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Sample records for identify reaction intermediate

  1. Identifying reaction intermediates and catalytic active sites through in situ characterization techniques

    SciTech Connect

    Foster, Andrew J.; Lobo, Raul F

    2010-01-01

    This tutorial review centers on recent advances and applications of experimental techniques that help characterize surface species and catalyst structures under in situ conditions. We start by reviewing recent applications of IR spectroscopy of working catalysis, emphasizing newer approaches such as Sum Frequency Generation and Polarization Modulation-infrared reflection absorption spectroscopy. This is followed by a section on solid-state NMR spectroscopy for the detection of surface species and reaction intermediates. These two techniques provide information mainly about the concentration and identity of the prevalent surface species. The following sections center on methods that provide structural and chemical information about the catalyst surface. The increasingly important role of high-pressure X-ray photoelectron spectroscopy in catalyst characterization is evident from the new and interesting information obtained on supported catalysts as presented in recent reports. X-Ray absorption spectroscopy (XANES and EXAFS) is used increasingly under reaction conditions to great advantage, although is inherently limited to systems where the bulk of the species in the sample are surface species. However, the ability of X-rays to penetrate the sample has been used cleverly by a number of groups to understand how changing reaction conditions change the structure and composition of surface atoms on supported catalyst.

  2. Intermediate energy heavy ion reactions

    NASA Astrophysics Data System (ADS)

    Grégoire, C.; Tamain, B.

    The intermediate energy heavy ion induced reactions are extensively studied for several years. In this paper, we try to summarize the present knowledge. The peripheral reactions appear to be intermediate between the fragmentation and the deep inelastic regimes. Many questions remain open concerning the energy relaxation mechanisms and an eventual participant zone creation. In the case of central collisions, it has been shown that very hot nuclei can be built. The fusion limits are discussed and the very hot nuclei properties are considered. In some cases, hot spot formation or compression effects could play a role. Multifragmentation is discussed as a possible decay channel. In all these aspects, a difficult question concerns the validity of the temperature concept and more generally of collective thermodynamical variables. Such collective effects have been investigated in pion production experiments. Les réactions induites par ions lourds d'énergie intermédiaire sont très étudiées depuis quelques années. Dans cet article, nous essayons de résumer l'état actuel des connaissances. Les mécanismes mis en jeu dans les collisions périphériques sont intermédiaires entre les collisions très inélastiques et la fragmentation. La cible joue clairement un rôle déterminant et des effets importants de champ moyen demeurent. De nombreuses questions restent sans réponse comme par exemple les mécanismes de relaxation d'énergie ou l'existence d'une éventuelle zone participante. Dans le cas des collisions centrales, il a pu être montré que des noyaux très chauds sont fabriqués. Les limites au processus de fusion et les propriétés des noyaux très chauds sont discutées. Dans certains cas, des effets de compression ou de points chauds peuvent être envisagés. La multifragmentation est une voie de désexcitation possible. Une importante question concerne la validité du concept de température et plus généralement la notion de variable collective équilibrée. Des effets collectifs peuvent être responsables de la production de pions.

  3. Characterization of reaction intermediates by ion spectroscopy.

    PubMed

    Roithov, Jana

    2012-01-21

    In the last decade, we have experienced massive progress in spectroscopic methods for mass-selected ions. The aim of this tutorial review is to present action spectroscopy as a powerful tool for the investigation of ionic reaction intermediates. Examples span from ultraviolet and infrared photodissociation spectroscopy of model reaction intermediates to applications of infrared multiphoton dissociation spectroscopy (IRMPD) to intermediates directly sampled from reaction mixtures. The first example of double resonance IR-UV spectroscopy of model intermediates in an organometallic reaction is also mentioned. PMID:21792393

  4. Intermediate Compounds and Intermediate Reactions in the Synthesis of Oligonucleotides

    NASA Astrophysics Data System (ADS)

    Zarytova, V. F.; Knorre, Dmitrii G.

    1985-02-01

    The principal features of the phosphorylation of nucleosides and other alcohols by phosphoric acid monoesters and diesters in the presence of the most widely used condensing agents (arenesulphonyl chlorides, arenesulphonyl azolides, carbodiimides, mixtures of arenesulphonyl chlorides with azoles and pyridines) are described. Data concerning the intermediate compounds and intermediate reactions in the oligonucleotides synthesis as well as model processes, obtained mainly with the aid of 31P NMR, are discussed. The bibliography includes 67 references.

  5. Transfer and breakup reactions at intermediate energies

    SciTech Connect

    Stokstad, R.G.

    1986-04-01

    The origin of the quasi-elastic peak in peripheral heavy-ion reactions is discussed in terms of inelastic scattering and transfer reactions to unbound states of the primary projectile-like fragment. The situation is analogous to the use of reverse kinematics in fusion reactions, a technique in which the object of study is moving with nearly the beam velocity. It appears that several important features of the quasi-elastic peak may be explained by this approach. Projectile-breakup reactions have attractive features for the study of nuclear structure. They may also be used to determine the partition of excitation energy in peripheral reactions. At intermediate energies, neutron-pickup reactions leading to four-body final states become important. Examples of experiments are presented that illustrate these points. 15 refs., 14 figs.

  6. A pentacyclic reaction intermediate of riboflavin synthase

    PubMed Central

    Illarionov, Boris; Eisenreich, Wolfgang; Bacher, Adelbert

    2001-01-01

    The S41A mutant of riboflavin synthase from Escherichia coli catalyzes the formation of riboflavin from 6,7-dimethyl-8-ribityllumazine at a very low rate. Quenching of presteady-state reaction mixtures with trifluoroacetic acid afforded a compound with an absorption maximum at 412 nm (pH 1.0) that can be converted to a mixture of riboflavin and 6,7-dimethyl-8-ribityllumazine by treatment with wild-type riboflavin synthase. The compound was shown to qualify as a kinetically competent intermediate of the riboflavin synthase-catalyzed reaction. Multinuclear NMR spectroscopy, using various 13C- and 15N-labeled samples, revealed a pentacyclic structure arising by dimerization of 6,7-dimethyl-8-ribityllumazine. Enzyme-catalyzed fragmentation of this compound under formation of riboflavin can occur easily by a sequence of two elimination reactions. PMID:11404482

  7. 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…

  8. 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

  9. 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.

  10. (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)

  11. Cluster Productions in Intermediate-Energy Proton-Nucleus Reactions

    SciTech Connect

    Iwamoto, Hiroki; Uozumi, Yusuke

    2008-04-17

    We propose a model to describe cluster productions within the framework of the intranuclear cascade (INC) model. In our model, combination of the 'surface coalescence' and the 'knockout' is implemented to describe cluster productions in intermediate-energy nuclear reactions. In the present work, the basic ingredients of our INC model are defined and applied to nucleon and cluster productions for the proton-nucleus reactions. Although our INC model has some difficulties and room for improvement, it gives a good overall agreement with experimental data of not only nucleon productions but also cluster productions at intermediate energies.

  12. The structure of the Guanine Nucleotide Exchange Factor Rlf in complex with the small G-protein Ral identifies conformational intermediates of the exchange reaction and the basis for the selectivity.

    PubMed

    Popovic, Milica; Schouten, Arie; Rensen-de Leeuw, Marije; Rehmann, Holger

    2016-02-01

    CDC25 homology domain (CDC25-HD) containing Guanine Nucleotide Exchange Factors (GEFs) initiate signalling by small G-proteins of the Ras-family. Each GEF acts on a small subset of the G-proteins only, thus providing signalling selectivity. Rlf is a GEF with selectivity for the G-proteins RalA and RalB. Here the crystal structure of Rlf in complex with Ral is determined. The Rlf·Ral complex crystallised into two different crystal forms, which represent different steps of the exchange reaction. Thereby general insight in the CDC25-HD catalysed nucleotide exchange is obtained. In addition, the basis for the selectivity of the interaction is investigated. The exchange activity is monitored by the use of recombinant proteins. Selectivity determinants in the binding interface are identified and confirmed by a mutational study. PMID:26687416

  13. Quantum mechanical investigations on the role of neutral and negatively charged enamine intermediates in organocatalyzed reactions

    NASA Astrophysics Data System (ADS)

    Hubin, Pierre O.; Jacquemin, Denis; Leherte, Laurence; Vercauteren, Daniel P.

    2014-04-01

    The proline-catalyzed aldol reaction is the seminal example of asymmetric organocatalysis. Previous theoretical and experimental studies aimed at identifying its mechanism in order to rationalize the outcome of this reaction. Here, we focus on key steps with modern first principle methods, i.e. the M06-2X hybrid exchange-correlation functional combined to the solvation density model to account for environmental effects. In particular, different pathways leading to the formation of neutral and negatively charged enamine intermediates are investigated, and their reactivity towards two electrophiles, i.e. an aldehyde and a benzhydrylium cation, are compared. Regarding the self-aldol reaction, our calculations confirm that the neutral enamine intermediate is more reactive than the negatively charged one. For the reaction with benzhydrylium cations however, the negatively charged enamine intermediate is more reactive.

  14. DFT research on the dehydroxylation reaction of pyrophyllite 2. Characterization of reactants, intermediates, and transition states along the reaction path.

    PubMed

    Molina-Montes, Esther; Donadio, Davide; Hernndez-Laguna, Alfonso; Sainz-Daz, C Ignacio

    2008-07-17

    We delineate the dehydroxylation reaction of pyrophyllite in detail by localizing the complete reaction path on the free energy surface obtained previously by Car-Parrinello molecular dynamics and the implemented metadynamics algorithm ( Molina-Montes et al. J. Phys. Chem. B 2008, 112, 7051 ). All intermediates were identified, and a transition state search was also undertaken with the PRFO algorithm. The characterization of this reaction and the atomic rearrangement in the intermediates and products at quantum mechanical level were performed for the two reaction paths found previously: (i) direct dehydroxylation through the octahedral hole (cross mechanism) or between contiguous hydroxyl groups (on-site mechanism) and (ii) two-step dehydroxylation assisted by apical oxygens for each of the two steps. New intermediates were found and determined structurally. The structural variations found for all intermediates and transition states are in agreement with experimental results. The formation of these structures indicates that the dehydroxylation process is much more complex than a first-order reaction and can explain the wide range of temperatures for completing the reaction, and these results can be extrapolated to the dehydroxylation of other dioctahedral 2:1 phyllosilicates. PMID:18563890

  15. Mechanistic and spectroscopic identification of initial reaction intermediates for prenal decomposition on a platinum model catalyst.

    PubMed

    Haubrich, J; Loffreda, D; Delbecq, F; Sautet, P; Jugnet, Y; Krupski, A; Becker, C; Wandelt, K

    2011-04-01

    The prediction of a reaction mechanism and the identification of the corresponding chemical intermediates is a major challenge in surface science and heterogeneous catalysis, due to a complex network of elementary steps and surface species. Here we demonstrate how to overcome this difficulty by tracking the temperature dependent formation of the initial reaction intermediates and identifying the decomposition pathways in the case of prenal, an ?,?-unsaturated aldehyde, on the Pt(111) model catalyst surface by combining vibrational spectroscopy, thermal reaction/desorption spectroscopy (TPRS) experiments and detailed theoretical analysis. TPRS characterization of this reaction up to 600 K shows a series of desorption states of H(2) (?280 K, 410 K and 473 K) and CO (?414 K), giving valuable insights into the sequence of elementary steps suggesting that the loss of hydrogen and the carbonyl functions are among the first elementary steps. HREELS experiments recorded after annealing to specific temperatures result in complex spectra, which can be assigned to several subsequently formed and transformed surface intermediates. Starting from stable prenal adsorption structures, complementary DFT calculations allow the determination of the most likely reaction pathway for the initial decomposition steps and the identification of the corresponding intermediates by comparison with HREELS. The decomposition occurs from the strongly bonded prenal adsorption structures via a dehydro-?(3)-tri?(CCC)-H1 intermediate to the highly stable ?(1)-isobutylidyne species at high temperatures. PMID:21344078

  16. 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. PMID:22875684

  17. Dehydropericyclic Reactions: Symmetry-Controlled Routes to Strained Reactive Intermediates.

    PubMed

    Skraba-Joiner, Sarah L; Johnson, Richard P; Agarwal, Jay

    2015-12-01

    The conceptual dehydrogenation of pericyclic reactions yields dehydropericyclic processes, which usually lead to strained or reactive intermediates. This is a simple scheme for inventing new chemical reactions. Computational results on two novel dehydropericyclic reactions are presented here. Conjugated enynes undergo a singlet-state photoisomerization that transposes the methylene carbon. We previously suggested excited-state closure to 1,2-cyclobutadiene followed by thermal ring opening. CCSD(T)//DFT computations show two minima of similar energy corresponding to 1,2-cyclobutadiene, one chiral and closed shell and the second a planar diradical. The chiral structure has a low barrier to ring opening and may best explain results on enyne photoisomerization. The first examples of 1,3-diyne + yne cycloadditions to give o-benzynes were reported in 1997. Computations on intramolecular versions of this tridehydro (-3H2) Diels-Alder reaction support a concerted mechanism for the parent triyne (1,3,8-nonatriyne); however, a slight electronic advantage in the concerted path may be outweighed by the difference in entropy of activation for sequential vs simultaneous formation of two new ring bonds. PMID:26418846

  18. 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.

  19. Crystal structures of intermediates in the nitroalkane oxidase reaction.

    PubMed

    Hroux, Annie; Bozinovski, Dragana M; Valley, Michael P; Fitzpatrick, Paul F; Orville, Allen M

    2009-04-21

    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 A 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 [Valley, M. P., and Fitzpatrick, P. F. (2003) J. Am. Chem. Soc. 125, 8738-8739]. 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. PMID:19265437

  20. 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.

  1. Biosynthesis of vitamin B2: diastereomeric reaction intermediates of archaeal and non-archaeal riboflavin synthases.

    PubMed

    Illarionov, Boris; Eisenreich, Wolfgang; Schramek, Nicholas; Bacher, Adelbert; Fischer, Markus

    2005-08-01

    The dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase affords riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. A pentacyclic adduct of two 6,7-dimethyl-8-ribityllumazines has been identified earlier as a catalytically competent reaction intermediate of the Escherichia coli enzyme. Acid quenching of reaction mixtures of riboflavin synthase of Methanococcus jannaschii, a paralog of 6,7-dimethyl-8-ribityllumazine synthase devoid of similarity with riboflavin synthases of eubacteria and eukaryotes, afforded a compound whose optical absorption and NMR spectra resemble that of the pentacyclic E. coli riboflavin synthase intermediate, whereas the circular dichroism spectra of the two compounds have similar envelopes but opposite signs. Each of the compounds could serve as a catalytically competent intermediate for the enzyme by which it was produced, but not vice versa. All available data indicate that the respective pentacyclic intermediates of the M. jannaschii and E. coli enzymes are diastereomers. PMID:15944152

  2. Excited states, electron-transfer reactions, and intermediates in bacterial photosynthetic reaction centers

    SciTech Connect

    Boxer, S.G.; Goldstein, R.A.; Lockhart, D.J.; Middendorf, T.R.; Takiff, L. )

    1989-12-28

    The three-dimensional structure of a photosynthetic reaction center has recently been obtained at atomic resolution using x-ray crystallography by Deisenhofer, Epp, Miki, Huber, and Michel (J. Mol. Biol. 1984, 180, 385-398; Nature 1985, 318, 618-624). This breakthrough provides the fundamental structural information needed to understand the mechanisms of the initial energy- and electron-transfer steps in photosynthesis. The structure reveals the distances among the reactive bacteriochlorophylls and quinones as well as the location of all nearby solvent molecules, the amino acids of the reaction center protein. Thus, the reaction center provides a complex but well-defined solid-state reactive system for the study of fundamental physical and chemical processes with implications and applications well beyond this specific system. We review recent studies of the reaction intermediates and mechanism of electron transfer in which the energetics and reaction dynamics have been perturbed with external electric and magnetic fields. Electron-transfer mechanisms which have been proposed are reviewed critically in light of the available data, and electron transfer in the reaction center is compared with electron transfer in other biological and nonbiological systems.

  3. Spectroscopic features of cytochrome P450 reaction intermediates.

    PubMed

    Luthra, Abhinav; Denisov, Ilia G; Sligar, Stephen G

    2011-03-01

    Cytochromes P450 constitute a broad class of heme monooxygenase enzymes with more than 11,500 isozymes which have been identified in organisms from all biological kingdoms [1]. These enzymes are responsible for catalyzing dozens chemical oxidative transformations such as hydroxylation, epoxidation, N-demethylation, etc., with very broad range of substrates [2,3]. Historically these enzymes received their name from 'pigment 450' due to the unusual position of the Soret band in UV-vis absorption spectra of the reduced CO-saturated state [4,5]. Despite detailed biochemical characterization of many isozymes, as well as later discoveries of other 'P450-like heme enzymes' such as nitric oxide synthase and chloroperoxidase, the phenomenological term 'cytochrome P450' is still commonly used as indicating an essential spectroscopic feature of the functionally active protein which is now known to be due to the presence of a thiolate ligand to the heme iron [6]. Heme proteins with an imidazole ligand such as myoglobin and hemoglobin as well as an inactive form of P450 are characterized by Soret maxima at 420nm [7]. This historical perspective highlights the importance of spectroscopic methods for biochemical studies in general, and especially for heme enzymes, where the presence of the heme iron and porphyrin macrocycle provides rich variety of specific spectroscopic markers available for monitoring chemical transformations and transitions between active intermediates of catalytic cycle. PMID:21167809

  4. Spectroscopic features of cytochrome P450 reaction intermediates

    PubMed Central

    Luthra, Abhinav; Denisov, Ilia G.; Sligar, Stephen G.

    2010-01-01

    Preface Cytochromes P450 constitute a broad class of heme monooxygenase enzymes with more than 11,500 isozymes which have been identified in organisms from all biological kingdoms [1]. These enzymes are responsible for catalyzing dozens chemical oxidative transformations such as hydroxylation, epoxidation, N-demethylation, etc., with very broad range of substrates [2-3]. Historically these enzymes received their name from pigment 450 due to the unusual position of the Soret band in UV-Vis absorption spectra of the reduced CO-saturated state [4-5]. Despite detailed biochemical characterization of many isozymes, as well as later discoveries of other P450-like heme enzymes such as nitric oxide synthase and chloroperoxidase, the phenomenological term cytochrome P450 is still commonly used as indicating an essential spectroscopic feature of the functionally active protein which is now known to be due to the presence of a thiolate ligand to the heme iron [6]. Heme proteins with an imidazole ligand such as myoglobin and hemoglobin as well as an inactive form of P450 are characterized by Soret maxima at 420 nm [7]. This historical perspective highlights the importance of spectroscopic methods for biochemical studies in general, and especially for heme enzymes, where the presence of the heme iron and porphyrin macrocycle provides rich variety of specific spectroscopic markers available for monitoring chemical transformations and transitions between active intermediates of catalytic cycle. PMID:21167809

  5. Capturing fleeting intermediates in a catalytic CH amination reaction cycle

    PubMed Central

    Perry, Richard H.; Cahill, Thomas J.; Roizen, Jennifer L.; Du Bois, Justin; Zare, Richard N.

    2012-01-01

    We have applied an ambient ionization technique, desorption electrospray ionization MS, to identify transient reactive species of an archetypal CH amination reaction catalyzed by a dirhodium tetracarboxylate complex. Using this analytical method, we have detected previously proposed short-lived reaction intermediates, including two nitrenoid complexes that differ in oxidation state. Our findings suggest that an Rh-nitrene oxidant can react with hydrocarbon substrates through a hydrogen atom abstraction pathway and raise the intriguing possibility that two catalytic CH amination pathways may be operative in a typical bulk solution reaction. As highlighted by these results, desorption electrospray ionization MS should have broad applicability for the mechanistic study of catalytic processes. PMID:23091019

  6. Radical cation intermediates in N-dealkylation reactions.

    PubMed

    Guengerich, F P; Okazaki, O; Seto, Y; Macdonald, T L

    1995-07-01

    1. A number of mechanistic possibilities exist for P450-catalysed N-dealkylation and have been considered over the years, including C- and N-hydroxylation and sequential electron transfer (SET). With peroxidases the evidence strongly favours SET and free radicals can be detected. Any mechanism must account for lack of incorporation of label from H218O into product by P450s and the high kinetic deuterium isotope effects that are seen in N-dealkylation reactions catalysed by peroxidases but not P450s. 2. Several lines of evidence support a role for SET in P450 amine oxidations, including Hammett analysis, products of dihydropyridine oxidations, and products of mechanism-based inhibition by strained cycloalkylamines. 3. The hypothesis was considered that the P450s act via base catalysis to deprotonate the aminium radical generated by SET, since the pKa has been estimated to be approximately 9. Dihydropyridine aminium radicals have low pKa (< 4) and are generally considered to have considerable kinetic acidity. None of the haemoproteins under consideration (including the peroxidases and haemoglobin) showed high kinetic hydrogen isotope effects for the oxidation of [4-2H]- or [4-3H]-labelled 1,4-dihydropyridines. These results are consonant with the view that P450s catalyse the deprotonation of N,N-dialkylaniline aminium radicals. 4. Since low isotope effects were seen with biomimetic metalloporphyrin models as well as P450s, the deprotonation is attributed to the (FeO)2+ entity, expected to be a strong base, and not the apoprotein. Thus, the FeO moiety of peroxidases is shielded, consistent with evidence by others that SET occurs through the porphyrin edge. Both P450s and peroxidases catalysed the oxidative N-demethylation of aminopyrine and N,N-dimethylaminothioanisole; however, only the peroxidases generated the stable coloured aminium radicals. 5. The rates of N-demethylation of variously para-substituted N,N-dimethylanilines can be used to undertake Hammett or Marcus analysis. The former yields rho = -0.6 and the latter an apparent E1/2 of approximately 1.8 for the formal (FeO)3+ entity of P4502B1. 6. Even in the oxidation of N,N-dialkylanilines, a finite rate of N-oxidation is seen (approximately 0.1% of N-dealkylation). The simplest paradigm has N-oxygenation and N-dealkylation both proceeding from a common aminium radical intermediate. PMID:7483667

  7. Reaction Intermediates Kinetics in Solution Investigated by Electrospray Ionization Mass Spectrometry: Diaurated Complexes.

    PubMed

    Jašíková, Lucie; Anania, Mariarosa; Hybelbauerová, Simona; Roithová, Jana

    2015-10-28

    A new method to investigate the reaction kinetics of intermediates in solution by electrospray ionization mass spectrometry is presented. The method, referred to as delayed reactant labeling, allows investigation of a reaction mixture containing isotopically labeled and unlabeled reactants with different reaction times. It is shown that we can extract rate constants for the degradation of reaction intermediates and investigate the effects of various reaction conditions on their half-life. This method directly addresses the problem of the relevance of detected gaseous ions toward the investigated reaction solution. It is demonstrated for geminally diaurated intermediates formed in the gold mediated addition of methanol to alkynes. Delayed reactant labeling allows us to directly link the kinetics of the diaurated intermediates with the overall reaction kinetics determined by NMR spectroscopy. It is shown that the kinetics of protodeauration of these intermediates mirrors the kinetics of the addition of methanol demonstrating they are directly involved in the catalytic cycle. Formation as well as decomposition of diaurated intermediates can be drastically slowed down by employing bulky ancillary ligands at the gold catalyst; the catalytic cycle then proceeds via monoaurated intermediates. The reaction is investigated for 1-phenylpropyne (Ph-CC-CH3) using [AuCl(PPh3)]/AgSbF6 and [AuCl(IPr)]/AgSbF6 as model catalysts. Delayed reactant labeling is achieved by using a combination of CH3OH and CD3OH or Ph-CC-CH3 and Ph-CC-CD3. PMID:26430872

  8. 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.

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

    PubMed

    Benitez, F Javier; Acero, Juan L; Real, Francisco J; Roldn, Gloria; Rodrguez, 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 (1?M) 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. PMID:24953706

  10. 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

  11. Pre-steady-state kinetic analysis of riboflavin synthase using a pentacyclic reaction intermediate as substrate.

    PubMed

    Illarionov, Boris; Haase, Ilka; Fischer, Markus; Bacher, Adelbert; Schramek, Nicholas

    2005-02-01

    Riboflavin synthase catalyses a mechanistically complex dismutation affording riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H )-pyrimidinedione from 6,7-dimethyl-8-ribityllumazine. A pentacyclic adduct (compound 2 ) of two substrate molecules was used as substrate for pre-steady-state kinetic analysis. Whereas the wild-type enzyme catalyses the decomposition of compound 2 into a mixture of riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H )-pyrimidinedione, as well as into two equivalents of 6,7-dimethyl-8-ribityllumazine, a H102Q mutant enzyme predominantly catalyses the former reaction. Stopped-flow experiments with this mutant enzyme failed to identify a reaction intermediate between compound 2 and riboflavin. However, the apparent rate constants for the formation of riboflavin as observed by stopped-flow and quenched-flow experiments were significantly different, thus suggesting that the reaction proceeds via a significantly populated intermediate, the absorbance of which is similar to that of compound 2 . An F2A mutant enzyme converts compound 2 predominantly into 6,7-dimethyl-8-ribityllumazine. Stopped-flow experiments using compound 2 as substrate indicated a slight and rapid initial increase in absorbance at 310 nm, followed by a slower decrease. This finding, in conjunction with different apparent rates for the formation of 6,7-dimethyl-8-ribityllumazine, suggests the involvement of a significantly populated intermediate in the transition between compound 2 and 6,7-dimethyl-8-ribityllumazine, the optical spectrum of which is similar to that of compound 1. PMID:15843156

  12. Two-neutron interferometry in low- and intermediate-energy heavy-ion reactions

    SciTech Connect

    Tagliente, G.; Colonna, N.; Ghetti, R.; De Filippo, E.

    1999-11-16

    Two-nucleon interferometry can be used in low- and intermediate-energy heavy ion reactions to probe the space-time evolution of hot and possibly compressed nuclear systems. At low energy, angle-gated correlation functions have allowed to succesfully extract the lifetime of moderately excited compound nuclei. At intermediate energy, two-neutron interferometry has been used to obtain information on the contribution of different mechanisms to the reaction dynamics.

  13. 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

  14. Elusive Reaction Intermediates in Solution Explored by ESI-MS: Reverse Periscope for Mechanistic Investigations.

    PubMed

    Iacobucci, Claudio; Reale, Samantha; De Angelis, Francesco

    2016-02-01

    Just as periscopes allow a submarine to visually search for objects above the surface of the sea, in a reversed periscope fashion electrospray mass spectrometry (ESI-MS) can analyze the compounds at the gas phase/liquid phase interface for chemical entities which may exist in solution. The challenge is the identification and structural characterization of key elusive reaction intermediates in chemical transformations, intermediates which are able to explain how chemical processes occur. This Minireview summarizes recent selected publications on the use of ESI-MS techniques for studying solution intermediates of homogeneous chemical reactions. PMID:26799781

  15. 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

  16. 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…

  17. Identifying the Tautomeric Form of a Deoxyguanosine-Estrogen Quinone Intermediate

    PubMed Central

    Stack, Douglas E.

    2015-01-01

    Mechanistic insights into the reaction of an estrogen o-quinone with deoxyguanosine has been further investigated using high level density functional calculations in addition to the use of 4-hyroxycatecholestrone (4-OHE1) regioselectivity labeled with deuterium at the C1-position. Calculations using the M06-2X functional with large basis sets indicate the tautomeric form of an estrogen-DNA adduct present when glycosidic bonds cleavage occurs is comprised of an aromatic A ring structure. This tautomeric form was further verified by use of deuterium labelling of the catechol precursor use to form the estrogen o-quinone. Regioselective deuterium labelling at the C1-position of the estrogen A ring allows discrimination between two tautomeric forms of a reaction intermediate either of which could be present during glycosidic bond cleavage. HPLC-MS analysis indicates a reactive intermediate with a m/z of 552.22 consistent with a tautomeric form containing no deuterium. This intermediate is consistent with a reaction mechanism that involves: (1) proton assisted Michael addition; (2) re-aromatization of the estrogen A ring; and (3) glycosidic bond cleavage to form the known estrogen-DNA adduct, 4-OHE1-1-N7Gua. PMID:26378590

  18. 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.

  19. 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.

  20. Neutron Spectra from Intermediate-Energy Nucleus-Nucleus Reactions

    SciTech Connect

    Iwase, Hiroshi; Iwata, Yoshiyuki; Nakamura, Takashi; Gudima, Konstantin; Mashnik, Stepan; Sierk, Arnold; Prael, Richard

    2005-05-24

    Double-differential cross sections of neutron production at angles from 0 to 110 degrees from many reactions induced by light and medium nuclei on targets from 12C to 208Pb, at several incident energies from 95 to 600 MeV/nucleon have been measured recently at the Institute of Physical and Chemical Research (RIKEN) Ring Cyclotron in Japan and at the Heavy-Ion Medical Accelerator of the National Institute of Radiological Science in Chiba, Japan using the time-of-flight technique. We have analyzed all these new measurements using the Quantum Molecular Dynamics (QMD) model, the Oak Ridge intranuclear cascade model HIC, the ISABEL intranuclear cascade model from LAHET, and the Los Alamos version of the Quark-Gluon String Model code LAQGSM03. On the whole, all four models used here describe reasonably well most of the measured neutron spectra, although different models agree differently with data from specific reactions and some serious discrepances are observed for some reactions. We present here some illustrative results from our study, discuss possible reasons for some of the observed discrepancies and try to outline ways to further improve the tested codes in order to address these problems.

  1. Ketene as a Reaction Intermediate in the Carbonylation of Dimethyl Ether to Methyl Acetate over Mordenite.

    PubMed

    Rasmussen, Dominik B; Christensen, Jakob M; Temel, Burcin; Studt, Felix; Moses, Poul Georg; Rossmeisl, Jan; Riisager, Anders; Jensen, Anker D

    2015-06-15

    Unprecedented insight into the carbonylation of dimethyl ether over Mordenite is provided through the identification of ketene (CH2CO) as a reaction intermediate. The formation of ketene is predicted by detailed DFT calculations and verified experimentally by the observation of doubly deuterated acetic acid (CH2DCOOD), when D2O is introduced in the feed during the carbonylation reaction. PMID:25967363

  2. Study of intermediates from transition metal excited-state electron-transfer reactions

    SciTech Connect

    Hoffman, M.Z.

    1992-07-31

    Conventional and fast-kinetics techniques of photochemistry, photophysics, radiation chemistry, and electrochemistry were used to study the intermediates involved in transition metal excited-state electron-transfer reactions. These intermediates were excited state of Ru(II) and Cr(III) photosensitizers, their reduced forms, and species formed in reactions of redox quenchers and electron-transfer agents. Of particular concern was the back electron-transfer reaction between the geminate pair formed in the redox quenching of the photosensitizers, and the dependence of its rate on solution medium and temperature in competition with transformation and cage escape processes. (DLC)

  3. Study of intermediates from transition metal excited-state electron-transfer reactions

    NASA Astrophysics Data System (ADS)

    Hoffman, M. Z.

    1992-07-01

    Conventional and fast-kinetics techniques of photochemistry, photophysics, radiation chemistry, and electrochemistry were used to study the intermediates involved in transition metal excited-state electron-transfer reactions. These intermediates were excited state of Ru(II) and Cr(III) photosensitizers, their reduced forms, and species formed in reactions of redox quenchers and electron-transfer agents. Of particular concern was the back electron-transfer reaction between the geminate pair formed in the redox quenching of the photosensitizers, and the dependence of its rate on solution medium and temperature in competition with transformation and cage escape processes.

  4. Crystal Structure of Reaction Intermediates in Pyruvate Class II Aldolase

    PubMed Central

    Coincon, Mathieu; Wang, Weijun; Sygusch, Jurgen; Seah, Stephen Y. K.

    2012-01-01

    Crystal structures of divalent metal-dependent pyruvate aldolase, HpaI, in complex with substrate and cleavage products were determined to 1.8–2.0 Å resolution. The enzyme·substrate complex with 4-hydroxy-2-ketoheptane-1,7-dioate indicates that water molecule W2 bound to the divalent metal ion initiates C3–C4 bond cleavage. The binding mode of the aldehyde donor delineated a solvent-filled capacious binding locus lined with predominantly hydrophobic residues. The absence of direct interactions with the aldehyde aliphatic carbons accounts for the broad specificity and lack of stereospecific control by the enzyme. Enzymatic complex structures formed with keto acceptors, pyruvate, and 2-ketobutyrate revealed bidentate interaction with the divalent metal ion by C1-carboxyl and C2-carbonyl oxygens and water molecule W4 that is within close contact of the C3 carbon. Arg70 assumes a multivalent role through its guanidinium moiety interacting with all active site enzymatic species: C2 oxygen in substrate, pyruvate, and ketobutyrate; substrate C4 hydroxyl; aldehyde C1 oxygen; and W4. The multiple interactions made by Arg70 stabilize the negatively charged C4 oxygen following proton abstraction, the aldehyde alignment in aldol condensation, and the pyruvate enolate upon aldol cleavage as well as support proton exchange at C3. This role is corroborated by loss of aldol cleavage ability and pyruvate C3 proton exchange activity and by a 730-fold increase in the dissociation constant toward the pyruvate enolate analog oxalate in the R70A mutant. Based on the crystal structures, a mechanism is proposed involving the two enzyme-bound water molecules, W2 and W4, in acid/base catalysis that facilitates reversible aldol cleavage. The same reaction mechanism promotes decarboxylation of oxaloacetate. PMID:22908224

  5. Solving the structure of reaction intermediates by time-resolved synchrotron x-ray absorption spectroscopy.

    PubMed

    Wang, Qi; Hanson, Jonathan C; Frenkel, Anatoly I

    2008-12-21

    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. PMID:19102533

  6. Identifying a Highly Active Copper Catalyst for KA(2) Reaction of Aromatic Ketones.

    PubMed

    Cai, Yujuan; Tang, Xinjun; Ma, Shengming

    2016-02-01

    The well-established A(3) coupling reaction of terminal alkynes, aldehydes, and amines provides the most straightforward approach to propargylic amines. However, the related reaction of ketones, especially aromatic ketones, is still a significant challenge. A highly efficient catalytic protocol has been developed for the coupling of aromatic ketones with amines and terminal alkynes, in which Cu(I) , generated in situ from the reduction of CuBr2 with sodium ascorbate, has been identified as the highly efficient catalyst. Since propargylic amines are versatile synthetic intermediates and important units in pharmaceutical products, such an advance will greatly stimulate research interest involving the previously unavailable propargylic amines. PMID:26660459

  7. Dynamical effects of spin-dependent interactions in low- and intermediate-energy heavy-ion reactions

    NASA Astrophysics Data System (ADS)

    Xu, Jun; Li, Bao-An; Shen, Wen-Qing; Xia, Yin

    2015-10-01

    It is well known that noncentral nuclear forces, such as the spin-orbital coupling and the tensor force, play important roles in understanding many interesting features of nuclear structures. However, their dynamical effects in nuclear reactions are poorly known because only the spin-averaged observables are normally studied both experimentally and theoretically. Realizing that spin-sensitive observables in nuclear reactions may convey useful information about the in-medium properties of noncentral nuclear interactions, besides earlier studies using the time-dependent Hartree-Fock approach to understand the effects of spin-orbital coupling on the threshold energy and spin polarization in fusion reactions, some efforts have been made recently to explore the dynamical effects of noncentral nuclear forces in intermediate-energy heavy-ion collisions using transport models. The focus of these studies has been on investigating signatures of the density and isospin dependence of the form factor in the spin-dependent single-nucleon potential. Interestingly, some useful probes were identified in the model studies but so far there are still no data to compare with. In this brief review, we summarize the main physics motivations as well as the recent progress in understanding the spin dynamics and identifying spin-sensitive observables in heavy-ion reactions at intermediate energies. We hope the interesting, important, and new physics potentials identified in the spin dynamics of heavy-ion collisions will stimulate more experimental work in this direction.

