxygen atom transfer (OAT) reactions. In the case of iron-peroxo intermediates

  11. Experiments in intermediate energy physics

    SciTech Connect

    Dehnhard, D.

    2003-02-28

    Research in experimental nuclear physics was done from 1979 to 2002 primarily at intermediate energy facilities that provide pion, proton, and kaon beams. Particularly successful has been the work at the Los Alamos Meson Physics Facility (LAMPF) on unraveling the neutron and proton contributions to nuclear ground state and transition densities. This work was done on a wide variety of nuclei and with great detail on the carbon, oxygen, and helium isotopes. Some of the investigations involved the use of polarized targets which allowed the extraction of information on the spin-dependent part of the triangle-nucleon interaction. At the Indiana University Cyclotron Facility (IUCF) we studied proton-induced charge exchange reactions with results of importance to astrophysics and the nuclear few-body problem. During the first few years, the analysis of heavy-ion nucleus scattering data that had been taken prior to 1979 was completed. During the last few years we created hypernuclei by use of a kaon beam at Brookhaven National Laboratory (BNL) and an electron beam at Jefferson Laboratory (JLab). The data taken at BNL for a study of the non-mesonic weak decay of the A particle in a nucleus are still under analysis by our collaborators. The work at JLab resulted in the best resolution hypernuclear spectra measured thus far with magnetic spectrometers.

  12. Membrane Fission: Model for Intermediate Structures

    PubMed Central

    Kozlovsky, Yonathan; Kozlov, Michael M.

    2003-01-01

    Membrane budding-fission is a fundamental process generating intracellular carriers of proteins. Earlier works were focused only on formation of coated buds connected to the initial membrane by narrow membrane necks. We present the theoretical analysis of the whole pathway of budding-fission, including the crucial stage where the membrane neck undergoes fission and the carrier separates from the donor membrane. We consider two successive intermediates of the reaction: 1), a constricted membrane neck coming out of aperture of the assembling protein coat, and 2), hemifission intermediate resulting from self-fusion of the inner monolayer of the neck, while its outer monolayer remains continuous. Transformation of the constricted neck into the hemifission intermediate is driven by the membrane stress produced in the neck by the protein coat. Although apparently similar to hemifusion, the fission is predicted to have an opposite dependence on the monolayer spontaneous curvature. Analysis of the further stages of the process demonstrates that in all practically important cases the hemifission intermediate decays spontaneously into two separate membranes, thereby completing the fission process. We formulate the “job description” for fission proteins by calculating the energy they have to deliver and the radii of the protein coat aperture which have to be reached to drive the fission process. PMID:12829467

  13. Long-lived glycosyl-enzyme intermediate mimic produced by formate re-activation of a mutant endoglucanase lacking its catalytic nucleophile.

    PubMed Central

    Viladot, J L; Canals, F; Batllori, X; Planas, A

    2001-01-01

    The mutant E134A 1,3-1,4-beta-glucanase from Bacillus licheniformis, in which the catalytic nucleophilic residue has been removed by mutation to alanine, has its hydrolytic activity rescued by exogenous formate in a concentration-dependent manner. A long-lived alpha-glycosyl formate is detected and identified by (1)H-NMR and matrix-assisted laser desorption ionization-time-of-flight-MS. The intermediate is kinetically competent, since it is, at least partially, enzymically hydrolysed, and able to act as a glycosyl donor in transglycosylation reactions. This transient compound represents a true covalent glycosyl-enzyme intermediate mimic of the proposed covalent intermediate in the reaction mechanism of retaining glycosidases. PMID:11256951

  14. Exemplary Dissemination Programs for Intermediate Units Serving Rural Schools.

    ERIC Educational Resources Information Center

    Edington, Everett; Hays, Leonard

    Utilizing information derived from documents, site visits, correspondence, and personal interviews re: 6 intermediate education units serving rural schools which were initially identified via a mail survey, this report describes intermediate education units with exemplary information dissemination programs. Varying considerably, each program is…

  15. BLUF Domain Function Does Not Require a Metastable Radical Intermediate State

    PubMed Central

    2014-01-01

    BLUF (blue light using flavin) domain proteins are an important family of blue light-sensing proteins which control a wide variety of functions in cells. The primary light-activated step in the BLUF domain is not yet established. A number of experimental and theoretical studies points to a role for photoinduced electron transfer (PET) between a highly conserved tyrosine and the flavin chromophore to form a radical intermediate state. Here we investigate the role of PET in three different BLUF proteins, using ultrafast broadband transient infrared spectroscopy. We characterize and identify infrared active marker modes for excited and ground state species and use them to record photochemical dynamics in the proteins. We also generate mutants which unambiguously show PET and, through isotope labeling of the protein and the chromophore, are able to assign modes characteristic of both flavin and protein radical states. We find that these radical intermediates are not observed in two of the three BLUF domains studied, casting doubt on the importance of the formation of a population of radical intermediates in the BLUF photocycle. Further, unnatural amino acid mutagenesis is used to replace the conserved tyrosine with fluorotyrosines, thus modifying the driving force for the proposed electron transfer reaction; the rate changes observed are also not consistent with a PET mechanism. Thus, while intermediates of PET reactions can be observed in BLUF proteins they are not correlated with photoactivity, suggesting that radical intermediates are not central to their operation. Alternative nonradical pathways including a keto–enol tautomerization induced by electronic excitation of the flavin ring are considered. PMID:24579721

  16. Observation by sup 13 C NMR of the EPSP synthase tetrahedral intermediate bound to the enzyme active site

    SciTech Connect

    Anderson, K.S.; Sammons, R.D.; Leo, G.C.; Sikorski, J.A. ); Benesi, A.J.; Johnson, K.A. )

    1990-02-13

    Direct observation of the tetrahedral intermediate in the EPSP synthase reaction pathway was provided by {sup 13}C NMR by examining the species bound to the enzyme active site under internal equilibrium conditions and using (2-{sup 13}C)PEP as a spectroscopic probe. The tetrahedral center of the intermediate bound to the enzyme gave a unique signal appearing at 104 ppm. Separate signals were observed for free EPSP and EPSP bound to the enzyme in a ternary complex with phosphate. These peak assignments account for the quantitation of the species bound to the enzyme and liberated upon quenching with either triethylamine or base. A comparison of quenching with acid, base, or triethylamine was conducted. After long times of incubation during the NMR measurement, a signal at 107 ppm appeared. The compound giving rise to this resonance was isolated and identified as an EPSP ketal. The rate of formation of the EPSP ketal was very slow establishing that it is a side product of the normal enzymatic reaction. To look for additional signals that might arise from a covalent adduct which has been postulated to arise from reaction of enzyme with PEP, and NMR experiment was performed with an analogue of S3P lacking the 4- and 5-hydroxyl groups. All of these results reaffirm identification of the tetrahedral species as the only observable intermediate in the EPSP synthase reaction.

  17. Development of a Multiplexed Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) Assay to Identify Common Members of the Subgenera Culex (Culex) and Culex (Phenacomyia) in Guatemala

    PubMed Central

    Kent, Rebekah J.; Deus, Stephen; Williams, Martin; Savage, Harry M.

    2010-01-01

    Morphological differentiation of mosquitoes in the subgenera Culex (Culex) and Culex (Phenacomyia) in Guatemala is difficult, with reliable identification ensured only through examination of larval skins from individually reared specimens and associated male genitalia. We developed a multiplexed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay to identify common Cx. (Cux.) and Cx. (Phc.). Culex (Cux.) chidesteri, Cx. (Cux.) coronator, Cx. (Cux.) interrogator, Cx. (Cux.) quinquefasciatus, Cx. (Cux.) nigripalpus/Cx. (Cux.) thriambus, and Cx. (Phc.) lactator were identified directly with a multiplexed primer cocktail comprising a conserved forward primer and specific reverse primers targeting ribosomal DNA (rDNA). Culex nigripalpus and Cx. thriambus were differentiated by restriction digest of homologous amplicons. The assay was developed and optimized using well-characterized specimens from Guatemala and the United States and field tested with unknown material from Guatemala. This assay will be a valuable tool for mosquito identification in entomological and arbovirus ecology studies in Guatemala. PMID:20682869

  18. Deformylation Reaction by a Nonheme Manganese(III)-Peroxo Complex via Initial Hydrogen-Atom Abstraction.

    PubMed

    Barman, Prasenjit; Upadhyay, Pranav; Faponle, Abayomi S; Kumar, Jitendra; Nag, Sayanta Sekhar; Kumar, Devesh; Sastri, Chivukula V; de Visser, Sam P

    2016-09-05

    Metal-peroxo intermediates are key species in the catalytic cycles of nonheme metalloenzymes, but their chemical properties and reactivity patterns are still poorly understood. The synthesis and characterization of a manganese(III)-peroxo complex with a pentadentate bispidine ligand system and its reactivity with aldehydes was studied. Manganese(III)-peroxo can react through hydrogen-atom abstraction reactions instead of the commonly proposed nucleophilic addition reaction. Evidence of the mechanism comes from experiments which identify a primary kinetic isotope effect of 5.4 for the deformylation reaction. Computational modeling supports the established mechanism and identifies the origin of the reactivity preference of hydrogen-atom abstraction over nucleophilic addition.

  19. [Intermediate endpoints in clinical research].

    PubMed

    Peters, Sanne A E; Groenwold, Rolf H H; Bots, Michiel L

    2013-01-01

    An intermediate variable such as blood pressure is part of the causal pathway of mechanisms to a clinical outcome, e.g. myocardial infarction. An intervention affects a clinical outcome through its effect on that intermediate variable. In studies designed to assess the effects of interventions an intermediate variable may be used as surrogate for clinical outcomes. Such an endpoint is also known as an intermediate endpoint. Intervention studies with intermediate endpoints are commonly performed in medical research to evaluate the effects of an intervention on clinical outcomes. Intervention studies with an intermediate endpoint are conducted in a smaller study population and with a shorter duration of follow-up than studies using clinical outcomes. An intermediate variable is not eligible as an intermediate endpoint when the intervention also affects other biological mechanisms that subsequently affect the clinical endpoint. Due to a smaller sample size and shorter study duration, side effects of intervention are more difficult to evaluate in studies with an intermediate endpoint than in studies with clinical endpoints.

  20. Structure and reactivity of bis(silyl) dihydride complexes (PMe(3))(3)Ru(SiR(3))(2)(H)(2): model compounds and real intermediates in a dehydrogenative C-Si bond forming reaction.

    PubMed

    Dioumaev, Vladimir K; Yoo, Bok R; Procopio, Leo J; Carroll, Patrick J; Berry, Donald H

    2003-07-23

    A series of stable complexes, (PMe(3))(3)Ru(SiR(3))(2)(H)(2) ((SiR(3))(2) = (SiH(2)Ph)(2), 3a; (SiHPh(2))(2), 3b; (SiMe(2)CH(2)CH(2)SiMe(2)), 3c), has been synthesized by the reaction of hydridosilanes with (PMe(3))(3)Ru(SiMe(3))H(3) or (PMe(3))(4)Ru(SiMe(3))H. Compounds 3a and 3c adopt overall pentagonal bipyramidal geometries in solution and the solid state, with phosphine and silyl ligands defining trigonal bipyramids and ruthenium hydrides arranged in the equatorial plane. Compound 3a exhibits meridional phosphines, with both silyl ligands equatorial, whereas the constraints of the chelate in 3c result in both axial and equatorial silyl environments and facial phosphines. Although there is no evidence for agostic Si-H interactions in 3a and 3b, the equatorial silyl group in 3c is in close contact with one hydride (1.81(4) A) and is moderately close to the other hydride (2.15(3) A) in the solid state and solution (nu(Ru.H.Si) = 1740 cm(-)(1) and nu(RuH) = 1940 cm(-)(1)). The analogous bis(silyl) dihydride, (PMe(3))(3)Ru(SiMe(3))(2)(H)(2) (3d), is not stable at room temperature, but can be generated in situ at low temperature from the 16e(-) complex (PMe(3))(3)Ru(SiMe(3))H (1) and HSiMe(3). Complexes 3b and 3d have been characterized by multinuclear, variable temperature NMR and appear to be isostructural with 3a. All four complexes exhibit dynamic NMR spectra, but the slow exchange limit could not be observed for 3c. Treatment of 1 with HSiMe(3) at room temperature leads to formation of (PMe(3))(3)Ru(SiMe(2)CH(2)SiMe(3))H(3) (4b) via a CH functionalization process critical to catalytic dehydrocoupling of HSiMe(3) at higher temperatures. Closer inspection of this reaction between -110 and -10 degrees C by NMR reveals a plethora of silyl hydride phosphine complexes formed by ligand redistribution prior to CH activation. Above ca. 0 degrees C this mixture converts cleanly via silane dehydrogenation to the very stable tris(phosphine) trihydride carbosilyl complex 4b

  1. Intermediate BL Lac objects

    NASA Astrophysics Data System (ADS)

    Bondi, M.; Marchã, M. J. M.; Dallacasa, D.; Stanghellini, C.

    2001-08-01

    The 200-mJy sample, defined by Marchã et al., contains about 60 nearby, northern, flat-spectrum radio sources. In particular, the sample has proved effective at finding nearby radio-selected BL Lac objects with radio luminosities comparable to those of X-ray-selected objects, and low-luminosity flat-spectrum weak emission-line radio galaxies (WLRGs). The 200-mJy sample contains 23 BL Lac objects (including 6 BL Lac candidates) and 19 WLRGs. We will refer to these subsamples as the 200-mJy BL Lac sample and the 200-mJy WLRG sample, respectively. We have started a systematic analysis of the morphological pc-scale properties of the 200-mJy radio sources using VLBI observations. This paper presents VLBI observations at 5 and 1.6GHz of 14 BL Lac objects and WLRGs selected from the 200-mJy sample. The pc-scale morphology of these objects is briefly discussed. We derive the radio beaming parameters of the 200-mJy BL Lac objects and WLRGs and compare them with those of other BL Lac samples and with a sample of FR I radio galaxies. The overall broad-band radio, optical and X-ray properties of the 200-mJy BL Lac sample are discussed and compared with those of other BL Lac samples, radio- and X-ray-selected. We find that the 200-mJy BL Lac objects fill the gap between HBL and LBL objects in the colour-colour plot, and have intermediate αXOX as expected in the spectral energy distribution unification scenario. Finally, we briefly discuss the role of the WLRGs.