  8. Reactions of benzylamines with methylamine dehydrogenase. Evidence for a carbanionic reaction intermediate and reaction mechanism similar to eukaryotic quinoproteins.

    PubMed

    Davidson, V L; Jones, L H; Graichen, M E

    1992-04-01

    It had been previously reported that aromatic amines were not substrates for the bacterial quinoprotein methylamine dehydrogenase. In this study, benzylamine-dependent activity was also not observed in the steady-state assay of this enzyme with the artificial electron acceptor phenazine ethosulfate (PES). Benzylamines did, however, stoichiometrically reduce the protein-bound tryptophan tryptophylquinone (TTQ) prosthetic group and acted as reversible competitive inhibitors of methylamine oxidation when the enzyme was assayed with PES. When methylamine dehydrogenase activity was monitored using a steady-state assay which employed its physiological electron acceptor amicyanin instead of PES, very low but detectable benzylamine-dependent activity was observed. The reactions of a series of para-substituted benzylamines with methylamine dehydrogenase were examined. A Hammett plot of the log of Ki values for the competitive inhibition by these amines against sigma p exhibited a negative slope. Rapid kinetic measurements allowed the determination of values of k3 and Ks for the reduction of TTQ by each of these amines. A Hammett plot of log k3 versus sigma p exhibited a positive slope, which suggests that the oxidation of these amines by methylamine dehydrogenase proceeds through a carbanionic reaction intermediate. A negative slope was observed for the correlation between log Ks and sigma p. Plots of log k3 and log Ks against substituent constants which reflected either resonance or field/inductive parameters for each para substituent indicated that the magnitude of k3 was primarily influenced by field/inductive effects while Ks was primarily influenced by resonance effects. No correlation was observed between either k3 or Ks and the relative hydrophobicity of the para-substituted benzylamines or steric parameters.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1554720

  9. Trapping and Characterization of a Reaction Intermediate in Carbapenem Hydrolysis by B. cereus Metallo-?-lactamase

    PubMed Central

    Tioni, Mariana F.; Llarrull, Leticia I.; Poeylaut-Palena, Andrs A.; Mart, Marcelo A.; Saggu, Miguel; Periyannan, Gopal R.; Mata, Ernesto G.; Bennett, Brian; Murgida, Daniel H.; Vila, Alejandro J.

    2009-01-01

    Metallo-?-lactamases hydrolyze most ?-lactam antibiotics. The lack of a successful inhibitor for them is related to the previous failure to characterize a reaction intermediate with a clinically useful substrate. Stopped-flow experiments together with rapid freeze-quench EPR and Raman spectroscopies were used to characterize the reaction of Co(II)-BcII with imipenem. These studies show that Co(II)-BcII is able to hydrolyze imipenem both in the mono- and dinuclear forms. In contrast to the situation met for penicillin, the species that accumulates during turnover is an enzyme-intermediate adduct in which the ?-lactam bond has already been cleaved. This intermediate is a metal-bound anionic species, with a novel resonant structure, that is stabilized by the metal ion at the DCH or Zn2 site. This species has been characterized based on its spectroscopic features. This represents a novel, previously unforeseen intermediate, that is related to the chemical nature of carbapenems, as confirmed by the finding of a similar intermediate for meropenem. Since carbapenems are the only substrates cleaved by B1, B2 and B3 lactamases, the identification of this intermediate could be exploited as a first step towards the design of transition state based inhibitors for all three classes of metallo-?-lactamases. PMID:18980308

  10. Synthesis of a potential intermediate for TMC-95A via an organocatalyzed aldol reaction.

    PubMed

    Pearson, Anthony J; Panda, Santanu; Bunge, Scott D

    2013-10-01

    N-Prolinylanthranilamide-based pseudopeptide organocatalyst 14 was shown to promote enantioselective direct aldol reaction of 7-iodoisatin and 2,2-dimethyl-1,3-dioxan-5-one with 90% conversion (75% isolated yield), 90% enantioselectivity, and 23:1 diastereoselectivity. To demonstrate the synthetic utility of this chemistry, the racemic aldol reaction product was converted in five steps to a potential intermediate for construction of the natural product TMC-95A. PMID:24024913

  11. International chemical identifier for reactions (RInChI).

    PubMed

    Grethe, Guenter; Goodman, Jonathan M; Allen, Chad Hg

    2013-01-01

    The IUPAC International Chemical Identifier (InChI) provides a method to generate a unique text descriptor of molecular structures. Building on this work, we report a process to generate a unique text descriptor for reactions, RInChI. By carefully selecting the information that is included and by ordering the data carefully, different scientists studying the same reaction should produce the same RInChI. If differences arise, these are most likely the minor layers of the InChI, and so may be readily handled. RInChI provides a concise description of the key data in a chemical reaction, and will help enable the rapid searching and analysis of reaction databases. PMID:24152584

  12. Recent developments in methods for identifying reaction coordinates

    PubMed Central

    Li, Wenjin; Ma, Ao

    2014-01-01

    In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the reaction coordinates based on limited information from molecular dynamics simulations. In this review, we provide a brief survey over a number of major methods developed in the past decade, some of which are discussed in greater detail, to provide an overview of the problems that are partially solved and challenges that still remain. A particular emphasis has been placed on methods for identifying reaction coordinates that are related to the committor. PMID:25197161

  13. Reaction of arynes with vinylogous amides: nucleophilic addition to the ortho-quinodimethide intermediate.

    PubMed

    Li, Ran; Wang, Xuemei; Wei, Zhibin; Wu, Chunrui; Shi, Feng

    2013-09-01

    The reaction of arynes with vinylogous amides containing no free N-H bonds proceeds in a [2 + 2] cycloaddition fashion at ambient temperature. The electronic properties of the vinylogous amides allow for the cycloadducts undergoing a facile ring-opening process, leading to electronically biased ortho-quinodimethide intermediates. Subsequent nucleophilic addition with alcohols affords 2-substituted benzaldehydes or ketones. PMID:23957502

  14. Production of projectile-like-fragments with light systems in mass asymmetric, intermediate energy reactions

    NASA Astrophysics Data System (ADS)

    Quinlan, Michael; Pawelczak, Iwona; T\\ Oke, Jan; Schr"Oder, Udo

    2009-05-01

    The reactions ^40,48Ca + ^112,124Sn at a bombarding energy of 45 MeV/A were studied with the 4? charged particle detector array, CHIMERA, at the Laboratori Nazionali del Sud in Catania, Italy. Measured observables were the charged particle multiplicities, their individual energy, charge, and in some cases, isotopic identity. Of particular interest is the production of intermediate mass fragments and their correlations with projectile-like fragments (PLFs) formed in the reaction. Data concerning the production of PLFs will be presented; specifically their charge, energy, and angular distributions. The reaction mechanism and isotopic effects with be discussed.

  15. Study of intermediates from transition metal excited-state electron-transfer reactions

    SciTech Connect

    Hoffman, M.Z.

    1991-12-31

    During this period, conventional and fast-kinetics techniques of photochemistry, photophysics, radiation chemistry, and electrochemistry were used for the characterization of the intermediates that are involved in transition metal excited-state electron-transfer reactions. The intermediates of interest were the excited states of Ru(II) and Cr(III) photosensitizers, their reduced forms, and the species formed in the reactions of redox quenchers and electron-transfer agents. Of particular concern has been the back electron-transfer reaction between the geminate pair formed in the redox quenching of the photosensitizers, and the dependence of its rate on solution medium and temperature in competition with transformation and cage escape processes.

  16. Isotope effects, dynamic matching, and solvent dynamics in a Wittig reaction. Betaines as bypassed intermediates.

    PubMed

    Chen, Zhuo; Nieves-Quinones, Yexenia; Waas, Jack R; Singleton, Daniel A

    2014-09-24

    The mechanism of the Wittig reaction of anisaldehyde with a stabilized ylide was studied by a combination of (13)C kinetic isotope effects, conventional calculations, and molecular dynamics calculations in a cluster of 53 THF molecules. The isotope effects support a cycloaddition mechanism involving two sequential transition states associated with separate C-C and P-O bond formations. However, the betaine structure in between the two transition states is bypassed as an equilibrated intermediate in most trajectories. The role of the dynamics of solvent equilibration in the nature of mechanistic intermediates is discussed. PMID:25208686

  17. Isotope Effects, Dynamic Matching, and Solvent Dynamics in a Wittig Reaction. Betaines as Bypassed Intermediates

    PubMed Central

    2015-01-01

    The mechanism of the Wittig reaction of anisaldehyde with a stabilized ylide was studied by a combination of 13C kinetic isotope effects, conventional calculations, and molecular dynamics calculations in a cluster of 53 THF molecules. The isotope effects support a cycloaddition mechanism involving two sequential transition states associated with separate CC and PO bond formations. However, the betaine structure in between the two transition states is bypassed as an equilibrated intermediate in most trajectories. The role of the dynamics of solvent equilibration in the nature of mechanistic intermediates is discussed. PMID:25208686

  18. An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

    NASA Technical Reports Server (NTRS)

    Jackels, C. F.

    1985-01-01

    Ab initio quantum chemical techniques are used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types are identified. Basis sets of polarized double zeta quality and large scale configuration interaction wave functions are utilized. Based on electronic energies, the covalently bonded HOOOH species is 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen bonded HO---HO2 species has an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen bonded form is planar, possesses one relatively normal hydrogen bond, and has the lowest energy 3A' and 1A' states that are essentially degenerate. The 1A" and 3A" excited states produced by rotation of the unpaired OH electron into the molecular plane are very slightly bound.

  19. An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

    NASA Technical Reports Server (NTRS)

    Jackels, C. F.; Phillips, D. H.

    1986-01-01

    Ab initio quantum chemical techniques have been used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types were identified. Basic sets of polarized double-zeta quality and large scale configuration interaction wave functions have been utilized. Based upon electronic energies, the covalently-bonded HOOOH species is found to be 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen-bonded HO-HO2 species is found to have an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen-bonded form is found to be planar, to possess one relatively 'normal' hydrogen bond, and to have lowest energy 3A-prime and 1A-prime states that are essentially degenerate. The 1A-double prime and 3A-double prime excited states produced by rotation of the unpaired OH electron into the molecular plane are found to be very slightly bound.

  20. The Role of Phosphate in a Multistep Enzymatic Reaction: Reactions of the Substrate and Intermediate in Pieces

    PubMed Central

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

    2015-01-01

    Several mechanistically unrelated enzymes utilize the binding energy of their substrates 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 enzymephosphodianion interactions to the reaction coordinate. PMID:25642788

  1. 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.

  2. 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

    2015-02-01

    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). PMID:25553776

  3. The crystallographic structure of thermoNicotianamine synthase with a synthetic reaction intermediate highlights the sequential processing mechanism.

    PubMed

    Dreyfus, Cyril; Larrouy, Manuel; Cavelier, Florine; Martinez, Jean; Pignol, David; Arnoux, Pascal

    2011-05-28

    We determined the three-dimensional structure of a complex between an archaeal nicotianamine synthase homologue and a chemically synthesised reaction intermediate. This structure suggests that the enzymes cavity allows both an ordered substrate binding and provides energetic coupling of the reaction intermediate formation and translocation. PMID:21487608

  4. 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; Dale, 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.

  5. Paramagnetic intermediates in reactions of the components of catalytic systems of the Ziegler type. Reactions of azo and azomethine complexes of Ni(II) with diethylaluminum chloride

    SciTech Connect

    Abbasov, Ya.A.; Ismailov, E.G.; Medzhidov, A.A.

    1988-04-01

    The intermediate paramagnetic particles, i.e., radical particles, complexes of Ni(I), and Ni/sub n/(O) aggregates, formed as a result of the reaction of azo and azomethine complexes of Ni(II) with Et/sub 2/AlCl in solvent media (toluene, THF, heptane) have been identified with the aid of ESR. The possibility of the stabilization of reactive intermediate complexes of Ni(I) by organophosphorus ligands (DPPE and TPP) has been demonstrated, and the magnetic-resonance parameters of their adducts have been determined. It has been postulated that the formation of radical particles occurs as a result of the coordination of the nitrogen atoms of the azo or azomethine ligands by the organoaluminum compound followed by splitting of the -N=N or -CH=N bonds.

  6. 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.

  7. 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.

  8. Random sampling of the Greens 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 Greens 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.

  9. Deriving reaction mechanisms from kinetic spectroscopy. Application to late rhodopsin intermediates.

    PubMed Central

    Szundi, I; Lewis, J W; Kliger, D S

    1997-01-01

    A general algebraic approach to the kinetic analysis of time-dependent absorption data is presented that allows the calculation of possible kinetic schemes. The kinetic matrices of all possible reaction mechanisms are calculated from experimental eigenvalues and eigenvectors derived from the decay constants and amplitude spectra (b-spectra) of the global exponential fit to the time-dependence of the absorption data. The eigenvalues are directly related to the decay constants, and the eigenvectors are obtained by decomposing the b-spectra into spectral components representing the intermediates. The analysis method is applied to the late intermediates (lumi, meta I, meta I-380, and meta II) of the rhodopsin photoreaction. The b-spectra are decomposed into lumi, meta I, meta-380, and rhodopsin spectra. The meta-380 component is partitioned into isospectral meta I-380 and meta II components based on physical criteria. The calculated kinetic matrices yield a number of reaction mechanisms (linear scheme with back reactions, branched schemes with equilibrium steps, and a variety of square models) consistent with the photolysis data at 25 degrees C. The problems associated with isospectral intermediates (meta I-380 and meta II) are treated successfully with this method. PMID:9251787

  10. 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)...

  11. 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 CO? from the carboxyphosphate intermediate to biotin. PMID:26020841

  12. 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. PMID:26397164

  13. Aspartate aminotransferase: the kinetic barriers facing the covalent intermediates on the reaction pathway

    SciTech Connect

    Kirsch, J.F.; Julin, D.A.; McLeish, M.; Wiesinger, H.

    1986-05-01

    The intermediates, aldimine (A), quinonoid (Q) and ketimine (K), along the transaminase reaction coordinate were probed by isotope transfer and solvent exchange kinetics. Less than 0.003% of /sup 3/H is transferred from C/sub ..cap alpha../(/sup 3/H)-aspartate to pyridoxamine phosphate in the cytoplasmic aspartate aminotransferase (cAATase) reaction implying either that Q does not exist as a kinetically competent intermediate or that there is a rapid exchange of isotope with solvent. The ratio of the rate constants for C/sub ..cap alpha../ hydrogen exchange vs keto acid product formation (k/sub exge//k/sub prod/) are 2.5 and 0.5 for the reactions of cAATase with C/sub ..cap alpha../ (/sup 2/H)-aspartate and mitochondrial (m) AATase with C/sub ..cap alpha../(/sup 2/H)-glutamate respectively. The latter reaction was also probed from the ..cap alpha..-keto-glutarate side with carbonyl 0-18 enriched keto acid. This experiment gave k/sub exge//k/sub prod/ = 1.0 for oxygen-18 exchange in ..cap alpha..-ketoglutarate versus amino acid formation. The two exchange experiments with mAATase are interpreted in terms of a model in which the rate constant for diffusion of water from the active site is comparable with those for product forming steps.

  14. Folylpolyglutamate synthetase: direct evidence for an acyl phosphate intermediate in the enzyme-catalyzed reaction

    SciTech Connect

    Banerjee, R.; McGuire, J.J.; Shane, B.; Coward, J.K.

    1986-05-01

    The nature of the intermediate in the reaction catalyzed by folylpoly-..gamma..-glutamate synthetase (FPGS) has been investigated. Incubation of ..cap alpha..,..gamma..-(/sup 18/O)methotrexate with ATP, glutamate, and FPGS resulted in the formation of (/sup 18/O)phosphate, thus providing strong evidence for the formation of a ..gamma..-glutamyl phosphate during catalysis. The inorganic phosphate formed in the enzyme-catalyzed reaction was separated from other products and substrates by chromatography on DEAE-cellulose, then converted to the trimethyl ester, and analyzed by mass spectroscopy. Stoichiometric formation of (/sup 18/O)phosphate was observed in the case of the E. coli enzyme, isolated from a transformant containing the cloned FPGS-dihydrofolate synthetase (folC) gene. In addition, /sup 31/P-NMR analysis of the phosphate isolated from the reaction using E. coli FPGS showed the expected /sup 18/O-isotopic perturbations due to both singly bonded and doubly bonded P-/sup 18/O species. Similar experiments were carried out with FPGS isolated from hog liver. In this case, the small amounts of pure enzyme available precluded use of the NMR technique. However, mass spectral analysis of the derivatized phosphate product revealed the presence of (/sup 18/O)-trimethyl phosphate, thus indicating that the reaction catalyzed by the mammalian enzyme also proceeds via an acyl phosphate intermediate.

  15. Investigations of the structure and reactions of the intermediate in the chlorination of resorcinol

    SciTech Connect

    Heasley, V.L.; Anderson, M.E.; Combes, D.S.; Elias, D.S.; Gardner, J.T.; Hernandez, M.L.; Moreland, R.J.; Shellhamer, D.F. . Dept. of Chemistry)

    1993-09-01

    The investigation reported here describes an attempt to establish the structure of the intermediate that undergoes ring-opening in the chlorination of resorcinol and its chloro-derivatives in a nucleophilic solvent such as H[sub 2]O or CH[sub 3]OH. The evidence suggests that the pentachloride and not the tetrachloride is the intermediate that reacts with the nucleophiles. Chlorination reactions were conducted in Ch[sub 3]OH/H[sub 2]O. The structures of the early-generation products from incorporation of CH[sub 3]OH were sufficiently stable to be characterized. These products implicated the pentachloride. Resorcinol, di- and trichlororesorcinol, and the pentachloride gave the same products. The mechanisms of the ring-opening and the reactions leading to the products are described in detail. The assumption is made that the same or similar reactions are involved in the aqueous chlorination of resorcinol, but that decarboxylation and solvolysis reactions rapidly degrade the products immediately following ring-opening.

  16. Evidence for an imino intermediate in the T4 endonuclease V reaction.

    PubMed

    Dodson, M L; Schrock, R D; Lloyd, R S

    1993-08-17

    Reductive methylation and site-directed mutagenesis experiments have implicated the N-terminal alpha-amino group of T4 endonuclease V in the glycosylase and abasic lyase activities of the enzyme. NMR studies have confirmed the involvement of the N-terminal alpha-amino group in the inhibition of enzyme activity by reductive methylation. A mechanism accounting for these results predicts that a (imino) covalent enzyme-substrate intermediate is formed between the protein N-terminal alpha-amino group and C1' of the 5'-deoxyribose of the pyrimidine dimer substrate subsequent to (or concomitantly with) the glycosylase step. Experiments to verify the existence of this intermediate indicated that enzyme inhibition by cyanide was substrate-dependent, a result classically interpreted to imply an imino reaction intermediate. In addition, sodium borohydride reduction of the intermediate formed a stable dead-end enzyme-substrate product. This product was formed whether ultraviolet light-irradiated high molecular weight DNA or duplex oligonucleotides containing a defined thymine-thymine cyclobutane dimer were used as substrate. The duplex oligonucleotide substrates demonstrated a well-defined gel shift. This will facilitate high-resolution footprinting of the enzyme on the DNA substrate. PMID:8347626

  17. Progress in applyiong the FKK multistep reaction theory to intermediate-energy data evaluation

    SciTech Connect

    Chadwick, M.B.; Young, P.G.

    1994-07-01

    Recent developments to the physics modeling in the FKK-GNASH code system are reviewed. We describe modifications to include a linking of multistep direct and multistep compound processes, which are important when the incident energy is less than about 30 MeV. A model for multiple preequilibrium emission is given, and compared with experimental measurements of proton reactions on {sup 90}Zr at 160 MeV. We also give some preliminary observations concerning FKK calculations which use both normal and non-normal DWBA matrix elements. We describe the application of the FKK-GNASH code to a range of nuclear data applications, including intermediate energy reactions of importance in the accelerator transmutation of waste, and fast neutron and proton cancer radiation treatment. We outline areas where further work is needed for the accurate modeling of nuclear reactions using the FKK theory.

  18. Exploiting Acyl and Enol Azolium Intermediates via NHeterocyclic Carbene Catalyzed Reactions of Alpha-Reducible Aldehydes

    PubMed Central

    Vora, Harit U.; Wheeler, Philip

    2013-01-01

    N-heterocyclic carbenes are well known for their role in catalyzing benzoin and Stetter reactions: the generation of acyl anion equivalents from simple aldehydes to react with a variety of electrophiles. However, when an aldehyde bearing a leaving group or unsaturation adjacent to the acyl anion equivalent is subjected to an NHC, a new avenue of reactivity is unlocked, leading to a number of novel transformations which can generate highly complex products from simple starting materials, many of which are assembled through unconventional bond disconnections. The field of these new reactions - those utilizing ?-reducible aldehydes to access previously unexplored catalytic intermediates has expanded rapidly in the past eight years. This review aims to provide the reader with a historical perspective on the underlying discoveries that led to the current state of the art, a mechanistic description of these reactions, and a summary of the recent advances in this area. PMID:23538785

  19. 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

  20. 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.

  1. 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. PMID:23724731

  2. A modular array for neutron spectroscopy in low- and intermediate-energy heavy-ion reactions

    NASA Astrophysics Data System (ADS)

    Colonna, N.; Celano, L.; D'Erasmo, G.; Fiore, E. M.; Fiore, L.; Paticchio, V.; Tagliente, G.; Antuofermo, G.; Iacobelli, G.; Sacchetti, M.; Vasta, P.; Pantaleo, A.

    1996-02-01

    An array for neutron spectroscopy in low and intermediate-energy heavy-ion reactions is here described. The array is made of cylindrical liquid scintillator cells 6.3 cm in radius and 12.7 cm thick. The detectors are mounted on a mechanical structure that allows to easily position the detectors in a wide range of angles and distances from the target. The performances of a single detector, as well as those of the whole apparatus are described. Examples of experimental configurations, used in recent experiments, are presented.

  3. Photocatalytic removal of pesticide dichlorvos from indoor air: a study of reaction parameters, intermediates and mineralization.

    PubMed

    Sleiman, Mohamad; Ferronato, Corinne; Chovelon, Jean-Marc

    2008-04-15

    This paper presents for the first time the investigation of TiO2 photocatalysis for the removal of pesticides in gas phase. Dichlorvos was used as a model pesticide, and experiments were carried out using both static and dynamic reaction systems to explore the different aspects of the process. Thus, adsorption, reaction kinetics, and the influence of several operational parameters such as relative humidity (RH), inlet concentration, flow rate, and association of TiO2 with activated carbon (AC) were all examined in detail. Furthermore, a special attention was devoted to the analysis of reaction products by means of various analytical techniques such as Fourier transform infrared spectroscopy, automated thermal desorption technique coupled to gas chromatography-mass spectrometry instrument, gas chromatography equipped with a pulse discharge helium photoionization detector, and ion chromatography. The results showed an immediate and total removal of dichlorvos at ppbv levels (50-350 ppbv) along with a high mineralization extent (50-85%) into harmless final products (CO2, HCl, PO43-). Moreover, RH was found to significantly affectthe mineralization extent and the formation of reaction intermediates. On the basis of identification data, direct charge transfer and chlorine radical (Cl*) attack were shown to play a key role in the reaction mechanism at low RH, whereas at high RH, HO* radicals were the predominant active species. PMID:18497160

  4. 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

  5. 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.

  6. Direct Observation of Intermediates Involved in the Interruption of the Bischler-Napieralski Reaction.

    PubMed

    White, Kolby L; Mewald, Marius; Movassaghi, Mohammad

    2015-08-01

    The first mechanistic investigation of electrophilic amide activation of ?,?-disubstituted tertiary lactams and the direct observation of key intermediates by in situ FTIR, (1)H, (13)C, and (19)F NMR in our interrupted Bischler-Napieralski-based synthetic strategy to the aspidosperma alkaloids, including a complex tetracyclic diiminium ion, is discussed. The reactivity of a wide range of pyridines with trifluoromethanesulfonic anhydride was systematically examined, and characteristic IR absorption bands for the corresponding N-trifluoromethanesulfonylated pyridinium trifluoromethanesulfonates were assigned. The reversible formation of diiminium ether intermediates was studied, providing insight into divergent mechanistic pathways as a function of the steric environment of the amide substrate and stoichiometry of reagents. Importantly, when considering base additives during electrophilic amide activation, more hindered ?-quaternary tertiary lactams require the use of non-nucleophilic pyridine additives in order to avoid deactivation via a competing desulfonylation reaction. The isolation and full characterization of a tetracyclic iminium trifluoromethanesulfonate provided additional correlation between in situ characterization of sensitive intermediates and isolable compounds involved in this synthetic transformation. PMID:26166404

  7. Multifragmentation in intermediate energy {sup 129}Xe-induced heavy-ion reactions

    SciTech Connect

    Tso, Kin

    1996-05-01

    The {sup 129}Xe-induced reactions on {sup nat}Cu, {sup 89}Y, {sup 165}Ho, and {sup 197}Au at bombarding energies of E/A = 40 & 60 MeV have been studied theoretically and experimentally in order to establish the underlying mechanism of multifragmentation at intermediate energy heavy-Ion collisions. Nuclear disks formed in central heavy-ion collisions, as simulated by means of Boltzmann-like kinetic equations, break up into several fragments due to a new kind of Rayleigh-like surface instability. A sheet of liquid, stable in the limit of non-interacting surfaces, is shown to become unstable due to surface-surface interactions. The onset of this instability is determined analytically. A thin bubble behaves like a sheet and is susceptible to the surface instability through the crispation mode. The Coulomb effects associated with the depletion of charges in the central cavity of nuclear bubbles are investigated. The onset of Coulomb instability is demonstrated for perturbations of the radial mode. Experimental intermediate-mass-fragment multiplicity distributions for the {sup 129}Xe-induced reactions are shown to be binomial at each transverse energy. From these distributions, independent of the specific target, an elementary binary decay probability p can be extracted that has a thermal dependence. Thus it is inferred that multifragmentation is reducible to a combination of nearly independent emission processes. If sequential decay is assumed, the increase of p with transverse energy implies a contraction of the emission time scale. The sensitivity of p to the lower Z threshold in the definition of intermediate-mass-fragments points to a physical Poisson simulations of the particle multiplicities show that the weak auto-correlation between the fragment multiplicity and the transverse energy does not distort a Poisson distribution into a binomial distribution. The effect of device efficiency on the experimental results has also been studied.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Reaction of coordinated dinitrogen. 12. Identification of intermediates in the conversion of molybdenum-bound dinitrogen into ammonia and hydrazine. Factors affecting the ammonia-forming reaction

    SciTech Connect

    Bossard, G.E.; George, T.A.; Howell, D.B.; Koczon, L.M.; Lester, R.K.

    1983-07-06

    When bis(dinitrogen) complexes of molybdenum and tungsten are treated with an excess of strong acid, with few exceptions, a complex containing the hydrazido(2-) ligand has been identified either as a product in the reaction or as an intermediate on the way to the formation of ammonia and hydrazine. In the case of those molybdenum complexes that produce ammonia, the stoichiometry of the reaction can be represented by eq 1 and 2: (1) )Mo/sup 0/(N/sub 2/)/sub 2/) ..-->../sup H/sup +// )Mo(NNH/sub 2/)) + N/sub 2/, (2) )Mo(NNH/sub 2/)) ..-->../sup H/sup +// 1/2N/sub 2/ + HN/sub 4//sup +/ + )Mo(III)), with a molybdenum(III) complex as the final molybdenum-containing product. Here the identification of two isomeric hydrazido(2-) complexes are reported upon, that are formed as a mixture in the reaction of excess HBr in tetrahydrofuran (THF) solution with trans-(Mo(N/sub 2/)/sub 2/(triphos)(PPh/sub 3/)), where triphos = PhP(CH/sub 2/CH/sub 2/PPh/sub 2/)/sub 2/. From this mixture of hydrazido(2-) complexes ammonia and a trace of hydrazine are produced in THF solution, but in benzene or toluene solution more hydrazine than ammonia is produced. On the basis of data presented, reversible phosphine dissociation is the next recognizable step toward ammonia formation.

  13. 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.

  14. Investigation of the O+allyl addition/elimination reaction pathways from the OCH(2)CHCH(2) radical intermediate.

    PubMed

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

    2008-08-28

    These experiments study the preparation of and product channels resulting from OCH(2)CHCH(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(2)CHCH(2) radicals; these undergo a facile ring opening to the OCH(2)CHCH(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 kcalmol. To elucidate the product channels resulting from the OCH(2)CHCH(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(3)H(4)O (acrolein)+H, C(2)H(4)+HCO (formyl radical), and H(2)CO (formaldehyde)+C(2)H(3). A small signal from C(2)H(2)O (ketene) product is also detected. The measured velocity distributions and relative signal intensities at me=27, 28, and 29 at two photoionization energies show that the most exothermic product channel, C(2)H(5)+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 calculated at the CCSD(T)/aug-cc-pVQZ level of theory, although a clean determination of the barrier energy to H+acrolein is precluded by the substantial partitioning into rotational energy during the photolytic production of the nascent radicals. We compare the measured branching fraction to the H+acrolein product channel with a statistical prediction based on the calculated transition states. PMID:19044817

  15. 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.

  16. Direct observation of intermediates in a thermodynamically controlled solid-state dynamic covalent reaction.

    PubMed

    Belenguer, Ana M; Lampronti, Giulio I; Wales, David J; Sanders, Jeremy K M

    2014-11-19

    We present the first polymorph interconversion study that uses solid-state dynamic covalent chemistry (DCC). This system exhibits unexpected and rich behavior, including the observation that under appropriate conditions the polymorph interconversion of a heterodimer proceeds through reversible covalent chemistry intermediates, and this route is facilitated by one of the two disulfide homodimers involved in the reaction. Furthermore, we demonstrate experimentally that in all cases a dynamic equilibrium is reached, meaning that changing the milling conditions affects the free energy difference between the two polymorphs and thus their relative stability. We suggest that this effect is due to the surface solvation energy combined with the high surface to volume ratio of the nanocrystalline powder. PMID:25314624

  17. Synthesis of ultrastable copper sulfide nanoclusters via trapping the reaction intermediate: potential anticancer and antibacterial applications.

    PubMed

    Wang, Hong-Yin; Hua, Xian-Wu; Wu, Fu-Gen; Li, Bolin; Liu, Peidang; Gu, Ning; Wang, Zhifei; Chen, Zhan

    2015-04-01

    Copper-based nanomaterials have broad applications in electronics, catalysts, solar energy conversion, antibiotics, tissue imaging, and photothermal cancer therapy. However, it is challenging to prepare ultrasmall and ultrastable CuS nanoclusters (NCs) at room temperature. In this article, a simple method to synthesize water-soluble, monodispersed CuS NCs is reported based on the strategy of trapping the reaction intermediate using thiol-terminated, alkyl-containing short-chain poly(ethylene glycol)s (HS-(CH2)11-(OCH2CH2)6-OH, abbreviated as MUH). The MUH-coated CuS NCs have superior stability in solutions with varied pH values and are stable in pure water for at least 10 months. The as-prepared CuS NCs were highly toxic to A549 cancer cells at a concentration of higher than 100 ?M (9.6 ?g/mL), making them be potentially applicable as anticancer drugs via intravenous administration by liposomal encapsulation or by direct intratumoral injection. Besides, for the first time, CuS NCs were used for antibacterial application, and 800 ?M (76.8 ?g/mL) CuS NCs could completely kill the E. coli cells through damaging the cell walls. Moreover, the NCs synthesized here have strong near-infrared (NIR) absorption and can be used as a candidate reagent for photothermal therapy and photoacoustic imaging. The method of trapping the reaction intermediate for simple and controlled synthesis of nanoclusters is generally applicable and can be widely used to synthesize many metal-based (such as Pt, Pd, Au, and Ag) nanoclusters and nanocrystals. PMID:25785786

  18. Reaction mechanism of pyridoxal 5'-phosphate synthase. Detection of an enzyme-bound chromophoric intermediate.

    PubMed

    Raschle, Thomas; Arigoni, Duilio; Brunisholz, Ren; Rechsteiner, Helene; Amrhein, Nikolaus; Fitzpatrick, Teresa B

    2007-03-01

    Vitamin B6 is an essential metabolite in all organisms. De novo synthesis of the vitamin can occur through either of two mutually exclusive pathways referred to as deoxyxylulose 5-phosphate-dependent and deoxyxylulose 5-phosphate-independent. The latter pathway has only recently been discovered and is distinguished by the presence of two genes, Pdx1 and Pdx2, encoding the synthase and glutaminase subunit of PLP synthase, respectively. In the presence of ammonia, the synthase alone displays an exceptional polymorphic synthetic ability in carrying out a complex set of reactions, including pentose and triose isomerization, imine formation, ammonia addition, aldol-type condensation, cyclization, and aromatization, that convert C3 and C5 precursors into the cofactor B6 vitamer, pyridoxal 5'-phosphate. Here, employing the Bacillus subtilis proteins, we demonstrate key features along the catalytic path. We show that ribose 5-phosphate is the preferred C5 substrate and provide unequivocal evidence that the pent(ul)ose phosphate imine occurs at lysine 81 rather than lysine 149 as previously postulated. While this study was under review, corroborative crystallographic evidence has been provided for imine formation with the corresponding lysine group in the enzyme from Thermotoga maritima (Zein, F., Zhang, Y., Kang, Y.-N., Burns, K., Begley, T. P., and Ealick, S. E. (2006) Biochemistry 45, 14609-14620). We have detected an unanticipated covalent reaction intermediate that occurs subsequent to imine formation and is dependent on the presence of Pdx2 and glutamine. This step most likely primes the enzyme for acceptance of the triose sugar, ultimately leading to formation of the pyridine ring. Two alternative structures are proposed for the chromophoric intermediate, both of which require substantial modifications of the proposed mechanism. PMID:17189272

  19. A chemometric method to identify enzymatic reactions leading to the transition from glycolytic oscillations to waves

    NASA Astrophysics Data System (ADS)

    Zimnyi, Lszl; Khoroshyy, Petro; Mair, Thomas

    2010-06-01

    In the present work we demonstrate that FTIR-spectroscopy is a powerful tool for the time resolved and noninvasive measurement of multi-substrate/product interactions in complex metabolic networks as exemplified by the oscillating glycolysis in a yeast extract. Based on a spectral library constructed from the pure glycolytic intermediates, chemometric analysis of the complex spectra allowed us the identification of many of these intermediates. Singular value decomposition and multiple level wavelet decomposition were used to separate drifting substances from oscillating ones. This enabled us to identify slow and fast variables of glycolytic oscillations. Most importantly, we can attribute a qualitative change in the positive feedback regulation of the autocatalytic reaction to the transition from homogeneous oscillations to travelling waves. During the oscillatory phase the enzyme phosphofructokinase is mainly activated by its own product ADP, whereas the transition to waves is accompanied with a shift of the positive feedback from ADP to AMP. This indicates that the overall energetic state of the yeast extract determines the transition between spatially homogeneous oscillations and travelling waves.

  20. 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 Alzheimers 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

  1. 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.

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

    DOE PAGESBeta

    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

  3. 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. Reactivity of a mononuclear copper(II)-alkylperoxide complex has also been examined to get insights into the intrinsic reactivity of copper(II)-peroxide species, which is usually considered as a sluggish oxidant or just a precursor of copper-oxyl radical type reactive species. However, our studies have unambiguously demonstrated that copper(II)-alkylperoxide complex can be a direct oxidant for C-H bond activation of organic substrates, when the C-H bond activation is coupled with O-O bond cleavage (concerted mechanism). The reactivity studies of these mononuclear copper(II) active-oxygen species (superoxide and alkylperoxide) will provide significantly important insights into the catalytic mechanism of copper monooxygenases as well as copper-catalyzed oxidation reactions in synthetic organic chemistry. PMID:26086527

  4. 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.

  5. Solution speciation, kinetics, and observing reaction intermediates in the alkylation of oxidovanadium compounds.

    PubMed

    Fautch, Jessica M; Wilker, Jonathan J

    2010-06-01

    Contact with environmental alkylating agents brings about modification of DNA bases, mispairing, mutations, and cancer. Nucleophilic compounds may be able to consume these toxins, thereby providing an alternative reaction pathway and preventing DNA damage. Owing to promising results from animal trials, oxidovanadium compounds present a potential class of nucleophilic complexes for preventing cancer. We are studying the reactivity of alkylating toxins with oxidovanadium-ligand compounds. The complexes K[VO(2)(salhyph(R)(2))], where salhyph is the salicylidenehydrazide ligand, are the focus of this study. By changing the electron donating or withdrawing ability of the -R substituents upon the salhyph(R)(2) ligand (R = -NO(2), -H, -CH(3), -OCH(3)), a family of compounds is obtained to investigate. Conductivity measurements reveal significant ion-pairing of all compounds in dimethyl sulfoxide (DMSO) solutions. Kinetic analysis shows that this ion-pairing causes a reduction in reaction rates. Reactivity of K[VO(2)(salhyph(R)(2))] is attributed exclusively to the non-ion-paired "free" [VO(2)(salhyph(R)(2))](-) anion in solution. Both (1)H and (51)V NMR spectroscopic studies show that direct alkylation of K[VO(2)(salhyph(H)(2))].CH(3)OH generates a VO(OCH(2)CH(3))(salhyph(H)(2)) intermediate which then protonates to release CH(3)CH(2)OH and a proposed [VO(salhyph(H)(2))](+) compound. Upon hydrolysis the dinuclear {[VO(salhyph(H)(2))](2)O} end product is formed. This mechanistic understanding and ability to exert control over reactions between inorganic compounds and alkylating toxins may aid in the future development of pharmaceuticals for preventing DNA damage. PMID:20420457

  6. Weak interaction processes in supernovae: New probes using charge exchange reaction at intermediate energies

    NASA Astrophysics Data System (ADS)

    Frekers, Dieter

    2005-04-01

    Spin-isospin-flip excitations in nuclei at vanishing momentum transfer are generally referred to as Gamov-Teller (GT) transitions. They are being studied because the simplicity of the excitation makes them an ideal probe for testing nuclear structure models. In astrophysics, GT transitions provide an important input for model calculations and element formation during the explosive phase of a massive star at the end of its life-time. GT transitions in the β- direction (also referred to as isospin lowering T< transitions) have extensively been studied through (p,n) and (3He,t) charge-exchange reactions [B.D. Anderson et al., Phys. Rev. C 36 (1987) 2195, B.D. Anderson et al., Phys. Rev. C 43 (1991) 50, J. Rapaport et al., Phys. Rev. C 24 (1981) 335, H. Akimune et al., Nucl. Phys. A 569 (1994) 245c, Y. Fujita et al., Phys. Lett. B 365 (1996) 29]. The generally good resolution allows easy extraction of the GT distribution and the total B(GT-) strength in the final nucleus. On the other hand, determination of B(GT+) strength through a charge-exchange reaction in the T> direction were mostly done with secondary neutron beams, and as such, they come with significant experimental difficulties. TRIUMF has pioneered this field in the late 80's and early 90's with a rich and highly successful (n,p) program using a several hundred MeV neutron beam from a 7Li(p,n)7Be reaction [R. Helmer, Can. J. Phys. 65 (1987) 588]. In this paper we present the (d,2He) reaction at intermediate energies as another and potentially even more powerful tool for charge-exchange reactions in the T>, resp. β+ direction. The key issue here will be the high resolution of order 100 keV, which provides new and sometimes unexpected insight into nuclear structure phenomena. This program has been launched at the AGOR Superconducting Cyclotron Facility at the KVI Groningen. By now, it covers a wide field of physics questions ranging from few-body physics, the structure of halo-nuclei, to questions pertaining to the dynamics of supernova explosions and nuclear synthesis, and more recently to the measurements of (ββ) decay matrix elements and the determination of half-lives of (ββ) decaying nuclei.

  7. 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 hydroperoxides of low volatility formed in the gas phase are partitioned into the particle phase to contribute to the SOA formation. Here, we propose a new oligomer formation mechanism including sequential addition of Criegee intermediates to hydroperoxides. REFERENCE: (1)Kroll, J. H.; Seinfeld, J. H. Chemistry of Secondary Organic Aerosol: Formation and Evolution of Low-Volatility Organics in the Atmosphere. Atmos. Environ. 2008, 42, 3593-3624. (2)Sadezky, A.; Chaimbault, P.; Mellouki, A.; Roempp, A.; Winterhalter, R.; Le Bras, G.; Moortgat, G. K. Formation of Secondary Organic Aerosol and Oligomers from the Ozonolysis of Enol Ethers. Atmos. Chem. Phys. 2006, 6, 5009-5024. (3)Sadezky, A.; Winterhalter, R.; Kanawati, B.; Roempp, A.; Spengler, B.; Mellouki, A.; Le Bras, G.; Chaimbault, P.; Moortgat, G. K. Oligomer Formation during Gas-Phase Ozonolysis of Small Alkenes and Enol Ethers: New Evidence for the Central Role of the Criegee Intermediate as Oligomer Chain Unit. Atmos. Chem. Phys. 2008, 8, 2667-2699. (4)Klotz, B.; Barnes, I.; Imamura, T. Product Study of the Gas-Phase Reactions of O3, OH and NO3 Radicals with Methyl Vinyl Ether. Phys. Chem. Chem. Phys. 2004, 6, 1725-1734.

  8. Capturing reaction paths and intermediates in Cre-loxP recombination using single-molecule fluorescence

    PubMed Central

    Pinkney, Justin N. M.; Zawadzki, Pawel; Mazuryk, Jaroslaw; Arciszewska, Lidia K.; Sherratt, David J.; Kapanidis, Achillefs N.

    2012-01-01

    Site-specific recombination plays key roles in microbe biology and is exploited extensively to manipulate the genomes of higher organisms. Cre is a well studied site-specific recombinase, responsible for establishment and maintenance of the P1 bacteriophage genome in bacteria. During recombination, Cre forms a synaptic complex between two 34-bp DNA sequences called loxP after which a pair of strand exchanges forms a Holliday junction (HJ) intermediate; HJ isomerization then allows a second pair of strand exchanges and thus formation of the final recombinant product. Despite extensive work on the Cre-loxP system, many of its mechanisms have remained unclear, mainly due to the transient nature of complexes formed and the ensemble averaging inherent to most biochemical work. Here, we address these limitations by introducing tethered fluorophore motion (TFM), a method that monitors large-scale DNA motions through reports of the diffusional freedom of a single fluorophore. We combine TFM with Frster resonance energy transfer (FRET) and simultaneously observe both large- and small-scale conformational changes within single DNA molecules. Using TFMFRET, we observed individual recombination reactions in real time and analyzed their kinetics. Recombination was initiated predominantly by exchange of the bottom-strands of the DNA substrate. In productive complexes we used FRET distributions to infer rapid isomerization of the HJ intermediates and that a rate-limiting step occurs after this isomerization. We also observed two nonproductive synaptic complexes, one of which was structurally distinct from conformations in crystals. After recombination, the product synaptic complex was extremely stable and refractory to subsequent rounds of recombination. PMID:23184986

  9. X-ray absorption spectroscopy of reaction intermediates of lithium-sulfur batteries dissolved in polymer electrolytes

    NASA Astrophysics Data System (ADS)

    Wujcik, Kevin; Balsara, Nitash

    2013-03-01

    Lithium polysulfide reaction intermediates formed during the charge and discharge reactions of a lithium-sulfur battery are known to diffuse out of the cathode during cycling, thus lowering battery capacity and lifetime. While numerous techniques have been developed to confine intermediates to the battery cathode, little is known about the complex reaction mechanism responsible for their formation. Work to understand the reaction mechanism requires an experimental technique capable of distinguishing the various lithium polysulfide intermediates formed during the charge/discharge reactions. We report on the use of x-ray absorption spectroscopy (XAS) to distinguish lithium polysulfide molecules in polymer electrolytes. Polysulfide intermediates dissolved in poly(ethylene oxide) and a block copolymer of polystyrene-poly(ethylene oxide) were probed at the oxygen, carbon, and sulfur K-edges. Simulated x-ray spectra based on ab-initio molecular dynamics were used to interpret experimental x-ray spectra. Theories regarding the physical and chemical nature of the polysulfide-polymer electrolyte interaction were developed.

  10. A Pivotal Heme-transfer Reaction Intermediate in Cytochrome c Biogenesis*

    PubMed Central

    Mavridou, Despoina A. I.; Stevens, Julie M.; Mnkemeyer, Leonie; Daltrop, Oliver; di Gleria, Katalin; Kessler, Benedikt M.; Ferguson, Stuart J.; Allen, James W. A.

    2012-01-01

    c-Type cytochromes are widespread proteins, fundamental for respiration or photosynthesis in most cells. They contain heme covalently bound to protein in a highly conserved, highly stereospecific post-translational modification. In many bacteria, mitochondria, and archaea this heme attachment is catalyzed by the cytochrome c maturation (Ccm) proteins. Here we identify and characterize a covalent, ternary complex between the heme chaperone CcmE, heme, and cytochrome c. Formation of the complex from holo-CcmE occurs in vivo and in vitro and involves the specific heme-binding residues of both CcmE and apocytochrome c. The enhancement and attenuation of the amounts of this complex correlates completely with known consequences of mutations in genes for other Ccm proteins. We propose the complex is a trapped catalytic intermediate in the cytochrome c biogenesis process, at the point of heme transfer from CcmE to the cytochrome, the key step in the maturation pathway. PMID:22121193

  11. Kinetics and mechanisms of reactions involving small aromatic reactive intermediates. Annual report

    SciTech Connect

    Lin, M.C.

    1994-04-01

    Phenyl (C{sub 6}H{sub 5}), phenoxy (C{sub 6}H{sub 5}O) and benzyne (C{sub 6}H{sub 4}) are fundamentally important prototype molecules. C{sub 6}H{sub 5} and C{sub 6}H{sub 5}O are also very important reactive intermediates in hydrocarbon combustion systems, particularly with regard to soot formation chemistry, as well as to the combustion chemistry of aromatic additives in gasoline. The authors proposed to study the kinetics and mechanisms of these three benchmark reactive intermediates using two complementary laser diagnostic techniques -- laser resonance absorption (LRA) and resonance enhanced multiphoton ionization mass spectrometry (REMPI/MS). In the first year of this contractual work, they have employed a new type of LRA, i.e. the intra-cavity resonance absorption technique, to measure the rate constants for C{sub 6}H{sub 5} reactions, extending the limit of rate constant measurement down to 10{sup {minus}18} cm{sup 3}/s. They have tested this method for the following reactions: C{sub 6}H{sub 5} + HBr, CH{sub 2}O, O{sub 2}, C{sub 2}H{sub 2} and C{sub 2}H{sub 4} at 297 K and obtained their rate constants to be 3.0 {times} 10{sup {minus}11}, 1.2 {times} 10{sup {minus}14}, 1.0 {times} 10{sup {minus}16}, 7.0 {times} 10{sup {minus}18} and 6.7 {times} 10{sup {minus}18} cm{sup 3}/s, respectively. In the second study, the REMPI spectroscopy of C{sub 6}H{sub 5} is being investigated with the two laser pump-probe surface photolysis method. The desorbed C{sub 6}H{sub 5} photofragment is ionized by (1+1) MPI in the spectral range 200--260 nm. Similarly, the NO photofragment is also detected by (1+1) MPI in the same spectral region. The detailed photofragmentation of the absorbed C{sub 6}H{sub 5}NO at 193 and 248 nm is being analyzed presently and a new experiment with acetophenone on a quartz surface is under way.

  12. 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 as being younger than 500 Myr. The intermediate-age stars could be as yet unknown members of a population formed in a starburst ~100 Myr ago. Finding no young (~a few Myr) stars at RSgr A ∗ = 0.5-3 pc favors the in situ formation scenario for the presence of the young stars at RSgr A ∗< 0.5 pc, although we do not completely exclude the possible existence of unknown young, massive stars in the region from our observations. Furthermore, the different spatial distributions of the young and the intermediate-age stars imply that the Galactic NSC is an aggregate of stars that were born in different places and under a variety of physical conditions. The reduced spectra as FITS files are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/588/A49

  13. The Genome Sequence of the Emerging Common Midwife Toad Virus Identifies an Evolutionary Intermediate within Ranaviruses

    PubMed Central

    Mavian, Carla; Lpez-Bueno, Alberto; Balseiro, Ana; Casais, Rosa; Alcam, Antonio

    2012-01-01

    Worldwide amphibian population declines have been ascribed to global warming, increasing pollution levels, and other factors directly related to human activities. These factors may additionally be favoring the emergence of novel pathogens. In this report, we have determined the complete genome sequence of the emerging common midwife toad ranavirus (CMTV), which has caused fatal disease in several amphibian species across Europe. Phylogenetic and gene content analyses of the first complete genomic sequence from a ranavirus isolated in Europe show that CMTV is an amphibian-like ranavirus (ALRV). However, the CMTV genome structure is novel and represents an intermediate evolutionary stage between the two previously described ALRV groups. We find that CMTV clusters with several other ranaviruses isolated from different hosts and locations which might also be included in this novel ranavirus group. This work sheds light on the phylogenetic relationships within this complex group of emerging, disease-causing viruses. PMID:22301140

  14. Intermediates in the cation reactions in solution probed by an in situ surface enhanced Raman scattering method

    NASA Astrophysics Data System (ADS)

    Tan, Chih-Shan; Chen, Hung-Ying; Chen, Hsueh-Szu; Gwo, Shangjr; Chen, Lih-Juann

    2015-09-01

    For chemical reactions in liquid state, such as catalysis, understanding of dynamical changes is conducive to practical applications. Solvation of copper salts in aqueous solution has implications for life, the environment, and industry. In an ongoing research, the question arises that why the color of aqueous CuCl2 solution changes with solution concentration? In this work, we have developed a convenient and efficient in situ surface enhanced Raman scattering technique to probe the presence of many intermediates, some of them are responsible for color change, in crystallization of aqueous copper chloride solution. The versatility of the novel technique was confirmed in the identification of five intermediates states in the transition from CdS to MoS2 nanowires in solution. The facile in situ method is expected to be widely applicable in probing intermediate states in a variety of chemical reactions in solution.

  15. Intermediates in the cation reactions in solution probed by an in situ surface enhanced Raman scattering method

    PubMed Central

    Tan, Chih-Shan; Chen, Hung-Ying; Chen, Hsueh-Szu; Gwo, Shangjr; Chen, Lih-Juann

    2015-01-01

    For chemical reactions in liquid state, such as catalysis, understanding of dynamical changes is conducive to practical applications. Solvation of copper salts in aqueous solution has implications for life, the environment, and industry. In an ongoing research, the question arises that why the color of aqueous CuCl2 solution changes with solution concentration? In this work, we have developed a convenient and efficient in situ surface enhanced Raman scattering technique to probe the presence of many intermediates, some of them are responsible for color change, in crystallization of aqueous copper chloride solution. The versatility of the novel technique was confirmed in the identification of five intermediates states in the transition from CdS to MoS2 nanowires in solution. The facile in situ method is expected to be widely applicable in probing intermediate states in a variety of chemical reactions in solution. PMID:26333518

  16. Compound nucleus emission of intermediate mass fragments in the 6Li+Ag reaction at 156 MeV

    NASA Astrophysics Data System (ADS)

    Grotowski, K.; Ilnicki, J.; Kozik, T.; ?ukasik, J.; Micek, S.; Sosin, Z.; Wieloch, A.; Heide, N.; Jelitto, H.; Kiener, I.; Rebel, H.; Zagromski, S.; Cole, A. J.

    1989-06-01

    It is shown that emission of intermediate mass fragments in a wide range of masseanand angles can be well described by sequential binary decay of the equilibrated compound system produced in the 26 MeV/A 6Li+Ag reaction.

  17. Identification of transient intermediates in the bisphosphatase reaction of rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase by 31P-NMR spectroscopy.

    PubMed Central

    Okar, D A; Kakalis, L T; Narula, S S; Armitage, I M; Pilkis, S J

    1995-01-01

    31P-NMR spectroscopy was used to identify reaction intermediates during catalytic turn-over of the fructose-2,6-bisphosphatase domain (Fru-2,6-P2ase) of the bifunctional enzyme, 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase. When fructose-2,6-bisphosphate (Fru-2,6-P2) was added to the enzyme, the 31P-NMR spectrum showed three resonances in addition to those of free substrate: the phosphohistidine (His-P) intermediate, the C-6 phosphoryl group of fructose-6-phosphate bound to the phosphoenzyme, and phosphate generated by the hydrolysis of substrate. Direct analysis of the alkali-denatured phospho-enzyme intermediate by 1H-31P heteronuclear multiple quantum-filtered coherence spectroscopy confirmed the formation of 3-N-phosphohistidine. Binding of fructose 6-phosphate to the bisphosphatase was detected by a down-field shift and broadening of the C-6 phosphoryl resonance. The down-field shift was greater in the presence of the phosphoenzyme intermediate. Inhibition of Fru-2,6-P2 hydrolysis by fructose 6-phosphate and Fru-2,6-P2 was shown to involve binding of the sugar phosphates to the phosphoenzyme. This study provides new experimental evidence in support of the reaction mechanism of Fru-2,6-P2ase and suggests that the steady-state His-P intermediate exists primarily in the E-P.fructose 6-phosphate complex. These results lay a solid foundation for the use of 31P-NMR magnetization transfer studies to provide an in-depth analysis of the bisphosphatase reaction mechanism. PMID:7755565

  18. 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.

  19. 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.

  20. 15N{31P} REDOR NMR Studies of the Binding of Phosphonate Reaction Intermediate Analogues to Saccharomyces cerevisiae Lumazine Synthase

    PubMed Central

    Yu, Tsyr-Yan; O'Connor, Robert D.; Sivertsen, Astrid C.; Chiauzzi, Colby; Poliks, Barbara; Fischer, Markus; Bacher, Adelbert; Haase, Ilka; Cushman, Mark; Schaefer, Jacob

    2009-01-01

    Lumazine synthase catalyzes the reaction of 5-amino-6-D-ribitylamino-2,4(1H,3H)-pyrimidinedione (1) with (S)-3,4-dihydroxybutanone 4-phosphate (2) to afford 6,7-dimethyl-8-D-ribityllumazine (3), the immediate biosynthetic precursor of riboflavin. The overall reaction implies a series of intermediates that are incompletely understood. The 15N{31P} REDOR NMR spectra of three metabolically stable phosphonate reaction intermediate analogues complexed to Saccharomyces cerevisiae lumazine synthase have been obtained at 7 and 12 T. Distances from the phosphorus atoms of the ligands to the side chain nitrogens of Lys92, His97, Arg136, and His148 have been determined. These distances were used in combination with the X-ray crystal coordinates of one of the intermediate analogues complexed with the enzyme in a series of distance-restrained molecular dynamics simulations. The resulting models indicate mobility of the Lys92 side chain, which could facilitate the exchange of inorganic phosphate eliminated from the substrate in one reaction, with the organic phosphate-containing substrate necessary for the next reaction. PMID:19117095

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

    PubMed

    Fukutome, Asuka; Kawamoto, Haruo; Saka, Shiro

    2015-07-01

    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. PMID:26099988

  2. The use of the magnetic field effect for studying a chemiluminescent chemical reaction in aqueous solution. Reaction rate constants and lifetimes of intermediate molecules

    NASA Astrophysics Data System (ADS)

    Triebel, Michael M.; Totrov, Maxim M.; Zorinyants, George E.; Frankevich, Eugene L.

    1993-11-01

    The phase shift magnetic field effect technique is applied for investigation of the chemiluminescent (ChL) reaction of luminol oxidation by potassium ferricyanide in aqueous alkali solution. The external modulated magnetic field changed the rate constant of recombination of luminol radicals. Rate constants of intermediate stages of the reaction are obtained: 10 8 M -1 s -1 for diazaquinone reaction with hydrogen peroxide, 2 X 10 6 M -1 s -1 for diazaquinone hydrolysis and 2 X 10 5 s -1 for the decomposition of hydroperoxide, which is a precursor of the light emitter.

  3. The reductive half-reaction of xanthine oxidase. Identification of spectral intermediates in the hydroxylation of 2-hydroxy-6-methylpurine.

    PubMed

    McWhirter, R B; Hille, R

    1991-12-15

    The reaction of xanthine oxidase with 2-hydroxy-6-methylpurine (also called 2-oxo-6-methylpurine) has been studied under both anaerobic and aerobic conditions. Reaction of enzyme with substoichiometric concentrations of hydroxymethylpurine in aerobic 0.1 M 3-(cyclohexylamino)propanesulfonic acid, 0.1 N KCl, 0.3 mM EDTA, pH 10.0, exhibits two reaction intermediates detectable by UV-visible spectrophotometry. The rate constants for formation of the first intermediate, conversion of the first to the second, and the decay of the second to give oxidized enzyme are 18, 1.2, and 0.13 s-1, respectively. The difference spectra of these two intermediates relative to oxidized enzyme are characterized by absorbance maxima at 470 and 540 nm, respectively, with extinction changes (relative to oxidized enzyme) of approximately 410 M-1 cm-1. The 0.13 s-1 decay of the second intermediate agrees well with kcat of 0.11 s-1 determined under the same conditions. Based on a comparison of the kinetics of the reaction as monitored by UV-visible absorption and electron paramagnetic resonance spectrometry, it is concluded that these spectral intermediates arise from the molybdenum center of the enzyme in the MoIV and MoV valence states, respectively, the latter corresponding to the species exhibiting the "very rapid" MoV EPR signal known to be formed in the course of the reaction. This conclusion is supported by the results of experiments using cytochrome c reduction to follow the formation of superoxide production in the course of the aerobic reaction of xanthine oxidase with substoichiometric hydroxymethylpurine, which demonstrate unequivocally that the species exhibiting the very rapid EPR signal is formed by one-electron oxidation of a MoIV species rather than direct one-electron reduction of MoVI by substrate. No evidence is found for the formation of any of the MoV EPR signals designated "rapid" in the present studies, and it is concluded that this species is not a bona fide catalytic intermediate in the reductive half-reaction of xanthine oxidase. PMID:1660883

  4. 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

  5. Intermediate in the O?O Bond Cleavage Reaction of an Extradiol Dioxygenase

    SciTech Connect

    Kovaleva, Elena G.; Lipscomb, John D.

    2009-02-16

    The reactive oxy intermediate of the catalytic cycle of extradiol aromatic ring-cleaving dioxygenases is formed by binding the catecholic substrate and O{sub 2} in adjacent ligand positions of the active site metal [usually Fe(II)]. This intermediate and the following Fe(II)-alkylperoxo intermediate resulting from oxygen attack on the substrate have been previously characterized in a crystal of homoprotocatechuate 2,3-dioxygenase (HPCD). Here a subsequent intermediate in which the O-O bond is broken to yield a gem diol species is structurally characterized. This new intermediate is stabilized in the crystal by using the alternative substrate, 4-sulfonylcatechol, and the Glu323Leu variant of HPCD, which alters the crystal packing.

  6. Glutathione-Complexed Iron-Sulfur Clusters. Reaction Intermediates and Evidence for a Template Effect Promoting Assembly and Stability

    PubMed Central

    Qi, Wenbin; Li, Jingwei; Chain, C. Y; Pasquevich, G.A.; Pasquevich, A. F.; Cowan, J. A.

    2013-01-01

    Assembly and stabilization of a glutathione-complexed [2Fe-2S] cluster is promoted by aggregation of glutathione. The cluster core selects the tetramer species from a collection of equilibrating solution aggregate species, and in turn the core is stabilized toward hydrolytic degradation. Studies of glutathione derivatives, in combination with mass spectrometric and Mssbauer investigations provide insight on reaction intermediates during formation of [2Fe-2S](GS)42-. PMID:23739324

  7. L-myo-inosose-1 as a probable intermediate in the reaction catalyzed by myo-inositol oxygenase

    SciTech Connect

    Naber, N.I.; Swan, J.S.; Hamilton, G.A.

    1986-11-04

    In previous investigations, it was necessary to have Fe(II) and cysteine present in order to assay the catalytic activity of purified hog kidney myo-inositol oxygenase. In the present study it was found that, if this purified nonheme iron enzyme is slowly frozen in solution with glutathione and stored at -20 degrees C, it is fully active in the absence of activators if catalase is present to remove adventitious H/sub 2/O/sub 2/. With this simpler assay system it was possible to clarify the effects of several variables on the enzymic reaction. Thus, the maximum velocity is pH-dependent with a maximum around pH 9.5, but the apparent Km for myo-inositol (air atmosphere) remains constant at 5.0 mM throughout a broad pH range. The enzyme is quite specific for its substrate myo-inositol, is very sensitive to oxidants and reductants, but is not affected by a variety of complexing agents, nucleotides, sulfhydryl reagents, etc. In other experiments it was found that L-myo-inosose-1, a potential intermediate in the enzymic reaction, is a potent competitive inhibitor (Ki = 62 microM), while other inososes and a solution thought to contain D-glucodialdehyde, another potential intermediate, are weak inhibitors. Also, both a kinetic deuterium isotope effect (kH/kD = 2.1) and a tritium isotope effect (kH/kT = 7.5) are observed for the enzymic reaction when (1-2H)- and (1-3H)-myo-inositol are used as reactants. These latter results are considered strong evidence that the oxygenase reaction proceeds by a pathway involving L-myo-inosose-1 as an intermediate rather than by an alternative pathway that would have D-glucodialdehyde as the intermediate.

  8. Characterization of manganese(V)-oxo polyoxometalate intermediates and their properties in oxygen-transfer reactions.

    PubMed

    Khenkin, Alex M; Kumar, Devesh; Shaik, Sason; Neumann, Ronny

    2006-12-01

    A manganese(III)-substituted polyoxometalate, [alpha2-P2MnIII(L)W17O61]7- (P2W17MnIII), was studied as an oxidation catalyst using iodopentafluorobenzene bis(tifluoroacetate) (F5PhI(TFAc)2) as a monooxygen donor. Pink P2W17MnIII turns green upon addition of F5PhI(TFAc)2. The 19F NMR spectrum of F5PhI(TFAc)2 with excess P2W17MnIII at -50 degrees C showed the formation of an intermediate attributed to P2W17MnIII-F5PhI(TFAc)2 that disappeared upon warming. The 31P NMR spectra of P2W17MnIII with excess F5PhI(TFAc)2 at -50 and -20 degrees C showed a pair of narrow peaks attributed to a diamagnetic, singlet manganese(V)-oxo species, P2W17MnV=O. An additional broad peak at -10.6 ppm was attributed to both the P2W17MnIII-F5PhI(TFAc)2 complex and a paramagnetic, triplet manganese(V)-oxo species. The electronic structure and reactivity of P2W17MnV=O were modeled by DFT calculations using the analogous Keggin compound, [PMnV=OW11O39]4-. Calculations with a pure functional, UBLYP, showed singlet and triplet ground states of similar energy. Further calculations using both the UBLYP and UB3LYP functionals for epoxidation and hydroxylation of propene showed lowest lying triplet transition states for both transformations, while singlet and quintet transition states were of higher energy. The calculations especially after corrections for the solvent effect indicate that [PMnV=OW11O39]4- should be highly reactive, even more reactive than analogous MnV=O porphyrin species. Kinetic measurements of the reaction of P2W17MnV=O with 1-octene indicated, however, that P2W17MnV=O was less reactive than a MnV=O porphyrin. The experimental enthalpy of activation confirmed that the energy barrier for epoxidation is low, but the highly negative entropy of activation leads to a high free energy of activation. This result originates in our view from the strong solvation of the highly charged polyoxometalate by the polar solvent used and adventitious water. The higher negative charge of the polyoxometalate in the transition versus ground state leads to electrostriction of the solvent molecules and to a loss of degrees of freedom, resulting in a highly negative entropy of activation and slower reactions. PMID:17132012

  9. Imaging Consecutive Steps of O2 Reaction with Hydroxylated TiO₂(110): Identification of HO₂ and Terminal OH Intermediates

    SciTech Connect

    Du, Yingge; Deskins, N. Aaron; Zhang, Zhenrong; Dohnalek, Zdenek; Dupuis, Michel; Lyubinetsky, Igor

    2009-01-15

    We report results of the combined experimental and theoretical investigation of the molecular oxygen reaction with a partially hydroxylated TiO₂(110) surface. The consecutive steps of both primary and secondary site-specific reactions have been tracked with high-resolution scanning tunneling microscopy (STM). For the first time, we have directly imaged stable, adsorbed hydroperoxyl (HO₂) species, which is believed to be a key intermediate in many heterogeneous photochemical processes but generally metastable and “elusive” until now. We also found terminal hydroxyl groups, another critical but never directly observed intermediates. A conclusive evidence that O₂ reacts spontaneously with a single bridging OH group as an initial reaction step is provided. The experimental results are supported by density functional theory (DFT) calculations that have determined species energies and configurations. Reported observations provide a basis for a consistent description of the elementary reaction steps and offer molecular-level insight into the underlying reaction mechanisms. In a broader perspective, the results are expected to have far reaching implications for various catalytic systems involving the interconversion of O₂ and H₂O.

  10. Spectroscopic Analyses on Reaction Intermediates Formed during Chlorination of Alkanes with NaOCl Catalyzed by a Nickel Complex.

    PubMed

    Draksharapu, Apparao; Codol, Zoel; Gmez, Laura; Lloret-Fillol, Julio; Browne, Wesley R; Costas, Miquel

    2015-11-16

    The spectroscopic, electrochemical, and crystallographic characterization of [((Me,H)PyTACN)Ni(II)(CH3CN)2](OTf)2 (1) ((Me,H)PyTACN = 1-(2-pyridylmethyl)-4,7-dimethyl-1,4,7-triazacyclononane, OTf = CF3SO3) is described together with its reactivity with NaOCl. 1 catalyzes the chlorination of alkanes with NaOCl, producing only a trace amount of oxygenated byproducts. The reaction was monitored spectroscopically and by high resolution electrospray-mass spectrometry (ESI-MS) with the aim to elucidate mechanistic aspects. NaOCl reacts with 1 in acetonitrile to form the transient species [(L)Ni(II)-OCl(S)](+) (A) (L = (Me,H)PyTACN, S = solvent), which was identified by ESI-MS. UV/vis absorption, electron paramagnetic resonance, and resonance Raman spectroscopy indicate that intermediate A decays to the complex [(L)Ni(III)-OH(S)](2+) (B) presumably through homolytic cleavage of the O-Cl bond, which liberates a Cl() atom. Hydrolysis of acetonitrile to acetic acid under the applied conditions results in the formation of [(L)Ni(III)-OOCCH3(S)](2+) (C), which undergoes subsequent reduction to [(L)Ni(II)-OOCCH3(S)](2+) (D), presumably via reaction with OCl(-) or ClO2(-). Subsequent addition of NaOCl to [(L)Ni(II)-OOCCH3(S)](+) (D) regenerates [(L)Ni(III)-OH(S)](2+) (B) to a much greater extent and at a faster rate. Addition of acids such as acetic and triflic acid enhances the rate and extent of formation of [(L)Ni(III)-OH(S)](2+) (B) from 1, suggesting that O-Cl homolytic cleavage is accelerated by protonation. Overall, these reactions generate Cl() atoms and ClO2 in a catalytic cycle where the nickel center alternates between Ni(II) and Ni(III). Chlorine atoms in turn react with the C-H bonds of alkanes, forming alkyl radicals that are trapped by Cl() to form alkyl chlorides. PMID:26540133

  11. New model catalysts (platinum nanoparticles) and new techniques (SFG and STM) for studies of reaction intermediates and surface restructuring at high pressures during catalytic reactions

    NASA Astrophysics Data System (ADS)

    Somorjai, G. A.