  2. Printing. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Seivert, Chester

    Several intermediate performance objectives and corresponding criterion measures are listed for each of 13 terminal objectives for an intermediate printing course. The materials were developed for a two-semester (3 hours daily) course with specialized classroom, shop, and practical experiences designed to enable the student to develop proficiency…

  3. Masonry. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Thompson, Moses

    Several intermediate performance objectives and corresponding criterion measures are listed for each of 13 terminal objectives for an intermediate masonry course. These materials, developed for a two-semester (3 hours daily) course, are designed to provide the student with the skills and knowledge necessary for entry level employment in the field…

  4. Welding. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Vincent, Kenneth

    Several intermediate performance objectives and corresponding criterion measures are listed for each of nine terminal objectives for an intermediate welding course. The materials were developed for a 36-week (3 hours daily) course designed to prepare the student for employment in the field of welding. Electric welding and specialized (TIG & MIG)…

  5. Dee-Mack Intermediate School

    ERIC Educational Resources Information Center

    Northwest Evaluation Association, 2012

    2012-01-01

    Frank Reliford, the Principal at Dee-Mack Intermediate since 2005, is familiar to almost every child in the community. 260 Students attend Reliford's school, and their status is a point of pride: Dee-Mack Intermediate is consistently one of the highest performing schools in the state. The change in student performance correlates to the…

  6. Intermediate dosimetric quantities.

    PubMed

    Kellerer, A M; Hahn, K; Rossi, H H

    1992-04-01

    The transfer of energy from ionizing radiation to matter involves a series of steps. In wide ranges of their energy spectra photons and neutrons transfer energy to an irradiated medium almost exclusively by the production of charged particles which ionize and thereby produce electrons that can ionize in turn. The examination of these processes leads to a series of intermediate quantities. One of these is kerma, which has long been employed as a measure of the energy imparted in the first of the interactions. It depends only on the fluence of uncharged particles and is therefore--unlike absorbed dose and electron fluence--insensitive to local differences of receptor geometry and composition. An analogous quantity for charged-particle fields, cema (converted energy per unit mass), is defined, which quantifies the energy imparted in terms of the interactions of charged particles, disregarding energy dissipation by secondary electrons. Cema can be expressed as an integral over the fluence of ions times their stopping power. However, complications arise when the charged particles are electrons, and when their fluence cannot be separated from that of the secondaries. The resulting difficulty can be circumvented by the definition of reduced cema. This quantity corresponds largely to the concept employed in the cavity theory of Spencer and Attix. In reduced cema not all secondary electrons but all electrons below a chosen cutoff energy, delta, are considered to be absorbed locally. When the cutoff energy is reduced, cema approaches absorbed dose and thereby becomes sensitive to highly local differences in geometry or composition. With larger values of delta, reduced cema is a useful parameter to specify the dose-generating potential of a charged-particle field 'free in air' or in vacuo. It is nearly equal to the mean absorbed dose in a sphere with radius equal to the range of electrons of energy delta. Reduced cema is a function of the fluence at the specified location at

  7. Noncanonical reactions of flavoenzymes.

    PubMed

    Sobrado, Pablo

    2012-11-05

    Enzymes containing flavin cofactors are predominantly involved in redox reactions in numerous cellular processes where the protein environment modulates the chemical reactivity of the flavin to either transfer one or two electrons. Some flavoenzymes catalyze reactions with no net redox change. In these reactions, the protein environment modulates the reactivity of the flavin to perform novel chemistries. Recent mechanistic and structural data supporting novel flavin functionalities in reactions catalyzed by chorismate synthase, type II isopentenyl diphosphate isomerase, UDP-galactopyranose mutase, and alkyl-dihydroxyacetonephosphate synthase are presented in this review. In these enzymes, the flavin plays either a direct role in acid/base reactions or as a nucleophile or electrophile. In addition, the flavin cofactor is proposed to function as a "molecular scaffold" in the formation of UDP-galactofuranose and alkyl-dihydroxyacetonephosphate by forming a covalent adduct with reaction intermediates.

  8. Cycloaddition reactions of ICNO

    NASA Astrophysics Data System (ADS)

    Pasinszki, Tibor; Krebsz, Melinda; Hajgató, Balázs

    2009-05-01

    The mechanism and selectivity of cycloaddition reactions of iodonitrile oxide, ICNO, have been studied with theoretical methods for the first time using MR-AQCC coupled-cluster and B3LYP DFT methods. Calculations have predicted that the favoured ICNO dimerisation process is a multi-step reaction to diiodofuroxan involving dinitrosoethylene-like intermediates. The ICNO cycloaddition with nitriles and ethynyl derivatives is a synchronous process favouring the formation of 1,2,4-oxadiazole and 1,2-oxazole derivatives, respectively. The cycloaddition reactions of ICNO have been studied experimentally by generating ICNO from AgCNO and iodine. Diiodofuroxan is obtained, however, even at the presence of nitriles.

  9. Mössbauer- and EPR-Snapshots of an Enzymatic Reaction: The Cytochrome P450 Reaction Cycle

    NASA Astrophysics Data System (ADS)

    Schünemann, V.; Jung, C.; Lendzian, F.; Barra, A.-L.; Teschner, T.; Trautwein, A. X.

    2004-12-01

    In this communication we present a complimentary Mössbauer- and EPR-study of the time dependance of the reaction of substrate free P450cam with peracetic acid within a time region ranging from 8 ms up to 5 min. An Fe(IV) species as well as a tyrosyl radical residing on the amino acid residue Tyr96 have been identified as reaction intermediates. These species possibly are formed by the reduction of compound I by means of transferring an electron from Tyr 96 to the heme moiety.

  10. Determination of the dissociation kinetics of a transient intermediate.

    PubMed

    Asam, M R; Glish, G L

    1999-02-01

    Tandem mass spectrometry provides information on the dissociation pathways of gas-phase ions by providing a link between product ions and parent ions. However, there exists a distinct possibility that a parent ion does not dissociate directly to the observed product ion, but that the reaction proceeds through unobserved reaction intermediates. This work describes the discovery and kinetic analysis of an unobserved reaction intermediate with a quadrupole ion trap. [a4 - NH3] ions formed from [YG beta FL + H] ions dissociate to [(F*YG - NH3) - CO] ions. It is expected, however, from previous results, that [F*YG - NH3] ions should form prior to [(F*YG - NH3) - CO] ions. Double-resonance experiments are used to demonstrate the existence of intermediate [F*YG - NH3] ions. Various kinetic analyses are then performed using traditional collision-induced dissociation kinetics and double-resonance experiments. The phenomenological rates of formation and decay of peptide rearrangement ion dissociation products are determined by curve fitting decay and formation data generated with the kinetics experiments. The data generated predict an observable level of the intermediate in a time frame accessible but previously not monitored. By examining early product-ion formation, the intermediate ions, [F*YG - NH3]+, are observed.

  11. 1,4-benzothiazines as key intermediates in the biosynthesis of red hair pigment pheomelanins.

    PubMed

    Di Donato, Paola; Napolitano, Alessandra

    2003-10-01

    Following the discovery of cysteinyldopas as the early intermediates in the biogenesis of pheomelanins, the typical red hair pigments, the reactivity of the biosynthetic precursors under biomimetic conditions was extensively investigated. As a result, the early stages of pheomelanogenesis were envisaged as involving oxidative cyclization of cysteinyldopas, mainly the 5-S-isomer, to 1,4-benzothiazine (BTZ) intermediates which undergo oxidative polymerization leading eventually to the pigments. In the last decade, several aspects of the chemistry and biosynthesis of pheomelanins were re-examined. In particular, (i) transient BTZ intermediates were identified by pulse radiolytic techniques and NMR analysis; (ii) the effect of reaction conditions and additives on the rearrangement vs. redox exchange reaction paths of such intermediates were investigated in detail; (iii) the mechanism of the oxidative polymerization of BTZs was characterized by the first isolation of oligomer species, and (iv) the pigment eventually resulting from oxidation of 5-S-cysteinyldopa (CD) was directly analyzed by spectroscopic and chemical methodologies in comparison with pheomelanins isolated from human hair. These advances led eventually to an integrated picture of the biogenetic route highlighting the intervention of various chemical and enzymatic factors which affect the kinetics of the different steps and the nature of the key benzothiazine precursors. A likely biogenetic route was also postulated for the delta2,2'-bi(2H-1,4-benzothiazine) pigments, termed trichochromes, whose origin had remained an open issue since their first isolation from red human hair and avian feathers. Finally, a more detailed description of the structure of pheomelanin pigments in terms of the monomer units, their mode of linking, and postsynthetic modifications was gained.

  12. 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

    temperatures, the formation of stabilized methylphenylperoxy radicals becomes significant. A further important reaction channel is available only to the 2-methylphenyl isomer, where 6-methylene-2,4-cyclohexadiene-1-one (ortho-quinone methide, o-QM) is produced via an intramolecular hydrogen transfer from the methyl group to the peroxy radical in 2-methylphenylperoxy, with subsequent loss of OH. The decomposition of o-QM to benzene + CO reveals a potentially important new pathway for the conversion of toluene to benzene during combustion. A number of the important products of toluene combustion proposed in this study are known to be precursors of polyaromatic hydrocarbons that are involved in soot formation. Reactions leading to the important unsaturated oxygenated intermediates identified in this study, and the further reactions of these intermediates, are not included in current aromatic oxidation mechanisms.

  13. Correlations in intermediate energy two-proton removal reactions.

    PubMed

    Wimmer, K; Bazin, D; Gade, A; Tostevin, J A; Baugher, T; Chajecki, Z; Coupland, D; Famiano, M A; Ghosh, T K; Grinyer, G F; Hodges, R; Howard, M E; Kilburn, M; Lynch, W G; Manning, B; Meierbachtol, K; Quarterman, P; Ratkiewicz, A; Sanetullaev, A; Simpson, E C; Stroberg, S R; Tsang, M B; Weisshaar, D; Winkelbauer, J; Winkler, R; Youngs, M

    2012-11-16

    We report final-state-exclusive measurements of the light charged fragments in coincidence with (26)Ne residual nuclei following the direct two-proton removal from a neutron-rich (28)Mg secondary beam. A Dalitz-plot analysis and comparisons with simulations show that a majority of the triple-coincidence events with two protons display phase-space correlations consistent with the (two-body) kinematics of a spatially correlated pair-removal mechanism. The fraction of such correlated events, 56(12)%, is consistent with the fraction of the calculated cross section, 64%, arising from spin S=0 two-proton configurations in the entrance-channel (shell-model) (28)Mg ground state wave function. This result promises access to an additional and more specific probe of the spin and spatial correlations of valence nucleon pairs in exotic nuclei produced as fast secondary beams.

  14. Criegee intermediates in the indoor environment. New insights

    SciTech Connect

    Shallcross, D. E.; Taatjes, C. A.; Percival, C. J.

    2014-03-25

    Criegee intermediates are formed in the ozonolysis of alkenes and play an important role in indoor chemistry, notably as a source of OH radicals. Recent studies have shown that these Criegee intermediates react very quickly with NO2, SO2, and carbonyls, and in this study, steady-state calculations are used to inspect the potential impact of these data on indoor chemistry. It is shown that these reactions could accelerate NO3 formation and SO2 removal in the indoor environment significantly. In addition, reaction between Criegee intermediates and halogenated carbonyls could provide a significant loss process indoors, where currently one does not exist.

  15. Tachyon field in intermediate inflation

    SciTech Connect

    Campo, Sergio del; Herrera, Ramon; Toloza, Adolfo

    2009-04-15

    The tachyonic inflationary universe model in the context of intermediate inflation is studied. General conditions for this model to be realizable are discussed. In the slow-roll approximation, we describe in great detail the characteristics of this model.

  16. Adventures in Reactive Intermediate Chemistry: A Perspective and Retrospective.

    PubMed

    Moss, Robert A

    2017-03-03

    I review aspects of my research on reactive intermediates, specifically the physical organic chemistry of carbenes and carbocations. The topics treated include carbenoids, carbenic philicity, absolute rates of carbene/alkene additions, the diazirine exchange reaction and derived carbenes, carbene equilibria, carbocations from diazotates, and carbocations from alkoxychlorocarbenes. The essay concludes with observations on the protean nature of physical organic chemistry.

  17. Modeling the Reaction of Fe Atoms with CCl4

    SciTech Connect

    Camaioni, Donald M.; Ginovska, Bojana; Dupuis, Michel

    2009-01-05

    The reaction of zero-valent iron with carbon tetrachloride (CCl4) in gas phase was studied using density functional theory. Temperature programmed desorption experiments over a range of Fe and CCl4 coverages on a FeO(111) surface, demonstrate a rich surface chemistry with several reaction products (C2Cl4, C2Cl6, OCCl2, CO, FeCl2, FeCl3) observed. The reactivity of Fe and CCl4 was studied under three stoichiometries, one Fe with one CCl4, one Fe with two CCl4 molecules and two Fe with one CCl4, modeling the environment of the experimental work. The electronic structure calculations give insight into the reactions leading to the experimentally observed products and suggest that novel Fe-C-Cl containing species are important intermediates in these reactions. The intermediate complexes are formed in highly exothermic reactions, in agreement with the experimentally observed reactivity with the surface at low temperature (30 K). This initial survey of the reactivity of Fe with CCl4 identifies some potential reaction pathways that are important in the effort to use Fe nano-particles to differentiate harmful pathways that lead to the formation of contaminants like chloroform (CHCl3) from harmless pathways that lead to products such as formate (HCO2-) or carbon oxides in water and soil. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  18. Reaction of tetracycline with biologically relevant chloramines.

    PubMed

    Benavides, J; Barrias, P; Piro, N; Arenas, A; Orrego, A; Pino, E; Villegas, L; Dorta, E; Aspée, A; López-Alarcón, C

    2017-05-05

    Helicobacter pylori (H. pylori) infection triggers inflammatory processes with the consequent production of hypochlorous acid (HOCl), monochloramine (NH2Cl), and protein-derived chloramines. As the therapy for eradicating H. pylori is partially based on the use of tetracycline, we studied the kinetic of its consumption elicited by HOCl, NH2Cl, N-chloro-n-butylamine (NHCl-But, used as a lysine-derived chloramine model), and lysozyme-derived chloramines. In the micromolar concentration range, tetracycline reacted rapidly with HOCl, generating in the first few seconds intermediates of short half-life. In contrast, a slow tetracycline consumption was observed in the presence of high NH2Cl and NHCl-But concentrations (millimolar range). Similar chlorinated products of tetracycline were identified by mass spectrometry, in the presence of HOCl and NH2Cl. These results evidenced that tautomers of tetracycline are pivotal intermediates in all reactions. In spite of the low reactivity of chloramines towards tetracycline, it is evident that, in the concentration range where they are produced in a H. pylori infection (millimolar range), the reactions lead to oxidation and/or chlorination of tetracycline. This kind of reactions, which were also observed triggered by lysozyme-derived chloramines, could limit the efficiency of the tetracycline-based therapy.

  19. Acyl silicates and acyl aluminates as activated intermediates in peptide formation on clays

    NASA Technical Reports Server (NTRS)

    White, D. H.; Kennedy, R. M.; Macklin, J.

    1984-01-01

    Glycine reacts with heating on dried clays and other minerals to give peptides in much better yield than in the absence of mineral. This reaction was proposed to occur by way of an activated intermediate such as an acyl silicate or acyl aluminate analogous to acyl phosphates involved in several biochemical reactions including peptide bond synthesis. The proposed mechanism has been confirmed by trapping the intermediate, as well as by direct spectroscopic observation of a related intermediate. The reaction of amino acids on periodically dried mineral surfaces represents a widespead, geologically realistic setting for prebiotic peptide formation via in situ activation.

  20. Serotype specific polymerase chain reaction identifies a higher prevalence of streptococcus mutans serotype k and e in a random group of children with dental caries from the Southern region of India

    PubMed Central

    Rao, Arun Prasad; Austin, Ravi David

    2014-01-01

    Background: The development of dental caries has been associated with the oral prevalence of Streptococcus mutans. Four serotypes of S. mutans have been reported, namely serotype c, e, f, and k that are classified based on the composition and linkages of cell wall polysaccharides, response to physiological reactions, sero-specificity and 16s rRNA homology. Although the oral prevalence of S. mutans serotype c in Indian subjects with or without caries is known, the prevalence of the other three serotypes, e, f, and k are not known. Hence in this study, we have investigated the occurrence of the e, f, and k serotypes in children with or without caries within the age group of 6-12 years. Materials and Methods: Genomic DNA isolated from whole saliva of caries active (CA) and caries free (CF) groups were first screened for the presence of S. mutans by strain specific polymerase chain reaction (PCR). Those samples that tested positive for the presence of S. mutans were further analyzed by serotype specific PCR to identify the prevalence of the serotypes. Results: Strain specific PCR indicated a higher prevalence of S. mutans in CA group (80%) relative to CF group (43%). Further analysis of the S. mutans positive samples in both groups indicated a higher prevalence of serotype k and e, followed by serotype f in CA group. Conclusion: The present data clearly establishes a novel S. mutans serotype prevalence hierarchy in children from this region, compared with those that have been reported elsewhere. Besides, the data are also clinically significant as the occurrence of serotype k has been associated with infective endocarditis. PMID:25191062

  1. Identifying Hazards

    EPA Pesticide Factsheets

    The federal government has established a system of labeling hazardous materials to help identify the type of material and threat posed. Summaries of information on over 300 chemicals are maintained in the Envirofacts Master Chemical Integrator.

  2. Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase

    PubMed Central

    Minges, Alexander; Ciupka, Daniel; Winkler, Christian; Höppner, Astrid; Gohlke, Holger; Groth, Georg

    2017-01-01

    Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP- and Pi-dependent formation of phosphoenolpyruvate from pyruvate in C4 -plants, but the reverse reaction forming ATP in bacteria and protozoa. The multi-domain enzyme is considered an efficient molecular machine that performs one of the largest single domain movements in proteins. However, a comprehensive understanding of the proposed swiveling domain motion has been limited by not knowing structural intermediates or molecular dynamics of the catalytic process. Here, we present crystal structures of PPDKs from Flaveria, a model genus for studying the evolution of C4 -enzymes from phylogenetic ancestors. These structures resolve yet unknown conformational intermediates and provide the first detailed view on the large conformational transitions of the protein in the catalytic cycle. Independently performed unrestrained MD simulations and configurational free energy calculations also identified these intermediates. In all, our experimental and computational data reveal strict coupling of the CD swiveling motion to the conformational state of the NBD. Moreover, structural asymmetries and nucleotide binding states in the PPDK dimer support an alternate binding change mechanism for this intriguing bioenergetic enzyme. PMID:28358005

  3. Learning to predict chemical reactions.

    PubMed

    Kayala, Matthew A; Azencott, Chloé-Agathe; Chen, Jonathan H; Baldi, Pierre

    2011-09-26

    Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles, respectively, are not high throughput, are not generalizable or scalable, and lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry data set consisting of 1630 full multistep reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top-ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of nonproductive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system

  4. Learning to Predict Chemical Reactions

    PubMed Central

    Kayala, Matthew A.; Azencott, Chloé-Agathe; Chen, Jonathan H.

    2011-01-01

    Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles respectively are not high-throughput, are not generalizable or scalable, or lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry dataset consisting of 1630 full multi-step reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval, problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of non-productive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system

  5. Detection of an intermediate of photosynthetic water oxidation.

    PubMed

    Clausen, Juergen; Junge, Wolfgang

    2004-07-22

    The oxygen that we breathe is produced by photosystem II of cyanobacteria and plants. The catalytic centre, a Mn4Ca cluster, accumulates four oxidizing equivalents before oxygen is formed, seemingly in a single reaction step 2H2O<==>O2 + 4H+ + 4e-. The energy and cycling of this reaction derives solely from light. No intermediate oxidation product of water has been detected so far. Here, we shifted the equilibrium of the terminal reaction backward by increasing the oxygen pressure and monitoring (by absorption transients in the near-ultraviolet spectrum) the electron transfer from bound water into the catalytic centre. A tenfold increase of ambient oxygen pressure (2.3 bar) half-suppressed the full progression to oxygen. The remaining electron transfer at saturating pressure (30 bar) was compatible with the formation of a stabilized intermediate. The abstraction of four electrons from water was probably split into at least two electron transfers: mildly endergonic from the centre's highest oxidation state to an intermediate, and exergonic from the intermediate to oxygen. There is little leeway for photosynthetic organisms to push the atmospheric oxygen concentration much above the present level.

  6. Benzoxazinone-Mediated Triazine Degradation: A Proposed Reaction Mechanism.

    PubMed

    Willett, C D; Lerch, R N; Lin, C-H; Goyne, K W; Leigh, N D; Roberts, C A

    2016-06-22

    The role of benzoxazinones (Bx, 2-hydroxy-2H-1,4-benzoxazin-3(4H)-one) in triazine resistance in plants has been studied for over half a century. In this research, fundamental parameters of the reaction between DIBOA-Glc (2-β-d-glucopyranosyloxy-4-hydroxy-1,4-benzoxazin-3-one) and atrazine (ATR, 6-chloro-N-ethyl-N'-(1-methylethyl)-1,3,5-triazine-2,4-diamine) were examined. Through a series of experiments employing a variety of chromatographic and spectroscopic techniques, the DIBOA-Glc/ATR reaction was characterized in terms of reactant and product kinetics, stoichiometry, identification of a reaction intermediate, and reaction products formed. Results of these experiments demonstrated that the reaction mechanism proceeds via nucleophilic attack of the hydroxamic acid moiety of DIBOA-Glc at the C-2 position of the triazine ring to form hydroxyatrazine (HA, 2-hydroxy-4-ethylamino-6-isopropylamino-s-triazine), with associated degradation of DIBOA-Glc. Degradation of reactants followed first-order kinetics with a noncatalytic role of DIBOA-Glc. A reaction intermediate was identified as a DIBOA-Glc-HA conjugate, indicating a 1:1 DIBOA-Glc:ATR stoichiometry. Reaction products included HA and Cl(-), but definitive identification of DIBOA-Glc reaction product(s) was not attained. With these reaction parameters elucidated, DIBOA-Glc can be evaluated in terms of its potential for a myriad of applications, including its use to address the problem of widespread ATR contamination of soil and water resources.

  7. Compact intermediates in RNA folding

    SciTech Connect

    Woodson, S.A.

    2011-12-14

    Large noncoding RNAs fold into their biologically functional structures via compact yet disordered intermediates, which couple the stable secondary structure of the RNA with the emerging tertiary fold. The specificity of the collapse transition, which coincides with the assembly of helical domains, depends on RNA sequence and counterions. It determines the specificity of the folding pathways and the magnitude of the free energy barriers to the ensuing search for the native conformation. By coupling helix assembly with nascent tertiary interactions, compact folding intermediates in RNA also play a crucial role in ligand binding and RNA-protein recognition.

  8. Intermediate and Definitive Cleft Rhinoplasty.

    PubMed

    Gary, Celeste; Sykes, Jonathan M

    2016-11-01

    Intermediate and definitive cleft rhinoplasties are a challenging part of definitive cleft care. The anatomy of the cleft nose is severely affected by the structural deficits associated with congenital orofacial clefting. A comprehensive understanding of the related anatomy is crucial for understanding how to improve the appearance and function in patients with secondary cleft nasal deformities. Timing of intermediate and definitive rhinoplasty should be carefully considered. A thorough understanding of advanced rhinoplasty techniques is an important part of providing adequate care for patients with these deformities.

  9. Intermediate tax sanctions: an overview.

    PubMed

    Peregrine, M W

    1997-07-01

    New federal tax law applies intermediate tax sanctions when tax-exempt organizations enter into so-called excess benefit transactions with corporate insiders. The sanctions take the form of a two-tiered penalty excise tax, which is assessed not on the tax-exempt organization itself but on the insider who receives the excess benefit and the organizational managers and board members who knowingly participate in an improper transaction. The intermediate tax sanctions, therefore, present tax-planning challenges for tax-exempt hospitals and integrated delivery systems as well as for 501(c)(4) HMOs. Forthcoming treasury regulations are expected to add clarity to the new law.

  10. Barrierless tautomerization of Criegee intermediates via acid catalysis.

    PubMed

    Kumar, Manoj; Busch, Daryle H; Subramaniam, Bala; Thompson, Ward H

    2014-11-14

    The tautomerization of Criegee intermediates via a 1,4 β-hydrogen atom transfer to yield a vinyl hydroperoxide has been examined in the absence and presence of carboxylic acids. Electronic structure calculations indicate that the organic acids catalyze the tautomerization reaction to such an extent that it becomes a barrierless process. In contrast, water produces only a nominal catalytic effect. Since organic acids are present in parts-per-billion concentrations in the troposphere, the present results suggest that the acid-catalyzed tautomerization, which can also result in formation of hydroxyl radicals, may be a significant pathway for Criegee intermediates.

  11. Keto-Enol Thermodynamics of Breslow Intermediates.

    PubMed

    Paul, Mathias; Breugst, Martin; Neudörfl, Jörg-Martin; Sunoj, Raghavan B; Berkessel, Albrecht

    2016-04-20

    Breslow intermediates, first postulated in 1958, are pivotal intermediates in carbene-catalyzed umpolung. Attempts to isolate and characterize these fleeting amino enol species first met with success in 2012 when we found that saturated bis-Dipp/Mes imidazolidinylidenes readily form isolable, though reactive diamino enols with aldehydes and enals. In contrast, triazolylidenes, upon stoichiometric reaction with aldehydes, gave exclusively the keto tautomer, and no isolable enol. Herein, we present the synthesis of the "missing" keto tautomers of imidazolidinylidene-derived diamino enols, and computational thermodynamic data for 15 enol-ketone pairs derived from various carbenes/aldehydes. Electron-withdrawing substituents on the aldehyde favor enol formation, the same holds for N,N'-Dipp [2,6-di(2-propyl)phenyl] and N,N'-Mes [2,4,6-trimethylphenyl] substitution on the carbene component. The latter effect rests on stabilization of the diamino enol tautomer by Dipp substitution, and could be attributed to dispersive interaction of the 2-propyl groups with the enol moiety. For three enol-ketone pairs, equilibration of the thermodynamically disfavored tautomer was attempted with acids and bases but could not be effected, indicating kinetic inhibition of proton transfer.

  12. NN and Nd Scattering with Intermediate Dibaryons

    NASA Astrophysics Data System (ADS)

    Platonova, Maria N.

    2017-03-01

    Excitation of intermediate dibaryon resonances in hadronic processes accompanied by high momentum transfers is considered. It is shown that some basic features of NN inelastic scattering with single- or double-pion production can be effectively described by taking into account the short-range s-channel dibaryon excitation along with peripheral t-channel meson-exchange processes. In particular, isovector dibaryons with I(J^P)=1(2^+), 1(3^-) and 1(2^-) are shown to play an important role in reproducing the cross sections and especially polarization observables in the basic single-pion production reaction pp → dπ ^+, while an isoscalar I(J^P)=0(3^+) dibaryon is crucial for describing the basic double-pion production process pn → d (π π )_0. Possible generalization of resonance (dibaryon) mechanisms considered in NN scattering to Nd elastic and inelastic scattering is also discussed.

  13. Identification of triclosan intermediates produced by oxidative degradation using TiO2 in pure water and their endocrine disrupting activities.

    PubMed

    Sankoda, K; Matsuo, H; Ito, M; Nomiyama, K; Arizono, K; Shinohara, R

    2011-05-01

    The photodegradation pathways of 2-(2,4-dichlorophenoxy)-5-chlorophenol (triclosan) in water were studied. The main purposes were to identify structures of intermediates derived by radical reaction using TiO(2) advanced oxidation processes and to evaluate the endocrine disrupting activities in treated triclosan during oxidative reactions. Intermediates such as dichlorophenols, 2,8-dibenzo-p-dioxin, tetrachlorinated diphenyl ether (tetraclosan) and hydroxylated triclosan were produced by photoreaction. The estrogen, thyroid hormone and retinoid X receptor activities of the treated triclosan were measured with the yeast two-hybrid assay. It was found that tetraclosan and 2,4-dichlorophenol have stronger thyroid hormone activities than triclosan in the presence of S9.

  14. Non-enzymatic synthesis of the coenzymes, uridine diphosphate glucose and cytidine diphosphate choline, and other phosphorylated metabolic intermediates

    NASA Technical Reports Server (NTRS)

    Mar, A.; Dworkin, J.; Oro, J.

    1987-01-01

    Using urea and cyanamide, the two condensing agents considered to have been present on the primitive earth, uridine diphosphate glucose (UDPG), cytidine diphosphate choline (CDP-choline), glucose-1-phosphate (G1P), and glucose-6-phosphate (G6P) were synthesized under simulated prebiotic conditions. The reaction products were separated and identified using paper chromatography, thin layer chromatography, enzymatic analyses, and ion-pair reverse-phase high performance liquid chromatography. The possibility of nonenzymatic synthesis of metabolic intermediates on the primitive earth from simple precursors was thus demonstrated.

  15. Material Voices: Intermediality and Autism

    ERIC Educational Resources Information Center

    Trimingham, Melissa; Shaughnessy, Nicola

    2016-01-01

    Autism continues to be regarded enigmatically; a community that is difficult to access due to perceived disruptions of interpersonal connectedness. Through detailed observations of two children participating in the Arts and Humanities Research Council funded project "Imagining Autism: Drama, Performance and Intermediality as Interventions for…

  16. Learning through Literature: Geography, Intermediate.

    ERIC Educational Resources Information Center

    Sterling, Mary Ellen

    This resource book provides specific strategies and activities for integrating the intermediate geography curriculum with related children's literature selections. The book includes the following sections: (1) "World Geography Overview"; (2) "Oceans"; (3) "Polar Regions"; (4) "Islands"; (5) "Rain Forests"; (6) "Mountains"; (7) "Forests"; (8)…

  17. Intermediality and the Child Performer

    ERIC Educational Resources Information Center

    Budd, Natasha

    2016-01-01

    This report details examples of praxis in the creation and presentation of "Joy Fear and Poetry": an intermedial theatre performance in which children aged 7-12 years generated aesthetic gestures using a range of new media forms. The impetus for the work's development was a desire to make an intervention into habituated patterns of…

  18. AIDS Elementary/Intermediate Curriculum.

    ERIC Educational Resources Information Center

    Kellogg, Nancy Rader

    This Acquired Immune Deficiency Syndrome (AIDS) Curriculum was developed for intermediate elementary (5th, 6th, and 7th grade) students. It is an integrated unit that encompasses health, science, social studies, math, and language arts. The curriculum is comprised of nine class activities designed to meet the following objectives: (1) to determine…

  19. Conversation at the Intermediate Level

    ERIC Educational Resources Information Center

    Dunlop, Ian

    1975-01-01

    Discusses the use of free conversation, especially with regard to vocabulary. Recommends group discussion in the FL, using, at the intermediate level, limited, familiar vocabulary. At a higher level, words from a special technical vocabulary may be introduced, aurally and visually. A teaching example ("Traffic") is given with thorough…

  20. Materials System for Intermediate Temperature Solid Oxide Fuel Cell

    SciTech Connect

    Uday B. Pal; Srikanth Gopalan

    2005-01-24

    AC complex impedance spectroscopy studies were conducted between 600-800 C on symmetrical cells that employed strontium-and-magnesium-doped lanthanum gallate electrolyte, La{sub 0.9}Sr{sub 0.1}Ga{sub 0.8}Mg{sub 0.2}O{sub 3} (LSGM). The objective of the study was to identify the materials system for fabrication and evaluation of intermediate temperature (600-800 C) solid oxide fuel cells (SOFCs). The slurry-coated electrode materials had fine porosity to enhance catalytic activity. Cathode materials investigated include La{sub 1-x}Sr{sub x}MnO{sub 3} (LSM), LSCF (La{sub 1-x}Sr{sub x}Co{sub y}Fe{sub 1-y}O{sub 3}), a two-phase particulate composite consisting of LSM-doped-lanthanum gallate (LSGM), and LSCF-LSGM. The anode materials were Ni-Ce{sub 0.85}Gd{sub 0.15}O{sub 2} (Ni-GDC) and Ni-Ce{sub 0.6}La{sub 0.4}O{sub 2} (Ni-LDC) composites. Experiments conducted with the anode materials investigated the effect of having a barrier layer of GDC or LDC in between the LSGM electrolyte and the Ni-composite anode to prevent adverse reaction of the Ni with lanthanum in LSGM. For proper interpretation of the beneficial effects of the barrier layer, similar measurements were performed without the barrier layer. The ohmic and the polarization resistances of the system were obtained over time as a function of temperature (600-800 C), firing temperature, thickness, and the composition of the electrodes. The study revealed important details pertaining to the ohmic and the polarization resistances of the electrode as they relate to stability and the charge-transfer reactions that occur in such electrode structures.

  1. Potential Energy Surfaces for the Reactions of HO2 Radical with CH2O and HO2 in CO2 Environment.

    PubMed

    Masunov, Artëm E; Atlanov, Arseniy A; Vasu, Subith S

    2016-10-06

    We report on potential energies for the transition state, reactant, and product complexes along the reaction pathways for hydrogen transfer reactions to hydroperoxyl radical from formaldehyde H2CO + HO2 → HCO + H2O2 and another hydroperoxyl radical 2HO2 → H2O2 + O2 in the presence of one carbon dioxide molecule. Both covalently bonded intermediates and weak intermolecular complexes are identified and characterized. We found that reactions that involve covalent intermediates have substantially higher activation barriers and are not likely to play a role in hydrogen transfer kinetics. The van der Waals complexation with carbon dioxide does not affect hydrogen transfer from formaldehyde, but it lowers the barrier for hydroperoxyl self-reaction by nearly 3 kcal/mol. This indicates that CO2 environment is likely to have catalytic effect on HO2 self-reaction, which needs to be included in kinetic combustion mechanisms in supercritical CO2.