    1997-11-01

    Single-crystal surfaces have long served us well as model catalysts; however, a new type of model catalyst has been prepared using electron beam lithography. Ordered arrays of platinum nano-particles in the 2.5-50 nm size range are deposited on oxide substrates (silica, alumina, and titania) of 1 cm 2 surface area, and are used in catalyzed surface reactions at high pressures (atmospheres). Their preparation, cleaning, and reactivity is discussed. Scanning tunneling microscopy (STM) and vibrational spectroscopy by sum frequency generation (SFG) can be utilized to monitor the substrate and adsorbate structure, respectively, over a fourteen order of magnitude pressure range (10 -10-10 4 Torr). As a consequence, we can monitor the surface structure and reaction intermediates during high pressure catalytic reactions. An STM that operates at both high pressure (atmosphere) and high temperature has been constructed and utilized to monitor platinum (111) and (110) surface structure during chemisorption of H 2, O 2 and CO, and during catalytic reactions of olefin hydrogenation and hydrogenolysis. Changes of surface structure upon chemisorption and during reactions have been monitored. Catalysis by the platinum tip was also detected in the presence of H 2 or O 2 at high pressures and 300 K, leading to hydrogenation or oxidation of carbonaceous deposits with nanometer spatial resolution. Vibrational spectroscopy using SFG has been used to monitor pressure dependent changes in the chemisorption of CO and NO over Pt(111). Bonding which is similar to that in Pt m(CO) n (where n/m > 1 ) clusters and for an incommensurate CO overlayer is observed above 100 Torr. Reaction intermediates that form during ethylene, propylene, and isobutene hydrogenation, as well as CO oxidation, at atmospheric pressures and 300 K were monitored by SFG. The dominant reacting species that hydrogenate are the weakly ?-bonded olefins, while the strongly chemisorbed alkylidyne and di-? bonded species are spectators during the reaction. From quantitative measurement of coverages, the absolute turnover rates can be determined.

  12. 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 Mller-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)2R113}(-) (M = Ni or Co) versus the distance between the chlorine atom leaving during reduction and the corresponding carbon atom showed an energy barrier to electron transfer (the first stage of R113 catalytic reduction), while DFT optimization of the {Ni(L2)R113}(-) adduct showed barrier-free decomposition. The difference between the stabilities of the {Ni(L1)2R113}(-) and {Ni(L2)R113}(-) adducts correlates with the difference between the catalytic activities of Ni(L1)2 and Ni(L2) in the electrochemical reduction of R113. PMID:25623515

  13. The major/minor concept: dependence of the selectivity of homogeneously catalyzed reactions on reactivity ratio and concentration ratio of the intermediates.

    PubMed

    Schmidt, Thomas; Dai, Zhenya; Drexler, Hans-Joachim; Hapke, Marko; Preetz, Angelika; Heller, Detlef

    2008-07-01

    The homogeneously catalyzed asymmetric hydrogenation of prochiral olefins with cationic Rh(I) complexes is one of the best-understood selection processes. For some of the catalyst/substrate complexes, experimental proof points out the validation of the major/minor principle; the concentration-deficient minor substrate complex, which has very high reactivity, yields the excess enantiomer. As exemplified by the reaction system of [Rh(dipamp)(MeOH)2]+/methyl (Z)-alpha-acetamidocinnamate (dipamp=1,2-bis((o-methoxyphenyl)phenylphosphino)ethane), all six of the characteristic reaction rate constants have been previously identified. Recently, it was found that the major substrate complex can also yield the major enantiomer (lock-and-key principle). The differential equation system that results from the reaction sequence can be solved numerically for different hydrogen partial pressures by including the known equilibrium constants. The result displays the concentration-time dependence of all species that exist in the catalytic cycle. On the basis of the known constants as well as further experimental evidence, this work focuses on the examination of all principal possibilities resulting from the reaction sequence and leading to different results for the stereochemical outcome. From the simulation, the following conclusions can be drawn: 1) When an intermediate has extreme reactivity, its stationary concentration can become so small that it can no longer be the source of product selectivity; 2) in principle, the major/minor and lock-and-key principles can coexist depending on the applied pressure; 3) thermodynamically determined intermediate ratios can be completely converted under reaction conditions for a selection process; and 4) the increase in enantioselectivity with increasing hydrogen partial pressure, a phenomenon that is experimentally proven but theoretically far from being well-understood, can be explained by applying both the lock-and-key as well as the major/minor principle. PMID:18543261

  14. The role of long-lived reactive oxygen intermediates in the reaction of ozone with aerosol particles

    NASA Astrophysics Data System (ADS)

    Shiraiwa, Manabu; Sosedova, Yulia; Rouvire, Aurlie; Yang, Hong; Zhang, Yingyi; Abbatt, Jonathan P. D.; Ammann, Markus; Pschl, Ulrich

    2011-04-01

    The heterogeneous reactions of O3 with aerosol particles are of central importance to air quality. They are studied extensively, but the molecular mechanisms and kinetics remain unresolved. Based on new experimental data and calculations, we show that long-lived reactive oxygen intermediates (ROIs) are formed. The chemical lifetime of these intermediates exceeds 100 seconds, which is much longer than the surface residence time of molecular O3 (~10-9 s). The ROIs explain and resolve apparent discrepancies between earlier quantum mechanical calculations and kinetic experiments. They play a key role in the chemical transformation and adverse health effects of toxic and allergenic air-particulate matter, such as soot, polycyclic aromatic hydrocarbons and proteins. ROIs may also be involved in the decomposition of O3 on mineral dust and in the formation and growth of secondary organic aerosols. Moreover, ROIs may contribute to the coupling of atmospheric and biospheric multiphase processes.

  15. Active intermediates of polyhydroxyalkanoate synthase from Aeromonas caviae in polymerization reaction.

    PubMed

    Numata, Keiji; Motoda, Yoko; Watanabe, Satoru; Tochio, Naoya; Kigawa, Takanori; Doi, Yoshiharu

    2012-11-12

    Polyhydroxyalkanoate (PHA) synthase from Aeromonas caviae FA440 (PhaC(Ac), BAA21815) is one of the most valuable PHA synthase, because of its function to synthesize a practical bioplastic, poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)]. However, biochemical activity and active intermediates of PhaC(Ac) have not been clarified until now. In the present study, a gene of PhaC(Ac) was cloned and overexpressed by a cell-free protein expression system. Both the polymerization activity and oligomerization behavior of the purified PhaC(Ac) were characterized in order to clarify the active intermediates of PhaC(Ac) based on the hydrodynamic diameters and specific activities of PhaC(Ac). The influences of a substrate, (R)-3-hydroxybutyryl-CoA (3HB-CoA), on the oligomerization of PhaC(Ac) (7.5 ?M) were also investigated, and then the Hill coefficient (n = 2.6 0.4) and the microscopic dissociation constant (K(m) = 77 5 ?M) were determined. Based on the results, the active intermediate of PhaC(Ac) was concluded to be the dimeric PhaC(Ac) containing 3HB-CoA as an activator for its dimerization. This information is critical for revealing the relationships between its dimerization and function in PHA synthesis. PMID:23043466

  16. Probing the Reaction Intermediates for the Watergas Shift over Inverse CeOx / Au(1 1 1) Catalysts

    SciTech Connect

    Senanayake, S.; Stacchiola, D; Evans, J; Estrella, M; Barrio, L; Perez, M; Hrbek, J; Rodriguez, J

    2010-01-01

    The water-gas shift (WGS) is an important reaction for the production of molecular H{sub 2} from CO and H{sub 2}O. An inverse CeO{sub x}/Au(1 1 1) catalyst exhibits a very good WGS activity, better than that of copper surfaces or Cu nanoparticles dispersed on a ZnO(0 0 0 {bar 1}) substrate which model current WGS industrial catalysts. In this work we report on intermediates likely to arise during the CO + H{sub 2}O reaction over CeO{sub x}/Au(1 1 1) using soft X-ray photoemission (sXPS) and near-edge X-ray absorption fine structure (NEXAFS). Several potential intermediates including formates (HCOO), carbonates (CO{sub 3}) and carboxylates (HOCO) are considered. Adsorption of HCOOH and CO{sub 2} is used to create both HCOO and CO{sub 3} on the CeO{sub x}/Au(1 1 1) surface, respectively. HCOO appears to have greater stability with desorption temperatures up to 600 K while CO{sub 3} only survives on the surface up to 300 K. On the CeO{sub x}/Au(1 1 1) catalysts, the presence of Ce{sup 3+} leads to the dissociation of H{sub 2}O to give OH groups. We demonstrate experimentally that the OH species are stable on the surface up to 600 K and interact with CO to yield weakly bound intermediates. When there is an abundance of Ce{sup 4+}, the OH concentration is diminished and the likely intermediates are carbonates. As the surface defects are increased and the Ce{sup 3+}/Ce{sup 4+} ratio grows, the OH concentration also grows and both carbonate and formate species are observed on the surface after dosing CO to H{sub 2}O/CeO{sub x}/Au(1 1 1). The addition of ceria nanoparticles to Au(1 1 1) is essential to generate an active WGS catalyst and to increase the production and stability of key reaction intermediates (OH, HCOO and CO{sub 3}).

  17. Probing the Reaction Intermediates for the Water-Gas Shift over Inverse CeOx/Au(111) Catalysts

    SciTech Connect

    Rodriguez, J.A.; Senanayake, S.D.; Stacchiola, D.; Evans, J.; Estrella, M.; Barrio-Pliego, L.; Prez, M.; Hrbek, J.

    2010-05-04

    The water-gas shift (WGS) is an important reaction for the production of molecular H{sub 2} from CO and H{sub 2}O. An inverse CeO{sub x}/Au(1 1 1) catalyst exhibits a very good WGS activity, better than that of copper surfaces or Cu nanoparticles dispersed on a ZnO(0 0 0 {bar 1}) substrate which model current WGS industrial catalysts. In this work we report on intermediates likely to arise during the CO + H{sub 2}O reaction over CeO{sub x}/Au(1 1 1) using soft X-ray photoemission (sXPS) and near-edge X-ray absorption fine structure (NEXAFS). Several potential intermediates including formates (HCOO), carbonates (CO{sub 3}) and carboxylates (HOCO) are considered. Adsorption of HCOOH and CO{sub 2} is used to create both HCOO and CO{sub 3} on the CeO{sub x}/Au(1 1 1) surface, respectively. HCOO appears to have greater stability with desorption temperatures up to 600 K while CO{sub 3} only survives on the surface up to 300 K. On the CeO{sub x}/Au(1 1 1) catalysts, the presence of Ce{sup 3+} leads to the dissociation of H{sub 2}O to give OH groups. We demonstrate experimentally that the OH species are stable on the surface up to 600 K and interact with CO to yield weakly bound intermediates. When there is an abundance of Ce{sup 4+}, the OH concentration is diminished and the likely intermediates are carbonates. As the surface defects are increased and the Ce{sup 3+}/Ce{sup 4+} ratio grows, the OH concentration also grows and both carbonate and formate species are observed on the surface after dosing CO to H{sub 2}O/CeO{sub x}/Au(1 1 1). The addition of ceria nanoparticles to Au(1 1 1) is essential to generate an active WGS catalyst and to increase the production and stability of key reaction intermediates (OH, HCOO and CO{sub 3}).

  18. N,O-Nucleosides from ene reactions of nitrosocarbonyl intermediates with the 3-methyl-2-buten-1-ol.

    PubMed

    Quadrelli, Paolo; Mella, Mariella; Carosso, Serena; Bovio, Bruna

    2013-01-18

    Nitrosocarbonyl intermediates undergo ene reactions with allylic alcohols, affording regioisomeric adducts in fair yields. Nitrosocarbonyl benzene reacts with 3-methyl-2-buten-1-ol and follows a Markovnikov orientation and abstracts preferentially the twix hydrogens over the lone ones. With the more sterically demanding nitrosocarbonyl mesitylene and anthracene, the Markovnikov directing effect is relieved and lone abstraction is observed, affording the 5-hydroxy-isoxazolidines that serve as synthons for the preparation of N,O-nucleoside analogues according to the Vorbrüggen protocol. PMID:23245669

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

    DOEpatents

    Maya, Leon (Oak Ridge, TN)

    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.

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

    DOEpatents

    Maya, Leon (Oak Ridge, TN)

    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.

  1. 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.

  2. On the chemistry of ethanol on basic oxides: revising mechanisms and intermediates in the Lebedev and Guerbet reactions.

    PubMed

    Chieregato, Alessandro; Velasquez Ochoa, Juliana; Bandinelli, Claudia; Fornasari, Giuseppe; Cavani, Fabrizio; Mella, Massimo

    2015-01-01

    A common way to convert ethanol into chemicals is by upgrading it over oxide catalysts with basic features; this method makes it possible to obtain important chemicals such as 1-butanol (Guerbet reaction) and 1,3-butadiene (Lebedev reaction). Despite their long history in chemistry, the details of the close inter-relationship of these reactions have yet to be discussed properly. Our present study focuses on reactivity tests, in?situ diffuse reflectance infrared Fourier transform spectroscopy, MS analysis, and theoretical modeling. We used MgO as a reference catalyst with pure basic features to explore ethanol conversion from its very early stages. Based on the obtained results, we formulate a new mechanistic theory able to explain not only our results but also most of the scientific literature on Lebedev and Guerbet chemistry. This provides a rational description of the intermediates shared by the two reaction pathways as well as an innovative perspective on the catalyst requirements to direct the reaction pathway toward 1-butanol or butadiene. PMID:25504787

  3. Direct evidence for an acyl phosphate intermediate in the folylpoly-. gamma. -glutamate synthetase and dihydrofolate synthetase-catalyzed reactions

    SciTech Connect

    Banerjee, R.

    1987-01-01

    The mechanism of the reactions catalyzed by two enzymes, namely dihydrofolate synthetase (DHFS) and folylpoly-..gamma..-glutamate synthetase (FPGS), has been investigated. The nature of the intermediate in each of the two reactions was monitored simultaneously in the multifunctional enzyme, FPGS/DHFS from E. coli. The latter was isolated from a transformant containing the cloned FPGS/DHFS gene. Incubation of (/sup 18/O)-H/sub 2/Pte and (/sup 17/O)-glutamate with ATP and the enzyme, resulted in the formation of (/sup 18/O)- and (/sup 17/O)-P/sub i/, thus providing strong evidence for the formation of an acyl phosphate species during catalysis of each reaction. The inorganic phosphate formed in the enzyme-catalyzed reaction was purified by chromatography on DEAE-cellulose, then converted to the trimethyl ester and analyzed by mass spectroscopy /sup 17/O NMR and /sup 31/P NMR. Stoichiometric formation of (/sup 17/O)- and (/sup 18/O)-Pi was observed. /sup 31/P NMR analysis showed the expected /sup 18/O-induced isotopic perturbations. The presence of (/sup 17/O)-trimethyl phosphate was revealed by /sup 17/O NMR. The mechanism of the FPGS-catalyzed reaction was also investigated with the antifolate (/sup 18/O)-methotrexate.

  4. Modeling the photochemical transformation of nitrobenzene under conditions relevant to sunlit surface waters: Reaction pathways and formation of intermediates.

    PubMed

    Vione, Davide; De Laurentiis, Elisa; Berto, Silvia; Minero, Claudio; Hatipoglu, Arzu; Cinar, Zekiye

    2016-02-01

    Nitrobenzene (NB) would undergo photodegradation in sunlit surface waters, mainly by direct photolysis and triplet-sensitized oxidation, with a secondary role of the OH reaction. Its photochemical half-life time would range from a few days to a couple of months under fair-weather summertime irradiation, depending on water chemistry and depth. NB phototransformation gives phenol and the three nitrophenol isomers, in different yields depending on the considered pathway. The minor OH role in degradation would make NB unsuitable as OH probe in irradiated natural water samples, but the selectivity towards OH could be increased by monitoring the formation of phenol from NB+OH. The relevant reaction would proceed through ipso-addition of OH on the carbon atom bearing the nitro-group, forming a pre-reactive complex that would evolve into a transition state (and then into a radical addition intermediate) with very low activation energy barrier. PMID:26688265

  5. 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.

  6. ENDOR structural characterization of a catalytically competent acylenzyme reaction intermediate of wild-type TEM-1 beta-lactamase confirms glutamate-166 as the base catalyst.

    PubMed

    Mustafi, D; Sosa-Peinado, A; Makinen, M W

    2001-02-27

    The catalytically competent active-site structure of a true acylenzyme reaction intermediate of TEM-1 beta-lactamase formed with the kinetically specific spin-labeled substrate 6-N-(2,2,5,5-tetramethyl-1-oxypyrrolinyl-3-carboxyl)-penicillanic acid isolated under cryoenzymologic conditions has been determined by angle-selected electron nuclear double resonance (ENDOR) spectroscopy. Cryoenzymologic experiments with use of the chromophoric substrate 6-N-[3-(2-furanyl)-propen-2-oyl]-penicillanic acid showed that the acylenzyme reaction intermediate could be stabilized in the -35 to -75 degrees C range with a half-life suitably long to allow freeze-quenching of the reaction species for ENDOR studies while a noncovalent Michaelis complex could be optically identified at temperatures only below -70 degrees C. The wild-type, Glu166Asn, Glu240Cys, and Met272Cys mutant forms of the mature enzyme were overexpressed in perdeuterated minimal medium to allow detection and assignment of proton resonances specific for the substrate and chemically modified amino acid residues in the active site. From analysis of the dependence of the ENDOR spectra on the setting of the static laboratory magnetic field H0, the dipolar contributions to the principal hyperfine coupling components were estimated to calculate the separations between the unpaired electron of the nitroxyl group and isotopically identified nuclei. These electron-nucleus distances were applied as constraints to assign the conformation of the substrate in the active site and of amino acid side chains by molecular modeling. Of special interest was that the ENDOR spectra revealed a water molecule sequestered in the active site of the acylenzyme of the wild-type protein that was not detected in the deacylation impaired Glu166Asn mutant. On the basis of the X-ray structure of the enzyme, the ENDOR distance constraints placed this water molecule within hydrogen-bonding distance to the carboxylate side chain of glutamate-166 as if it were poised for nucleophilic attack of the scissile ester bond. The ENDOR results provide experimental evidence of glutamate-166 in its functional role as the general base catalyst in the wild-type enzyme for hydrolytic breakdown of the acylenzyme reaction intermediate of TEM-1 beta-lactamase. PMID:11327860

  7. Direct observation of reaction intermediates for a well defined heterogeneous alkene metathesis catalyst

    PubMed Central

    Blanc, Frédéric; Berthoud, Romain; Copéret, Christophe; Lesage, Anne; Emsley, Lyndon; Singh, Rojendra; Kreickmann, Thorsten; Schrock, Richard R.

    2008-01-01

    Grafting of [W(≡NAr)(=CHtBu)(2,5-Me2NC4H2)2] on a silica partially dehydroxylated at 700°C (SiO2- (700)) generates the corresponding monosiloxy complex [(≡SiO)W(≡NAr)(=CHtBu)(2,5-Me2NC4H2)] as the major species (≈90%) along with [(≡SiO)W(≡NAr)(CH2tBu)(2,5-Me2NC4H2)2], according to mass balance analysis, IR, and NMR studies. This heterogeneous catalyst displays good activity and stability in the metathesis of propene. Very importantly, solid state NMR spectroscopy allows observation of the propagating alkylidene as well as stable metallacyclobutane intermediates. These species have the same reactivity as the initial surface complex [(≡SiO)W(≡NAr)(=CHtBu)(2,5-Me2NC4H2)], which shows that they are the key intermediates of alkene metathesis. PMID:18723685

  8. Direct observation of reaction intermediates for a well defined heterogeneous alkene metathesis catalyst.

    PubMed

    Blanc, Frdric; Berthoud, Romain; Copret, Christophe; Lesage, Anne; Emsley, Lyndon; Singh, Rojendra; Kreickmann, Thorsten; Schrock, Richard R

    2008-08-26

    Grafting of [W([triple bond]NAr)(=CHtBu)(2,5-Me(2)NC(4)H(2))(2)] on a silica partially dehydroxylated at 700 degrees C (SiO(2- (700))) generates the corresponding monosiloxy complex [([triple bond]SiO)W([triple bond]NAr)(=CHtBu)(2,5-Me(2)NC(4)H(2))] as the major species (approximately 90%) along with [([triple bond]SiO)W([triple bond]NAr)(CH(2)tBu)(2,5-Me(2)NC(4)H(2))(2)], according to mass balance analysis, IR, and NMR studies. This heterogeneous catalyst displays good activity and stability in the metathesis of propene. Very importantly, solid state NMR spectroscopy allows observation of the propagating alkylidene as well as stable metallacyclobutane intermediates. These species have the same reactivity as the initial surface complex [([triple bond]SiO)W([triple bond]NAr)(=CHtBu)(2,5-Me(2)NC(4)H(2))], which shows that they are the key intermediates of alkene metathesis. PMID:18723685

  9. 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 phobia). PMID:25451788

  10. High Resolution Reaction Intermediates of rabbit Muscle Fructose-1,6-bisphosphate Aldolase: Substrate Cleavage and Induced Fit

    SciTech Connect

    St-Jean,M.; Lafrance-Vanasse, J.; Liotard, B.; Sygusch, J.

    2005-01-01

    Crystal structures were determined to 1.8-Angstrom resolution of the glycolytic enzyme fructose-1, 6-bis(phosphate) aldolase trapped in complex with its substrate and a competitive inhibitor, mannitol-1, 6-bis(phosphate). The enzyme substrate complex corresponded to the postulated Schiff base intermediate and has reaction geometry consistent with incipient C3-C4 bond cleavage catalyzed by Glu-187, which is adjacent to the Schiff base forming Lys-229. Atom arrangement about the cleaved bond in the reaction intermediate mimics a pericyclic transition state occurring in non-enzymatic aldol condensations. Lys-146 hydrogen bonds the substrate C4 hydroxyl and assists substrate cleavage by stabilizing the developing negative charge on the C4 hydroxyl during proton abstraction. Mannitol-1, 6-bis(phosphate) forms a non-covalent complex in the active site whose binding geometry mimics the covalent carbinolamine precursor. Glu-187 hydrogen bonds the C2 hydroxyl of the inhibitor in the enzyme complex substantiating a proton transfer role by Glu-187 in catalyzing the conversion of the carbinolamine intermediate to Schiff base. Modeling of the acyclic substrate configuration into the active site shows Glu-187, in acid form, hydrogen bonding both substrate C2 carbonyl and C4 hydroxyl, thereby aligning the substrate ketose for nucleophilic attack by Lys-229. The multi-functional role by Glu-187 epitomizes a canonical mechanistic feature conserved in Schiff base forming aldolases catalyzing carbohydrate metabolism. Trapping of tagatose-1, 6-bis(phosphate), a diastereoisomer of fructose-1, 6-bis(phosphate), displayed stereospecific discrimination and reduced ketohexose binding specificity. Each ligand induces homologous conformational changes in two adjacent a-helical regions that promote phosphate binding in the active site.

  11. Vibrational spectrum of the lumi intermediate in the room temperature rhodopsin photo-reaction.

    PubMed

    Ujj, L; Jger, F; Atkinson, G H

    1998-03-01

    The vibrational spectrum (650-1750 cm(-1)) of the lumi-rhodopsin (lumi) intermediate formed in the microsecond time regime of the room-temperature rhodopsin (RhRT) photoreaction is measured for the first time using picosecond time-resolved coherent anti-Stokes Raman spectroscopy (PTR/CARS). The vibrational spectrum of lumi is recorded 2.5 micros after the 3-ps, 500-nm excitation of RhRT. Complementary to Fourier transform infrared spectra recorded at Rh sample temperatures low enough to freeze lumi, these PTR/CARS results provide the first detailed view of the vibrational degrees of freedom of room-temperature lumi (lumiRT) through the identification of 21 bands. The exceptionally low intensity (compared to those observed in bathoRT) of the hydrogen out-of-plane (HOOP) bands, the moderate intensity and absolute positions of C-C stretching bands, and the presence of high-intensity C==C stretching bands suggest that lumiRT contains an almost planar (nontwisting), all-trans retinal geometry. Independently, the 944-cm(-1) position of the most intense HOOP band implies that a resonance coupling exists between the out-of-plane retinal vibrations and at least one group among the amino acids comprising the retinal binding pocket. The formation of lumiRT, monitored via PTR/CARS spectra recorded on the nanosecond time scale, can be associated with the decay of the blue-shifted intermediate (BSI(RT)) formed in equilibrium with the bathoRT intermediate. PTR/CARS spectra measured at a 210-ns delay contain distinct vibrational features attributable to BSI(RT), which suggest that the all-trans retinal in both BSI(RT) and lumiRT is strongly coupled to part of the retinal binding pocket. With regard to the energy storage/transduction mechanism in RhRT, these results support the hypothesis that during the formation of lumiRT, the majority of the photon energy absorbed by RhRT transfers to the apoprotein opsin. PMID:9512045

  12. Use of crown ethers to isolate intermediates in ammonia-borane dehydrocoupling reactions.

    PubMed

    Less, Robert J; Garca-Rodrguez, Ral; Simmonds, Hayley R; Allen, Lucy K; Bond, Andrew D; Wright, Dominic S

    2016-02-23

    The presence of 18-crown-6 in the Lewis acid-promoted dehydrocoupling reaction of ammonia borane permits isolation of [(THF)BH2NH3](+) and [BH2(NH3)2](+) cations. [(THF)BH2NH3](+) reacts with Lewis bases to give either boron adducts or by deprotonation at nitrogen to give borazine and ammonia-borane. PMID:26853317

  13. Momentum distributions in stripping reactions of radioactive projectiles at intermediate energies

    NASA Astrophysics Data System (ADS)

    Bertulani, C. A.; Hansen, P. G.

    2004-09-01

    The theory of one-nucleon removal in the stripping reaction (inelastic breakup) on a light target is extended to cover two-dimensional momentum distributions of the reaction residues with the use of realistic profile functions for the core-target and nucleon-target interactions. Examples of the calculated projected parallel- and transverse momentum distributions are given. The transverse momentum distributions, projections on a Cartesian axis perpendicular to the beam direction, show an interesting intermingling of the stripping reaction with elastic scattering of the reaction residue on the target. We also obtain doubly differential distributions of the cross section on the parallel- and transverse-momentum variables. The distributions depend strongly on the value of the magnetic quantum number m . They will be of importance for evaluating acceptance corrections in experiments, and they lead to alignment with the possibility of anisotropic emission of subsequent gamma rays, an interesting spectroscopic tool. Experimental data for proton stripping of 8B agree with our calculations.

  14. Dearomative Indole Cycloaddition Reactions of Aza-Oxyallyl Cationic Intermediates: Modular Access to Pyrroloindolines.

    PubMed

    Acharya, Arjun; Anumandla, Devendar; Jeffrey, Christopher S

    2015-12-01

    A regioselective dearomative aza-(3 + 2) cycloaddition reaction of substituted indoles with ?-halohydroxamates has been developed. This transformation provides rapid access to highly functionalized pyrroloindolines that are represented in large number of bioactive compounds. The natural product, physostigmine, has been concisely synthesized utilizing this method. PMID:26562215

  15. 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

  16. Sensitivity of the blue loops of intermediate-mass stars to nuclear reactions

    SciTech Connect

    Halabi, Ghina M.; El Eid, Mounib

    2012-11-20

    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 mass range 5M{sub Circled-Dot-Operator} to 12M{sub Circled-Dot-Operator }. We show that the blue loops of stars in the mass range 5M{sub Circled-Dot-Operator} to 8M{sub Circled-Dot-Operator }, that is the range of super ABG stars, are severely affected by a modification of the important {sup 14}N(p,{gamma}){sup 15}O reaction rate. We also show that the blue loops can be restored if envelope overshooting is included, which is necessary to explain the observations of the Cepheid stars.

  17. 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.

  18. Evidence for a Tetraoxo Intermediate in a Reaction Between a Superoxometal Complex and Acylperoxyl Radicals

    SciTech Connect

    Pestovsky, Oleg; Harrata, Kamel A.; Bakac, Andreja

    2008-08-05

    The superoxo complex Cr{sub aq}({sup 18}O{sup 18}O){sup 2+} reacts with (CH{sub 3}){sub 3}C(O){sup 16}O{sup 16}O{sup {center_dot}} to generate quantitative yields of mixed-label dioxygen, {sup 18}O{sup 16}O, demonstrating that this cross-reaction involves head-to-head interaction between the metal-activated and alkyl-activated dioxygen.

  19. Observation of Organometallic and Radical Intermediates Formed during the Reaction of Methyl-Coenzyme M Reductase with Bromoethanesulfonate

    PubMed Central

    Li, Xianghui; Telser, Joshua; Hoffman, Brian M.; Gerfen, Gary; Ragsdale, Stephen W.

    2010-01-01

    Methyl-coenzyme M reductase (MCR) from methanogenic archaea catalyzes the final step of methane formation, in which methyl-coenzyme M (2-methylthioethane sulfonate, methyl-SCoM) is reduced with coenzyme B (N-7-mercaptoheptanolyl-threonine phosphate, CoBSH) to form methane and the heterodisulfide CoBS-SCoM. The active dimeric form of MCR contains two Ni(I)-F430 prosthetic groups, one in each monomer. This manuscript describes studies of the reaction of the active Ni(I) state of MCR (MCRred1) with BES (2-bromoethanesulfonate) and CoBSH or its analog, CoB6SH (N-6-mercaptohexanolyl-threonine phosphate), by transient kinetic measurements using EPR and UV-visible spectroscopy and by global fits of the data. This reaction is shown to lead to the formation of three intermediates, the first of which is assigned as an alkyl-Ni(III) species that forms as the active Ni(I)-MCRred1 state of the enzyme decays. Subsequently, a radical (MCRBES radical) is formed that was characterized by multifrequency electron paramagnetic resonance (EPR) studies at X (~ 9 GHz)-, Q (~35 GHz)- and D (~135 GHz)-bands and by electron-nuclear double resonance (ENDOR) spectroscopy. The MCRBES radical is characterized by g-values at 2.00340 and 1.99832 and includes a strongly coupled non-exchangeable proton with a hyperfine coupling constant of 50 MHz. Based on transient kinetic measurements, the formation and decay of the radical coincides with a species that exhibits absorption peaks at 426 nm and 575 nm. Isotopic substitution, multifrequency EPR and ENDOR spectroscopic experiments rule out the possibility that MCRBES is a tyrosyl radical and indicate that if a tyrosyl radical is formed during the reaction, it does not accumulate to detectable levels. The results provide support for a hybrid mechanism of methanogenesis by MCR that includes both alkyl-Ni and radical intermediates. PMID:20597483

  20. [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)

  1. Study of intermediates from transition metal excited-state electron-transfer reactions. [Annual] progress report, August 1, 1989--July 31, 1992

    SciTech Connect

    Hoffman, M.Z.

    1992-07-31

    Conventional and fast-kinetics techniques of photochemistry, photophysics, radiation chemistry, and electrochemistry were used to study the intermediates involved in transition metal excited-state electron-transfer reactions. These intermediates were excited state of Ru(II) and Cr(III) photosensitizers, their reduced forms, and species formed in reactions of redox quenchers and electron-transfer agents. Of particular concern was the back electron-transfer reaction between the geminate pair formed in the redox quenching of the photosensitizers, and the dependence of its rate on solution medium and temperature in competition with transformation and cage escape processes. (DLC)

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

    PubMed

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

    2015-12-15

    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 ?-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 because the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate. PMID:26323320

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

    DOE PAGESBeta

    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 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

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

    PubMed Central

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

    2015-01-01

    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 because the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate. PMID:26323320

  5. Reaction intermediates in aromatic-fuel combustion. Final report, 18 July 1984-17 July 1985

    SciTech Connect

    Sanders, W.A.

    1985-07-17

    There is increasing tendency in future fuels to have higher aromatic contents because partly of the change in fuel sources (such as coals and shale oils) and partly of the greater use of aromatic compounds as additives due to their high octane values. The chemistry of the oxidation of aromatic compound at combustion temperatures (T > 1500 K) is very complex and poorly understood. This study is part of a series of experiments being carried out to elucidate the oxidation mechanism of C6H6, the most important benchmark system for the aromatic compounds. The unimolecular decomposition of methylphenyl ether (anisole) was studied in incident shock waves covering the temperature range from 1000 to 1580 K and the pressure range from 0.4 to 0.9 atm. The carbon monoxide formed in the reaction, monitored by resonance absorption using a stabilized cw CO laser, could be satisfactorily accounted for by a four-reaction mechanism: C6H5OCH3 yields C6H50 + CH3; C6H5O yields CO + C5H5; CH3 + C6H5O yields o- and p-CH3C6H4OH; and CH3 + CH3 yields C2H6.

  6. Directly measuring reaction kinetics of ˙QOOH--a crucial but elusive intermediate in hydrocarbon autoignition.

    PubMed

    Zádor, Judit; Huang, Haifeng; Welz, Oliver; Zetterberg, Johan; Osborn, David L; Taatjes, Craig A

    2013-07-14

    Hydrocarbon autoignition has long been an area of intense fundamental chemical interest, and is a key technological process for emerging clean and efficient combustion strategies. Carbon-centered radicals containing an -OOH group, commonly denoted ˙QOOH radicals, are produced by isomerization of the alkylperoxy radicals that are formed in the first stages of oxidation. These ˙QOOH radicals are among the most critical species for modeling autoignition, as their reactions with O2 are responsible for chain branching below 1000 K. Despite their importance, no ˙QOOH radicals have ever been observed by any means, and only computational and indirect experimental evidence has been available on their reactivity. Here, we directly produce a ˙QOOH radical, 2-hydroperoxy-2-methylprop-1-yl, and experimentally determine rate coefficients for its unimolecular decomposition and its association reaction with O2. The results are supported by high-level theoretical kinetics calculations. Our experimental strategy opens up a new avenue to study the chemistry of ˙QOOH radicals in isolation. PMID:23689671

  7. Detection of spirorchiid trematodes in gastropod tissues by polymerase chain reaction: preliminary identification of an intermediate host of Learedius learedi.