  2. Pathophysiology of hemolytic transfusion reactions.

    PubMed

    Davenport, Robertson D

    2005-07-01

    Hemolytic transfusion reactions (HTR) are systemic reactions provoked by immunologic red blood cell (RBC) incompatibility. Clinical and experimental observations of such reactions indicate that they proceed through phases of humoral immune reaction, activation of phagocytes, productions of cytokine mediators, and wide-ranging cellular responses. HTR have many features in common with the systemic inflammatory response syndrome (SIRS). Knowledge of the pathophysiologic mechanisms in HTR suggest that newer biological agents that target complement intermediates or proinflammatory cytokines may be effective agents in the treatment of severe HTRs.

  3. Racemization in Prins Cyclization Reactions

    PubMed Central

    Jasti, Ramesh

    2008-01-01

    Isotopic labeling experiments were performed in order to elucidate a new mechanism for racemization in Prins cyclization reactions. The loss in optical activity for these reactions was shown to occur by 2-oxonia-Cope rearrangements by way of a (Z)-oxocarbenium ion intermediate. Reaction conditions such as solvent, temperature, and the nucleophile employed played a critical role in whether an erosion in enantiomeric excess was observed. Additionally, certain structural features of Prins cyclization precursors were also shown to be important for preserving optical purity in these reactions. PMID:17031979

  4. Special Relativity and Reactions with Unstable Nuclei

    SciTech Connect

    Bertulani, C.A.

    2005-10-14

    Dynamical relativistic effects are often neglected in the description of reactions with unstable nuclear beams at intermediate energies (ELab {approx_equal} 100 MeV/nucleon). Evidently, this introduces sizable errors in experimental analysis and theoretical descriptions of these reactions. This is particularly important for the experiments held in GANIL/France, MSU/USA, RIKEN/Japan and GSI/Germany. I review a few examples where relativistic effects have been studied in nucleus-nucleus scattering at intermediate energies.

  5. Finding intermediates in the O2 activation pathways of non-heme iron oxygenases.

    PubMed

    Kovaleva, E G; Neibergall, M B; Chakrabarty, S; Lipscomb, J D

    2007-07-01

    Intermediates in the reaction cycle of an oxygenase are usually very informative with respect to the chemical mechanism of O 2 activation and insertion. However, detection of these intermediates is often complicated by their short lifetime and the regulatory mechanism of the enzyme designed to ensure specificity. Here, the methods used to detect the intermediates in an extradiol dioxygenase, a Rieske cis-dihydrodiol dioxygenase, and soluble methane monooxygenase are discussed. The methods include the use of alternative, chromophoric substrates, mutagenesis of active site catalytic residues, forced changes in substrate binding order, control of reaction rates using regulatory proteins, and initialization of catalysis in crystallo.

  6. On the relative preference of enamine/iminium pathways in an organocatalytic Michael addition reaction.

    PubMed

    Patil, Mahendra P; Sunoj, Raghavan B

    2009-05-04

    The mechanism of the organocatalyzed Michael addition between propanal and methyl vinyl ketone is investigated using the density functional and ab intio methods. Different modes of substrate activation offered by a secondary amine (pyrrolidine) organocatalyst are reported. The electrophilic activation of enone (P-I) through the formation of an iminium ion, and nucleophilic activation of propanal (P-II) in the form of enamine have been examined by identifying the corresponding transition states. The kinetic preference for the formation of key intermediates is established in an effort to identify the competing pathways associated with the title reaction. A comparison of barriers associated with different pathways as well as intermediate formation allows us to provide a suitable mechanistic rationale for Michael addition reactions catalyzed by a secondary amine. The overall barriers for the C-C bond formation pathways involving enol or iminium intermediates are identified as higher than the enamine pathway. Additionally, the generation of iminium is found to be less favored as compared to enamine formation. The effect of co-catalyst/protic solvent on the energetics of the overall reaction is also studied using the cluster continuum approach. Significant reduction in the activation energies for each step of the reaction is predicted for the solvent-assisted models. The co-catalyst assisted addition of propanal-enamine to methyl vinyl ketone is identified as the most preferred pathway (P-IV) for the Michael addition reaction. The results are in concurrence with the available experimental reports on the rate acceleration by the use of a co-catalyst in this reaction.

  7. Picosecond Studies of Chemical Intermediates

    DTIC Science & Technology

    1991-05-01

    encapsulation significantly modify photoisomerization reaction rates. In the case of t-stilbene complexed to various cyclodextrins we directly observed...43 Figure 7.6 Schematic of equilibrium between tight and loose stilbene/ cyclodextrin complexes...how frictional effects due to the local (or "restricted") environment of the inner cyclodextrin cavity modifed the motion necessary for reaction

  8. Substrate radical intermediates in soluble methane monooxygenase.

    PubMed

    Liu, Aimin; Jin, Yi; Zhang, Jingyan; Brazeau, Brian J; Lipscomb, John D

    2005-12-09

    EPR spin-trapping experiments were carried out using the three-component soluble methane monooxygenase (MMO). Spin-traps 5,5-dimethyl-1-pyrroline N-oxide (DMPO), alpha-4-pyridyl-1-oxide N-tert-butylnitrone (POBN), and nitrosobenzene (NOB) were used to investigate the possible formation of substrate radical intermediates during catalysis. In contrast to a previous report, the NADH-coupled oxidations of various substrates did not produce any trapped radical species when DMPO or POBN was present. However, radicals were detected by these traps when only the MMO reductase component and NADH were present. DMPO and POBN were found to be weak inhibitors of the MMO reaction. In contrast, NOB is a strong inhibitor for the MMO-catalyzed nitrobenzene oxidation reaction. When NOB was used as a spin-trap in the complete MMO system with or without substrate, EPR signals from an NOB radical were detected. We propose that a molecule of NOB acts simultaneously as a substrate and a spin-trap for MMO, yielding the long-lived radical and supporting a stepwise mechanism for MMO.

  9. Mechanics of vimentin intermediate filaments

    NASA Technical Reports Server (NTRS)

    Wang, Ning; Stamenovic, Dimitrijie

    2002-01-01

    It is increasingly evident that the cytoskeleton of living cells plays important roles in mechanical and biological functions of the cells. Here we focus on the contribution of intermediate filaments (IFs) to the mechanical behaviors of living cells. Vimentin, a major structural component of IFs in many cell types, is shown to play an important role in vital mechanical and biological functions such as cell contractility, migration, stiffness, stiffening, and proliferation.

  10. Selective insertion of sulfur dioxide reduction intermediates on graphene oxide.

    PubMed

    Humeres, Eduardo; Debacher, Nito A; Smaniotto, Alessandra; de Castro, Karen M; Benetoli, Luís O B; de Souza, Eduardo P; Moreira, Regina de F P M; Lopes, Cristiane N; Schreiner, Wido H; Canle, Moisés; Santaballa, J Arturo

    2014-04-22

    Graphite microparticles (d50 6.20 μm) were oxidized by strong acids, and the resultant graphite oxide was thermally exfoliated to graphene oxide sheets (MPGO, C/O 1.53). Graphene oxide was treated with nonthermal plasma under a SO2 atmosphere at room temperature. The XPS spectrum showed that SO2 was inserted only as the oxidized intermediate at 168.7 eV in the S 2p region. Short thermal shocks at 600 and 400 °C, under an Ar atmosphere, produced reduced sulfur and carbon dioxide as shown by the XPS spectrum and TGA analysis coupled to FTIR. MPGO was also submitted to thermal reaction with SO2 at 630 °C, and the XPS spectrum in the S 2p region at 164.0 eV showed that this time only the nonoxidized episulfide intermediate was inserted. Plasma and thermal treatment produced a partial reduction of MPGO. The sequence of thermal reaction followed by plasma treatment inserted both sulfur intermediates. Because oxidized and nonoxidized intermediates have different reactivities, this selective insertion would allow the addition of selective types of organic fragments to the surface of graphene oxide.

  11. Detection and accumulation of tetrahedral intermediates in elastase catalysis.

    PubMed Central

    Fink, A L; Meehan, P

    1979-01-01

    Tetrahedral intermediates in the reaction of elastase with specific di- and tripeptide p-nitroanilide substrates have been detected, accumulated, and stabilized at high pH by using subzero temperatures and fluid aqueous/organic cryosolvents. The tetrahedral adducts are characterized by spectra with lambda max of 359 +/- 2 nm, compared with thata of 380 nm for p-nitroaniline and 315-320 nm for the substrates. The maximal concentration of intermediate that could be accumulated varied with the different substrates from 40 to 100% of the active enzyme present. The pH dependence of the reactions indicated that formation of the tetrahedral intermediates was rate-limiting at low pH (pK* = 7.0 at -39 degrees C) and that collapse to the acylenzymes was rate-determining at high pH. When corrected for the effect of temperature and cosolvent, the rate of intermediate formation was in good agreement with that measured at 25 degrees C in aqueous solution by stopped-flow techniques. PMID:36609

  12. Intermediate Temperature Solid Oxide Fuel Cell Development

    SciTech Connect

    S. Elangovan; Scott Barnett; Sossina Haile

    2008-06-30

    Solid oxide fuel cells (SOFCs) are high efficiency energy conversion devices. Present materials set, using yttria stabilized zirconia (YSZ) electrolyte, limit the cell operating temperatures to 800 C or higher. It has become increasingly evident however that lowering the operating temperature would provide a more expeditious route to commercialization. The advantages of intermediate temperature (600 to 800 C) operation are related to both economic and materials issues. Lower operating temperature allows the use of low cost materials for the balance of plant and limits degradation arising from materials interactions. When the SOFC operating temperature is in the range of 600 to 700 C, it is also possible to partially reform hydrocarbon fuels within the stack providing additional system cost savings by reducing the air preheat heat-exchanger and blower size. The promise of Sr and Mg doped lanthanum gallate (LSGM) electrolyte materials, based on their high ionic conductivity and oxygen transference number at the intermediate temperature is well recognized. The focus of the present project was two-fold: (a) Identify a cell fabrication technique to achieve the benefits of lanthanum gallate material, and (b) Investigate alternative cathode materials that demonstrate low cathode polarization losses at the intermediate temperature. A porous matrix supported, thin film cell configuration was fabricated. The electrode material precursor was infiltrated into the porous matrix and the counter electrode was screen printed. Both anode and cathode infiltration produced high performance cells. Comparison of the two approaches showed that an infiltrated cathode cells may have advantages in high fuel utilization operations. Two new cathode materials were evaluated. Northwestern University investigated LSGM-ceria composite cathode while Caltech evaluated Ba-Sr-Co-Fe (BSCF) based pervoskite cathode. Both cathode materials showed lower polarization losses at temperatures as low as 600

  13. Chronic candida endophthalmitis as a cause of intermediate uveitis

    PubMed Central

    Amin, Rowayda Mohamed; Hamdy, Islam; Osman, Ihab Mohamed

    2015-01-01

    Intermediate uveitis is a subset of intraocular inflammation where vitritis is the most consistent sign, with or without snowball opacities or snow banks over the pars plana. Some patients will have an associated underlying systemic disease such as sarcoidosis, multiple sclerosis, ocular tuberculosis, inflammatory bowel disease, possibly Behçet's disease and intraocular lymphoma, whereas some will be classified as pars planitis in case of the lack of an identifiable systemic disease association. Our patient, a 47-year-old woman, developed intermediate uveitis after cataract surgery in her right eye, was misdiagnosed as pars planitis, and received steroid monotherapy for 8 months. Her inflammation only fully resolved after vitrectomy with removal of the intraocular lens (IOL) and capsular bag. Oral fluconazole and intravitreal amphotericin B injection had failed to resolve her inflammation when Candida albicans was identified as the cause of her persistent intermediate uveitis. PMID:25870216

  14. Radical SAM catalysis via an organometallic intermediate with an Fe-[5'-C]-deoxyadenosyl bond.

    PubMed

    Horitani, Masaki; Shisler, Krista; Broderick, William E; Hutcheson, Rachel U; Duschene, Kaitlin S; Marts, Amy R; Hoffman, Brian M; Broderick, Joan B

    2016-05-13

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to cleave SAM to initiate diverse radical reactions. These reactions are thought to involve the 5'-deoxyadenosyl radical intermediate, which has not yet been detected. We used rapid freeze-quenching to trap a catalytically competent intermediate in the reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme. Characterization of the intermediate by electron paramagnetic resonance and (13)C, (57)Fe electron nuclear double-resonance spectroscopies reveals that it contains an organometallic center in which the 5' carbon of a SAM-derived deoxyadenosyl moiety forms a bond with the unique iron site of the [4Fe-4S] cluster. Discovery of this intermediate extends the list of enzymatic bioorganometallic centers to the radical SAM enzymes, the largest enzyme superfamily known, and reveals intriguing parallels to B12 radical enzymes.

  15. 4,6-Dinitrobenzofuroxan, an Important Explosive Intermediate.

    DTIC Science & Technology

    1983-02-01

    A major drawback to this method is that the intermediate picryl azide ( PiAz ) must be isolated then heated under reflux in xylene to give DNBF. PiAz is...NO, NO, PiCI PiAz The method of choice for preparation of DNB? could be either the nitration of BF or the "one-pot" reaction of PiCl with sodium azide

  16. Electrochemical incineration of 4-chlorophenol and the identification of products and intermediates by mass spectrometry

    SciTech Connect

    Johnson, S.K.; Houk, L.L.; Feng, J.; Houk, R.S.; Johnson, D.C. )

    1999-08-01

    This report summarizes results obtained as part of a larger effort to demonstrate the applicability of electrolytic procedures for the direct anodic (oxidative) degradation of toxic organic wastes. The authors refer to this process as electrochemical incineration (ECI) because the ultimate degradation products are equivalent to those achieved by thermal incineration processes. In this work, the ECI of 4-chlorophenol is achieved in an aqueous medium using a platinum anode coated with a quaternary metal oxide film containing Ti, Ru, Sn, and Sb oxides. The electrode is stable and active when used with a solid Nafion membrane without the addition of soluble supporting electrolyte. Liquid chromatography (LC), including reverse phase and ion exchange chromatography, is coupled with electrospray mass spectrometry (ES-MS) and used, along with gas chromatography-mass spectrometry (GC-MS) and measurements of pH, chemical oxygen demand (COD), and total organic carbon (TOC), to study the reaction and identify the intermediate products from the ECI of 4-chlorophenol. Twenty-six intermediate products are identified and reported. The most abundant of these products are benzoquinone, 4-chlorocatechol, maleic acid, succinic acid, malonic acid, and the inorganic anions chloride, chlorate, and perchlorate. After 24 h of ECI, a solution that initially contained 108 ppm 4-chlorophenol yields only 1 ppm TOC with 98% of the original chlorine remaining in the specified inorganic forms. LC-ES-MS and direct infusion ES-MS detection limits are between 80 ppb and 4 ppm for these intermediate products. Elemental analysis of the electrolyzed solutions by inductively coupled plasma mass spectrometry ICP-MS showed that only trace amounts of the metallic elements comprising the metal oxide film were present in the solution.

  17. Organic impurity profiling of methylone and intermediate compounds synthesized from catechol.

    PubMed

    Heather, Erin; Bortz, Adam; Shimmon, Ronald; McDonagh, Andrew M

    2016-11-25

    This work examined the synthesis and organic impurity profile of methylone prepared from catechol. The primary aim of this work was to determine whether the synthetic pathway used to prepare 3,4-methylenedioxypropiophenone could be ascertained through analysis of the synthesized methylone. The secondary aim was the structural elucidation and origin determination of the organic impurities detected in methylone and the intermediate compounds. The organic impurities present in the reaction products were identified using GC-MS and NMR spectroscopy. Six organic impurities were detected in 1,3-benzodioxole and identified as the 1,3-benzodioxole dimer, 1,3-benzodioxole trimer, [1,3] dioxolo[4,5-b]oxanthrene, 4,4'-, 4,5'-, and 5,5'-methylenebis-1,3-benzodioxole. Six organic impurities were detected in 3,4-methylenedioxypropiophenone and identified as (2-hydroxyphenyl) propanoate, [2-(chloromethoxy) phenyl] propanoate, (2-propanoyloxyphenyl)propanoate, 5-[1-(1,3-benzodioxol-5-yl)prop-1-enyl]-1,3-benzodioxole, (5E)- and (5Z)-7-(1,3-benzodioxol-5-yl)-5-ethylidene-6-methyl-cyclopenta[f][1,3]benzodioxole). Exploratory synthetic experiments were also conducted to unambiguously identify the organic impurities detected in 3,4-methylenedioxypropiophenone. Two organic impurities were detected in 5-bromo-3,4-methylenedioxypropiophenone and identified as [2-(chloromethoxy)phenyl] propanoate and 3,4-methylenedioxypropiophenone. Five organic impurities were detected in methylone and identified as 3,4-methylenedioxypropiophenone, 1-(1,3-benzodioxol-5-yl)-N-methyl-propan-1-imine, 1-(1,3-benzodioxol-5-yl)-2-methylimino-propan-1-one, 1-(1,3-benzodioxol-5-yl)-N1,N2-dimethyl-propane-1,2-diimine and butylated hydroxytoluene. The origin of these organic impurities was also ascertained, providing valuable insight into the chemical profiles of methylone and the intermediate compounds. However, neither the catechol precursor nor the 1,3-benzodioxole intermediate could be identified based on the

  18. MicroRNA profiling of human intermediate monocytes.

    PubMed

    Zawada, Adam M; Zhang, Lu; Emrich, Insa E; Rogacev, Kyrill S; Krezdorn, Nicolas; Rotter, Björn; Fliser, Danilo; Devaux, Yvan; Ziegler-Heitbrock, Loems; Heine, Gunnar H

    2017-03-01

    Among the three human monocyte subsets, intermediate CD14++CD16+ monocytes have been characterized as particularly proinflammatory cells in experimental studies and as potential biomarkers of cardiovascular risk in clinical cohorts. To further substantiate the distinct role of intermediate monocytes within human monocyte heterogeneity, we assessed subset-specific expression of miRNAs as central epigenetic regulators of gene expression. We hypothesized that intermediate monocytes have a distinct miRNA profile compared to classical and non-classical monocytes. By using small RNA-seq we analyzed 662 miRNAs in the three monocyte subsets. We identified 38 miRNAs that are differentially expressed in intermediate monocytes compared to both classical and non-classical monocytes with a p value of <10(-10), of which two miRNAs - miR-6087 (upregulated) and miR-150-5p (downregulated) - differed in their expression more than ten-fold. Pathway analysis of the 38 differentially expressed miRNAs linked intermediate monocytes to distinct biological processes such as gene regulation, cell differentiation, toll-like receptor signaling as well as antigen processing and presentation. Moreover, differentially expressed miRNAs were connected to those genes that we previously identified as markers of intermediate monocytes. In aggregation, we provide first genome-wide miRNA data in the context of monocyte heterogeneity, which substantiate the concept of monocyte trichotomy in human immunity. The identification of miRNAs that are specific for intermediate monocytes may allow to develop strategies, which particularly target this cell population while sparing the other two subsets.

  19. Error Analysis in Composition of Iranian Lower Intermediate Students

    ERIC Educational Resources Information Center

    Taghavi, Mehdi

    2012-01-01

    Learners make errors during the process of learning languages. This study examines errors in writing task of twenty Iranian lower intermediate male students aged between 13 and 15. A subject was given to the participants was a composition about the seasons of a year. All of the errors were identified and classified. Corder's classification (1967)…

  20. Vocabulary Learning Strategies of Iranian Upper-Intermediate EFL Learners

    ERIC Educational Resources Information Center

    Khatib, Mohammad; Hassanzadeh, Mohammad; Rezaei, Saeed

    2011-01-01

    This study examines the preferred vocabulary learning strategies of Iranian upper-intermediate EFL learners. In order to identify the aforementioned group in terms of language proficiency, a TOEFL test was administered to a population of 146 undergraduate EFL students at the university of Vali-e-Asr in Rafsanjan, Iran. Those scoring above 480 were…

  1. Reactions of aminomalononitrile with electrophiles. [simulating prebiotic conditions

    NASA Technical Reports Server (NTRS)

    Thanassi, J. W.

    1975-01-01

    Aminomalononitrile (HCN trimer) reacts with electrophiles such as aldehydes and acrylonitrile under very mild conditions of temperature and pH to produce intermediates which, after acid hydrolysis, yield amino acids. The following amino acids have been identified and quantitated: glycine, D,L-erythro- and D,L-threo-beta-hydroxyaspartic acids, D,L glutamic acid, and D,L-threonine and allo-threonine. The mechanism of their formation and the possible significance of these reactions in prebiotic syntheses are discussed.

  2. Role of Intermediate Filaments in Vesicular Traffic

    PubMed Central

    Margiotta, Azzurra; Bucci, Cecilia

    2016-01-01

    Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway. PMID:27120621

  3. Diphosphine is an intermediate in the photolysis of phosphine to phosphorus and hydrogen. [Jupiter atmospheric chemistry

    NASA Technical Reports Server (NTRS)

    Ferris, J. P.; Benson, R.

    1980-01-01

    The photolysis of phosphine to red phosphorus (P4) and hydrogen is investigated in light of the potential significance of the reaction in the atmospheric chemistry of Jupiter. It is reported that the photolysis of PH3 at room temperature by a 206.2-nm light source gave rise to a product identified by its UV and IR spectra and gas chromatographic retention time as P2H4, the yield of which is found to increase to a maximum and then decrease to 20% of the maximum value with illumination time. A mechanism for phosphine photolysis including diphosphine formation as an intermediate step is proposed, and it is concluded that P2H4 is a likely constituent of the atmospheres of the Jovian planets.

  4. Fates of imine intermediates in radical cyclizations of N-sulfonylindoles and ene-sulfonamides.

    PubMed

    Zhang, Hanmo; Hay, E Ben; Geib, Stephen J; Curran, Dennis P

    2015-01-01

    Two new fates of imine intermediates formed on radical cyclizations of ene-sulfonamides have been identified, reduction and hydration/fragmentation. Tin hydride-mediated cyclizations of 2-halo-N-(3-methyl-N-sulfonylindole)anilines provide spiro[indoline-3,3'-indolones] or spiro-3,3'-biindolines (derived from imine reduction), depending on the indole C2 substituent. Cyclizations of 2-haloanilide derivatives of 3-carboxy-N-sulfonyl-2,3-dihydropyrroles also presumably form spiro-imines as primary products. However, the lactam carbonyl group facilitates the ring-opening of these cyclic imines by a new pathway of hydration and retro-Claisen-type reaction, providing rearranged 2-(2'-formamidoethyl)oxindoles.

  5. Fates of imine intermediates in radical cyclizations of N-sulfonylindoles and ene-sulfonamides

    PubMed Central

    Zhang, Hanmo; Hay, E Ben; Geib, Stephen J

    2015-01-01

    Summary Two new fates of imine intermediates formed on radical cyclizations of ene-sulfonamides have been identified, reduction and hydration/fragmentation. Tin hydride-mediated cyclizations of 2-halo-N-(3-methyl-N-sulfonylindole)anilines provide spiro[indoline-3,3'-indolones] or spiro-3,3'-biindolines (derived from imine reduction), depending on the indole C2 substituent. Cyclizations of 2-haloanilide derivatives of 3-carboxy-N-sulfonyl-2,3-dihydropyrroles also presumably form spiro-imines as primary products. However, the lactam carbonyl group facilitates the ring-opening of these cyclic imines by a new pathway of hydration and retro-Claisen-type reaction, providing rearranged 2-(2'-formamidoethyl)oxindoles. PMID:26664585

  6. Reaction Pathways and Kinetics of a Cyanobacterial Neurotoxin β-N-Methylamino-L-Alanine (BMAA) during Chlorination.

    PubMed

    Chen, Yi-Ting; Chen, Wan-Ru; Liu, Zhi-Quan; Lin, Tsair-Fuh

    2017-02-07

    β-N-Methylamino-L-alanine (BMAA), a probable cause of the amyotrophic lateral sclerosis/parkinsonism-dementia complex (ALS/PDC), or Alzheimer's disease, has been identified in more than 20 cyanobacterial genera. However, its removal and fate in drinking water has never been reported before. In this study, the reaction of BMAA with chlorine, a common drinking-water oxidant/disinfectant, was investigated. A liquid chromatograph coupled with a triple quadrupole mass spectrometer was employed to quantify BMAA and its intermediates. Upon chlorination, four chlorinated intermediates, each with one or two chlorines, were identified. The disappearance of BMAA caused by chlorine follows a second-order reaction, with the rate constant k1 is 5.0 × 10(4) M(-1) s(-1) at pH ∼7.0. The chlorinated intermediates were found to further react with free chlorine, exhibiting a second-order rate constant k3 = 16.8 M(-1) s(-1). After all free chlorine was consumed, the chlorinated intermediates autodecomposed slowly with a first order rate constant k2 = 0.003 min(-1); when a reductant was added, these chlorinated intermediates were then reduced back to BMAA. The results as described shed a useful light on the reactivity, appearance, and removal of BMAA in the chlorination process of a drinking-water system.

  7. Detailed mechanism of the autoxidation of N-hydroxyurea catalyzed by a superoxide dismutase mimic Mn(III) porphyrin: formation of the nitrosylated Mn(II) porphyrin as an intermediate.

    PubMed

    Kalmár, József; Biri, Bernadett; Lente, Gábor; Bányai, István; Budimir, Ana; Biruš, Mladen; Batinić-Haberle, Ines; Fábián, István

    2012-10-14

    The in vitro autoxidation of N-hydroxyurea (HU) is catalyzed by Mn(III)TTEG-2-PyP(5+), a synthetic water soluble Mn(III) porphyrin which is also a potent mimic of the enzyme superoxide dismutase. The detailed mechanism of the reaction is deduced from kinetic studies under basic conditions mostly based on data measured at pH = 11.7 but also including some pH-dependent observations in the pH range 9-13. The major intermediates were identified by UV-vis spectroscopy and electrospray ionization mass spectrometry. The reaction starts with a fast axial coordination of HU to the metal center of Mn(III)TTEG-2-PyP(5+), which is followed by a ligand-to-metal electron transfer to get Mn(II)TTEG-2-PyP(4+) and the free radical derived from HU (HU˙). Nitric oxide (NO) and nitroxyl (HNO) are minor intermediates. The major pathway for the formation of the most significant intermediate, the {MnNO} complex of Mn(II)TTEG-2-PyP(4+), is the reaction of Mn(II)TTEG-2-PyP(4+) with NO. We have confirmed that the autoxidation of the intermediates opens alternative reaction channels, and the process finally yields NO(2)(-) and the initial Mn(III)TTEG-2-PyP(5+). The photochemical release of NO from the {MnNO} intermediate was also studied. Kinetic simulations were performed to validate the deduced rate constants. The investigated reaction has medical implications: the accelerated production of NO and HNO from HU may be utilized for therapeutic purposes.

  8. Detailed Mechanism of the Autoxidation of N-hydroxyurea Catalyzed by a Superoxide Dismutase Mimic Mn(III) Porphyrin: Formation of the Nitrosylated Mn(II) Porphyrin as an Intermediate

    PubMed Central

    Kalmár, József; Biri, Bernadett; Bányai, István; Budimir, Ana; Biruš, Mladen; Batinić-Haberle, Ines; Fábián, István

    2012-01-01

    The in vitro autoxidation of N-hydroxyurea (HU) is catalyzed by MnIIITTEG-2-PyP5+, a synthetic water soluble Mn(III) porphyrin which is also a potent mimic of the enzyme superoxide dismutase. The detailed mechanism of the reaction is deduced from kinetic studies under basic conditions mostly based on data measured at pH = 11.7 but also including some pH-dependent observations in the pH range 9 – 13. The major intermediates were identified by UV-vis spectroscopy and electrospray ionization mass spectrometry. The reaction starts with a fast axial coordination of HU to the metal center of MnIIITTEG-2-PyP5+, which is followed by a ligand-to-metal electron transfer to get MnIITTEG-2-PyP4+ and the free radical derived from HU (HU•). Nitric oxide (NO) and nitroxyl (HNO) are minor intermediates. The major pathway for the formation of the most significant intermediate, the {MnNO} complex of MnIITTEG-2-PyP4+, is the reaction of MnIITTEG-2-PyP4+ with NO. We have confirmed that the autoxidation of the intermediates open alternative reaction channels, and the process finally yields NO2− and the initial MnIIITTEG-2-PyP5+. The photochemical release of NO from the {MnNO} intermediate was also studied. Kinetic simulations were performed to validate the deduced rate constants. The investigated reaction has medical implications: the accelerated production of NO and HNO from HU may be utilized for therapeutic purposes. PMID:22911446

  9. Lithium Cell Reactions.

    DTIC Science & Technology

    1983-12-01

    SUPPLEMENTARY NOTES It. KEY WORDS (Continue on reverse .,ide if necessary and Identify by block number) Batteries Thionyl Chloride Batteries Lithium ...Batteries Lithium Cells Primary Batteries Thionyl Chloride Cells Non Rechargeable Batteries Electrochemical Reactions 20. ABSTRACT (Continue on reverse...INVESTIGATION OF CHEMICAL, ELECTROCHEMICAL AND PARASITIC REACTIONS IN LITHIUM - THIONYL CHLORIDE CELLS .......................................... 1 1.0 IN TRO D UC

  10. Applications of Reaction Rate

    ERIC Educational Resources Information Center

    Cunningham, Kevin

    2007-01-01

    This article presents an assignment in which students are to research and report on a chemical reaction whose increased or decreased rate is of practical importance. Specifically, students are asked to represent the reaction they have chosen with an acceptable chemical equation, identify a factor that influences its rate and explain how and why it…

  11. Catalytic degradation of recalcitrant pollutants by Fenton-like process using polyacrylonitrile-supported iron (II) phthalocyanine nanofibers: Intermediates and pathway.

    PubMed

    Zhu, Zhexin; Chen, Yi; Gu, Yan; Wu, Fei; Lu, Wangyang; Xu, Tiefeng; Chen, Wenxing

    2016-04-15

    Iron (II) phthalocyanine (FePc) molecules were isolated in polyacrylonitrile (PAN) nanofibers by electrospinning to prevent the formation of dimers and oligomers. Carbamazepine (CBZ) and Rhodamine B (RhB) degradation was investigated during a Fenton-like process with FePc/PAN nanofibers. Classical quenching tests with isopropanol and electron paramagnetic resonance tests with 5,5-dimethyl-pyrroline-oxide as spin-trapping agent were performed to determine the formation of active species during hydrogen peroxide (H2O2) decomposition by FePc/PAN nanofibers. After eight recycles for CBZ degradation over the FePc/PAN nanofibers/H2O2 system, the removal ratios of CBZ remained at 99%. Seven by-products of RhB and twelve intermediates of CBZ were identified using ultra-performance liquid chromatography and high-resolution mass spectrometry. Pathways of CBZ and RhB degradation were proposed based on the identified intermediates. As the reaction proceeded, all CBZ and RhB aromatic nucleus intermediates decreased and were transformed to small acids, but also to potentially toxic epoxide-containing intermediates and acridine, because of the powerful oxidation ability of •OH in the catalytic system.

  12. EGRET sources at intermediate galactic latitude

    NASA Technical Reports Server (NTRS)

    Halpern, Jules P. (Principal Investigator)

    1996-01-01

    This paper presents the abstracts of four papers (using ROSAT data) that are submitted to refereed journals during the current reporting period. The papers are: (1) Extreme x-ray variability in the narrow-line QSO PHL 1092; (2) The Geminga pulsar (soft x-ray variability and an EUVE observation); (3) a broad-band x-ray study of the geminga pulsar; and (4) Classification of IRAS-selected x-ray galaxies in the ROSAT all-sky survey. The abstracts of these papers are given in the next four sections of this report, and their status is given in the Appendix. Finally, two new projects (De-identifying a non-AGN and EGRET sources at intermediate galactic latitude) for which ROSAT data were recently received are currently being studied under this grant. A summary of work in progress on these new projects is given in the last two sections of this report.