    PubMed

    Stacy, Brian A; Frankovich, Thomas; Greiner, Ellis; Alleman, A Rick; Herbst, Lawrence H; Klein, Paul; Bolten, Alan; McIntosh, Antoinette; Jacobson, Elliott R

    2010-08-01

    Marine spirorchiid trematodes are associated with morbidity and mortality in sea turtles worldwide. The intermediate hosts remain unknown, and discovery efforts are hindered by the large number and great diversity of potential hosts within sea turtle habitats, as well the potential for low prevalence and overdispersion. A high-throughput DNA extraction and polymerase chain reaction-based method was developed to detect the internal transcribed spacer 2 (ITS2) region of the ribosomal gene of 2 spirorchiid genera, Learedius and Hapalotrema , within pooled samples of gastropod tissues. A model system consisting of freshwater snail ( Pomacea bridgesii ) tissues and DNA extracts spiked with adult Learedius learedi and known quantities of spirorchiid DNA was used to develop and test the technique. Threshold of detection was found to be equivalent to an early prepatent infection within 1.5 g of gastropod tissue. This technique was used to screen approximately 25 species of marine gastropods at a captive facility where green turtles ( Chelonia mydas ) become infected by L. learedi . The parasite was detected in a sample of knobby keyhole limpet ( Fissurella nodosa ), thus providing the first evidence of an intermediate host for a marine spirorchiid trematode. This technique has many potential applications in trematode life cycle discovery studies. PMID:20496958

  8. Extending the Kawai-Kerman-McVoy Statistical Theory of Nuclear Reactions to Intermediate Structure via Doorways

    SciTech Connect

    Arbanas, Goran; Bertulani, C. A.; Dean, D. J.; Kerman, A. K.; Roche, K. J.

    2011-01-01

    Kawai, Kerman, and McVoy have shown that a statistical treatment of many open channels that are coupled by direct reactions leads to modifications of the Hauser- Feshbach expression for energy-averaged cross section (Ann. of Phys. 75 (1973) 156). The energy averaging interval for this cross section is on the order of the width of single particle resonances, 1MeV, revealing only a gross structure in the cross section. When the energy-averaging interval is decreased down to a width of a doorway state 0.1 MeV, a so-called intermediate structure may be observed in cross sections. We extend the Kawai-Kerman-McVoy theory into the intermediate structure by leveraging a theory of doorway states developed by Feshbach, Kerman, and Lemmer (Ann. of Phys. 42 (1967) 230). As a byproduct of the extension, an alternative derivation of the central result of the Kawai-Kerman-McVoy theory is suggested. We quantify the effect of the approximations used in derivation by performing numerical computations for a large set of compound nuclear states.

  9. H2O2/TiO2 photocatalytic oxidation of metol. Identification of intermediates and reaction pathways.

    PubMed

    Aceituno, Mnica; Stalikas, Constantine D; Lunar, Loreto; Rubio, Soledad; Prez-Bendito, Dolores

    2002-08-01

    The applicability of H2O2 to increase the efficiency of TiO2 photocatalytic degradations was investigated. The photographic developer metol [N-methyl-p-aminophenol] that does not adsorb on the surface of TiO2 particulates was used as a model for this purpose. It was proved that metol was mineralised under oxidation with H2O2/TiO2/UV through different thermal and photochemical reactions. Identification of intermediates by both HPLC-electron impact-MS and HPLC-electrospray ionisation-MS helped to elucidate the role of H2O2 and TiO2 in the degradation process and to establish degradation pathways. Intermediates yielded were partially oxygenated aromatic species and dimers, which were amenable to oxidation. The optimal degradation conditions found for mineralisation were 0.4 M H2O2, 5 mg/ml TiO2, pH 9 and irradiation centred at 360 nm (4.9 mW/cm2). The use of oxidants opens an interesting medium to the treatment of effluents containing a diversity of organics since they increase substantially the efficiency of TiO2 photocatalytic degradations. PMID:12230204

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

    SciTech Connect

    Calaza, Florencia; Chen, Tsung-Liang; Mullins, David R; Xu, Ye; Overbury, Steven {Steve} H

    2015-01-01

    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 CeO2surface, 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. 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.

  11. Plastic scintillator detectors for the study of transfer and breakup reactions at intermediate energies

    SciTech Connect

    Schmidt, H.R.; Bantel, M.; Chan, Y.D.; Gazes, S.M.; Kamermans, R.; Albiston, C.; Wald, S.; Stokstad, R.G.

    1984-10-01

    The detection of light particles associated with projectile like fragments can be used to separate transfer and breakup reactions provided the detectors cover a large solid angle. Three detection systems are described: (1) a ..pi.. detector in the shape of a cube, 20 cm on a side, (2) a X-Y position sensitive ..delta..E-E detector having an area of 20 x 20 cm/sup 2/, and (3) a multi-element detector consisting of eight position sensitive strips. The latter two detectors are of the phoswich type having the thin element of NE102 (tau = 2.5 ns) and the thick element of NE115 (tau = 225 ns). The performance characteristics of the three detectors are described. 6 references, 13 figures.

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

    PubMed Central

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

    2015-01-01

    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 ?,?-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. PMID:26601202

  13. 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. PMID:26601202

  14. Plastic scintillator detectors for the study of transfer and breakup reactions at intermediate energies

    NASA Astrophysics Data System (ADS)

    Schmidt, H. R.; Bantel, M.; Chan, Y. D.; Gazes, S. M.; Kamermans, R.; Albiston, C.; Wald, S.; Stokstad, R. G.

    1984-10-01

    The detection of light particles associated with projectile like fragments can be used to separate transfer and breakup reactions provided the detectors cover a large solid angle. Three detection systems are described: (1) 4-pi detector in the shape of a cube, 20 cm on a side, (2) a X-Y position sensitive (delta) E-E detector having an area of 20 x 20 cm, and (3) a multielement detector consisting of eight position sensitive strips. The latter two detectors are of the phoswich type having the thin element of NE102 (tau = 2.5 ns) and the thick element of NE115 (tau = 225 ns). The performance characteristics of the three detectors are described.

  15. Trapping the P+B(L)- initial intermediate state of charge separation in photosynthetic reaction centers from Rhodobacter capsulatus.

    PubMed

    Carter, Brett; Boxer, Steven G; Holten, Dewey; Kirmaier, Christine

    2009-03-31

    The short-lived (<1 ps) initial intermediate state P(+)B(L)(-) in the photoinduced charge separation process of the bacterial photosynthetic reaction center has been trapped in two D(LL)-based Rhodobacter capsulatus mutants that have Tyr at position M208 and lack the bacteriopheophytin electron acceptor H(L). Transient state P(+)B(L)(-) is characterized by a 1017 nm bacteriochlorophyll anion absorption band and decays by charge recombination with a lifetime of several hundred picoseconds at 295 K. P(+)B(L)(-) is not observed in an otherwise identical mutant that has Phe at M208, which appears to make the state thermodynamically inaccessible from the excited primary electron donor P*. PMID:19245209

  16. A Dianionic Phosphorane Intermediate and Transition States in an Associative AN+DN Mechanism for the RibonucleaseA Hydrolysis Reaction

    SciTech Connect

    Elsasser, Brigitta M.; Valiev, Marat; Weare, John H.

    2009-03-25

    The RNaseA enzyme efficiently cleaves phosphodiester bonds in the RNA backbone. Phosphoryl transfer plays a central role in many biochemical reactions, and this is one of the most studied enzymes. However, there remains considerable controversy about the reaction mechanism. Most of this debate centers around the roles of the conserved residues, structures of the transition state or states, the possibility of a stable intermediate, and the charge and structure of this intermediate. In this communication we report calculations of the mechanism of the hydrolysis step in this reaction using a comprehensive QM/MM theoretical approach that includes a high level calculation of the interactions in the QM region, free energy estimates along an NEB optimized reaction path, and the inclusion of the interaction of the protein surroundings and solvent. Contrary to prior calculations we find a stable pentacoordinated dianionic phosphorane intermediate in the reaction path supporting an AN+DN reaction mechanism. In the transition state in the path from the reactant to the intermediate state (with barrier of 3.96 kcal/mol and intermediate stability of 2.21 kcal/mol) a proton from the attacking water is partially transferred to the His119 residue and the PO bond only partially formed from the remaining nucleophilic OH? species (bond order (BO) 0.11). In passing from the intermediate to the product state (barrier 13.22 kcal/mol) the PO bond on the cyclic phosphorane intermediate is nearly broken (BO 0.28) and the transfer of the proton from the Lys41 is almost complete (Lys41-H BO 0.87). In the product state a proton has been transferred from Lys41 to the O2? position of the sugar. The role of Lys41 as the catalytic acid is a result of the relative positioning of the Lys41 and His12 in the catalytic site. This configuration is supported by calculations and docking studies.

  17. Two-proton and two-neutron correlation functions for intermediate-energy heavy-ion reactions

    NASA Astrophysics Data System (ADS)

    Gaff, Sally Janine

    Two-particle intensity interferometry is used to study the space-time characteristics of the reaction zone formed in intermediate-energy heavy ion reactions. The results are compared to appropriate models. Because of the recently reported discrepancies between BUU calculations and measured two-proton correlation functions at beam energies E/A > 100 MeV, a two-proton correlation function has been measured for the reaction 16O + 197Au at E/A = 200 MeV. The measured total correlation function agrees with the BUU predictions, but the dependence of the correlation function on the total momentum predicted by the BUU model is larger than the data show. In the evaporative regime, questions arise in interpreting charged particle correlations because of the Coulomb field of the heavy residue. Therefore, in this energy region two-neutron correlation functions were measured. Two-neutron correlation functions for the reaction 40Ar + 165Ho at E/A = 25 MeV are presented and comparisons made to models. Corrections and event selection are made for the coincident neutrons to eliminate the effects of crosstalk and background scattering. These corrections are compared to two independent simulations. The experimental results show a strong correlation at q = 0, which is comparable to emission from the surface of a sphere with a radius of 7 fm and an exponential lifetime of 700 fm/c. An evaporative model with and without preequilibrium corrections was compared to the data. The measured lifetime is within a factor of two of the lifetime the evaporative model predicts. This comparison provides a useful test of the statistical models used for fission lifetime measurements.

  18. 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 CH 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)OOH. 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.

  19. Mechanistic origins of chemo- and regioselectivity of Ru(II)-catalyzed reactions involving ortho-alkenylarylacetylene, alkyne, and methanol: the crucial role of a chameleon-like intermediate.

    PubMed

    Dang, Yanfeng; Qu, Shuanglin; Tao, Yuan; Song, Chunyu; Wang, Zhi-Xiang

    2014-10-01

    M06-DFT computations have been applied to understand four catalytic systems which involved [Ru(Cp*)(MeCN)3]PF6 or [Ru(Tp)(PPh3)(MeCN)2]PF6 as mediator and ortho-alkenylarylacetylene, terminal alkyne, and methanol as reactants. Potentially, the products of these systems could be dihydrobiphenylenes, 1,3-dienyl ether, and naphthalene. Remarkably, each system afforded product selectively. Our computed mechanisms successfully account for the chemo- and regioselectivities of these systems. Furthermore, the study demonstrates that the chameleon-like mono(carbene) intermediates formed via the intermolecular alkyne-alkyne oxidative coupling play a crucial role to complete the reactions. According to their geometric and electronic structures, three resonance structures were introduced to characterize their reactivity properties, which address the features of the classical alkyne-alkyne oxidative coupling intermediates, mono(carbene) species, and electrophilicity of the intermediates, respectively. The reactivity properties lead to three channels isomerizing the intermediates to three isomers. Surprisingly, the bis(carbene) isomers, which are similar to the bis(carbene) intermediates generally considered to be crucial in the neutral RuCp*Cl-catalyzed systems, are accessible but not reactive enough to continue the subsequent reaction steps partially due to aromaticity. The other two isomers continue subsequent reaction steps. These findings may help not only to understand the four specific catalytic reactions but also to advance the [2 + 2 + 2] synthetic methodology. PMID:25222525

  20. 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. PMID:25493718

  1. Degradation of 2,4-dihydroxibenzoic acid by vacuum UV process in aqueous solution: kinetic, identification of intermediates and reaction pathway.

    PubMed

    Azrague, Kamal; Pradines, Vincent; Bonnefille, Eric; Claparols, Catherine; Maurette, Marie-Thrse; Benoit-Marqui, Florence

    2012-10-30

    2,4-Dihydroxybenzoic acid (2,4-DHBA) is found frequently as a pollutant in natural waters and represents a threat to water quality because it is a precursor to the formation of quinones which are highly toxic. The degradation of 2,4-DHBA using the vacuum UV photolysis of water has been investigated. Irradiation was carried out in an annular photoreactor equipped with a Xe-excimer lamp situated in the centre and emitting at 172 nm. The degradation kinetic followed a pseudo first order and the reaction has been found to be very heterogeneous, especially at low concentration. Impacts of oxygen or temperature have also been investigated but no effect has been shown. LC-MS and HPLC-UV combined with other analytical techniques allowed the identification of the formation of trihydroxybenzoc acids and trihydroxybenzenes which underwent a ring opening, conducting to the formation of aliphatic products named ?, ?, ? and ?. These products were in turn degraded successively into malec acid, malic and succinic acid, malonic acid, glyoxalic acid and oxalic acid before reaching the complete mineralization in about 180 min. The proposed reaction pathway has shown to be very different from the one observed for the TiO(2) photocatalysis which involves only holes (h(+)) without any formation of aromatic intermediates. The different behaviours of 2,4-DHBA towards the h(+) and HO make it a good probe to identify involved entities. PMID:22975258

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

    NASA Astrophysics Data System (ADS)

    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 63736 s -1 and 13.81.410 6 M -1 s -1, respectively, for hydrolysis catalyzed by TEM-1 ?-lactamase of E. coli, and 0.50.04 s -1 and 3.90.410 4 M -1 s -1 for hydrolysis catalyzed by the ?-lactamase of Enterobacter cloacae P99. We have also observed "burst kinetics" for the hydrolysis of SLPPEN with P99 ?-lactamase, indicative of formation of an acylenzyme reaction intermediate. In DMSO:H 2O (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 C was ?3 min, suitable for optical characterization. The observation of burst kinetics in the hydrolysis of SLPPEN catalyzed by P99 ?-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.

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

    NASA Astrophysics Data System (ADS)

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

    1990-04-01

    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.

  4. 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.

  5. 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) / k(SCI + SO2), of 3.5 (±1.8). This result suggests that SCIs may contribute to the oxidation of DMS in the atmosphere and that this process could therefore influence new particle formation in regions impacted by emissions of unsaturated hydrocarbons and DMS.

  6. Formation of 2,5-dimethyl-4-hydroxy-3(2H)-furanone through methylglyoxal: a Maillard reaction intermediate.

    PubMed

    Wang, Yu; Ho, Chi-Tang

    2008-08-27

    The caramel-like aroma compound, 2,5-dimethyl-4-hydroxy-3(2H)-furanone (DMHF) was quantified and verified by HPLC and GC-MS in the Maillard reaction based on methylglyoxal (MG). The reaction was performed in the 0.5 M phosphate buffer by heating MG with or without either glycine or cysteine at 120 degrees C for 1 h. MG alone or MG with cysteine could produce increased level of DMHF with pH increased, whereas MG with glycine had contrary trend. Experiments using a 1:1 mixture of [(13)C6]glucose and [(12)C6]glucose indicate that in the presence of glycine or cysteine, glucose skeleton kept intact during DMHF formation since a 1:1 mixture of [(13)C6]DMHF and [(12)C6]DMHF was formed. Acetylformoin was detected in the glucose with amino acid reaction system as a precursor of DMHF, while in the MG reaction systems, acetylformoin could not be identified. It is suggested different pathways of DMHF formation via MG and glucose. PMID:18593173

  7. Perturbation of cellular proteostasis networks identifies pathways that modulate precursor and intermediate but not mature levels of frataxin

    PubMed Central

    Nabhan, Joseph F.; Gooch, Renea L.; Piatnitski Chekler, Eugene L.; Pierce, Betsy; Bulawa, Christine E.

    2015-01-01

    Friedreichs Ataxia is a genetic disease caused by expansion of an intronic trinucleotide repeat in the frataxin (FXN) gene yielding diminished FXN expression and consequently disease. Since increasing FXN protein levels is desirable to ameliorate pathology, we explored the role of major cellular proteostasis pathways and mitochondrial proteases in FXN processing and turnover. We targeted p97/VCP, the ubiquitin proteasome pathway (UPP), and autophagy with chemical inhibitors in cell lines and patient-derived cells. p97 inhibition by DBeQ increased precursor FXN levels, while UPP and autophagic flux modulators had variable effects predominantly on intermediate FXN. Our data suggest that these pathways cannot be modulated to influence mature functional FXN levels. We also targeted known mitochondrial proteases by RNA interference and discovered a novel protease PITRM1 that regulates intermediate FXN levels. Treatment with the aforementioned chemical and genetic modulators did not have a differential effect in patient cells containing lower amounts of FXN. Interestingly, a number of treatments caused a change in total amount of FXN protein, without an effect on mature FXN. Our results imply that regulation of FXN protein levels is complex and that total amounts can be modulated chemically and genetically without altering the absolute amount of mature FXN protein. PMID:26671574

  8. Perturbation of cellular proteostasis networks identifies pathways that modulate precursor and intermediate but not mature levels of frataxin.

    PubMed

    Nabhan, Joseph F; Gooch, Renea L; Piatnitski Chekler, Eugene L; Pierce, Betsy; Bulawa, Christine E

    2015-01-01

    Friedreich's Ataxia is a genetic disease caused by expansion of an intronic trinucleotide repeat in the frataxin (FXN) gene yielding diminished FXN expression and consequently disease. Since increasing FXN protein levels is desirable to ameliorate pathology, we explored the role of major cellular proteostasis pathways and mitochondrial proteases in FXN processing and turnover. We targeted p97/VCP, the ubiquitin proteasome pathway (UPP), and autophagy with chemical inhibitors in cell lines and patient-derived cells. p97 inhibition by DBeQ increased precursor FXN levels, while UPP and autophagic flux modulators had variable effects predominantly on intermediate FXN. Our data suggest that these pathways cannot be modulated to influence mature functional FXN levels. We also targeted known mitochondrial proteases by RNA interference and discovered a novel protease PITRM1 that regulates intermediate FXN levels. Treatment with the aforementioned chemical and genetic modulators did not have a differential effect in patient cells containing lower amounts of FXN. Interestingly, a number of treatments caused a change in total amount of FXN protein, without an effect on mature FXN. Our results imply that regulation of FXN protein levels is complex and that total amounts can be modulated chemically and genetically without altering the absolute amount of mature FXN protein. PMID:26671574

  9. Models for reactions of acetylene on platinum(111): a vinyl(acetylene)triplatinum complex and evidence for an ethylidyne intermediate

    SciTech Connect

    Rashidi, M.; Puddephatt, R.J.

    1988-07-01

    Reaction of (Pt/sub 3/(..mu../sub 3/-H)(..mu..-dppm)/sub 3/)/sup +/ (1) with excess acetylene gives (Pt/sub 3/(CH=CH/sub 2/)(..mu../sub 3/-eta/sup 2/(parallel)-HCCH)(..mu..-dppm)/sub 3/)/sup +/, where dppm = Ph/sub 2/PCH/sub 2/PPh/sub 2/. Deuterium-labeling studies indicate that H-D scrambling occurs within the vinyl group but not in the acetylene ligand. For example, (Pt/sub 3/(..mu../sub 3/-D)(..mu..-dppm)/sub 3/)/sup +/ with HCCH gave (Pt/sub 3/(CH==CH/sub 7/-d/sub 1/)(..mu../sub 3/-eta/sup 2/(parallel)-HCCH)(..mu..-dppm)/sub 3/)/sup +/, in which the deuterium label was distributed randomly in all three possible positions in the vinyl group. It is possible that this scrambling occurs by way of a short-lived ethylidyne intermediate. The complex is fluxional, due to rotation of the acetylene ligand, at room temperature. Similar reaction of 1 with excess propyne gives (Pt/sub 3/(CH=CHMe)(..mu../sub 3/-eta/sup 2/(**)-MeCCH)(..mu..-dppm)/sub 3/)/sup +/, but this complex is not fluxional at room temperature and is formed selectively by cis insertion of propyne into the Pt-H groups. There is a strong resemblance to the chemistry resulting from chemisorption of acetylene on a Pt(111) surface, thus providing a clear example of the value of coordinatively unsaturated clusters as mimics of metal surfaces.

  10. pH-jump studies at subzero temperatures on an intermediate in the reaction of xanthine oxidase with xanthine.

    PubMed Central

    Tsopanakis, A D; Tanner, S J; Bray, R C

    1978-01-01

    Xanthine oxidase is stable and active in aqueous dimethyl sulphoxide solutions of up to at least 57% (w/w). Simple techniques are described for mixing the enzyme in this solvent at--82 degrees C, with its substrate, xanthine. When working at high pH values under such conditions, no reaction occurred, as judged by the absence of e.p.r. signals. On warming to--60 degrees C, for 10 min, however, the Very Rapid molybdenum(V) e.p.r. signal was obtained. This signal did not change on decreasing the pH, while maintaining the sample in liquid nitrate reductase, caused its molybdenum(V) e.p.r. signal to change from the high-pH to the low-pH form. These findings are not compatible with the conclusions of Edmondson, Ballou, Van Heuvelen, Palmer & Massey [J. Biol. Chem. (1973) 248, 6135-6144], that the Very Rapid signal is in prototropic equilibrium with the Rapid signal, and should be important in understanding the mechanism of action of the enzyme. They emphasize the unique nature of the intermediate represented by the Very Rapid e.p.r. signal. The possible value of the pK for loss of an exchangeable proton from the Rapid signal is discussed. PMID:33666

  11. Photocatalytic degradation of herbicide bentazone in aqueous suspension of TiO2: mineralization, identification of intermediates and reaction pathways.

    PubMed

    Mir, Niyaz A; Haque, M M; Khan, A; Muneer, M; Vijayalakshmi, S

    2014-01-01

    Semiconductor-mediated hydrogen peroxide-assisted photocatalytic degradation of a selected herbicide, Bentazone (1) has been investigated in aqueous suspensions of TiO2 under a variety of conditions. The degradation was studied by monitoring the depletion in total organic carbon content as a function of irradiation time. The degradation kinetics was investigated under different conditions such as type of TiO2 (Anatase/Anatase-Rutile mixture), reaction pH, catalyst dosage and hydrogen peroxide (H202) concentration. The degradation rates were found to be strongly influenced by all the above parameters. Titanium dioxide Degussa P25 was found to be more efficient as compared with other two commercially available TiO2 powders like Hombikat UV100 and PC500 from Millennium Inorganic Chemicals. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of the irradiated mixture of Bentazone (1) indicates the formation of several intermediate products which have been characterized on the basis of molecular ion/mass fragmentation pattern and also on comparison with the National Institute of Standards and Technology (NIST) library. Plausible mechanism for the formation of different products during photocatalytic treatment of Bentazone in the presence of TiO2 has been proposed. The use of H202 substantially increased the efficiency of TiO2 photocatalytic degradation. PMID:24600881

  12. 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.

  13. Identifying Nuclear Reaction Rates That Are Important For (44) TI Supernova Nucleosynthesis

    NASA Astrophysics Data System (ADS)

    The, L.-S.; Meyer, B. S.; Clayton, D. D.

    1997-05-01

    Large excesses of (44) Ca in certain presolar graphite and silicon carbide grains give strong evidence for (44) Ti production in supernovae. Furthermore, recent detection of the (44) Ti gamma -line from the Cas A SNR by CGRO/COMPTEL shows that radioactive (44) Ti is produced in supernovae. In this work we study the conditions needed for (44) Ti production in alpha-rich freezeouts in core-collapse supernovae as a function of peak temperature and density. We survey the key nuclear reactions governing (44) Ti production by varying their cross sections. We identify and rank their importance. We find (44) Ti production is most sensitive to variations in the rates of the reactions (44) Ti(alpha ,p)(47) V, alpha (2alpha ,gamma )(12) C, and (45) V(p,gamma )(46) Cr. Because many of these rates are unknown experimentally, our results suggest the most important targets for future cross section measurements.

  14. 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 leads to the dissociation of H2O2 from Cr(III), while in the H+-independent reaction, CraqOOH2+ is transformed to Cr(V). Both scavengers rapidly remove Cr(V) and simplify both the kinetics and products by impeding formation of Cr(IV, V, VI). Syntheses, Reactivity, and Thermodynamic Considerations LRhR2+. Macrocyclic rhodium(II) complexes LRh(H 2O)2+ (L = L1= cyclam and L2 = meso-Me6-cyclam) react with alkyl hydroperoxides R(CH3)2COOH to generate the corresponding rhodium(III) alkyls LRh(H2O)R2+ (R = CH3, C2 H5, PhCH2). Methyl and benzyl complexes can also be prepared by bimolecular group transfer from alkyl cobaloximes (dmgX) 2(H2O)CoR (where R = CH3, CH2Ph and dmgX is either dimethylglyoxime or a BF2-capped derivative of dmg) to LRh(H2O)2+. When R = C2H5, C3H7 or C4H9, the mechanism changes from group transfer to hydrogen atom abstraction from the coordinated alkyl and produces LRh(H2O)H2+ and an a-olefin. The new LRh(H2O)R2+ complexes were characterized by solution NMR and by crystal structure analysis. They exhibit great stability in aqueous solution at room temperature, but undergo efficient Rh-C bond cleavage upon photolysis. 'Green' Model for Decarboxylation of Biomass Derived Acids via Photolysis of in situ formed Metal-Carboxylate Complexes. Photolysis of aqueous solutions containing propionic acid and Fe 3+ aq in the absence of oxygen generates a mixture of hydrocarbons (ethane, ethylene and butane), carbon dioxide, and Fe2+. Photolysis in the presence of O2 yields catalytic amounts of hydrocarbon products. When halide ions are present during photolysis; nearly quantitative yields of ethyl halides are produced via extraction of a halide atom from FeX2+ by ethyl radical. The rate constants for ethyl radical reactions with FeCl2+ (k = 4.0 (+/- 0.5) x 106 M-1s-1) and with FeBr 2+ (k = 3.0 (+/- 0.5) x 107 M-1s -1) were determined via competition reactions. Irradiation of solutions containing aqueous Cu2+ salts and linear carboxylic acids yield alpha-olefins selectively. This process is made catalytic by the introduction of O2. Photochemical decarboxylation of propionic acid in the presence of Cu2+ generates ethylene and Cu +. Longer-chain acids also yield alpha olefins as exclusive products. In the absence of continued purging with O2 to aid removal of olefin, Cu+(olefin) complexes accumulate and catalytic activity slows dramatically due to depletion of Cu2+. The results underscore the profound effect that the choice of metal ions, the medium, and reaction conditions exert on the photochemistry of carboxylic acids. Free Oxygen Atom in Solution from 4-Benzoylpyridine N-Oxide Excited Singlet. Photolysis of 4-benzoylpyridine N-oxide (BPyO) in the presence of quenchers of the triplet excited state produces up to 41% O(3P) (as determined by generation of ethylene upon scavenging with cyclopentene). In the absence of 3BPyO* quenchers a maximum of 13% O(3P) relative to consumed BPyO is obtained. The remaining products are hydroxylated-4-benzoylpyridine and 4-benzoylpyridine. Additionally, the rate of BPyO consumption (as determined by UV-vis) decreases in the presence of 3BPyO* quenching agents. Second order rate constants for 3BPyO* quenching were determined. A mechanism for photochemical deoxygenation of BPyO is proposed on the basis of kinetic data and product distribution under various conditions. Additionally, comparisons are made between the observed intermediates and similar triplet excited states and radical anions.

  15. Using EMMA and MIX analysis to assess mixing ratios and to identify hydrochemical reactions in groundwater.

    PubMed

    Tubau, Isabel; Vzquez-Su, Enric; Jurado, Anna; Carrera, Jess

    2014-02-01

    This study presents a methodology using an end-member mixing analysis (EMMA) and MIX to compute mixing ratios and to identify hydrochemical reactions in groundwater. The methodology consists of (1) identifying the potential sources of recharge, (2) characterising recharge sources and mixed water samples using hydrogeochemistry, (3) selecting chemical species to be used in the analysis and (4) calculating mixing ratios and identification of hydrochemical reactions in groundwater. This approach has been applied in the Bess River Delta area, where we have collected 51 groundwater samples and a long data register of the hydrogeochemistry of the Bess River created by the Catalan Water Agency is also available. The EMMA performed in the Bess River suggests that 3 end-members are required to explain its temporal variability, accounting for the species chloride, sulphate, sodium, bicarbonate, calcium, magnesium, potassium, ammonium, total nitrogen, and electrical conductivity. One river end-member is from the wet periods (W1), and two are from dry periods (D1 and D2). These end-members have been used to compute mixing ratios in groundwater samples because the Bess River is considered the main recharge source for the aquifer. Overall, dry season end-members dominated over the wet season end-member, in a proportion of 4:1. Moreover, when departures from the mixing line exist, geochemical processes might be identified. Redox processes, carbonate dissolution/precipitation and ion exchange processes may occur in Bess Delta aquifer. PMID:24246935

  16. An Oxyferrous Heme/Protein-based Radical Intermediate Is Catalytically Competent in the Catalase Reaction of Mycobacterium tuberculosis Catalase-Peroxidase (KatG)*S?

    PubMed Central

    Suarez, Javier; Ranguelova, Kalina; Jarzecki, Andrzej A.; Manzerova, Julia; Krymov, Vladimir; Zhao, Xiangbo; Yu, Shengwei; Metlitsky, Leonid; Gerfen, Gary J.; Magliozzo, Richard S.

    2009-01-01

    A mechanism accounting for the robust catalase activity in catalase-peroxidases (KatG) presents a new challenge in heme protein enzymology. In Mycobacterium tuberculosis, KatG is the sole catalase and is also responsible for peroxidative activation of isoniazid, an anti-tuberculosis pro-drug. Here, optical stopped-flow spectrophotometry, rapid freeze-quench EPR spectroscopy both at the X-band and at the D-band, and mutagenesis are used to identify catalase reaction intermediates in M. tuberculosis KatG. In the presence of millimolar H2O2 at neutral pH, oxyferrous heme is formed within milliseconds from ferric (resting) KatG, whereas at pH 8.5, low spin ferric heme is formed. Using rapid freeze-quench EPR at X-band under both of these conditions, a narrow doublet radical signal with an 11 G principal hyperfine splitting was detected within the first milliseconds of turnover. The radical and the unique heme intermediates persist in wild-type KatG only during the time course of turnover of excess H2O2 (1000-fold or more). Mutation of Met255, Tyr229, or Trp107, which have covalently linked side chains in a unique distal side adduct (MYW) in wild-type KatG, abolishes this radical and the catalase activity. The D-band EPR spectrum of the radical exhibits a rhombic g tensor with dual gx values (2.00550 and 2.00606) and unique gy (2.00344) and gz values (2.00186) similar to but not typical of native tyrosyl radicals. Density functional theory calculations based on a model of an MYW adduct radical built from x-ray coordinates predict experimentally observed hyperfine interactions and a shift in g values away from the native tyrosyl radical. A catalytic role for an MYW adduct radical in the catalase mechanism of KatG is proposed. PMID:19139099

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

    PubMed Central

    Skerry, Amy E.; Spelke, Elizabeth S.

    2014-01-01

    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. PMID:24321623

  18. Study of intermediates from transition metal excited-state electron-transfer reactions. Progress report, August 1, 1989--December 31, 1991

    SciTech Connect

    Hoffman, M.Z.

    1991-12-31

    During this period, conventional and fast-kinetics techniques of photochemistry, photophysics, radiation chemistry, and electrochemistry were used for the characterization of the intermediates that are involved in transition metal excited-state electron-transfer reactions. The intermediates of interest were the excited states of Ru(II) and Cr(III) photosensitizers, their reduced forms, and the species formed in the reactions of redox quenchers and electron-transfer agents. Of particular concern has been the back electron-transfer reaction between the geminate pair formed in the redox quenching of the photosensitizers, and the dependence of its rate on solution medium and temperature in competition with transformation and cage escape processes.

  19. Imaging Consecutive Steps of O2 Reaction with Hydroxylated TiO2(110): Identification of HO2 and Terminal OH Intermediates

    SciTech Connect

    Du, Yingge; Deskins, N. Aaron; Zhang, Zhenrong; Dohnalek, Zdenek; Dupuis, Michel; Lyubinetsky, Igor

    2009-01-15

    The hydroperoxyl (HO2) species is believed to be a key intermediate in many heterogeneous photochemical processes, but generally metastable and thus hard to prove. We report here that for the first time, we directly imaged stable, adsorbed HO2 species during O2 reaction with a partially hydroxylated TiO2(110). We also found terminal hydroxyl groups, another critical but never directly observed intermediates. By imaging species and tracking site-specific reactions with high-resolution scanning tunneling microscopy, and determining the energies and configurations with density functional theory calculations, we provide molecular-level insight into the underlying reaction mechanisms. These results are expected to have far reaching implications for various catalytic systems involving the interconversion of O2 and H2O.

  20. Heme-bound nitroxyl, hydroxylamine, and ammonia ligands as intermediates in the reaction cycle of cytochrome c nitrite reductase: a theoretical study.