  13. A Caged, Destabilized Free Radical Intermediate in the Q Cycle

    PubMed Central

    Vennam, Preethi R.; Fisher, Nicholas; Krzyaniak, Matthew D.; Kramer, David M.

    2013-01-01

    The Rieske/cytochrome b complexes, also known as cytochrome bc complexes, catalyze a unique oxidant-induced reduction reaction at their quinol oxidase sites (Qo), in which substrate hydroquinone reduces two distinct electron transfer chains, one through a series of high-potential electron carriers, the second through low-potential cytochrome b. This reaction is a critical step in energy storage by the Q-cycle. The semiquinone intermediate in this reaction can reduce O2 to produce deleterious superoxide. It is yet unknown how the enzyme controls this reaction, though numerous models are proposed. In previous work we trapped a Q-cycle semiquinone anion intermediate, termed SQo, in bacterial cyt bc1 by rapid freeze-quenching. In this work, we apply pulsed EPR techniques to determine the location and properties of SQo in the mitochondrial complex. In contrast to semiquinone intermediates in other enzymes, SQo is not thermodynamically stabilized, and may even be destabilized with respect to solution. It is trapped in the Qo at a site, which is distinct from previously described inhibitor-binding sites, yet sufficiently close to cytochrome bL to allow rapid electron transfer. The binding site and EPR analysis show that SQo is not stabilized by hydrogen bonds to proteins. The formation of SQo involves “stripping” of both substrate -OH protons during the initial oxidation step, as well as conformational changes of the semiquinone and Qo proteins. The resulting charged radical is kinetically trapped, rather than thermodynamically stabilized (as in most enzymatic semiquinone species), conserving redox energy to drive electron transfer to cytochrome bL, while minimizing certain Q-cycle bypass reactions including oxidation of pre-reduced cytochrome b and reduction of O2. PMID:24009094

  14. Cerium doped red mud catalytic ozonation for bezafibrate degradation in wastewater: Efficiency, intermediates, and toxicity.

    PubMed

    Xu, Bingbing; Qi, Fei; Sun, Dezhi; Chen, Zhonglin; Robert, Didier

    2016-03-01

    In this study, the performance of bezafibrate (BZF) degradation and detoxification in the aqueous phase using cerium-modified red mud (RM) catalysts prepared using different cerium sources and synthesis methods were evaluated. Experimental results showed that the surface cerium modification was responsible for the development of the catalytic activity of RM and this was influenced by the cerium source and the synthesis method. Catalyst prepared from cerium (IV) by precipitation was found to show the best catalytic activity in BZF degradation and detoxification. Reactive oxygen species including peroxides, hydroxyl radicals, and super oxide ions were identified in all reactions and we proposed the corresponding catalytic reaction mechanism for each catalyst that prepared from different cerium source and method. This was supported by the intermediates profiles that were generated upon BZF degradation. The surface and the structural properties of cerium-modified RM were characterized in detail by several analytical methods. Two interesting findings were made: (1) the surface texture (specific surface area and mesoporous volume) influenced the catalytic reaction pathway; and (2) Ce(III) species and oxygen vacancies were generated on the surface of the catalyst after cerium modification. This plays an important role in the development of the catalytic activity.

  15. Elucidation of intermediates and mechanisms in heterogeneous catalysis using infrared spectroscopy.

    PubMed

    Savara, Aditya; Weitz, Eric

    2014-01-01

    Infrared spectroscopy has a long history as a tool for the identification of chemical compounds. More recently, various implementations of infrared spectroscopy have been successfully applied to studies of heterogeneous catalytic reactions with the objective of identifying intermediates and determining catalytic reaction mechanisms. We discuss selective applications of these techniques with a focus on several heterogeneous catalytic reactions, including hydrogenation, deNOx, water-gas shift, and reverse-water-gas shift. The utility of using isotopic substitutions and other techniques in tandem with infrared spectroscopy is discussed. We comment on the modes of implementation and the advantages and disadvantages of the various infrared techniques. We also note future trends and the role of computational calculations in such studies. The infrared techniques considered are transmission Fourier transform infrared spectroscopy, infrared reflection-absorption spectroscopy, polarization-modulation infrared reflection-absorption spectroscopy, sum-frequency generation, diffuse reflectance infrared Fourier transform spectroscopy, attenuated total reflectance, infrared emission spectroscopy, photoacoustic infrared spectroscopy, and surface-enhanced infrared absorption spectroscopy.

  16. Nitrite dismutase reaction mechanism: kinetic and spectroscopic investigation of the interaction between nitrophorin and nitrite.

    PubMed

    He, Chunmao; Howes, Barry D; Smulevich, Giulietta; Rumpel, Sigrun; Reijerse, Edward J; Lubitz, Wolfgang; Cox, Nicholas; Knipp, Markus

    2015-04-01

    Nitrite is an important metabolite in the physiological pathways of NO and other nitrogen oxides in both enzymatic and nonenzymatic reactions. The ferric heme b protein nitrophorin 4 (NP4) is capable of catalyzing nitrite disproportionation at neutral pH, producing NO. Here we attempt to resolve its disproportionation mechanism. Isothermal titration calorimetry of a gallium(III) derivative of NP4 demonstrates that the heme iron coordinates the first substrate nitrite. Contrary to previous low-temperature EPR measurements, which assigned the NP4-nitrite complex electronic configuration solely to a low-spin (S = 1/2) species, electronic absorption and resonance Raman spectroscopy presented here demonstrate that the NP4-NO2(-) cofactor exists in a high-spin/low-spin equilibrium of 7:3 which is in fast exchange in solution. Spin-state interchange is taken as evidence for dynamic NO2(-) coordination, with the high-spin configuration (S = 5/2) representing the reactive species. Subsequent kinetic measurements reveal that the dismutation reaction proceeds in two discrete steps and identify an {FeNO}(7) intermediate species. The first reaction step, generating the {FeNO}(7) intermediate, represents an oxygen atom transfer from the iron bound nitrite to a second nitrite molecule in the protein pocket. In the second step this intermediate reduces a third nitrite substrate yielding two NO molecules. A nearby aspartic acid residue side-chain transiently stores protons required for the reaction, which is crucial for NPs' function as nitrite dismutase.

  17. Displays for future intermediate UAV

    NASA Astrophysics Data System (ADS)

    Desjardins, Daniel; Metzler, James; Blakesley, David; Rister, Courtney; Nuhu, Abdul-Razak

    2008-04-01

    The Dedicated Autonomous Extended Duration Airborne Long-range Utility System (DAEDALUS) is a prototype Unmanned Aerial Vehicle (UAV) that won the 2007 AFRL Commander's Challenge. The purpose of the Commander's Challenge was to find an innovative solution to urgent warfighter needs by designing a UAV with increased persistence for tactical employment of sensors and communication systems. DAEDALUS was chosen as a winning prototype by AFRL, AFMC and SECAF. Follow-on units are intended to fill an intermediate role between currently fielded Tier I and Tier II UAV's. The UAV design discussed in this paper, including sensors and displays, will enter Phase II for Rapid Prototype Development with the intent of developing the design for eventual production. This paper will discuss the DAEDALUS UAV prototype system, with particular focus on its communications, to include the infrared sensor and electro-optical camera, but also displays, specifically man-portable.

  18. Intermediate superconductive magnetic energy storage

    SciTech Connect

    Masuda, M.; Fujino, H.; Iwamoto, M.; Murakomi, M.; Shintomi, T.; Veda, K.

    1983-05-01

    In the past decade, the superconducting magnetic energy storage (SMES) for application to peak shaving in utility has been investigated in a manner to construct the huge superconducting coil in bed rock. To confine the strong electromagnetic forces accompanied with the high magnetic field, megaton structures, no matter how they will be constructed in a liquid helium temperature, are needed. To meet such a requirement, the revolutionary idea was proposed that the superconducting coil would be constructed on the underground bed rock. Here presented is a 10 MWh unit as an intermediate SMES that is a milestone along the distant way of RandD of SMES against 1,000 - 10,000 MWh unit which advocate the replacement of the hydro-pumped station. Therefore, even if the 10 MWh unit would not function as a storage in the utility network, its design should also consider the same situation.

  19. Microleakage of intermediate restorative materials.

    PubMed

    Lim, K C

    1990-03-01

    This study compares the microleakage of a glass ionomer cement, Ketac Fil, used without cavity conditioning, with the established intermediate restorative materials, Cavit-W, and a reinforced zinc oxide-eugenol cement, Kalzinol. Microleakage was assessed using an electrochemical technique. At the end of 30 days, the materials tested, listed in decreasing order of microleakage, were Cavit-W, Ketac Fil inserted without cavity conditioning, Kalzinol, and the control group of Ketac Fil inserted into conditioned cavities. There was no significant difference in the microleakage observed in Ketac Fil restorations inserted without cavity conditioning and Kalzinol (p = 0.450), while the differences between the other groups were highly significant (p less than 0.001).

  20. INTERMEDIATE FILAMENTS IN SMOOTH MUSCLE

    PubMed Central

    Tang, Dale D.

    2008-01-01

    The intermediate filament (IF) network is one of the three cytoskeletal systems in smooth muscle. The type III IF proteins vimentin and desmin are major constituents of the network in smooth muscle cells and tissues. Lack of vimentin or desmin impairs contractile ability of various smooth muscle preparations, implying their important role for smooth muscle force development. The IF framework has long been viewed as a fixed cytostructure that solely provides mechanical integrity for the cell. However, recent studies suggest that the IF cytoskeleton is dynamic in mammalian cells in response to various external stimulation. In this review, the structure and biological properties of IF proteins in smooth muscle are summarized. The role of IF proteins in the modulation of smooth muscle force development and redistribution/translocation of signaling partners (such as p130 Crk-associated substrate, CAS) is depicted. This review also summarizes our latest understanding on how the IF network may be regulated in smooth muscle. PMID:18256275

  1. Nucleoprotein complex intermediates in HIV-1 integration

    PubMed Central

    Li, Min; Craigie, Robert

    2012-01-01

    Integration of retroviral DNA into the host genome is an essential step in the viral replication cycle. The viral DNA, made by reverse transcription in the cytoplasm, forms part of a large nucleoprotein complex called the preintegration complex (PIC). The viral integrase protein is the enzyme within the PIC that is responsible for integrating the viral DNA into the host genome. Integrase is tightly associated with the viral DNA within the PIC as demonstrated by functional assays. Integrase protein catalyzes the key DNA cutting and joining steps of integration in vitro with DNA substrates that mimic the ends of the viral DNA. Under most in vitro assay conditions the stringency of the reaction is relaxed; most products result from “half-site” integration in which only one viral DNA end is integrated into one strand of target DNA rather than concerted integration of pairs of DNA as occurs with PICs and in vivo. Under these relaxed conditions catalysis appears to occur without formation of the highly stable nucleoprotein complexes that is characteristic of the association of integrase with viral DNA in the PIC. Here we describe methods for the assembly of nucleoprotein complex intermediates in HIV-1 DNA integration from purified HIV-1 integrase and substrates that mimic the viral DNA ends. PMID:19232539

  2. Reactions of methanethiol on cobalt-covered Mo(110)

    SciTech Connect

    Chen, D.A.; Friend, C.M.; Xu, H.

    1996-03-20

    The reactions of methanethiol on cobalt overlayers grown on Mo(110) were studied using a temperature-programmed reaction and X-ray photoelectron and high-resolution electron energy loss spectroscopies. Methyl thiolate was identified as the reaction intermediate on the basis of X-ray photoelectron and high resolution electron energy loss data. Methane, methyl radical, and H{sub 2} were the only gaseous products. The peak temperature for methane production from methyl thiolate hydrogenolysis was relatively insensitive to the Co coverage and geometric structure of the Co layer. However, less methyl radical formation was observed as the Co coverage increased from 1 to 2.5 monolayers. The selectivity for hydrocarbon formation was essentially the same, nearly 48{+-}5%, for all Co coverages. The total amount of methyl thiolate deposited in the initial S-H bond breaking was independent of Co coverage. At 400 K, sulfur-induced structural rearrangement of the Co overlayer was insignificant and therefore did not affect the reaction of methanethiol. The mixed Co-S overlayer had a substantially lower activity for the methanethiol reaction than any of the clean surfaces; the total amount of reaction on both the sulfur and Co-S overlayers was 30% that of the clean Mo(110) and pure Co overlayers. 53 refs., 5 figs., 1 tab.

  3. Chemical redox reactions in ES-MS: Study of electrode reactions

    SciTech Connect

    Zhou, Feimeng; VAn Berkel, G.J.

    1995-12-31

    The authors previously demonstrated that chemical redox reactions can be used to ionize neutral commpounds for electrospray mass spectrometric (ES-MS) detection. Two different compounds, viz, C{sub 60}F{sub 48} and {beta}-carotene were used to demonstrate the utility of chemical redox reactions with on-line ES-MS for the elucidation of mechanisms of complicated electron transfer reactions and for the kinetic study of electrode reactions in which relatively short-lived intermediates are involved.

  4. The nitric oxide producing reactions of hydroxyurea.

    PubMed

    King, S Bruce

    2003-03-01

    Hydroxyurea is used to treat a variety of cancers and sickle cell disease. Despite this widespread use, a complete mechanistic understanding of the beneficial actions of this compound remains to be understood. Hydroxyurea inhibits ribonucleotide reductase and increases the levels of fetal hemoglobin, which explains a portion of the effects of this drug. Administration of hydroxyurea to patients results in a significant increase in levels of iron nitrosyl hemoglobin, nitrite and nitrate suggesting the in vivo metabolism of hydroxyurea to nitric oxide. Formation of nitric oxide from hydroxyurea may explain a portion of the observed effects of hydroxyurea treatment. At the present, the mechanism or mechanisms of nitric oxide release, the identity of the in vivo oxidant and the site of metabolism remain to be identified. Chemical oxidation of hydroxyurea produces nitric oxide and nitroxyl, the one-electron reduced form of nitric oxide. These oxidative pathways generally proceed through the nitroxide radical (2) or C-nitrosoformamide (3). Biological oxidants, including both iron and copper containing enzymes and proteins, also convert hydroxyurea to nitric oxide or its decomposition products in vitro and these reactions also occur through these intermediates. A number of other reactions of hydroxyurea including the reaction with ribonucleotide reductase and irradiation demonstrate the potential to release nitric oxide and should be further investigated. Gaining an understanding of the metabolism of hydroxyurea to nitric oxide will provide valuable information towards the treatment of these disorders and may lead to the development of better therapeutic agents.

  5. Insights into the Competing Mechanisms and Origin of Enantioselectivity for N-Heterocyclic Carbene-Catalyzed Reaction of Aldehyde with Enamide

    NASA Astrophysics Data System (ADS)

    Qiao, Yan; Chen, Xinhuan; Wei, Donghui; Chang, Junbiao

    2016-12-01

    Hydroacylation reactions and aza-benzoin reactions have attracted considerable attention from experimental chemists. Recently, Wang et al. reported an interesting reaction of N-heterocyclic carbene (NHC)-catalyzed addition of aldehyde to enamide, in which both hydroacylation and aza-benzoin reactions may be involved. Thus, understanding the competing relationship between them is of great interest. Now, density functional theory (DFT) investigation was performed to elucidate this issue. Our results reveal that enamide can tautomerize to its imine isomer with the assistance of HCO3‑. The addition of NHC to aldehydes formed Breslow intermediate, which can go through cross-coupling with enamide via hydroacylation reaction or its imine isomer via aza-benzoin reaction. The aza-benzoin reaction requires relatively lower free energy barrier than the hydroacylation reaction. The more polar characteristic of C=N group in the imine isomers, and the more advantageous stereoelectronic effect in the carbon-carbon bond forming transition states in aza-benzoin pathway were identified to determine that the imine isomer can react with the Breslow intermediate more easily. Furthermore, the origin of enantioselectivities for the reaction was explored and reasonably explained by structural analyses on key transition states. The work should provide valuable insights for rational design of switchable NHC-catalyzed hydroacylation and aza-benzoin reactions with high stereoselectivity.

  6. Insights into the Competing Mechanisms and Origin of Enantioselectivity for N-Heterocyclic Carbene-Catalyzed Reaction of Aldehyde with Enamide

    PubMed Central

    Qiao, Yan; Chen, Xinhuan; Wei, Donghui; Chang, Junbiao

    2016-01-01

    Hydroacylation reactions and aza-benzoin reactions have attracted considerable attention from experimental chemists. Recently, Wang et al. reported an interesting reaction of N-heterocyclic carbene (NHC)-catalyzed addition of aldehyde to enamide, in which both hydroacylation and aza-benzoin reactions may be involved. Thus, understanding the competing relationship between them is of great interest. Now, density functional theory (DFT) investigation was performed to elucidate this issue. Our results reveal that enamide can tautomerize to its imine isomer with the assistance of HCO3−. The addition of NHC to aldehydes formed Breslow intermediate, which can go through cross-coupling with enamide via hydroacylation reaction or its imine isomer via aza-benzoin reaction. The aza-benzoin reaction requires relatively lower free energy barrier than the hydroacylation reaction. The more polar characteristic of C=N group in the imine isomers, and the more advantageous stereoelectronic effect in the carbon-carbon bond forming transition states in aza-benzoin pathway were identified to determine that the imine isomer can react with the Breslow intermediate more easily. Furthermore, the origin of enantioselectivities for the reaction was explored and reasonably explained by structural analyses on key transition states. The work should provide valuable insights for rational design of switchable NHC-catalyzed hydroacylation and aza-benzoin reactions with high stereoselectivity. PMID:27905524

  7. Ozone dissociation to oxygen affected by Criegee intermediate.

    PubMed

    Wei, Wen-Mei; Zheng, Ren-Hui; Pan, Yue-Li; Wu, Yun-Kai; Yang, Fan; Hong, Shi

    2014-03-06

    The detailed potential energy surfaces for the reactions of Criegee intermediate (CI, H2COO) and formaldehyde (H2CO) with ozone (O3) have been investigated at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-311++G(2d,2p) level of theory, respectively. New alternative reaction mechanisms, to the one previously proposed (J. Phys. Chem. Lett. 2013, 4, 2525) have been found. The lower barrier of the new mechanism shows that it is easy for H2COO + O3 to dissociate to formaldehyde and oxygen. For the reactions of H2CO with O3 to produce H2COO and O2, we find relatively high energy barriers, which makes the ozone dissociation to oxygen unlikely to be catalyzed by CI.

  8. Intermediate P* from Soluble Methane Monooxygenase Contains a Diferrous Cluster

    PubMed Central

    Banerjee, Rahul; Meier, Katlyn K.; Münck, Eckard; Lipscomb, John D.

    2013-01-01

    During a single turnover of the hydroxylase component (MMOH) of soluble methane monooxygenase from Methylosinus trichosporium OB3b, several discrete intermediates are formed. The diiron cluster of MMOH is first reduced to the FeIIFeII state (Hred). O2 binds rapidly at a site away from the cluster to form the FeIIFeII intermediate O, which converts to an FeIIIFeIII-peroxo intermediate P and finally to the FeIVFeIV intermediate Q. Q binds and reacts with methane to yield methanol and water. The rate constants for these steps are increased by a regulatory protein, MMOB. Previously reported transient kinetic studies have suggested that an intermediate P* forms between O and P in which the g = 16 EPR signal characteristic of the reduced diiron cluster of Hred and O is lost. This was interpreted as signaling oxidation of the cluster, but low accumulation of P* prevented further characterization. In this study, three methods to directly detect and trap P* are applied together to allow its spectroscopic and kinetic characterization. First, the MMOB mutant His33Ala is used to specifically slow the decay of P* without affecting its formation rate, leading to its nearly quantitative accumulation. Second, spectra-kinetic data collection is used to provide a sensitive measure of the formation and decay rate constants of intermediates as well as their optical spectra. Finally, the substrate furan is included to react with Q and quench its strong chromophore. The optical spectrum of P* closely mimics those of Hred and O, but it is distinctly different from that of P. The reaction cycle rate constants allowed prediction of the times for maximal accumulation of the intermediates. Mössbauer spectra of rapid freeze quench samples at these times show that the intermediates are formed at almost exactly the predicted levels. The Mössbauer spectra show that the diiron cluster of P*, quite unexpectedly, is in the FeIIFeII state. Thus, the loss of the g = 16 EPR results from a change of

  9. Intermediate P* from soluble methane monooxygenase contains a diferrous cluster.

    PubMed

    Banerjee, Rahul; Meier, Katlyn K; Münck, Eckard; Lipscomb, John D

    2013-06-25

    During a single turnover of the hydroxylase component (MMOH) of soluble methane monooxygenase from Methylosinus trichosporium OB3b, several discrete intermediates are formed. The diiron cluster of MMOH is first reduced to the Fe(II)Fe(II) state (H(red)). O₂ binds rapidly at a site away from the cluster to form the Fe(II)Fe(II) intermediate O, which converts to an Fe(III)Fe(III)-peroxo intermediate P and finally to the Fe(IV)Fe(IV) intermediate Q. Q binds and reacts with methane to yield methanol and water. The rate constants for these steps are increased by a regulatory protein, MMOB. Previously reported transient kinetic studies have suggested that an intermediate P* forms between O and P in which the g = 16 EPR signal characteristic of the reduced diiron cluster of H(red) and O is lost. This was interpreted as signaling oxidation of the cluster, but a low level of accumulation of P* prevented further characterization. In this study, three methods for directly detecting and trapping P* are applied together to allow its spectroscopic and kinetic characterization. First, the MMOB mutant His33Ala is used to specifically slow the decay of P* without affecting its formation rate, leading to its nearly quantitative accumulation. Second, spectra-kinetic data collection is used to provide a sensitive measure of the formation and decay rate constants of intermediates as well as their optical spectra. Finally, the substrate furan is included to react with Q and quench its strong chromophore. The optical spectrum of P* closely mimics those of H(red) and O, but it is distinctly different from that of P. The reaction cycle rate constants allowed prediction of the times for maximal accumulation of the intermediates. Mössbauer spectra of rapid freeze-quench samples at these times show that the intermediates are formed at almost exactly the predicted levels. The Mössbauer spectra show that the diiron cluster of P*, quite unexpectedly, is in the Fe(II)Fe(II) state. Thus, the

  10. Kinetics of a Criegee intermediate that would survive high humidity and may oxidize atmospheric SO2.

    PubMed

    Huang, Hao-Li; Chao, Wen; Lin, Jim Jr-Min

    2015-09-01

    Criegee intermediates are thought to play a role in atmospheric chemistry, in particular, the oxidation of SO2, which produces SO3 and subsequently H2SO4, an important constituent of aerosols and acid rain. However, the impact of such oxidation reactions is affected by the reactions of Criegee intermediates with water vapor, because of high water concentrations in the troposphere. In this work, the kinetics of the reactions of dimethyl substituted Criegee intermediate (CH3)2COO with water vapor and with SO2 were directly measured via UV absorption of (CH3)2COO under near-atmospheric conditions. The results indicate that (i) the water reaction with (CH3)2COO is not fast enough (kH2O < 1.5 × 10(-16) cm(3) s(-1)) to consume atmospheric (CH3)2COO significantly and (ii) (CH3)2COO reacts with SO2 at a near-gas-kinetic-limit rate (kSO2 = 1.3 × 10(-10) cm(3) s(-1)). These observations imply a significant fraction of atmospheric (CH3)2COO may survive under humid conditions and react with SO2, very different from the case of the simplest Criegee intermediate CH2OO, in which the reaction with water dimer predominates in the CH2OO decay under typical tropospheric conditions. In addition, a significant pressure dependence was observed for the reaction of (CH3)2COO with SO2, suggesting the use of low pressure rate may underestimate the impact of this reaction. This work demonstrates that the reactivity of a Criegee intermediate toward water vapor strongly depends on its structure, which will influence the main decay pathways and steady-state concentrations for various Criegee intermediates in the atmosphere.

  11. Kinetics of a Criegee intermediate that would survive high humidity and may oxidize atmospheric SO2

    PubMed Central

    Huang, Hao-Li; Chao, Wen; Lin, Jim Jr-Min

    2015-01-01

    Criegee intermediates are thought to play a role in atmospheric chemistry, in particular, the oxidation of SO2, which produces SO3 and subsequently H2SO4, an important constituent of aerosols and acid rain. However, the impact of such oxidation reactions is affected by the reactions of Criegee intermediates with water vapor, because of high water concentrations in the troposphere. In this work, the kinetics of the reactions of dimethyl substituted Criegee intermediate (CH3)2COO with water vapor and with SO2 were directly measured via UV absorption of (CH3)2COO under near-atmospheric conditions. The results indicate that (i) the water reaction with (CH3)2COO is not fast enough (kH2O < 1.5 × 10−16 cm3s−1) to consume atmospheric (CH3)2COO significantly and (ii) (CH3)2COO reacts with SO2 at a near–gas-kinetic-limit rate (kSO2 = 1.3 × 10−10 cm3s−1). These observations imply a significant fraction of atmospheric (CH3)2COO may survive under humid conditions and react with SO2, very different from the case of the simplest Criegee intermediate CH2OO, in which the reaction with water dimer predominates in the CH2OO decay under typical tropospheric conditions. In addition, a significant pressure dependence was observed for the reaction of (CH3)2COO with SO2, suggesting the use of low pressure rate may underestimate the impact of this reaction. This work demonstrates that the reactivity of a Criegee intermediate toward water vapor strongly depends on its structure, which will influence the main decay pathways and steady-state concentrations for various Criegee intermediates in the atmosphere. PMID:26283390

  12. Analysis of the citric acid cycle intermediates using gas chromatography-mass spectrometry.

    PubMed

    Kombu, Rajan S; Brunengraber, Henri; Puchowicz, Michelle A

    2011-01-01

    Researchers view analysis of the citric acid cycle (CAC) intermediates as a metabolomic approach to identifying unexpected correlations between apparently related and unrelated pathways of metabolism. Relationships of the CAC intermediates, as measured by their concentrations and relative ratios, offer useful information to understanding interrelationships between the CAC and metabolic pathways under various physiological and pathological conditions. This chapter presents a relatively simple method that is sensitive for simultaneously measuring concentrations of CAC intermediates (relative and absolute) and other related intermediates of energy metabolism using gas chromatography-mass spectrometry.

  13. Myofibroblasts reaction in urothelial carcinomas.

    PubMed

    Alexa, Aurora; Baderca, Flavia; Lighezan, Rodica; Izvernariu, D

    2009-01-01

    The myofibroblast is a connective tissue cell with intermediate features between the fibroblast and the smooth muscle cell and unknown origin, which normally is present in only a few organs, but with increased incidence in malignancies. The patterns of myofibroblastic reaction may be synchronous, metachronous and mixed. The presence of the myofibroblasts has been demonstrated into the stroma of breast carcinomas, particularly in firm, retracted tumors with no inflammatory infiltrate. The present literature lacks data regarding the presence and the behavior of the myofibroblasts in urothelial carcinomas. Fifty-nine urothelial carcinoma specimens from patients admitted into the Urology Clinic of the Emergency County Hospital of Timisoara between 1999 and 2004 were stained with usual HE stain for the morphological diagnosis and immunohistochemically stained with smooth muscle actin, vimentin, and desmin for the detection of myofibroblasts. In biopsies sampled from normal urinary bladder and in urothelial carcinomas of the superior urinary tract Ta, we have not noticed any cells with myofibroblast morphology or immunophenotype. In Ta tumors, no matter the differentiation grade, we have not noticed myofibroblasts neither between the tumor cells nor at distance. The myofibroblasts were identified in seven of the 26 (26.92%) tumors in T1 stage. In T2 and T3 stage tumors the number of myofibroblasts differs from case to case, being significantly higher in tumors with high differentiation grade, G3.

  14. A common intermediate for N2 formation in enzymes and zeolites: side-on Cu-nitrosyl complexes.

    PubMed

    Kwak, Ja Hun; Lee, Jong H; Burton, Sarah D; Lipton, Andrew S; Peden, Charles H F; Szanyi, János

    2013-09-16

    Side on! Combined FTIR and NMR studies revealed the presence of a side-on nitrosyl species in the zeolite Cu-SSZ-13. This intermediate is very similar to those found in nitrite reductase enzyme systems. The identification of this intermediate led to the proposal of a reaction mechanism that is fully consistent with the results of both kinetic and spectroscopic studies.

  15. Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase

    SciTech Connect

    Knoot, Cory J.; Purpero, Vincent M.; Lipscomb, John D.

    2014-12-29

    Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe3+ to activate O2 and catecholic substrates for reaction. The inability of Fe3+ to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated in this paper using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surrounding solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe3+ species, and the anhydride-Fe3+ intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe2+-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe2+ intermediate that could bind O2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Finally, structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage.

  16. Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase

    DOE PAGES

    Knoot, Cory J.; Purpero, Vincent M.; Lipscomb, John D.

    2014-12-29

    Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe3+ to activate O2 and catecholic substrates for reaction. The inability of Fe3+ to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated in this paper using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surrounding solution. The X-ray crystalmore » structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe3+ species, and the anhydride-Fe3+ intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe2+-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe2+ intermediate that could bind O2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Finally, structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage.« less

  17. Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase

    PubMed Central

    Knoot, Cory J.; Purpero, Vincent M.; Lipscomb, John D.

    2015-01-01

    Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe3+ to activate O2 and catecholic substrates for reaction. The inability of Fe3+ to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated here using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surrounding solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe3+ species, and the anhydride-Fe3+ intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe2+-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe2+ intermediate that could bind O2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage. PMID:25548185

  18. Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase.

    PubMed

    Knoot, Cory J; Purpero, Vincent M; Lipscomb, John D

    2015-01-13

    Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe(3+) to activate O2 and catecholic substrates for reaction. The inability of Fe(3+) to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated here using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surrounding solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe(3+) species, and the anhydride-Fe(3+) intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe(2+)-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe(2+) intermediate that could bind O2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage.

  19. Identification of thioether intermediates in the reductive transformation of gonyautoxins into saxitoxins by thiols.

    PubMed

    Sato, S; Sakai, R; Kodama, M

    2000-08-21

    O-Sulfate group of gonyautoxin I and IV is transformed into methylene to form neosaxitoxin by thiols such as glutathione, a common cellular scavenger, in mild conditions. We isolated the intermediate of this conversion and propose that this reaction proceeds through formation of thiohemiketal, 1,2 shift to form stable thioether intermediate, and then redox exchange at sulfur atom to form the final product.

  20. Wind Variability in Intermediate Luminosity B Supergiants

    NASA Technical Reports Server (NTRS)

    Massa, Derck

    1996-01-01

    This study used the unique spectroscopic diagnostics of intermediate luminosity B supergiants to determine the ubiquity and nature of wind variability. Specifically, (1) A detailed analysis of HD 64760 demonstrated massive ejections into its wind, provided the first clear demonstration of a 'photospheric connection' and ionization shifts in a stellar wind; (2) The international 'IUE MEGA campaign' obtained unprecedented temporal coverage of wind variability in rapidly rotating stars and demonstrated regularly repeating wind features originating in the photosphere; (3) A detailed analysis of wind variability in the rapidly rotating B1 Ib, gamma Ara demonstrated a two component wind with distinctly different mean states at different epochs; (4) A follow-on campaign to the MEGA project to study slowly rotating stars was organized and deemed a key project by ESA/NASA, and will obtain 30 days of IUE observations in May-June 1996; and (5) A global survey of archival IUE time series identified recurring spectroscopic signatures, identified with different physical phenomena. Items 4 and 5 above are still in progress and will be completed this summer in collaboration with Raman Prinja at University College, London.

  1. Morphological and Ultrastructural Changes in Tissues of Intermediate and Definitive Hosts Infected by Protostrongylid Lungworms (Nematoda: Metastrongyloidea)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cellular and sub-cellular mechanisms involved in tissue responses to larval and adult lungworms (Protostrongylidae) were respectively explored through experimental and natural infections in molluscan intermediate (Xeropicta candacharica) and ruminant definitive hosts (Ovis aries). Reaction to develo...