    PubMed

    Bykov, Dmytro; Plog, Matthias; Neese, Frank

    2014-01-01

    In this article, we consider, in detail, the second half-cycle of the six-electron nitrite reduction mechanism catalyzed by cytochrome c nitrite reductase. In total, three electrons and four protons must be provided to reach the final product, ammonia, starting from the HNO intermediate. According to our results, the first event in this half-cycle is the reduction of the HNO intermediate, which is accomplished by two PCET reactions. Two isomeric radical intermediates, HNOH() and H2NO(), are formed. Both intermediates are readily transformed into hydroxylamine, most likely through intramolecular proton transfer from either Arg114 or His277. An extra proton must enter the active site of the enzyme to initiate heterolytic cleavage of the N-O bond. As a result of N-O bond cleavage, the H2N(+) intermediate is formed. The latter readily picks up an electron, forming H2N(+), which in turn reacts with Tyr218. Interestingly, evidence for Tyr218 activity was provided by the mutational studies of Lukat (Biochemistry 47:2080, 2008), but this has never been observed in the initial stages of the overall reduction process. According to our results, an intramolecular reaction with Tyr218 in the final step of the nitrite reduction process leads directly to the final product, ammonia. Dissociation of the final product proceeds concomitantly with a change in spin state, which was also observed in the resonance Raman investigations of Martins et al. (J Phys Chem B 114:5563, 2010). PMID:24271207

  1. Identifiability of parameters and behaviour of MCMC chains: a case study using the reaction norm model.

    PubMed

    Shariati, M M; Korsgaard, I R; Sorensen, D

    2009-04-01

    Markov chain Monte Carlo (MCMC) enables fitting complex hierarchical models that may adequately reflect the process of data generation. Some of these models may contain more parameters than can be uniquely inferred from the distribution of the data, causing non-identifiability. The reaction norm model with unknown covariates (RNUC) is a model in which unknown environmental effects can be inferred jointly with the remaining parameters. The problem of identifiability of parameters at the level of the likelihood and the associated behaviour of MCMC chains were discussed using the RNUC as an example. It was shown theoretically that when environmental effects (covariates) are considered as random effects, estimable functions of the fixed effects, (co)variance components and genetic effects are identifiable as well as the environmental effects. When the environmental effects are treated as fixed and there are other fixed factors in the model, the contrasts involving environmental effects, the variance of environmental sensitivities (genetic slopes) and the residual variance are the only identifiable parameters. These different identifiability scenarios were generated by changing the formulation of the model and the structure of the data and the models were then implemented via MCMC. The output of MCMC sampling schemes was interpreted in the light of the theoretical findings. The erratic behaviour of the MCMC chains was shown to be associated with identifiability problems in the likelihood, despite propriety of posterior distributions, achieved by arbitrarily chosen uniform (bounded) priors. In some cases, very long chains were needed before the pattern of behaviour of the chain may signal the existence of problems. The paper serves as a warning concerning the implementation of complex models where identifiability problems can be difficult to detect a priori. We conclude that it would be good practice to experiment with a proposed model and to understand its features before embarking on a full MCMC implementation. PMID:19320765

  2. Challenges in enhancing student learning in intermediate mechanics: Identifying the need for a tutorial approach to instruction

    NASA Astrophysics Data System (ADS)

    Ambrose, Bradley

    2005-03-01

    One area of ongoing physics education research at Grand Valley State University is to probe the conceptual understanding and reasoning skills of advanced undergraduates as they make the transition from a traditional sequence in introductory calculus-based physics to their first course in upper-level mechanics. [1] The results thus far are consistent with findings from other investigations in upper division courses, which indicate that persistent difficulties with fundamental concepts can hinder meaningful learning of advanced topics. To address this problem, the tutorial approach developed at the University of Washington [2] is being adapted and incorporated into the intermediate mechanics course. Evidence from ungraded quizzes (pretests) and course exams will be presented to illustrate the presence of specific difficulties and the effectiveness of the modified instructional approach. [1] B.S. Ambrose, Am. J. Phys. 72 (4), 453 -- 459 (2004). [2] L.C. McDermott, P.S. Shaffer, and the Physics Education Group at the University of Washington, Tutorials in Introductory Physics (Prentice-Hall, Upper Saddle River, NJ, 2002).

  3. Reaction rate uncertainties and the operation of the NeNa and MgAl chains during HBB in intermediate-mass AGB stars

    NASA Astrophysics Data System (ADS)

    Izzard, Robert; Lugaro, Maria; Illadis, Christian; Karakas, Amanda

    We study the effect of uncertainties in the proton-capture reaction rates of the NeNa and MgAl chains on nucleosynthesis due to the operation of hot bottom burning (HBB) in intermediate-mass asymptotic giant branch (AGB) stars. HBB nucleosynthesis is associated with the production of sodium, radioactive 26 Al and the heavy magnesium isotopes, and it is possibly responsible for the O, Na, Mg and Al abundance anomalies observed in globular cluster stars. We model HBB with an analytic code based on full stellar evolution models so we can quickly cover a large parameter space. The reaction rates are varied first individually, then all together. This creates a knock-on effect, where an increase of one reaction rate affects production of an isotope further down the reaction chain. We find the yields of 22 Ne, 23 Na and 26 Al to be the most susceptible to current nuclear reaction rate uncertainties.

  4. Adsorption and oxidation of formaldehyde on a polycrystalline Pt film electrode: An in situ IR spectroscopy search for adsorbed reaction intermediates

    PubMed Central

    Behm, R Jürgen

    2014-01-01

    Summary As part of a mechanistic study of the electrooxidation of C1 molecules we have systematically investigated the dissociative adsorption/oxidation of formaldehyde on a polycrystalline Pt film electrode under experimental conditions optimizing the chance for detecting weakly adsorbed reaction intermediates. Employing in situ IR spectroscopy in an attenuated total reflection configuration (ATR-FTIRS) with p-polarized IR radiation to further improve the signal-to-noise ratio, and using low reaction temperatures (3 °C) and deuterium substitution to slow down the reaction kinetics and to stabilize weakly adsorbed reaction intermediates, we could detect an IR absorption band at 1660 cm−1 characteristic for adsorbed formyl intermediates. This assignment is supported by an isotope shift in wave number. Effects of temperature, potential and deuterium substitution on the formation and disappearance of different adsorbed species (COad, adsorbed formate, adsorbed formyl), are monitored and quantified. Consequences on the mechanism for dissociative adsorption and oxidation of formaldehyde are discussed. PMID:24991512

  5. SABER: a computational method for identifying active sites for new reactions.

    PubMed

    Nosrati, Geoffrey R; Houk, K N

    2012-05-01

    A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. PMID:22492397

  6. Fuel-Specific Influences on the Composition of Reaction Intermediates in Premixed Flames of Three C5H10O2 Ester Isomers

    SciTech Connect

    Yang, B.; Cool, T. A.; Westbrook, Charles K.; Hansen, N.; Kohse-Hoinghaus, K.

    2011-01-01

    Measurements of the composition of reaction intermediates in low-pressure premixed flat flames of three simple esters, the methyl butanoate (MB), methyl isobutanoate (MIB), and ethyl propanoate (EP) isomers of C{sub 5}H{sub 10}O{sub 2}, enable further refinement and validation of a detailed chemical reaction mechanism originally developed in modeling studies of similar flames of methyl formate, methyl acetate, ethyl formate, and ethyl acetate. Photoionization mass spectrometry (PIMS), using monochromated synchrotron radiation, reveals significant differences in the compositions of key reaction intermediates between flames of the MB, MIB, and EP isomers studied under identical flame conditions. Detailed kinetic modeling describes how these differences are related to molecular structures of each of these isomers, leading to unique fuel destruction pathways. Despite the simple structures of these small esters, they contain structural functional groups expected to account for fuel-specific effects observed in the combustion of practical biodiesel fuels. The good agreement between experimental measurements and detailed reaction mechanisms applicable to these simple esters demonstrates that major features of each flame can be predicted with reasonable accuracy by building a hierarchical reaction mechanism based on three factors: (1) unimolecular decomposition of the fuel, especially by complex bond fission; (2) H-atom abstraction reactions followed by ?-scission of the resulting radicals, leading to nearly all of the intermediate species observed in each flame; (3) the rates of H-atom abstraction reactions for each alkoxy or alkyl group (i.e., methoxy, ethoxy, methyl, ethyl, propyl) are effectively the same as in other ester fuels with the same structural groups.

  7. A Dianionic Phosphorane Intermediate and Transition States in an Associative AN+DN Mechanism for the RibonucleaseA Hydrolysis Reaction

    SciTech Connect

    Elsasser, Brigitta M.; Valiev, Marat; Weare, John H.

    2009-02-26

    The ubiquitous presence of phosphoryl transfer as central step in many metabolic, signaling, energy storage, etc. enzymatic reactions requires that the details of the reaction mechanisms (e.g. reaction paths, transition state stabilization and structure, etc.) that leads to their remarkable rates in protein catalytic environments be understood1. It is expected that most of these reactions proceed through a pathway that includes a penta- coordinated phosphorane species. However, the nature of the bonding and the protonation of the structure in this region and the possibility of stable intermediates as the system passes along the reaction path through the transitions state (TS) are currently topics of considerable debate1a,b,c. Typically nucleophilic substitution reactions are classified in terms of extremes of two bonding situations along the reaction path: in a dissociative mechanism the substrate phosphate bridging bond is broken and the bond to the entering nucleophilic group is not yet formed leaving a metastable metaphosphate (PO3-) intermediate (a DN+AN reaction); in an associative mechanism in the extreme case a metastable pentacoordinated phosphorane species with nearly equivalent bonds is present in the TS, whose subsequent dissociation leads to the product state (an AN+DN reaction). Recently we published a computational study of the phosphoryl transfer step of a major class of enzymes, the serine kinases2a,b involved in signal transduction. These calculations2b support a dissociative mechanism (DNAN,) for this family of enzymes with unstable metaphosphate structure in loose transition state with total bond order of 22%.

  8. Studies on the mechanism of the peroxyoxalate chemiluminescence reaction: part 2. Further identification of intermediates using 2D EXSY 13C nuclear magnetic resonance spectroscopy.

    PubMed

    Tonkin, Sarah A; Bos, Richard; Dyson, Gail A; Lim, Kieran F; Russell, Richard A; Watson, Simon P; Hindson, Christopher M; Barnett, Neil W

    2008-05-01

    Further consideration has been given to the reaction pathway of a model peroxyoxalate chemiluminescence system. Again utilising doubly labelled oxalyl chloride and anhydrous hydrogen peroxide, 2D EXSY (13)C nuclear magnetic resonance (NMR) spectroscopy experiments allowed for the characterisation of unknown products and key intermediate species on the dark side of the peroxyoxalate chemiluminescence reaction. Exchange spectroscopy afforded elucidation of a scheme comprised of two distinct mechanistic pathways, one of which contributes to chemiluminescence. (13)C NMR experiments carried out at varied reagent molar ratios demonstrated that excess amounts of hydrogen peroxide favoured formation of 1,2-dioxetanedione: the intermediate that, upon thermolysis, has been long thought to interact with a fluorophore to produce light. PMID:18420048

  9. Facile detection of acyl and peptidyl intermediates on thiotemplate carrier domains via phosphopantetheinyl elimination reactions during tandem mass spectrometry.

    PubMed

    Dorrestein, Pieter C; Bumpus, Stefanie B; Calderone, Christopher T; Garneau-Tsodikova, Sylvie; Aron, Zachary D; Straight, Paul D; Kolter, Roberto; Walsh, Christopher T; Kelleher, Neil L

    2006-10-24

    With the emergence of drug resistance and the genomic revolution, there has been a renewed interest in the genes that are responsible for the generation of bioactive natural products. Secondary metabolites of one major class are biosynthesized at one or more sites by ultralarge enzymes that carry covalent intermediates on phosphopantetheine arms. Because such intermediates are difficult to characterize in vitro, we have developed a new approach for streamlined detection of substrates, intermediates, and products attached to a phosphopantetheinyl arm of the carrier site. During vibrational activation of gas-phase carrier domains, facile elimination occurs in benchtop and Fourier-transform mass spectrometers alike. Phosphopantetheinyl ejections quickly reduce >100 kDa megaenzymes to <1000 Da ions for structural assignment of intermediates at <0.007 Da mass accuracy without proteolytic digestion. This "top down" approach quickly illuminated diverse acyl intermediates on the carrier domains of the nonribosomal peptide synthetases (NRPSs) or polyketide synthases (PKSs) found in the biosynthetic pathways of prodigiosin, pyoluteorin, mycosubtilin, nikkomycin, enterobactin, gramicidin, and several proteins from the orphan pksX gene cluster from Bacillus subtilis. By focusing on just those regions undergoing covalent chemistry, the method delivered clean proof for the reversible dehydration of hydroxymethylglutaryl-S-PksL via incorporation of 2H or 18O from the buffer. The facile nature of this revised assay will allow diverse laboratories to spearhead their NRPS-PKS projects with benchtop mass spectrometers. PMID:17042494

  10. Bromide ion promoted. beta. -elimination in. cap alpha. -bromo ester substrates. Evidence for an intermediate in the E2C reaction

    SciTech Connect

    Kwart, H.; Gaffney, A.

    1983-12-02

    The TDKIE (temperature dependence of the kinetic isotope effect) criteria of transition state geometry in H-transfer reactions have been applied in the title reactions; a bent transition state consistent with the geometry of the E2C reaction has been verified by the results of intramolecular and intermolecular competition modes of determining k/sub H/k/sub D/ as a function of temperature. The extraordinary magnitude measured for the ..cap alpha.. secondary deuterium isotope effect in the E2C mechanism is reconciled with a very loose transition state and an acute angle of H-abstraction in the course of rearward approach to C/sub ..cap alpha../ by the promoter base. The virtual identity of the inter- and intramolecular isotope effects can be correlated by the assumption of a reaction intermediate of trigonal-bipyramid structure surrounding C/sub ..cap alpha../ and in which the extractable H and D atoms are equally available to the action of the promoter base. The properties of this intermediate, by way of contrast with the transition state of an S/sub N/2 process, are discussed in detail. 7 tables, 2 figures.

  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. Protein vivisection reveals elusive intermediates in folding.

    PubMed

    Zheng, Zhongzhou; Sosnick, Tobin R

    2010-04-01

    Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here, we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu-->Glu(-)) to destabilize and unfold a specific region of the protein. We applied this strategy to ubiquitin, reversibly trapping a folding intermediate in which the beta5-strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high-energy states. PMID:20144618

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

    PubMed

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

    2014-12-01

    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

  14. 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

  15. Identifying cluster subtypes for intentions to have colorectal cancer screening among non-compliant intermediate-risk siblings of individuals with colorectal cancer

    PubMed Central

    Manne, Sharon L.; Coups, Elliot J.; Winkel, Gary; Markowitz, Arnold; Meropol, Neal J.; Lesko, Samuel M.; Jacobsen, Paul B.; Haller, Daniel; Jandorf, Lina; Peterson, Susan K.

    2009-01-01

    Although first-degree relatives of colorectal cancer (CRC) patients diagnosed at an early age are at increased risk for CRC, their compliance with colorectal cancer screening (CRCS) is not high. Relatively little is known about why these intermediate-risk family members do not comply with CRCS. Study aims were to identify subgroups of siblings of individuals diagnosed with CRC prior to age 61 who were not compliant with CRCS using cluster analysis and to identify demographical, medical and attitudinal correlates of cluster membership. A total of 421 siblings completed measures of pros, cons, processes of change, CRCS knowledge, physician and family CRCS support, CRC risk, severity, preventability, curability, closeness with the affected sibling, distress about the sibling's cancer and screening intentions. Three clusters characterized as ‘Positive about Screening’, ‘Uncertain about Screening’ and ‘Negative about Screening’ were identified. External validation revealed that those in the Positive about Screening cluster reported significantly stronger CRCS intentions than those who are Uncertain about Screening and Negative about Screening clusters. Results provide an empirical typology for understanding motivations for CRCS among at-risk family members and may lead to the development of more effective interventions to improve screening uptake. PMID:19654222

  16. Synthesis and electronic structure of bis(imino)pyridine iron metallacyclic intermediates in iron-catalyzed cyclization reactions.

    PubMed

    Hoyt, Jordan M; Sylvester, Kevin T; Semproni, Scott P; Chirik, Paul J

    2013-03-27

    The bis(imino)pyridine iron dinitrogen compound, ((iPr(TB))PDI)Fe(N2)2 ((iPr(TB))PDI = 2,6-(2,6-(i)Pr2-C6H3-N═C-(CH2)3)2(C5H1N)) is an effective precatalyst for the [2π + 2π] cycloaddition of diallyl amines as well as the hydrogenative cyclization of N-tosylated enynes and diynes. Addition of stoichiometric quantities of amino-substituted enyne and diyne substrates to ((iPr(TB))PDI)Fe(N2)2 resulted in isolation of catalytically competent bis(imino)pyridine iron metallacycle intermediates. A combination of magnetochemistry, X-ray diffraction, and Mössbauer spectroscopic and computational studies established S = 1 iron compounds that are best described as intermediate-spin iron(III) (SFe = 3/2) antiferromagnetically coupled to a chelate radical anion (SPDI = 1/2). Catalytically competent bis(imino)pyridine iron diene and metallacycles relevant to the [2π + 2π] cycloaddition were also isolated and structurally characterized. The combined magnetic, structural, spectroscopic, and computational data support an Fe(I)-Fe(III) catalytic cycle where the bis(imino)pyridine chelate remains in its one-electron reduced radical anion form. These studies revise a previous mechanistic proposal involving exclusively ferrous intermediates and highlight the importance of the redox-active bis(imino)pyridine chelate for enabling catalytic cyclization chemistry with iron. PMID:23448301

  17. 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. PMID:11674363

  18. Master equation analysis of thermal activation reactions: Energy-transfer constraints on falloff behavior in the decomposition of reactive intermediates with low thresholds

    SciTech Connect

    Tsang, W.; Bedanov, V.; Zachariah, M.R.

    1996-03-07

    This paper deals with the high-temperature decomposition of reactive intermediates with low reaction thresholds. If these intermediates are created in situ, for example, through radical chain processes, their initial molecular distribution functions may be characteristic of the bath temperature and, under certain circumstances, peak at energies above the reaction threshold. Such an ordering of reaction thresholds and distribution functions has some similarities to that found during chemical activation. This leads to consequences that are essentially the inverse (larger rate constants than those deduced from steady-state distributions) of the situation for stable compounds under shock-heated conditions and hence reduces falloff effects. To study this behavior, rate constants for the unimolecular decomposition of ally, ethyl, n-propyl, and n-hexyl radicals have been determined on the basis of the solution of the time-dependent master equation with specific rate constants from RRKM calculations. The time required for the molecules to attain steady-state distribution functions has been determined as a function of the energy-transfer parameter (the step size down) molecular size (heat capacity), high-pressure rate parameters, temperature, and pressure. At 101 kPa (1atm) pressure, unimolecular rate constants near 10{sup 7} s{sup -1} represent a lower boundary, above which steady-state assumptions become increasingly questionable. 21 refs., 7 figs., 1 tab.

  19. [The development of polymer immunoglobulin preparations to identify different serovars legionella pneumophilia in reaction of slide-agglutination].

    PubMed

    Karbyshev, G L; Narkevich, A N; Kochetkova, A P; Larionova, L V; Simakova, D I; Liukshina, E Iu; Lysova, L K; Terent'ev, A N; Shelokhovich, A I; Sokirkina, O G

    2013-03-01

    The article deals with the results of study targeted to develop polymer diagnostic preparation to identify epidemically significant serogroups Legionella pneumophilia. The preparation combines rate of record (1-5 min) of reaction of paragglutinining preparations with color visualization and demonstrative of reaction of volume agglomeration with polymer diagnosticums. The specially synthesized polymer microspheres were sensibilized with serums enriched with antibodies to lipopolysaccharide of corresponding serovar L. pneumophilia. The derived immunoglobulin diagnostic preparations detect agent of legionellesis in the reaction of slide-agglutination on glass during 1-5 min. The polymer diagnostic preparations provide positive reaction with culture of corresponding serovar and no reaction with other gomologic and geterologic agents of infectious diseases. PMID:23808028

  20. 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

  1. Influence of multiple sources on the two-neutron correlation function in Ni-induced, intermediate energy, heavy ion reactions

    NASA Astrophysics Data System (ADS)

    Ghetti, R.; Helgesson, J.; Colonna, N.; Jakobsson, B.; Anzalone, A.; Bellini, V.; Carln, L.; Cavallaro, S.; Celano, L.; de Filippo, E.; D'erasmo, G.; di Santo, D.; Fiore, E. M.; Fokin, A.; Geraci, M.; Giustolisi, F.; Kuznetsov, A.; Lanzan, G.; Mahboub, D.; Marrone, S.; Merchez, F.; Mrtensson, J.; Palazzolo, F.; Palomba, M.; Pantaleo, A.; Paticchio, V.; Riera, G.; Sperduto, M. L.; Sutera, C.; Tagliente, G.; Urrata, M.; Westerberg, L.

    2001-07-01

    The strength of the neutron-neutron correlation function from the E=45A MeV 58Ni+27Al, natNi, and 197Au reactions depends on the neutron parallel velocity. This indicates the presence of multiple sources of neutron emission. We find these sources consistent with a dissipative, binary reaction mechanism as it is described by, e.g., Boltzmann-Uehling-Uhlenbeck calculations.

  2. Reaction intermediate analogues for mandelate racemase: interaction between Asn 197 and the alpha-hydroxyl of the substrate promotes catalysis.

    PubMed

    St Maurice, M; Bearne, S L

    2000-11-01

    Mandelate racemase (MR) catalyzes the interconversion of the enantiomers of mandelic acid, stabilizing the altered substrate in the transition state by 26 kcal/mol relative to the substrate in the ground state. To understand the origins of this binding discrimination, carboxylate-, phosphonate-, and hydroxamate-containing substrate and intermediate analogues were examined for their ability to inhibit MR. Comparison of the competitive inhibition constants revealed that an alpha-hydroxyl function is required for recognition of the ligand as an intermediate analogue. Two intermediate analogues, alpha-hydroxybenzylphosphonate (alpha-HBP) and benzohydroxamate, were bound with affinities approximately 100-fold greater than that observed for the substrate. Furthermore, MR bound alpha-HBP enantioselectively, displaying a 35-fold higher affinity for the (S)-enantiomer relative to the (R)-enantiomer. In the X-ray structure of mandelate racemase [Landro, J. A., Gerlt, J. A., Kozarich, J. W., Koo, C. W., Shah, V. J., Kenyon, G. L., Neidhart, D. J., Fujita, J., and Petsko, G. A. (1994) Biochemistry 33, 635-643], the alpha-hydroxyl function of the competitive inhibitor (S)-atrolactate is within hydrogen bonding distance of Asn 197. To demonstrate the importance of the alpha-hydroxyl function in intermediate binding, the N197A mutant was constructed. The values of k(cat) for N197A were reduced 30-fold for (R)-mandelate and 179-fold for (S)-mandelate relative to wild-type MR; the values of k(cat)/K(m) were reduced 208-fold for (R)-mandelate and 556-fold for (S)-mandelate. N197A shows only a 3.5-fold reduction in its affinity for the substrate analogue (R)-atrolactate but a 51- and 18-fold reduction in affinity for alpha-HBP and benzohydroxamate, respectively. Thus, interaction between Asn 197 and the substrate's alpha-hydroxyl function provides approximately 3.5 kcal/mol of transition-state stabilization free energy to differentially stabilize the transition state relative to the ground state. PMID:11063568

  3. The Wittig Reaction: Generation, Observation and Reactivity of a Phosphorous Ylide Intermediate. An Experiment for the Advanced Organic Chemistry Laboratory Course

    NASA Astrophysics Data System (ADS)

    Breton, Gary W.

    1997-01-01

    An experiment has been devised that illustrates three important concepts in organic chemistry: the synthesis of an alkene via the Wittig reaction, characterization of a reactive intermediate by 1H NMR, and site - specific deuterium labelling. Deprotonation of ethyltriphenylphosphonium iodide (1) by methylsulfinyl carbanion (generated in situ by the reaction of NaH with DMSO-d6) results in the formation of the ylide, CH3CH-PPH3(2 -H). An ensuing, rapid deuterium exchange process between the deuterated solvent, and 2-H at the C-1 position affords CH3CD - PPH3 (2-D). The 1H NMR spectrum of 2-D was obtained, and the ylide was quenched with benzophenone to obtain 2-deutero-diphenylpropene (3) in 42% yield.

  4. 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.

  5. 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. PMID:20695491

  6. 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. PMID:26178082

  7. 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.

  8. Molecular structure determination for photogenerated intermediates in photoinduced electron transfer reactions using steady-state and transient XAFS

    SciTech Connect

    Chen, L.X.; Wasielewski, M.R.; Rajh, T.

    1996-10-01

    Many photoinduced electron transfer reactions are accompanied by nuclear rearrangements of the molecules involved. In order to understand the reactivities of the molecules and the reaction mechanisms, precise information on the molecular structural changes accompanying the electron transfer is often required. We present here conventional XAFS and transient energy dispersive XAFS studies on structures of excited and photoinduced charge separated state of porphyrin and porphyrin based supermolecules, and structures of TiO{sub 2} colloid and the heavymetal ions that bind to the colloid surfaces during photocatalytic reductions.

  9. 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. PMID:26074480

  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. Biotechnol. Bioeng. 2016;113: 661-674. 2015 Wiley Periodicals, Inc. PMID:26375179

  11. Kinetics and Mechanism of the Chlorite-Periodate System: Formation of a Short-Lived Key Intermediate OClOIO3 and Its Subsequent Reactions.

    PubMed

    Baranyi, Nóra; Csekő, György; Valkai, László; Xu, Li; Horváth, Attila K

    2016-03-01

    The chlorite-periodate reaction has been studied spectrophotometrically in acidic medium at 25.0 ± 0.1 °C, monitoring the absorbance at 400 nm in acetate/acetic acid buffer at constant ionic strength (I = 0.5 M). We have shown that periodate was exclusively reduced to iodate, but chlorite ion was oxidized to chlorate and chlorine dioxide via branching pathways. The stoichiometry of the reaction can be described as a linear combination of two limiting stoichiometries under our experimental conditions. Detailed initial rate studies have clearly revealed that the formal kinetic orders of hydrogen ion, chlorite ion, and periodate ion are all strictly one, establishing an empirical rate law to be d[ClO2]/dt = kobs[ClO2(-)][IO4(-)][H(+)], where the apparent rate coefficient (kobs) was found to be 70 ± 13 M(-2) s(-1). On the basis of the experiments, a simple four-step kinetic model with three fitted kinetic parameters is proposed by nonlinear parameter estimation. The reaction was found to proceed via a parallel oxygen transfer reaction leading to the exclusive formation of chlorate and iodate as well as via the formation of a short-lived key intermediate OClOIO3 followed by its further transformations by a sequence of branching pathways. PMID:26849795

  12. 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

  13. 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. PMID:25330363

  14. 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. PMID:24400595

  15. Infrared Spectroscopy of OHCH3OH: Hydrogen-Bonded Intermediate Along the Hydrogen Abstraction Reaction Path.

    PubMed

    Hernandez, Federico J; Brice, Joseph T; Leavitt, Christopher M; Pino, Gustavo A; Douberly, Gary E

    2015-07-23

    Substantial non-Arrhenius behavior has been previously observed in the low temperature reaction between the hydroxyl radical and methanol. This behavior can be rationalized assuming the stabilization of an association adduct in the entrance channel of the reaction, from which barrier penetration via quantum mechanical tunneling produces the CH3O radical and H2O. Helium nanodroplet isolation and a serial pick-up technique are used to stabilize the hydrogen bonded prereactive OHCH3OH complex. Mass spectrometry and infrared spectroscopy are used to confirm its production and probe the OH stretch vibrations. Stark spectroscopy reveals the magnitude of the permanent electric dipole moment, which is compared to ab initio calculations that account for wide-amplitude motion in the complex. The vibrationally averaged structure has Cs symmetry with the OH moiety hydrogen bonded to the hydroxyl group of methanol. Nevertheless, the zero-point level of the complex exhibits a wave function significantly delocalized over a bending coordinate leading to the transition state of the CH3O producing reaction. PMID:26135615

  16. The reaction systems CH{sub 3} + OH at intermediate temperatures. Appearance of a new product channel

    SciTech Connect

    Humpfer, R.; Oser, H.; Grotheer, H.H.; Just, T.

    1994-12-31

    In an extension of work at lower temperatures, the title reaction was measured directly in a flow reactor at temperatures up to 700 K and at pressures of 0.65 and 3.25 mbar. OH was used in an excess over CH{sub 3}. Both reactants along with the reaction products were monitored by mass spectrometry. CH{sub 3} profiles served as the major observable quantity for the extraction of rate data by using computer simulation. The fitted total rate coefficients were divided into individual channel rate coefficients by the mass spectrometric measurement of the reaction products. For CH{sub 3} + OH, this led to a rate coefficient, k{sub 1a}, into the stabilization channel, and another one, k{sub le + f}, referring to the sum of two H{sub 2}-eliminating channels yielding the biradical HCOH, and CH{sub 2}O. These latter channels have not been measured before. In order to distinguish between them, the authors switched from OH to OD so that these channels could be determined by their byproducts, H{sub 2} and HD, respectively. A comparison of the rate coefficients for both systems, i.e., CH{sub 3} + OH and CH{sub 3} + OD, indicates that, within error limits, no significant isotope effect takes place. By including previous measurements along with additional ones at 600 K, to be published elsewhere, the authors arrive at the channel rate coefficients.

  17. Determination of elementary rate constants by fitting detailed reaction mechanisms: Application to intermediate-temperature hydrocarbon kinetics

    NASA Astrophysics Data System (ADS)

    Scire, James J., Jr.

    Experimental elementary rate constant determinations are vital for the construction of reaction mechanisms and the verification of theoretical rate predictions. It is often difficult to obtain direct rate measurements, however, and the best determinations often come from fitting a detailed reaction mechanism to experimental data. In this work, techniques for assessing the mechanistic dependence of rate constants determined in this manner were developed. The techniques were used to design and evaluate flow reactor experiments for the determination of rate constants important in hydrocarbon combustion. First, local, first-order sensitivity coefficients were developed for rate constants determined by a least-squares fit to flow reactor data. These coefficients give the sensitivity of the determined rate constants to the remaining model parameters and experimental data. With uncertainty estimates for the model rate constants and experimental data the uncertainty in the proposed rate constant determinations could be estimated. Such estimates were used for experimental design, where these uncertainties were minimized through adjustment of the experimental conditions in a series of simulated flow reactor experiments. The local, first-order technique could also be used for error estimates once the experiments were completed. However, given the large parameter uncertainties and strong couplings typical of kinetic mechanisms, a globally valid technique was desirable. An importance-sampled Monte Carlo technique was developed to determine global probability distributions and regressions for the fit results. Flow reactor experiments were designed to determine rate constants for the reactions of methyl radicals with HO2 and O2 and of formaldehyde with HO2. These experiments were performed in a variable pressure flow reactor and new rate constant values were determined. The local technique was used to examine the mechanistic dependence of the results. Rigorous error bounds were developed and the limitations of the local technique were examined using the Monte Carlo technique. The new determinations gave a considerable reduction in uncertainty over the previous literature values. In addition, a system for in situ far-UV absorption spectrometry was developed to measure additional species and aid in rate measurements. This system was used in initial work toward rate constant determinations for the reaction of vinyl radicals with O2.

  18. 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.

  19. Reaction rate uncertainties and the operation of the NeNa and MgAl chains during HBB in intermediate-mass AGB stars

    NASA Astrophysics Data System (ADS)

    Izzard, R. G.; Lugaro, M.; Karakas, A. I.; Iliadis, C.; van Raai, M.

    2007-05-01

    Context: We test the effect of proton-capture reaction rate uncertainties on the abundances of the Ne, Na, Mg and Al isotopes processed by the NeNa and MgAl chains during hot bottom burning (HBB) in asymptotic giant branch (AGB) stars of intermediate mass between 4 and 6 M? and metallicities between Z = 0.0001 and 0.02. Aims: We provide uncertainty ranges for the AGB stellar yields, for inclusion in galactic chemical evolution models, and indicate which reaction rates are most important and should be better determined. Methods: We use a fast synthetic algorithm based on detailed AGB models. We run a large number of stellar models, varying one reaction per time for a very fine grid of values, as well as all reactions simultaneously. Results: We show that there are uncertainties in the yields of all the Ne, Na, Mg and Al isotopes due to uncertain proton-capture reaction rates. The most uncertain yields are those of 26Al and 23Na (variations of two orders of magnitude), 24Mg and 27Al (variations of more than one order of magnitude), 20Ne and 22Ne (variations between factors 2 and 7). In order to obtain more reliable Ne, Na, Mg and Al yields from IM-AGB stars the rates that require more accurate determination are: 22Ne(p,?)23Na, 23Na(p,?)24Mg, 25Mg(p,?)26Al, 26Mg(p,?)27Al and 26Al(p,?)27Si. Conclusions: Detailed galactic chemical evolution models should be constructed to address the impact of our uncertainty ranges on the observational constraints related to HBB nucleosynthesis, such as globular cluster chemical anomalies. Table 13 is only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/466/641

  20. 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

    2016-01-01

    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. PMID:26754774

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

    PubMed Central

    Xu, X.; Sumption, M. D.

    2016-01-01

    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. PMID:26754774

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

    NASA Astrophysics Data System (ADS)

    Xu, X.; Sumption, M. D.

    2016-01-01

    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.

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

    PubMed

    Bencivenni, Giorgio; Cesari, Riccardo; Nanni, Daniele; El Mkami, Hassane; Walton, John C

    2010-01-01

    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

  4. 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

  5. Elucidation of the order of oxidations and identification of an intermediate in the multistep clavaminate synthase reaction

    SciTech Connect

    Salowe, S.P.; Krol, W.J.; Iwata-Reuyl, D.; Townsend, C.A. )

    1991-02-26

    The enzyme clavaminate synthase (CS) catalyzes the formation of the first bicyclic intermediate in the biosynthetic pathway to the potent {beta}-lactamase inhibitor clavulanic acid. Previous work has led to the proposal that the cyclization/desaturation of the substrate proclavaminate proceeds in two oxidative steps, each coupled to a decarboxylation of {alpha}-ketoglutarate and a reduction of dioxygen to water. The authors have now employed kinetic isotope effect studies to determine the order of oxidations for CS purified from Streptomyces clavuligerus. Using (4{prime}RS)-(4{prime}-{sup 3}H,1-{sup 14}C)-rac-proclavaminate, a primary {sup T}(V/K) = 8.3 {plus minus} 0.2 was measured from ({sup 3}H)water release data, while an {alpha}-secondary {sup T}(V/K) = 1.06 {plus minus} 0.01 was determined from the changing {sup 3}H/{sup 14}C ratio of the product clavaminate. Values for the primary and {alpha}-secondary effects of 11.9 {plus minus} 1.7 and 1.12 {plus minus} 0.07, respectively, were obtained from the changing {sup 3}H/{sup 14}C ratio of the residual proclavaminate by using new equations derived for a racemic substrate bearing isotopic label at both primary and {alpha}-secondary positions. On the basis of the body of information available and the similarities to {alpha}-ketoglutarate-dependent dioxygenases, a comprehensive mechanistic scheme for CS is proposed to account for this unusual enzymatic transformation.