  2. Storage Stability and Improvement of Intermediate Moisture Foods, Phase 3

    NASA Technical Reports Server (NTRS)

    Labuza, T. P.

    1975-01-01

    Methods were determined for the improvement of shelf-life stability of intermediate moisture foods (IMF). Microbial challenge studies showed that protection against molds and Staphylococcus aureus could be achieved by a combination of antimicrobial agents, humectants and food acids. Potassium sorbate and propylene glycol gave the best results. It was also confirmed that the maximum in heat resistance shown by vegetative pathogens at intermediate water activities also occurred in a solid food. Glycols and sorbitol both achieve browning inhibition because of their action as a medium for reaction and effect on viscosity of the adsorbed phase. Chemical availability results showed rapid lysine loss before visual discoloration occurred. This is being confirmed with a biological test using Tetrahymena pyriformis W. Accelerated temperature tests show that effectiveness of food antioxidants against rancidity development can be predicted; however, the protection factor changes with temperature. BHA was found to be the best antioxidant for iron catalyzed oxidation.

  3. Monoclonal antibody aggregation intermediates visualized by atomic force microscopy.

    PubMed

    Lee, Hanjoo; Kirchmeier, Marc; Mach, Henryk

    2011-02-01

    Ubiquitous but highly variable processes of therapeutic protein aggregation remain poorly characterized, especially in the context of common infusion reactions and clinical immunogenicity. Among the numerous challenges is the characterization of intermediate steps that lead to the appearance of precipitates. Although the biophysical methods for elucidation of secondary and tertiary structures as well as overall size distribution are typically well established in the development laboratories, the use of molecular scale imaging techniques is still relatively rare due to low throughput and technical complexity. In this work, we present the use of atomic force microscopy to examine morphology of monoclonal antibody aggregates. Despite varying in primary structure as a result of different complementarity defining regions, most antibodies studied exhibited a similar aggregation intermediate consisting of several monomers. However, the manner of subsequent condensation of these oligomers appeared to differ between the antibodies, suggesting stability-dependent mechanisms.

  4. Mechanism of a C-H bond activation reaction in room-temperature alkane solution

    SciTech Connect

    Bromberg, S.E.; Yang, H.; Asplund, M.C.

    1997-10-10

    Chemical reactions that break alkane carbon-hydrogen (C-H) bonds are normally carried out under conditions of high temperature and pressure because these bonds are extremely strong ({approx} 100 kilocalories per mole), but certain metal complexes can activate C-H bonds in alkane solution under the mild conditions of room temperature and pressure. Time-resolved infrared experiments probing the initial femtosecond dynamics through the nano- and microsecond kinetics to the final stable products have been used to generate a detailed picture of the C-H activation reaction. Structures of all of the intermediates involved in the reaction of Tp*Rh(CO){sub 2} (Tp* = HB-Pz{sub 3}*, Pz* = 3,5-di-methylpyrazolyl) in alkane solution have been identified and assigned, and energy barriers for each reaction step from solvation to formation of the final alkyl hydride product have been estimated from transient lifetimes. 27 refs., 6 figs.

  5. The mechanism of a C-H Bond Activation reaction in roomtemperature alkane solution

    SciTech Connect

    Bromberg, Steven E.; Yang, Haw; Asplund, Matthew C.; Lian, T.; McNamara, B.K.; Kotz, K.T.; Yeston, J.S.; Wilkens, M.; Frei, H.; Bergman,Robert G.; Harris, C.B.

    1997-07-31

    Chemical reactions that break alkane carbon-hydrogen (C-H) bonds are normally carried out under conditions of high temperature and pressure because these bonds are extremely strong ({approx}100 kilocalories per mole), but certain metal complexes can activate C-H bonds in alkane solution under the mild conditions of room temperature and pressure. Time-resolved infrared experiments probing the initial femtosecond dynamics through the nano- and microsecond kinetics to the final stable products have been used to generate a detailed picture of the C-H activation reaction. Structures of all of the intermediates involved in the reaction of Tp*Rh(CO)2 (Tp* = HB-Pz3*, Pz* = 3,5-dimethylpyrazolyl) in alkane solution have been identified and assigned, and energy barriers for each reaction step from solvation to formation of the final alkylhydride product have been estimated from transient lifetimes.

  6. Interplay between chemical reactions and transport in structured spaces

    NASA Astrophysics Data System (ADS)

    Konkoli, Zoran

    2005-07-01

    The main motivation behind this study is to understand the interplay between the reactions and transport in a geometries that are not compact. Typical examples of compact geometries are a box or a sphere. A network made of containers C1,C2,…,CN and tubes is an example of the space that is structured and noncompact. In containers, particles react with the rate λ . Tubes connecting containers allow for the exchange of chemicals with the transport rate D . A situation is considered where a number of reactants is small and kinetics is noise dominated. A method is presented that can be used to calculate the average and higher moments of the reaction time. A number of different chemical reactions are studied and their performance compared in various ways. Two schemes are discussed in general, the reaction on a fixed geometry ensemble (ROGE) and the geometry on a fixed reaction ensemble, examples are given in the ROGE case. The most important findings are as follows. (i) There is a large number of reactions that run faster in a networklike geometry. Such reactions contain antagonistic catalytic influences in the intermediate stages of a reaction scheme that are best dealt with in a networklike structure. (ii) Antagonistic catalytic influences are hard to identify since they are strongly connected to the pattern of injected molecules (inject pattern) and depend on the choice of molecules that have to be synthesized at the end (task pattern). (iii) The reaction time depends strongly on the details of the inject and task patterns.

  7. Improved evidence for the existence of an intermediate phase during hydration of tricalcium silicate

    SciTech Connect

    Bellmann, Frank; Damidot, Denis; Moeser, Bernd; Skibsted, Jorgen

    2010-06-15

    Tricalcium silicate (Ca{sub 3}SiO{sub 5}) with a very small particle size of approximately 50 nm has been prepared and hydrated for a very short time (5 min) by two different modes in a paste experiment, using a water/solid-ratio of 1.20, and by hydration as a suspension employing a water/solid-ratio of 4000. A phase containing uncondensed silicate monomers close to hydrogen atoms (either hydroxyl groups or water molecules) was formed in both experiments. This phase is distinct from anhydrous tricalcium silicate and from the calcium-silicate-hydrate (C-S-H) phase, commonly identified as the hydration product of tricalcium silicate. In the paste experiment, approximately 79% of silicon atoms were present in the hydrated phase containing silicate monomers as determined from {sup 29}Sileft brace{sup 1}Hright brace CP/MAS NMR. This result is used to show that the hydrated silicate monomers are part of a separate phase and that they cannot be attributed to a hydroxylated surface of tricalcium silicate after contact with water. The phase containing hydrated silicate monomers is metastable with respect to the C-S-H phase since it transforms into the latter in a half saturated calcium hydroxide solution. These data is used to emphasize that the hydration of tricalcium silicate proceeds in two consecutive steps. In the first reaction, an intermediate phase containing hydrated silicate monomers is formed which is subsequently transformed into C-S-H as the final hydration product in the second step. The introduction of an intermediate phase in calculations of the early hydration of tricalcium silicate can explain the presence of the induction period. It is shown that heterogeneous nucleation on appropriate crystal surfaces is able to reduce the length of the induction period and thus to accelerate the reaction of tricalcium silicate with water.

  8. Synthetic high-pressure micas compositionally intermediate between the dioctahedral and trioctahedral mica series

    NASA Astrophysics Data System (ADS)

    Green, T. H.

    1982-03-01

    Intermediate-composition micas with octahedral occupancy ≳2.5 have been crystallized experimentally from natural phengite, 50% phengite+50% biotite, and synthetic basalt compositions in the pressure range 20 35 kb and temperatures of 800 1,000° C. Their compositions suggest a complete range of micas with octahedral occupancy between 3.0 and 2.5, but a very restricted range between 2.0 and 2.5. These 2.5-octahedral micas lie close to the new mica series proposed by Seifert and Schreyer (1965, 1971), with one end-member composition of K Mg2.5 (Si4O10) (OH2) which is extended by the present results into alumina-bearing members of the series (e. g. K Mg1.5 Al1.0 (Si3Al1.0O10) (OH)2). However, the possibility of interlayering of dioctahedral and trioctahedral micas to give an apparently intermediate composition cannot be ruled out. X-ray powder diffraction data on the critical 060 reflection for the phengite mix suggest a transitional change from a single phengite field, through a 2-phase phengite — 2.5-octahedral mica field to a single phase 2.5-octahedral mica field. Natural micas of similar composition have not so far been identified, due probably to the unlikelihood of obtaining a mineralogical record of an appropriate composition at the restricted pressure and temperature conditions apparently needed to stabilize the 2.5-octahedral mica phase. Nevertheless, such a phase may have an important role in mineral assemblages and melting reactions in the deep continental crust, subducted oceanic crust and in the upper mantle; evidence of its existence may be removed by later, lower-pressure reactions.

  9. Chromospheric Activity at Intermediate Ages

    NASA Astrophysics Data System (ADS)

    Giampapa, Mark; Stauffer, John; Deliyannis, Constantine; Sherry, William

    2005-08-01

    The calibration of the empirical relation between Ca II chromospheric strength and stellar age between 0.6 Gyr (Hyades) and 4.0 - 5 Gyr (M67 and the Sun) relies on the uncertain determination of ages for individual field stars in the solar neighborhood. We therefore propose to obtain WIYN/Hydra spectra of ~ 100 solar-type dwarf stars in the 1.8 Gyr old open cluster, NGC 752. This cluster contains a sample of solar-type dwarfs that is homogeneous in age and chemical composition. Furthermore, NGC 752 is the nearest-and hence brightest- cluster at an age ~ 2 Gyr. The results will yield an improved calibration of the age-activity relation at intermediate ages. In addition, we will determine if the chromospheric Ca II strengths for the solar-type stars in NGC 752 lie in the so-called "Vaughan-Preston Gap''- an apparent discontinuity in the Ca II H& K strength-(B-V) diagram found for field stars in the solar neighborhood. Our data will yield insight on the two proposed origins for the gap, namely, that it is a result of two different modes of dynamo action or that it is actually an artifact of a discontinuity in the local star formation rate. This is a resubmission of a previously approved proposal that was allocated two nights in 2004 November. The time was lost to instrument problems (Hydra gripper malfunctions) and weather. No usable data were obtained.

  10. Intermediate Filaments: Structure and Assembly.

    PubMed

    Herrmann, Harald; Aebi, Ueli

    2016-11-01

    Proteins of the intermediate filament (IF) supergene family are ubiquitous structural components that comprise, in a cell type-specific manner, the cytoskeleton proper in animal tissues. All IF proteins show a distinctly organized, extended α-helical conformation prone to form two-stranded coiled coils, which are the basic building blocks of these highly flexible, stress-resistant cytoskeletal filaments. IF proteins are highly charged, thus representing versatile polyampholytes with multiple functions. Taking vimentin, keratins, and the nuclear lamins as our prime examples, we present an overview of their molecular and structural parameters. These, in turn, document the ability of IF proteins to form distinct, highly diverse supramolecular assemblies and biomaterials found, for example, at the inner nuclear membrane, throughout the cytoplasm, and in highly complex extracellular appendages, such as hair and nails, of vertebrate organisms. Ultimately, our aim is to set the stage for a more rational understanding of the immediate effects that missense mutations in IF genes have on cellular functions and for their far-reaching impact on the development of the numerous IF diseases caused by them.

  11. Enhancement of entropic transport by intermediates.

    PubMed

    Mondal, Debasish

    2011-07-01

    Brownian particles confined in a two-dimensional enclosure that give rise to a bistable entropic potential are considered. With the introduction of an intermediate lobe, the mean first passage time from one lobe to another through the intermediate shows a turnover behavior with the variation of the stability of the entropic intermediate. The mean escape time shows a minimum for an optimal value of the barrier height of the intermediate state. A three-state model is proposed to explain the nonmonotonic behavior of the entropic transport.

  12. Thermal Runaway during Intermediate-Depth Earthquake Rupture

    NASA Astrophysics Data System (ADS)

    Prieto, German; Florez, Manuel; Barrett, Sarah; Beroza, Gregory; Pedraza, Patricia; Blanco, Jose; Poveda, Esteban

    2014-05-01

    Intermediate-depth earthquakes occur at depths of 50 to 300 km in subducting lithosphere. Despite their ubiquity in earthquake catalogs, their physical mechanism remains unclear because ambient temperatures and pressures are expected to lead to ductile, rather than brittle deformation. There are two leading explanations for the physical mechanism that enables these earthquakes. In the first, high pore pressure from metamorphic dehydration reactions in the subducting slab reduces the effective normal stress sufficiently to enable frictional failure. In the second, slow deformation generates heat, which leads to weakening, further deformation, and a self-localizing thermal shear runaway. We use the nest of intermediate-depth earthquakes under Bucaramanga, Colombia as recorded by the digital RSNC (Red Sísmica Nacional de Colombia) regional seismic network to explore these two possibilities. We observe a combination of high stress drop and low radiation efficiency for Mw 4-5 earthquakes in the Bucaramanga Nest that points to the importance of thermal effects. If we assume a cm-scale fault-zone width, this combination implies a temperature increase of 600-1,000ºC during earthquake failure, which suggests that substantial shear heating, and possibly partial melting, occurs during intermediate-depth earthquake failure. Our observations support thermal shear runaway as the mechanism for intermediate-depth earthquakes. This mechanism could help explain differences in their behavior, such as the paucity of aftershocks, compared to shallow earthquakes. Although we have inferred these mechanisms for intermediate depth earthquakes, it's likely that they would apply for rapid deformation on the deep extensions of fault zones as well - particularly during large earthquakes, such as the 2012 Mw 8.6 strike-slip event off Sumatra, which is inferred to have ruptured well into the oceanic mantle.

  13. Microfabricated electrochemiluminescence cell for chemical reaction detection

    DOEpatents

    Northrup, M. Allen; Hsueh, Yun-Tai; Smith, Rosemary L.

    2003-01-01

    A detector cell for a silicon-based or non-silicon-based sleeve type chemical reaction chamber that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The detector cell is an electrochemiluminescence cell constructed of layers of silicon with a cover layer of glass, with spaced electrodes located intermediate various layers forming the cell. The cell includes a cavity formed therein and fluid inlets for directing reaction fluid therein. The reaction chamber and detector cell may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The ECL cell may also be used in synthesis instruments, particularly those for DNA amplification and synthesis.

  14. Mineralization of the antibiotic levofloxacin in aqueous medium by electro-Fenton process: kinetics and intermediate products analysis.

    PubMed

    Yahya, Muna Sh; El Karbane, Miloud; Oturan, Nihal; El Kacemi, Kacem; Oturan, Mehmet A

    2016-01-01

    The present study investigates the feasibility of using electro-Fenton (EF) process for the oxidative degradation of antibiotic levofloxacin (LEV). The EF experiments have been performed in an electrochemical cell using a carbon-felt cathode. The effect of applied current in the range 60-500 mA and catalyst concentration in the range 0.05-0.5 mM on the kinetics of oxidative degradation and mineralization efficiency have been investigated. Degradation of LEV by hydroxyl radicals was found to follow pseudo-first-order reaction kinetics. The absolute rate constant for oxidative degradation of LEV by hydroxyl radical has been determined by a competition kinetics method and found to be (2.48 ± 0.18) × 10(9) M(-1) s(-1). An optimum current value of 400 mA and a catalyst (Fe(2+)) concentration of 0.1 mM were observed to be optimal for an effective degradation of LEV under our operating conditions. Mineralization of aqueous solution of LEV was performed by the chemical oxygen demand analysis and an almost mineralization degree (>91%) was reached at the end of 6 h of electrolysis. A number of intermediate products have been identified using high performance liquid chromatography and liquid chrmatography-mass spectrometry analyses. Based on these identified reaction intermediates, a plausible reaction pathway has been suggested for the mineralization process. The formation and evolution of [Formula: see text] and [Formula: see text] ions released to the medium during the process were also discussed.

  15. Intermediate filaments in nervous tissues

    PubM