  6. Calculated and measured battery voltages - thermodynamics aids in identifying electrochemical reactions. Final report, March-June 1984

    SciTech Connect

    DeVries, L.E.

    1985-02-01

    Both the open- and closed-circuit voltages of a battery depend on the thermodynamic conditions inside the cell. When the actual electrochemical reaction of a particular battery is unknown, thermodynamic calculations can help to identify it. Using thermodynamics data, the open-circuit voltages for alternatively electrochemical reactions can be calculated. When accurate data are available, the calculated voltage for the correct electrochemical reaction will agree to within millivolts with the measured value. For the Cl/sub 2/-Li molten salt system, the calculated and measured values are both 3.612V. For alkaline zinc batteries, the data indicate that Zn0 is the discharge product at the anode under ambient conditions. For the acid Mn02-Zn system, under the thermodynamic conditions, a two-electron reduction of MnO/sub 2/ occurs. Initially, in the alkaline MnO/sub 2/-Zn system. Mn(OH)/sub 4/ is the discharge product at the cathode.

  7. Inhibition of the SHV-1 beta-lactamase by sulfones: crystallographic observation of two reaction intermediates with tazobactam.

    PubMed

    Kuzin, A P; Nukaga, M; Nukaga, Y; Hujer, A; Bonomo, R A; Knox, J R

    2001-02-13

    Two species resulting from the reaction of the SHV-1 class A beta-lactamase with the sulfone inhibitor tazobactam have been trapped at 100 K and mapped by X-ray crystallography at 2.0 A resolution. An acyclic form of tazobactam is covalently bonded to the catalytic Ser70 side chain, and a second species, a five-atom vinyl carboxylic acid fragment of tazobactam, is bonded to Ser130. It is proposed that the electron density map of the crystal is a composite picture of two complexes, each with only a single bound species. It is estimated that the two complexes exist in the crystal in approximately equal populations. Results are discussed in relation to the mechanism-based inhibition of class A beta-lactamases by the similar inhibitors sulbactam and clavulanic acid. PMID:11327849

  8. 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

  9. 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…

  10. Fast determination of multiple-reaction intermediates for long-chain dicarboxylic Acid biotransformation by gas chromatography-flame ionization detector.

    PubMed

    Cho, Yong-Han; Lee, Hye-Jin; Lee, Jung-Eun; Kim, Soo-Jung; Park, Kyungmoon; Lee, Do Yup; Park, Yong-Cheol

    2015-05-01

    For the analysis of multiple-reaction intermediates for long-chain dicarboxylic acid biotransformation, simple and reproducible methods of extraction and derivatization were developed on the basis of gas chromatography with flame ionization detector (GC-FID) instead of mass spectrometry. In the derivatization step, change of the ratio of pyridine to MSTFA from 1:3 to 9:1 resulted in higher peak intensity (p = 0.021) and reproducibility (0.6%CV) when analyzing 32 g/l ricinoleic acid (RA). Extraction of RA and ?-hydroxyundec- 9-enoic acid with water containing 100 mM Tween 80 showed 90.4-99.9% relative extraction efficiency and 2-7%CV compared with those with hydrophobic ethyl acetate. In conclusion, reduction of the pyridine content and change of the extraction solvent to water with Tween 80 provided compatible derivatization and extraction methods to GC-FID-based analysis of longchain carboxylic acids. PMID:25737121

  11. Identifying genetic risk factors for serious adverse drug reactions: current progress and challenges

    PubMed Central

    Wilke, Russell A.; Lin, Debbie W.; Roden, Dan M.; Watkins, Paul B.; Flockhart, David; Zineh, Issam; Giacomini, Kathleen M.; Krauss, Ronald M.

    2009-01-01

    Serious adverse drug reactions (SADRs) are a major cause of morbidity and mortality worldwide. Some SADRs may be predictable, based upon a drug's pharmacodynamic and pharmacokinetic properties. Many, however, appear to be idiosyncratic. Genetic factors may underlie susceptibility to SADRs and the identification of predisposing genotypes may improve patient management through the prospective selection of appropriate candidates. Here we discuss three specific SADRs with an emphasis on genetic risk factors. These SADRs, selected based on wide-sweeping clinical interest, are drug-induced liver injury, statin-induced myotoxicity and drug-induced long QT and torsades de pointes. Key challenges for the discovery of predictive risk alleles for these SADRs are also considered. PMID:17971785

  12. Caught in the Act: The 1.5 Å Resolution Crystal Structures of the HIV-1 Protease and the I54V Mutant Reveal a Tetrahedral Reaction Intermediate

    SciTech Connect

    Kovalevsky, Andrey Y.; Chumanevich, Alexander A.; Liu, Fengling; Louis, John M.; Weber, Irene T.

    2008-03-21

    HIV-1 protease (PR) is the target for several important antiviral drugs used in AIDS therapy. The drugs bind inside the active site cavity of PR where normally the viral polyprotein substrate is bound and hydrolyzed. We report two high-resolution crystal structures of wild-type PR (PR{sub WT}) and the multi-drug-resistant variant with the I54V mutation (PR{sub I54V}) in complex with a peptide at 1.46 and 1.50 {angstrom} resolution, respectively. The peptide forms a gem-diol tetrahedral reaction intermediate (TI) in the crystal structures. Distinctive interactions are observed for the TI binding in the active site cavity of PR{sub WT} and PR{sub I54V}. The mutant PR{sub I54V}/TI complex has lost water-mediated hydrogen bond interactions with the amides of Ile50 and Ile50{prime} in the flap. Hence, the structures provide insight into the mechanism of drug resistance arising from this mutation. The structures also illustrate an intermediate state in the hydrolysis reaction. One of the gem-diol hydroxide groups in the PR{sub WT} complex forms a very short (2.3 {angstrom}) hydrogen bond with the outer carboxylate oxygen of Asp25. Quantum chemical calculations based on this TI structure are consistent with protonation of the inner carboxylate oxygen of Asp25{prime}, in contrast to several theoretical studies. These TI complexes and quantum calculations are discussed in relation to the chemical mechanism of the peptide bond hydrolysis catalyzed by PR.

  13. Direct Detection of the Oxygen Rebound Intermediates, Ferryl Mb and NO2, in the Reaction of metMyoglobin with Peroxynitrite

    PubMed Central

    Su, Jia; Groves, John T.

    2009-01-01

    Oxygenated hemoproteins are known to react rapidly with nitric oxide (NO) to produce peroxynitrite (PN) at the heme site. This process could lead either to attenuation of the effects of NO or to nitrosative protein damage. Peroxynitrite is a powerful nitrating and oxidizing agent that has been implicated in a variety of cell injuries. Accordingly, it is important to delineate the nature and variety of reaction mechanisms of PN reactions with heme proteins. Here we present direct evidence that ferrylMb and NO2 are both produced during the reaction of PN and metmyolgobin (metMb). Kinetic evidence indicates that these products evolve from initial formation of a caged radical intermediate [FeIV=O NO2]. This caged pair reacts mainly via internal return with a rate constant kr to form metMb and nitrate in an oxygen rebound scenario. Detectable amounts of ferrylMb are observed by stopped-flow spectrophotometry, appearing at a rate consistent with the rate, kobs, of heme-mediated PN decomposition. Freely-diffusing NO2, which is liberated concomitantly from the radical pair (ke), preferentially nitrates Tyr103 in horse heart myoglobin. The ratio of the rates of in-cage rebound and cage escape, kr/ke, was found to be ?10 by examining the nitration yields of fluorescein, an external NO2 trap. This rebound/escape model for the metMb/PN interaction is analogous to the behavior of alkyl hyponitrites and the well-studied geminate recombination processes of deoxymyoglobin with O2, CO and NO. The scenario is also similar to the step-wise events of substrate hydroxylation by cytochrome P450 and other oxygenases. It is likely, therefore, that the reaction of metMb with ONOO- and that of oxyMb with NO proceed through the same [FeIV=O NO2] caged radical intermediate and lead to similar outcomes. The results indicate that while oxyMb may reduce the concentration of intracellular NO, it would not eliminate the formation of NO2 as a decomposition product of peroxynitrite. PMID:19705829

  14. Intermediate products of sulfur disproportional reaction and their physical role in effusive to explosive submarine volcanic activity

    NASA Astrophysics Data System (ADS)

    Nakamura, K.; Takano, B.; Butterfield, D. A.; Resing, J.; Chadwick, W. W.; Embley, R. W.

    2009-12-01

    Recent direct observations of submarine volcanic activity in the Mariana Arc are giving us a chance to examine the role of volcanic gas in submarine volcanic conduits. Unlike subaerial volcanoes, where hydrogeologic conditions have different character from place to place, the overlying water mass above submarine volcanoes gives a uniform hydrographic setting. Currently, the places where we can directly observe submarine volcanic activity are located deeper than 400 m, which raises the boiling point of seawater to over 240 deg C. This situation allows us to examine the interaction of volcanic gases with ambient seawater at a shorter distance from the magma source than at subaerial volcanic settings. Arc volcano settings give us longer and more frequent opportunities to make observations and provide a more diverse range of submarine volcanism than ridge settings. Among the three major components of volcanic gases (i.e., H2O, CO2 and SO2), water follows a two phase boundary below the critical temperature after volatile components leave from the magmatic source. Milky sulfur sol bearing hydrothermal fluid is commonly observed throughout Mariana active sites. Most of the sulfur sol (colloidal elemental sulfur and polysulfides) might be formed by disproportional reaction of sulfur dioxide with seawater when water vapor shrinks to liquid water. The reaction creates not only sulfur sol but also various types of sulfite, which affects the pH of seawater. We detected short-lived sulfite species in the water column above several active Mariana volcanoes such as NW Rota-1, Daikoku and Nikko by on-board HPLC. Because most observations are made on the liquid phase side of H2O boundary, it is very hard to get data to investigate the physical and chemical sulfur sol forming process occurring on the vapor phase side or at the critical state (i.e., near the magma source process). Carbon dioxide behaves as a gas at a wide range of pressures and temperatures and carries heat and sulfur dioxide effectively and quickly to the seafloor. At Nikko Seamount carbon dioxide bubbles penetrated the intentionally excavated liquid sulfur pond beneath a hydrothermal vent. The bubbles have misty surfaces, which indicated progressive disproportional reaction of carried sulfur dioxide with ambient seawater. Although the temperature along most of the conduit up to the seafloor is above the freezing point of elemental sulfur, coalescence of sulfur sol, which creates masses of liquid sulfur, mostly occur when the mixture of hydrothermal fluid and volcanic gas leaves the two phase boundary of water near the seafloor. The polymerization state of liquid sulfur governs the resistance against volcanic gas flow near the surface of volcanic conduits. Several types of liquid sulfur spherules were sampled at NW Rota-1 eruption site.

  15. 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.

  16. 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

    2016-03-01

    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. WIREs Syst Biol Med 2016, 8:104-122. doi: 10.1002/wsbm.1323 For further resources related to this article, please visit the WIREs website. PMID:26559926

  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-(?-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)= 3780180M?1s?1, ?H1 = 26.41.7 kJ mol?1, ?S1 = ? 75.66.8 J mol?1K?1), and then convert more slowly (k2(?10 C)= 4173.2 M?1s?1, ?H2 = 47.11.4 kJ mol?1, ?S2 = ? 15.05.7 J mol?1K?1) to a species 3 with isotopically sensitive stretches at ?o-o (?18O) = 819(47) cm?1, kOO= 3.02 mdyn/, and ?Mn-O(?18O) = 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?1,2O2)}2+ (3) is shown to be bridging between two Mn(III) ions in an end-on trans-?-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 en route to a binuclear ?oxo bridged product derived from O2. Vibrational and metrical parameters for binuclear Mn-peroxo 3 are compared with those of related binuclear Fe- and Cu-peroxo compounds. PMID:23470101

  18. E-pharmacovigilance: development and implementation of a computable knowledge base to identify adverse drug reactions

    PubMed Central

    Neubert, Antje; Dormann, Harald; Prokosch, Hans-Ulrich; Bürkle, Thomas; Rascher, Wolfgang; Sojer, Reinhold; Brune, Kay; Criegee-Rieck, Manfred

    2013-01-01

    Aims Computer-assisted signal generation is an important issue for the prevention of adverse drug reactions (ADRs). However, due to poor standardization of patients' medical data and a lack of computable medical drug knowledge the specificity of computerized decision support systems for early ADR detection is too low and thus those systems are not yet implemented in daily clinical practice. We report on a method to formalize knowledge about ADRs based on the Summary of Product Characteristics (SmPCs) and linking them with structured patient data to generate safety signals automatically and with high sensitivity and specificity. Methods A computable ADR knowledge base (ADR-KB) that inherently contains standardized concepts for ADRs (WHO-ART), drugs (ATC) and laboratory test results (LOINC) was built. The system was evaluated in study populations of paediatric and internal medicine inpatients. Results A total of 262 different ADR concepts related to laboratory findings were linked to 212 LOINC terms. The ADR knowledge base was retrospectively applied to a study population of 970 admissions (474 internal and 496 paediatric patients), who underwent intensive ADR surveillance. The specificity increased from 7% without ADR-KB up to 73% in internal patients and from 19.6% up to 91% in paediatric inpatients, respectively. Conclusions This study shows that contextual linkage of patients' medication data with laboratory test results is a useful and reasonable instrument for computer-assisted ADR detection and a valuable step towards a systematic drug safety process. The system enables automated detection of ADRs during clinical practice with a quality close to intensive chart review. PMID:23586589

  19. Direct observation of unstable intermediate species in the reaction of trans-2-butene on ferrierite zeolite by picosecond infrared laser spectroscopy.

    PubMed

    Noguchi, Hidenori; Yoda, Eisuke; Ishizawa, Naoko; Kondo, Junko N; Wada, Akihide; Kobayashi, Hisayoshi; Domen, Kazunari

    2005-09-15

    The reaction dynamics of trans-2-butene adsorbed to acidic hydroxyl groups on the surface of ferrierite zeolite is examined by time-resolved spectroscopy using a tunable infrared picosecond pulse laser system. The transient absorption spectra measured by a two-color pump-probe technique at 188-243 K reveal bleaching and hot bands of the OD stretching mode 2 ps after excitation. This vibrationally excited state relaxes within 20 ps at 188 K, while the bleaching band includes a long-lifetime component that lasts for more than 100 ps at 243 K. Thus, the OD (isotope-exchanged hydroxy groups) stretching band does not entirely recover in this period and is mirrored by an analogous weakening of the CH bending band of the adsorbed trans-2-butene. Simultaneously, three new bands in CH stretching region were observed at 3045, 3095, and 3130 cm(-1). This result suggests the presence of a short-lived intermediate formed by reaction between the acidic hydroxyl groups and adsorbed trans-2-butene. PMID:16853197

  20. 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.

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

    DOEpatents

    Holzrichter, John F. (Berkeley, CA); Siekhaus, Wigbert J. (Berkeley, CA)

    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.

  2. A new strategy to identify rare blood donors: single polymerase chain reaction multiplex SNaPshot reaction for detection of 16 blood group alleles

    PubMed Central

    Latini, Flavia Roche Moreira; Gazito, Diana; Arnoni, Carine Prisco; Muniz, Janana Guilhem; de Medeiros Person, Rosangela; Carvalho, Fabricio Oliveira; Baleotti, Wilson; Castilho, Lilian; Barreto, Jos Augusto

    2014-01-01

    Background As an alternative to phenotyping, large-scale DNA-based assays, which are feasible for high-throughput donor red blood cell typing, were developed for determination of blood group polymorphisms. However, high-throughput genotyping platforms based on these technologies are still expensive and the inclusion of single nucleotide polymorphisms and analysis of the alleles depend on the manufacturers determination. To overcome this limitation and in order to develop an assay to enable the screening of rare donors, we developed a SNaPshot assay for analysis of nine single nucleotide polymorphisms related to antigens that are difficult to assess using conventional serology. Materials and methods The single polymerase chain reaction multiplex SNaPshot reaction was optimized to identify nine single nucleotide polymorphisms determining 16 alleles: KEL*3/KEL*4, KEL*6/KEL*7, DI*1/DI*2, DI*3/DI*4, YT*1/YT*2, CO*1/CO*2, DO*1/DO*2, DO*4, DO*5. We designed a single multiplex PCR with primers encompassing the blood group single nucleotide polymorphisms and performed an internal reaction with probe primers able to discriminate the alleles after fragment analysis. The SNaPshot assay was validated with 140 known alleles previously determined by PCR restriction fragment length polymorphism. Results We were able to simultaneous detect nine single nucleotide polymorphisms defining 16 blood group alleles on an assay based on a multiplex PCR combined with a single base extension using genomic DNA. Discussion This study demonstrates a robust genotyping strategy for conducting rare donor screening which can be applied in blood centers and could be an important tool for identifying antigen-negative donors and, therefore, for providing rare blood. PMID:23736910

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

    PubMed Central

    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. PMID:26161858

  4. Studies of intermediate-mass fragment emission in the 3He+natAg, 197Au reactions between 0.48 and 3.6 GeV

    NASA Astrophysics Data System (ADS)

    Yennello, S. J.; Kwiatkowski, K.; Pollacco, E. C.; Volant, C.; Cassagnou, Y.; Dayras, R.; Fields, D. E.; Harar, S.; Hourani, E.; Legrain, R.; Norbeck, E.; P?aneta, R.; Wile, J. L.; Yoder, N. R.; Viola, V. E.

    1993-09-01

    Intermediate-mass fragments formed in reactions of 3He ions with natAg and 197Au targets have been studied at five energies between 0.48 and 3.6 GeV. Inclusive measurements show that as the bombarding energy increases, there is a strong enhancement in fragment cross sections and a trend toward isotropic angular distributions. Between 0.90 and 1.8 GeV, a change in the emission mechanism is suggested by (1) kinetic energy spectra with high-energy tails that become distinctly flatter, (2) a broadening of the spectral Coulomb peaks toward lower energies, and (3) charge distributions that become constant, exhibiting a power-law exponent ?~=2.0. Exclusive studies of the 3He+natAg system at 0.90 and 3.6 GeV detected multifragment events with multiplicities up to four. The probability for high-multiplicity events increases about 40-fold between 0.90 and 3.6 GeV. At both energies, the kinetic energy spectra depend on multiplicity, especially when triggering on backward-emitted fragments. For multiplicity three events, a rapidity analysis of the data at 3.6 GeV is consistent with a single, relatively low source velocity, vS~=0.4 cm/ns. The data are compared with predictions of a coplanarity-sphericity calculation, the sequential statistical decay code GEMINI, and a hybrid intranuclear cascade/percolation model.

  5. Ab initio study of hypervalent sulfur hydrides as model intermediates in the interconversion reactions of compounds containing sulfur-sulfur bonds

    SciTech Connect

    Laitinen, R.S.; Pakkanen, T.A.; Steudel, R.

    1987-02-04

    Ab initio MO calculations involving the 4-31G* basis set have been used to predict the equilibrium geometries of the hypervalent sulfur hydrides H/sub 2/SS, (HS)/sub 2/SS, H/sub 2/S(SH)/sub 2/, H/sub 2/S(SSH)/sub 2/, and the cyclic H/sub 4/S/sub 4/. The energy changes in their formation from appropriate sulfanes H/sub 2/S/sub n/ (n = 1-4) have been studied with the 6-31G* basis set including the correction for the electron correlation by the second- and third-order Moeller-Plesset perturbation theory. The results are used to discuss the possible pathways in the interconversion reactions between various sulfur compounds containing cumulated SS bonds, for example, the formation of S/sub 7/ from S/sub 8/ for which hypervalent intermediates have been proposed recently. Comparison with experimental evidence is made whenever possible.

  6. Characterization of a succinyl-CoA radical-cob(II)alamin spin triplet intermediate in the reaction catalyzed by adenosylcobalamin-dependent methylmalonyl-CoA mutase.

    PubMed

    Mansoorabadi, Steven O; Padmakumar, Rugmini; Fazliddinova, Nisso; Vlasie, Monica; Banerjee, Ruma; Reed, George H

    2005-03-01

    The electron paramagnetic resonance (EPR) spectrum of an intermediate freeze trapped during the steady state of the reaction catalyzed by the adenosylcobalamin (AdoCbl)-dependent enzyme, methylmalonyl-CoA mutase, has been studied. The EPR spectrum is that of a hybrid triplet spin system created as a result of strong electron-electron spin coupling between an organic radical and the low-spin Co(2+) in cob(II)alamin. The spectrum was analyzed by simulation to obtain the zero-field splitting (ZFS) parameters and Euler angles relating the radical-to-cobalt interspin vector to the g axis system of the low-spin Co(2+). Labeling of the substrate with (13)C and (2)H was used to probe the identity of the organic radical partner in the triplet spin system. The patterns of inhomogeneous broadening in the EPR signals produced by [2'-(13)C]methylmalonyl-CoA and [2-(13)C]methylmalonyl-CoA as well as line narrowing resulting from deuterium substitution in the substrate were consistent with those expected for a succinyl-CoA radical wherein the unpaired electron was centered on the carbon alpha to the free carboxyate group of the rearranged radical. The interspin distance and the Euler angles were used to position this product radical into the active site of the enzyme. PMID:15736925

  7. Characterization of a Succinyl-CoA RadicalCob(II)alamin Spin Triplet Intermediate in the Reaction Catalyzed by Adenosylcobalamin-Dependent Methylmalonyl-CoA Mutase

    PubMed Central

    Mansoorabadi, Steven O.; Padmakumar, Rugmini; Fazliddinova, Nisso; Vlasie, Monica; Banerjee, Ruma; Reed, George H.

    2011-01-01

    The electron paramagnetic resonance (EPR) spectrum of an intermediate freeze trapped during the steady state of the reaction catalyzed by the adenosylcobalamin (AdoCbl)-dependent enzyme, methylmalonyl-CoA mutase, has been studied. The EPR spectrum is that of a hybrid triplet spin system created as a result of strong electronelectron spin coupling between an organic radical and the low-spin Co2+ in cob(II)alamin. The spectrum was analyzed by simulation to obtain the zero-field splitting (ZFS) parameters and Euler angles relating the radical-to-cobalt interspin vector to the g axis system of the low-spin Co2+. Labeling of the substrate with 13C and 2H was used to probe the identity of the organic radical partner in the triplet spin system. The patterns of inhomogeneous broadening in the EPR signals produced by [2?-13C]methylmalonyl-CoA and [2-13C]methylmalonyl-CoA as well as line narrowing resulting from deuterium substitution in the substrate were consistent with those expected for a succinyl-CoA radical wherein the unpaired electron was centered on the carbon ? to the free carboxyate group of the rearranged radical. The interspin distance and the Euler angles were used to position this product radical into the active site of the enzyme. PMID:15736925

  8. Combining Real-Time Polymerase Chain Reaction Using SYBR Green I Detection and Sequencing to Identify Vertebrate Bloodmeals in Fleas

    PubMed Central

    GRAHAM, CHRISTINE B.; BLACK, WILLIAM C.; BOEGLER, KAREN A.; MONTENIERI, JOHN A.; HOLMES, JENNIFER L.; GAGE, KENNETH L.; EISEN, REBECCA J.

    2015-01-01

    Programs that aim to control vector-borne zoonotic diseases require information on zoonotic hosts and on the feeding behavior of bridging vectors that are capable of transmitting pathogens from those hosts to humans. Here we describe an assay developed to identify bloodmeals in field-collected cat fleas (Ctenocephalides felis Bouch) to assess this species potential role as a Yersinia pestis bridging vector in a plague-endemic region of Uganda. Our assay uses a single primer set and SYBR Green I-based real-time polymerase chain reaction to amplify a segment of the 12S mitochondrial ribosomal RNA gene for identification by sequencing. The assay capitalizes on the sensitivity of real-time polymerase chain reaction and the specificity of sequencing and can be used to differentiate vertebrate bloodmeals to the genus or species level without a priori knowledge of the host community. Because real-time assays that detect vertebrate DNA are highly sensitive to human DNA contamination, we analyzed detection in artificially fed and unfed fleas to establish a Ct cutoff that optimized specificity without completely sacrificing sensitivity. Using the established cutoff, our assay detected human, rat, and goat DNA in artificially fed C. felis up to 72 h postfeeding. PMID:23270174

  9. A novel mixed valence form of Rhus vernicifera laccase and its reaction with dioxygen to give a peroxide intermediate bound to the trinuclear center.

    PubMed

    Zoppellaro, G; Sakurai, T; Huang, H

    2001-06-01

    Rhus vernicifera laccase, in a novel mixed valence state [T1oxT23red: type 1 Cu as Cu(II), and type 2 and 3 Cus as Cu(I)], was formed by reacting Cu(I) on the type 2 Cu-depleted laccase [T1oxT3red: type 1 Cu as Cu(II) and type 3 Cus as Cu(I)] under argon. Contrary to T1oxT3red, T1oxT23red was highly reactive with dioxygen, and gave the three transient bands at 340, 475, and 680 nm due to the two-electron reduced form of dioxygen [charge transfer bands from peroxide to Cu(II)]. The first order decays were highly dependent on pH, which led to the successful detection of the intermediate for ca. 2 h at pH 7.5. Another mixed valence derivative, T12oxT3red [type 1 and type 2 Cus as Cu(II), and type 3 Cus as Cu(I)] prepared through the action of Cu(II) on T1oxT3red was not reactive with dioxygen, but showed high enzyme activity as to the oxidation of N,N-dimethyl-p-phenylenediamine. The whole reaction mechanism of the reduction of dioxygen by laccase was proposed based on the present results together with data for the former detection and characterization of the three-electron reduced form of dioxygen [Huang, H. et al. (1999) J. Biol. Chem. 274, 46, 32718-32724]. PMID:11388911

  10. Kinetics of stabilised Criegee intermediates derived from alkene ozonolysis: reactions with SO2, H2O and decomposition under boundary layer conditions.

    PubMed

    Newland, Mike J; Rickard, Andrew R; Alam, Mohammed S; Vereecken, Luc; Muñoz, Amalia; Ródenas, Milagros; Bloss, William J

    2015-02-14

    The removal of SO2 in the presence of alkene-ozone systems has been studied for ethene, cis-but-2-ene, trans-but-2-ene and 2,3-dimethyl-but-2-ene, as a function of humidity, under atmospheric boundary layer conditions. The SO2 removal displays a clear dependence on relative humidity for all four alkene-ozone systems confirming a significant reaction for stabilised Criegee intermediates (SCI) with H2O. The observed SO2 removal kinetics are consistent with relative rate constants, k(SCI + H2O)/k(SCI + SO2), of 3.3 (±1.1) × 10(-5) for CH2OO, 26 (±10) × 10(-5) for CH3CHOO derived from cis-but-2-ene, 33 (±10) × 10(-5) for CH3CHOO derived from trans-but-2-ene, and 8.7 (±2.5) × 10(-5) for (CH3)2COO derived from 2,3-dimethyl-but-2-ene. The relative rate constants for k(SCI decomposition)/k(SCI + SO2) are -2.3 (±3.5) × 10(11) cm(-3) for CH2OO, 13 (±43) × 10(11) cm(-3) for CH3CHOO derived from cis-but-2-ene, -14 (±31) × 10(11) cm(-3) for CH3CHOO derived from trans-but-2-ene and 63 (±14) × 10(11) cm(-3) for (CH3)2COO. Uncertainties are ±2σ and represent combined systematic and precision components. These values are derived following the approximation that a single SCI is present for each system; a more comprehensive interpretation, explicitly considering the differing reactivity for syn- and anti-SCI conformers, is also presented. This yields values of 3.5 (±3.1) × 10(-4) for k(SCI + H2O)/k(SCI + SO2) of anti-CH3CHOO and 1.2 (±1.1) × 10(13) for k(SCI decomposition)/k(SCI + SO2) of syn-CH3CHOO. The reaction of the water dimer with CH2OO is also considered, with a derived value for k(CH2OO + (H2O)2)/k(CH2OO + SO2) of 1.4 (±1.8) × 10(-2). The observed SO2 removal rate constants, which technically represent upper limits, are consistent with decomposition being a significant, structure dependent, sink in the atmosphere for syn-SCI. PMID:25562069

  11. Hydrogen storage in LiAlH4 : predictions of the crystal structures and reaction mechanisms of intermediate phases from quantum mechanics.

    SciTech Connect

    Lee, Jai Young; Muller, Richard Partain; Kang, Jeung Ku; Goddard, William A., III

    2005-06-01

    We use the density functional theory and x-ray and neutron diffraction to investigate the crystal structures and reaction mechanisms of intermediate phases likely to be involved in decomposition of the potential hydrogen storage material LiAlH{sub 4}. First, we explore the decomposition mechanism of monoclinic LiAlH4 into monoclinic Li{sub 3}AlH{sub 6} plus face-centered cubic (fcc) Al and hydrogen. We find that this reaction proceeds through a five-step mechanism with an overall activation barrier of 36.9 kcal/mol. The simulated x ray and neutron diffraction patterns from LiAlH{sub 4} and Li{sub 3}AlH{sub 6} agree well with experimental data. On the other hand, the alternative decomposition of LiAlH{sub 4} into LiAlH2 plus H2 is predicted to be unstable with respect to that through Li{sub 3}AlH{sub 6}. Next, we investigate thermal decomposition of Li{sub 3}AlH{sub 6} into fcc LiH plus Al and hydrogen, occurring through a four-step mechanism with an activation barrier of 17.4 kcal/mol for the rate-limiting step. In the first and second steps, two Li atoms accept two H atoms from AlH{sub 6} to form the stable Li-H-Li-H complex. Then, two sequential H2 desorption steps are followed, which eventually result in fcc LiH plus fcc Al and hydrogen: Li{sub 3}AlH{sub 6}(monoclinic) {yields} 3 LiH(fcc) + Al(fcc) + 3/2 H{sub 2} is endothermic by 15.8 kcal/mol. The dissociation energy of 15.8 kcal/mol per formula unit compares to experimental enthalpies in the range of 9.8-23.9 kcal/mol. Finally, we explore thermal decomposition of LiH, LiH(s) + Al(s) {yields} LiAl(s) + 1/2 H{sub 2}(g) is endothermic by 4.6 kcal/mol. The B32 phase, which we predict as the lowest energy structure for LiAl, shows covalent bond characters in the Al-Al direction. Additionally, we determine that transformation of LiH plus Al into LiAlH is unstable with respect to transformation of LiH through LiAl.

  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 158E over the Shatsky Rise, or around 170E 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. 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, Hkon

    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. Efforts also should be also directed to identify blood donors with significant risk of bacteremia, at the time of donation in the first place as a high priority. The goal of this review is to highlights strategies for identifying both the sources of bacterial contamination of blood components in Norway and identifying donors with a higher risk of bacteremia at the time of donation. The key to achieving this goal is initiating continual revising and upgrading the Norwegian transfusion guidelines, based on the transfusion legislation and by introducing a relevant specialized donor bacterial questionnaire. PMID:25242310

  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 ?-meso carbon by a ferric hydroperoxide and is predicted to proceed via an isoporphyrin ?-cation intermediate. Here we report spectroscopic detection of a transient intermediate during oxidation by hHO-1 of ?-meso-phenylheme-IX, ?-meso-(p-methylphenyl)-mesoheme-III, and ?-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, 4259342604), only the ?-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 ?-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. 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

    2014-03-01

    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. PMID:24606361

  16. 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)

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    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 1H-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.

  17. 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.

  18. DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemicalprotein interactome

    PubMed Central

    Luo, Heng; Chen, Jian; Shi, Leming; Mikailov, Mike; Zhu, Huang; Wang, Kejian; He, Lin; Yang, Lun

    2011-01-01

    Identifying new indications for existing drugs (drug repositioning) is an efficient way of maximizing their potential. Adverse drug reaction (ADR) is one of the leading causes of death among hospitalized patients. As both new indications and ADRs are caused by unexpected chemicalprotein interactions on off-targets, it is reasonable to predict these interactions by mining the chemicalprotein interactome (CPI). Making such predictions has recently been facilitated by a web server named DRAR-CPI. This server has a representative collection of drug molecules and targetable human proteins built up from our work in drug repositioning and ADR. When a user submits a molecule, the server will give the positive or negative association scores between the users molecule and our library drugs based on their interaction profiles towards the targets. Users can thus predict the indications or ADRs of their molecule based on the association scores towards our library drugs. We have matched our predictions of drugdrug associations with those predicted via gene-expression profiles, achieving a matching rate as high as 74%. We have also successfully predicted the connections between anti-psychotics and anti-infectives, indicating the underlying relevance of anti-psychotics in the potential treatment of infections, vice versa. This server is freely available at http://cpi.bio-x.cn/drar/. PMID:21558322

  19. 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

    2016-03-16

    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)2NiO4±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 . Since the unfilled interstitial sites in the R-P phase serve to accommodate the adsorbed oxygen during incorporation, like vacancies in the perovskite structure , more 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 works to regulate the exchange rate, and how the contradiction between and is harmonized so that the latter in the R-P structure also positively promotes the incorporation rate in the ORR. PMID:26939545

  20. 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. PMID:26240023

  1. Electrospray ionization mass spectrometric investigations of [alpha]-dicarbonyl compounds--Probing intermediates formed in the course of the nonenzymatic browning reaction of l-ascorbic acid

    NASA Astrophysics Data System (ADS)

    Schulz, Anke; Trage, Claudia; Schwarz, Helmut; Kroh, Lothar W.

    2007-05-01

    A new method is presented which allows the simultaneous detection of various [alpha]-dicarbonyl compounds generated in the course of the nonenzymatic browning reaction initiated by thermal treatment of l-ascorbic acid, namely: glyoxal, methylglyoxal, diacetyl, 3-deoxy-l-pentosone, and l-threosoneE 3-Deoxy-l-threosone was successfully identified as a new C4-[alpha]-dicarbonyl structure for the first time in the degradation of Vitamin C by application of this non-chromatographic mass spectrometric approach. Moreover, a more detailed elucidation of the mechanistic scenario with respect to the oxidative and nonoxidative pathways is presented by using dehydro-l-ascorbic acid and 2,3-diketo-l-gulonic acid instead of l-ascorbic acid as a starting material. Furthermore, the postulated pathways are corroborated with the aid of 13C-isotopic labeling studies. The investigations were extended to baby food, and the successful detection of [alpha]-dicarbonyl compounds characteristic for Vitamin C degradation proved the matrix tolerance of the introduced method.

  2. 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.

  3. Unexpected NO transfer reaction between trans-[Ru(II)(NO+)(NH3)4(L)]3+ and Fe(III) species: observation of a heterobimetallic NO-bridged intermediate.

    PubMed

    Metzker, Gustavo; Lopes, Pietro P; da Silva, Augusto C H; da Silva, Sebastiao C; Franco, Douglas W

    2014-05-01

    The reaction between trans-[Ru(II)(NO(+))(NH3)4(L)](3+), L = ImN, IsN, Nic, P(OMe)3, P(OEt)3, and P(OH)(OEt)2, and the Fe(III) species [Fe(III)(TPPS)], metmyoglobin, and hemoglobin was monitored by UV-vis, EPR, and electrochemical techniques (DPV, CV). No reaction was observed when L = ImN, IsN, Nic, and P(OH)(OEt)2. However, when L = P(OMe)3 and P(OEt)3, the reaction was quantitative and the products were trans-[Ru(III)(H2O)(NH3)4(P(OR)3)](3+) and [Fe(II)(NO(+))] species. Reaction kinetics data and DFT calculations suggest a two-step reaction mechanism with the initial formation of a bridged [Ru-(μNO)-Fe] intermediate, which was confirmed through electrochemical techniques (E(0)' = -0.47 V vs NHE). The calculated specific rate constant values for the reaction were in the ranges k1 = 1.1 to 7.7 L mol(-1) s(-1) and k2 = 2.4 × 10(-3) to 11.4 × 10(-3) s(-1) for L = P(OMe)3 and P(OEt)3. The oxidation of the ruthenium center (Ru(II) to Ru(III)) containing the nitrosonium ligand suggests that NO can act as an electron transfer bridge between the two metal centers. PMID:24738470

  4. Remarkable reactions and intermediates in titanocene(IV) chemistry: migratory insertion reactions of 2,2-disubstituted-1-alkenes, intramolecular 1,5-? bond metathesis via ?-agostic interactions, and a rare example of a ?-agostic alkyltitanocene complex.

    PubMed

    Sauriol, Francoise; Sonnenberg, Jessica F; Chadder, Sarah J; Dunlop-Brire, Alexandre F; Baird, Michael C; Budzelaar, Peter H M

    2010-09-29

    The compound Cp(2)TiMe(2) reacts with [Ph(3)C][B(C(6)F(5))(4)] in CD(2)Cl(2) at 205 K to give, inter alia, [Cp(2)TiMe(CD(2)Cl(2))][B(C(6)F(5))(4)]. This solvent-separated ion pair reacts in turn with 2,4-dimethyl-1-pentene (DMP) to give a series of cationic species, the first being the alkene complex [Cp(2)TiMe(DMP)](+), which undergoes ready migratory insertion to form the ?-alkyl complex [Cp(2)Ti(CH(2)CMe(2)CH(2)CHMe(2))](+). The latter, which does not contain a ?-hydrogen atom, rearranges rapidly via an unprecedented 1,5-? bond metathesis reaction involving two isomeric ?-agostic species to give the ?-alkyl species [Cp(2)Ti(CH(2)CHMeCH(2)CMe(3))](+); this does contain a ?-hydrogen atom and, in concurrent processes, eliminates H(2) or 2,4,4-trimethyl-1-pentene (a major product) to form respectively the allylic complex [Cp(2)Ti{?(3)-(CH(2))(2)CCH(2)CMe(3)}](+) (a major product) or the hydride complex [Cp(2)TiH](+). The latter reacts reversibly with free DMP to give the insertion product [Cp(2)Ti(CH(2)CHMeCH(2)CHMe(2))](+) (V, a major product), in which the italicized hydrogen atom engages in a ?-agostic interaction with the metal atom. Compound V is a rare example of both a ?-agostic derivative of a group 4 metallocene and a ?-agostic compound of any metal in which the (1)H resonance of the agostic hydrogen can be identified in the (1)H NMR spectrum (? -3.43). Interestingly, a NOESY experiment on V indicates slow mutual exchange between the agostic hydrogen atom, the hydrogen atoms on C(1), and those of Me(2). These observations are consistent with the intermediacy of the allylic dihydrogen species [Cp(2)Ti(H(2)){?(3)-(CH(2))(2)CCH(2)CHMe(2)}](+), which loses H(2) to form [Cp(2)Ti{?(3)-(CH(2))(2)CCH(2)CHMe(2)}](+) (a minor product). Support for all steps of the proposed reaction scheme comes from product distributions, from labeling studies utilizing [Cp(2)Ti(CD(3))(CD(2)Cl(2))](+), and from extensive DFT calculations. The observed titanocene-based chemistry stands in stark contrast to that of the analogous zirconium system, in which the unusual but well-characterized cationic methyl alkene complex [Cp(2)ZrMe(DMP)](+) does not undergo migratory insertion and subsequent reactions. PMID:20812708

  5. Probing the sensitivity of the total nucleus-nucleus reaction cross section at intermediate energies to medium effects and isospin asymmetries

    SciTech Connect

    Sammarruca, Francesca; White, Larz

    2011-06-15

    This paper presents reaction cross-section predictions. These predictions are the result of a continuous pipeline that originates from a microscopic nuclear interaction. Density parameters and effective nucleon-nucleon cross sections (both involved in the reaction calculations) are by-products of the same equation of state. First, we perform tests of sensitivity to medium effects using reactions involving {sup 208}Pb, a stable but weakly isospin-asymmetric nucleus. We also show predictions for collisions of some neutron-rich isotopes of calcium and argon. We observe significant sensitivity of the reaction cross section to medium effects but very weak sensitivity to inclusion of isospin asymmetry in the effective nucleon-nucleon cross sections.

  6. 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. PMID:25000711

  7. Photon-induced neutron polarization from the {sup 2}H({gamma},n-vector){sup 1}H reaction within the NN-force model with an intermediate dibaryon

    SciTech Connect

    Kukulin, V. I.; Obukhovsky, I. T.; Pomerantsev, V. N.; Faessler, Amand; Grabmayr, Peter

    2008-04-15

    A model for the NN force, which is induced by the formation of an intermediate dibaryon dressed with {sigma}- and other meson fields, has been developed by the present authors in previous years. This model is applied to the deuteron photodisintegration processes with the main focus on the {gamma}-induced polarization P{sub y}{sup '} of the neutron at energies below E{sub {gamma}} < or approx. 30 MeV. The inclusion of the intermediate dibaryon leads to a model of the NN force completely different to the conventional NN potential models at short distances. Here the model is tested on the nucleonic level through comparison to rather similar predictions from the conventional NN potential model both for the total and differential cross sections and also for the spin polarization of the ejected neutrons. The predictions of the present model are at least of the same quality than those for the Nijmegen potential; the visible differences with experimental data for P{sub y}{sup '} still remain. However, in combination with the previous results a consistent description can be achieved simultaneously for many observables.

  8. Synthesis of novel synthetic intermediates from the reaction of benzimidazole and triazole carbenes with ketenimines and their application in the construction of spiro-pyrroles.

    PubMed

    Mo, Jun-Ming; Ma, Yang-Guang; Cheng, Ying

    2009-12-01

    2-(2-Alkoxycarbonyl-1-arylamino-1-propenyl)benzimidazolium and 5-(2-alkoxycarbonyl-1-arylamino-1-propenyl)triazolium salts were synthesized in good yields from the reaction of benzimidazole and triazole carbenes with ketenimines. Upon treatment with a base, both salts were converted into novel 1,3-dipoles which underwent [3+2] cycloaddition reactions with electron-deficient alkynes and allenes to produce benzimidazole-spiro-pyrroles or triazole-spiro-pyrroles. This work provides novel synthons for the construction of multifunctional spiro-pyrrole derivatives that are not easy accessible by other synthetic methods and are potentially amenable to further transformations. PMID:19907793

  9. Impact parameter dependence of intermediate-mass fragment formation in Ca+Sn heavy-ion reactions at 45 AMeV

    NASA Astrophysics Data System (ADS)

    Quinlan, Michael; Pawelczak, Iwona; Singh, Hardev; Toke, Jan; Schroder, Udo; Chimera Collaboration

    2011-04-01

    Charged products produced in collisions of Ca and Sn at 45 AMeV were measured by the CHIMERA multi-detector. The kinematical relationships between the reaction products were analyzed. Events consistent with the binary split of the PLF were examined and found to show characteristics consistent with a non-equilibrium formation mechanism. In particular, two distinct event classes were found and appear to be sensitive to the centrality of the collision. A comparison of the data with a number of reaction models will be discussed. This work was supported by the US Department of Energy Grant No. DE-FG02-88ER40414.

  10. Identifying the active site in nitrogen-doped graphene for the VO2+/VO2(+) redox reaction.

    PubMed

    Jin, Jutao; Fu, Xiaogang; Liu, Qiao; Liu, Yanru; Wei, Zhiyang; Niu, Kexing; Zhang, Junyan

    2013-06-25

    Nitrogen-doped graphene sheets (NGS), synthesized by annealing graphite oxide (GO) with urea at 700-1050 C, were studied as positive electrodes in a vanadium redox flow battery. The NGS, in particular annealed at 900 C, exhibited excellent catalytic performance in terms of electron transfer (ET) resistance (4.74 0.51 and 7.27 0.42 ? for the anodic process and cathodic process, respectively) and reversibility (?E = 100 mV, Ipa/Ipc = 1.38 at a scan rate of 50 mV s(-1)). Detailed research confirms that not the nitrogen doping level but the nitrogen type in the graphene sheets determines the catalytic activity. Among four types of nitrogen species doped into the graphene lattice including pyridinic-N, pyrrolic-N, quaternary nitrogen, and oxidic-N, quaternary nitrogen is verified as a catalytic active center for the [VO](2+)/[VO2](+) couple reaction. A mechanism is proposed to explain the electrocatalytic performance of NGS for the [VO](2+)/[VO2](+) couple reaction. The possible formation of a N-V transitional bonding state, which facilitates the ET between the outer electrode and reactant ions, is a key step for its high catalytic activity. PMID:23647240

  11. Basal Serum Thyroglobulin Measured by a Second-Generation Assay Is Equivalent to Stimulated Thyroglobulin in Identifying Metastases in Patients with Differentiated Thyroid Cancer with Low or Intermediate Risk of Recurrence

    PubMed Central

    Nakabashi, Cláudia C.D.; Kasamatsu, Teresa S.; Crispim, Felipe; Yamazaki, Claudia A.; Camacho, Cléber P.; Andreoni, Danielle M.; Padovani, Rosalia P.; Ikejiri, Elza S.; Mamone, Maria C.O.M.; Aldighieri, Flávia C.; Wagner, Jairo; Hidal, Jairo T.; Vieira, José G.H.; Biscolla, Rosa P.M.; Maciel, Rui M.B.

    2014-01-01

    Background Guidelines for the follow-up of differentiated thyroid cancer (DTC) recommend the measurement of TSH-stimulated thyroglobulin (s-Tg) instead of basal Tg on T4 therapy (b-Tg). However, these guidelines were established using first-generation Tg assays with a functional sensitivity (FS) of 0.5-1.0 ng/ml. Current more sensitive second-generation Tg assays (Tg2G; FS 0.05-0.10 ng/ml) have shown that low-risk DTC patients with undetectable b-Tg rarely have recurrences. Objectives This study was undertaken to compare b-Tg using a chemiluminescent Tg2G assay (Tg2GICMA; FS 0.1 ng/ml) with s-Tg in DTC patients with an intermediate risk of recurrence. Methods We evaluated 168 DTC patients with a low (n = 101) and intermediate (n = 67) risk of recurrence treated by total thyroidectomy (147 also treated with radioiodine), with a mean follow-up of 5 years. Results b-Tg was undetectable with the Tg2GICMA in 142 of 168 patients. s-Tg was <2 ng/ml in 138 of these 142 patients, and only 3 of these 138 (2%) presented metastases on cervical ultrasound (US). Of the 4 of 142 patients with s-Tg >2 ng/ml, 1 had cervical metastases seen after radioiodine. Furthermore, 26 of 168 patients presented detectable b-Tg with the Tg2GICMA; 17 of these 26 patients also presented s-Tg >2 ng/ml. In 10 of these 17 patients, metastases were detected. Cervical US or b-Tg were positive in 14 of 15 patients with recurrent disease. Globally, the sensitivity and negative predictive value of the Tg2GICMA plus US were 93 and 99%, respectively. Conclusion b-Tg measured with a Tg2GICMA and cervical US, used together, are equivalent to s-Tg in identifying metastases in patients with DTC with a low or intermediate risk of recurrence. PMID:24847465

  12. A small organic compound enhances the religation reaction of human topoisomerase I and identifies crucial elements for the religation mechanism

    PubMed Central

    Arn, Barbara; Coletta, Andrea; Tesauro, Cinzia; Zuccaro, Laura; Fiorani, Paola; Lentini, Sara; Galloni, Pierluca; Conte, Valeria; Floris, Barbara; Desideri, Alessandro

    2013-01-01

    The different steps of the human Top1 (topoisomerase I) catalytic cycle have been analysed in the presence of a pentacyclic-diquinoid synthetic compound. The experiments indicate that it efficiently inhibits the cleavage step of the enzyme reaction, fitting well into the catalytic site. Surprisingly the compound, when incubated with the binary topoisomeraseDNA cleaved complex, helps the enzyme to remove itself from the cleaved DNA and close the DNA gap, increasing the religation rate. The compound also induces the religation of the stalled enzymeCPT (camptothecin)DNA ternary complex. Analysis of the molecule docked over the binary complex, together with its chemical properties, suggests that the religation enhancement is due to the presence on the compound of two oxygen atoms that act as hydrogen acceptors. This property facilitates the deprotonation of the 5? DNA end, suggesting that this is the limiting step in the topoisomerase religation mechanism. PMID:23368812

  13. Identifying abiotic chlorinated ethene degradation: characteristic isotope patterns in reaction products with nanoscale zero-valent iron.

    PubMed

    Elsner, Martin; Chartrand, Michelle; Vanstone, Nancy; Couloume, Georges Lacrampe; Lollar, Barbara Sherwood

    2008-08-15

    Carbon isotope fractionation is of great interest in assessing chlorinated ethene transformation by nanoscale zero-valent iron at contaminated sites, particularly in distinguishing the effectiveness of an implemented abiotic degradation remediation scheme from intrinsic biotic degradation. Transformation of trichloroethylene (TCE), cis-dichloroethylene (cis-DCE), and vinyl chloride (VC) with two types of nanoscale iron materials showed different reactivity trends, but relatively consistent carbon isotope enrichment factors (epsilon) of -19.4 per thousand +/- 1.8 per thousand (VC), -21.7 per thousand +/- 1.8 per thousand (cis-DCE), and -23.5 per thousand +/- 2.8 per thousand (TCE) with one type of iron (FeBH), and from -20.9 per thousand +/- 1.1 per thousand to -26.5 per thousand +/- 1.5 per thousand (TCE) with the other (FeH2). Products of the dichloroelimination pathway (ethene, ethane, and acetylene) were consistently 10 per thousand more isotopically depleted than those of the hydrogenolysis pathway (cis-DCE from TCE, VC from cis-DCE), displaying a characteristic pattern that may serve as an indicator of abiotic dehalogenation reactions and as a diagnostic parameter for differentiating the effects of abiotic versus biotic degradation. In contrast, the product-related enrichment factors of each respective pathway varied significantly in different experiments. Because such variation would not be expected for independent pathways with constant kinetic isotope effects, our data give preliminary evidence that the two pathways may share an irreversible first reaction step with subsequent isotopically sensitive branching. PMID:18767652

  14. 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. PMID:23278484

  15. Diallyl Trisulfide Is a Fast H2S Donor, but Diallyl Disulfide Is a Slow One: The Reaction Pathways and Intermediates of Glutathione with Polysulfides.

    PubMed

    Liang, Dong; Wu, Haixia; Wong, Ming Wah; Huang, Dejian

    2015-09-01

    Diallyl trisulfide (DATS) reacts rapidly with glutathione (GSH) to release H2S through thiol-disulfide exchange followed by allyl perthiol reduction by GSH. Yet diallyl disulfide (DADS) only releases a minute amount of H2S via a sluggish reaction with GSH through an ?-carbon nucleophilic substitution pathway. The results clarify the misunderstanding of DADS as a rapid H2S donor, which is attributed to its DATS impurity. PMID:26301500

  16. Analysis of sensitivity of the reaction cross section and the forward scattering amplitude to the structure of the nuclear optical potential for intermediate-energy nucleons and antinucleons

    SciTech Connect

    Zavarzina, V.P.; Stepanov, A.V.

    1986-04-01

    Within the framework of the optical model with phenomenological optical potentials describing elastic scattering we calculate the total cross section, the reaction cross section, and the real part of the forward scattering amplitude for nucleons and antinucleons in the energy range 50--200 MeV for a broad range of nuclei. It is shown that with a significantly different spatial dependence of the real part of the optical potential (the Woods-Saxon form and the ''wine-bottle bottom'' form) the real parts of the proton forward scattering amplitude differ from each other by several times, while the difference in the total cross sections and reaction cross sections is not larger than tens of per cent. The calculations are performed in first-order perturbation theory in deviation of the wave function of the incident particle from the eikonal approximation. Comparison of the results of the approximate and exact calculations shows that the error of the approximate approach in the energy range considered is not larger than 10%. We compare our results with the results of calculations of the reaction cross section for antiprotons in light nuclei in the Glauber theory.

  17. Kinetic and spectroscopic properties of intermediates formed by the reaction of some oxidizing and reducing radicals with 2-mercaptothiazoline (2-MT) in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Mahal, H. S.; Mukherjee, T.

    1999-01-01

    Resonance-stabilized 2-MT rad radicals, generated pulse radiolytically in neutral aqueous solutions from 2-MT by the reaction with OH rad , Br rad , and Br rad -2 radicals have a broad absorption band between 300-550 nm. The rate constants for the reactions of OH rad , T1 2+, Cl rad -2, Br rad and Br rad -2 with 2-MT have been determined at pH 2.2 and 6 and are close to the diffusion controlled values. At pH 6 the OH rad radicals react only to an extent of 45% with 2-MT. The 2-MT rad radicals are able to oxidize phenothiazine [PH] drugs [ E1?0.8 V] and ABTS with k?2-510 9 dm 3 mol -1 s -1. The semi-reduced species have been formed by the reaction of e -aq with 2-MT with a k?5.710 9 dm 3mol -1s -1 at pH 7. They show ?max ranging from 300-325 nm depending on the solution pH. The radical p Ka has been measured, p Ka=6. The semi-reduced form of 2-MT efficiently reduced MV 2+ to MV rad +. Our results indicate that if 2-MT is to be used as a corrosion inhibitor it will be more conducive to use it under reducing conditions than under oxidizing conditions.

  18. Reaction Plane Determination at Intermediate Rapidity in √s_NN = 200 GeV Au-Au Collisions in PHENIX at RHIC-BNL

    NASA Astrophysics Data System (ADS)

    Norman, B.

    2004-10-01

    In mid-central heavy ion collisions, the nuclear overlap region is almond shaped. This spatial anisotropy leads to a momentum space anisotropy, which has symmetry about the plane defined by the beam axis and the impact parameter. This reaction plane (or event plane) can be determined in experiment using the final particle azimuthal distribution. The reaction plane resolution depends on particle multiplicity, azimuthal angle resolution, azimuthal hermeticity, and the amount of actual asymmetry that exists in the collision. We will present the effect of these factors on the resolution of the reaction plane for Au-Au collisions in general and more specifically for the pad planes of the PHENIX Multiplicity Vertex Detector (MVD). These pad planes are in the pseudorapidity range 1.8<|η|<2.6 on either side of the vertex region for which PHOBOS data (nucl-ex/0403025) suggest a v2 of about 4 percent for mid-central Au-Au collisions at √s_NN = 200 GeV.

  19. ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain Optimization Based on Genome-Scale Metabolic Network

    PubMed Central

    Xu, Zixiang; Zheng, Ping; Sun, Jibin; Ma, Yanhe

    2013-01-01

    Gene knockout has been used as a common strategy to improve microbial strains for producing chemicals. Several algorithms are available to predict the target reactions to be deleted. Most of them apply mixed integer bi-level linear programming (MIBLP) based on metabolic networks, and use duality theory to transform bi-level optimization problem of large-scale MIBLP to single-level programming. However, the validity of the transformation was not proved. Solution of MIBLP depends on the structure of inner problem. If the inner problem is continuous, Karush-Kuhn-Tucker (KKT) method can be used to reformulate the MIBLP to a single-level one. We adopt KKT technique in our algorithm ReacKnock to attack the intractable problem of the solution of MIBLP, demonstrated with the genome-scale metabolic network model of E. coli for producing various chemicals such as succinate, ethanol, threonine and etc. Compared to the previous methods, our algorithm is fast, stable and reliable to find the optimal solutions for all the chemical products tested, and able to provide all the alternative deletion strategies which lead to the same industrial objective. PMID:24348984

  20. The reaction of pristane (2,6,10,14-tetramethylpentadecane) with radiolytically generated reactive oxygen intermediates results in a stable genotoxic compound as assessed by the SOS chromotest.

    PubMed

    Janz, S; Brede, O; Müller, J

    1991-07-01

    The most widely studied model of plasmacytomagenesis is the induction of plasmacytomas in BALB/c mice by i.p. injections of the isoalkane pristane (2,6,10,14-tetramethylpentadecane). Employing a simple quantitative and well-established short-term bacterial genotoxicity assay, the SOS chromotest, as a model system, we have investigated whether pristane may potentially be involved in causing or modulating the genotoxic events thought to induce plasma cell tumorigenesis. We found that incorporation of pristane into the cell membranes enhance the SOS response in Escherichia coli PQ37 and PQ300 induced by gamma-radiation under hyperoxic conditions. Moreover, the oxidation of pristane by radiolytically generated reactive oxygen intermediates yielded a stable, genotoxic product active on E. coli PQ300, a SOS tester strain designed to detect oxidative genotoxins. We discuss these findings in relation to the tumor-promoting role of the chronic i.p. inflammation that accompanies plasmacytomagenesis and conclude that, under these specific conditions, pristane may possess a previously unrecognized genotoxic activity in its tumorigenic potential. PMID:2070489

  1. Carbamoyl-phosphate synthetase II of the mammalian CAD protein: kinetic mechanism and elucidation of reaction intermediates by positional isotope exchange

    SciTech Connect

    Meek, T.D.; Karsten, W.E.; DeBrosse, C.W.

    1987-05-05

    The kinetic mechanism of carbamoyl-phosphate synthetase II from Syrian hamster kidney cells has been determined at pH 7.2 and 37 degrees C. Initial velocity, product inhibition, and dead-end inhibition studies of both the biosynthetic and bicarbonate-dependent adenosinetriphosphatase (ATPase) reactions are consistent with a partially random sequential mechanism in which the ordered addition of MgATP, HCO/sub 3/-, and glutamine is followed by the ordered release of glutamate and Pi. Subsequently, the binding of a second MgATP is followed by the release of MgADP, which precedes the random release of carbamoyl phosphate and a second MgADP. Carbamoyl-phosphate synthetase II catalyzes beta gamma-bridge:beta-nonbridge positional oxygen exchange of (gamma-/sup 18/O)ATP in both the ATPase and biosynthetic reactions. Negligible exchange is observed in the strict absence of HCO3- (and glutamine or NH/sub 4/+). The ratio of moles of MgATP exchanged to moles of MgATP hydrolyzed (nu ex/nu cat) is 0.62 for the ATPase reaction, and it is 0.39 and 0.16 for the biosynthetic reaction in the presence of high levels of glutamine and NH/sub 4/+, respectively. The observed positional isotope exchange is suppressed but not eliminated at nearly saturating concentrations of either glutamine or NH/sub 4/+, suggesting that this residual exchange results from either the facile reversal of an E-MgADP-carboxyphosphate-Gln(NH/sub 4/+) complex or exchange within an E-MgADP-carbamoyl phosphate-MgADP complex, or both. In the /sup 31/P NMR spectra of the exchanged (gamma-/sup 18/O)ATP, the distribution patterns of /sup 16/O in the gamma-phosphorus resonances in all samples reflect an exchange mechanism in which a rotationally unhindered molecule of (/sup 18/O, /sup 16/O)Pi does not readily participate.

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

    SciTech Connect

    Ferguson, J.M.

    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.

  3. 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).

  4. A two-color laser photolysis method for determining reaction rates of short-lived intermediates by product analysis: application to the o-quinodimethane problem.

    PubMed

    Ouchi, Akihiko; Li, Zhong; Sakuragi, Masako; Majima, Tetsuro

    2003-01-29

    A time-delayed, two-color pulse laser photolysis technique was used for a kinetic study of short-lived transient species through product analysis, the determination of the rate constant of the cycloaddition of o-quinodimethane (1) and maleic anhydride (2) in room-temperature solutions. o-Quinodimethane (1) was generated from 1,2-bis[(phenylseleno)methyl]benzene (3) by the irradiation of a pulse of a KrF excimer laser (248 nm) in the presence of excess 2, and a successive pulse of a XeCl excimer laser (308 nm) was irradiated to the reaction mixture after varied delay times from 0 to 0.1 s for the decomposition of the remaining 1 to quench the cycloaddition reaction. The rate constant of the cycloaddition of 1 and 2 was 2.1 x 10(5) M(-1) s(-1), which was obtained by the analysis of the delay-time dependence of the product yields. PMID:12537511

  5. Infrared Spectra and Density Functional Calculations for Singlet CH2═SiX2 and Triplet HC-SiX3 and XC-SiX3 Intermediates in Reactions of Laser-Ablated Silicon Atoms with Di-, Tri-, and Tetrahalomethanes.

    PubMed

    Cho, Han-Gook; Andrews, Lester

    2016-03-21

    Reactions of laser-ablated silicon atoms with di-, tri-, and tetrahalomethanes in excess argon were investigated, and the products were identified from the matrix infrared spectra, isotopic shifts, and density functional theory energy, bond length, and frequency calculations. Dihalomethanes produce planar singlet silenes (CH2═SiX2), and tri- and tetrahalomethanes form triplet halosilyl carbenes (HC-SiX3 and XC-SiX3). The Si-bearing molecules identified are the most stable, lowest-energy product in the reaction systems. While the C-Si bond in the silene is a true double bond, the C-Si bond in the carbene is a shortened single bond enhanced by hyperconjugation of the two unpaired electrons on C to σ*(Si-X) orbitals, which contributes stabilization through a small amount of π-bonding and reduction of the HCSi or XCSi angles. The C-Si bond lengths in these carbenes (1.782 Å for HC-SiF3) are between the single-bond length in the unobserved first insertion intermediate (1.975 Å for CHF2-SiF) and the double-bond length in the silene (1.704 Å for CHF═SiF2). The silicon s(2)p(2) and titanium s(2)d(2) electron configurations produce similar primary products, but the methylidyne with Ti has a bond to carbon stronger than that of the halosilyl carbene. PMID:26918739

  6. Hybrid model analysis of intermediate energy (20< E ?<140 MeV) photonuclear reactions on232Th and235,238U

    NASA Astrophysics Data System (ADS)

    Ryckbosch, D.; Carlos, P.; Leprtre, A.

    1988-12-01

    The hybrid model code ALICE/LIVERMORE 82 (with fission option) has been used in the study of photonuclear reactions on232Th and235,238U (20< E ?<140 MeV). The total fission probabilities P f were calculated. A model was established for the decay of the fission fragments. This model, together with the code ALICE, allowed the calculation of the cross sections ? (i) for emission of at least i neutrons, and of the average multiplicity v and width W of the neutron distribution for238U. The theoretical results for P f , ? (i) , v and W show very good agreement with existing experimental data. It is shown that a comparison of the calculations with the available experimental data does not allow for a discrimination between the various photon absorption mechanisms proposed (single-particle absorption vs. quasi-deuteron mechanism).

  7. 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.

  8. Recoil studies of photonuclear reactions on natCu, natAg, natTa, and 197Au at intermediate energies

    NASA Astrophysics Data System (ADS)

    Fujiwara, I.; Haba, H.; Matsumura, H.; Sakamoto, K.; Miyamoto, Y.; Oura, Y.; Shibata, S.; Furukawa, M.

    1999-01-01

    The recoil properties of nuclides produced in the photonuclear reactions on natCu, natAg, natTa, and 197Au induced by bremsstrahlung of end-point energies (E o) of 250 to 1000 MeV have been investigated using the thick-target thick-catcher method. The obtained mean ranges of produced nuclides smoothly increase with an increase of the mass difference (?A) between products and target, and show E 0-independence at E 0?600 MeV, reflecting the limiting behavior above (3, 3) resonance region. The mean kinetic energies, T, deduced from the mean ranges show the following two components; (1) (?, xn) products by giant-resonance and/or quasi-deuteron resonance absorption, (2) (?, xnyp) products by mainly (3, 3) resonance absorption. Slightly rapid increase of T was found around ?A=15, 18, 24, and 25 for natCu, natAg, natTa and 197Au, respectively, reflecting a change in mechanism. Kinematic properties of the product nuclei were calculated by using the PICA (Photon-Induced Intranuclear Cascade Analysis) code. The T calculated by the PICA code at E 0=400 MeV well reproduced the experimental results of natCu, but the same calculation for natAg, natTa, and 197Au gave lower mean kinetic energies than the experimental results.

  9. Recoil studies of photonuclear reactions on natCu, natAg, natTa, and 197Au at intermediate energies

    NASA Astrophysics Data System (ADS)

    Fujiwara, I.; Haba, H.; Matsumura, H.; Sakamoto, K.; Miyamoto, Y.; Oura, Y.; Shibata, S.; Furukawa, M.

    1999-01-01

    The recoil properties of nuclides produced in the photonuclear reactions on natCu, natAg, natTa, and 197Au induced by bremsstrahlung of end-point energies ( E o) of 250 to 1000 MeV have been investigated using the thick-target thick-catcher method. The obtained mean ranges of produced nuclides smoothly increase with an increase of the mass difference (?A) between products and target, and show E 0-independence at E 0?600 MeV, reflecting the limiting behavior above (3, 3) resonance region. The mean kinetic energies, T, deduced from the mean ranges show the following two components; (1) (?, xn) products by giant-resonance and/or quasi-deuteron resonance absorption, (2) (?, xnyp) products by mainly (3, 3) resonance absorption. Slightly rapid increase of T was found around ?A=15, 18, 24, and 25 for natCu, natAg, natTa and 197Au, respectively, reflecting a change in mechanism. Kinematic properties of the product nuclei were calculated by using the PICA (Photon-Induced Intranuclear Cascade Analysis) code. The T calculated by the PICA code at E 0=400 MeV well reproduced the experimental results of natCu, but the same calculation for natAg, natTa, and 197Au gave lower mean kinetic energies than the experimental results.

  10. Partial methylation of two adjacent adenosines in ribosomes from Euglena gracilis chloroplasts suggests evolutionary loss of an intermediate stage in the methyl-transfer reaction.

    PubMed

    Van Buul, C P; Hamersma, M; Visser, W; Van Knippenberg, P H

    1984-12-11

    Bacterial, cytoplasmic and organellar ribosomes from a wide phylogenetic spectrum of organisms have a characteristic m6(2)Am6(2)A structure near the 3' end of the RNA of the small ribosomal subunit (SSU). We have studied one of the few exceptions to this extremely conserved post-transcriptionally modified sequence, i.e. dimethylation of only one of the two A's in chloroplasts from Euglena gracilis. It was established that only the A closest to the 5' end is dimethylated, the other one being unmodified. The methylation reaction was studied in vitro using ribosomes from a kasugamycin resistant mutant (ksgA) of Escherichia coli and purified methyl-transferase. Using limited amounts of the methyl donor S-adenosylmethionine (SAM) a partial level of methylation (50% of control) was attained. It is shown that in this case the 3' proximal A is dimethylated while the other is not. This suggests that dimethylation takes place in two successive stages. Apparently in E. gracilis chloroplasts the first stage of methylation does not occur. PMID:6440121

  11. Eleven new heaviest isotopes of elements Z = 105 to Z = 117 identified among the products of 249Bk+48Ca reactions

    SciTech Connect

    Oganessian, Yuri Ts.; Abdullin, F. Sh.; Bailey, P. D.; Benker, D. E.; Bennett, M. E.; Dmitriev, S.; Ezold, Julie G.; Hamilton, J. H.; Henderson, R.; Itkis, M. G.; Lobanov, Yu. V.; Mezentsev, A. N.; Moody, K.; Nelson, S. L.; Polyakov, A. N.; Porter, C. E.; Ramayya, A. V.; Riley, F. D.; Roberto, James B; Ryabinin, M. A.; Rykaczewski, Krzysztof Piotr; Taylor, R; Tsyganov, Yu. S.; Utyonkov, V.; Voinov, A. A.; Vostokin, G. K.; Wilk, P. A.

    2011-01-01

    The heaviest isotopes of elements Z = 117 to Z = 105, 294117, 293117, 290115, 289115, 286113, 285113, 282Rg, 281Rg, 278Mt, 274Bh, and 270Db, were identified by means of the Dubna gas-filled recoil separator among the products of the 249Bk + 48Ca reaction. The details of the observed six decay chains, indicating the production and decay of isotopes 293117 and 294117, 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.

  12. Radiolytic oxidation of 1,2,4-benzenetriol. An application of time-resolved resonance Raman spectroscopy to kinetic studies of reaction intermediates

    SciTech Connect

    Qin, L.; Tripathi, G.N.R.; Schuler, R.H.

    1987-03-26

    In acidic solution, 1,2,4-benzenetriol is rapidly oxidized by OH or N/sub 3/ to form a mixture of neutral 2,4- and 3,4-dihydroxyphenoxyl radicals. At higher pH these radicals deprotonate (pK/sub a/(1) = 4.75) to form the 2-hydroxy-p-benzosemiquinone radical anion which exhibits a prominent resonance Raman band at 1625 cm/sup -1/ attributable to the Wilson 8a ring stretching mode. In basic solutions this radical subsequently reacts with OH/sup -/ to form the radical dianion (pK/sub a/(2) = 8.85) in which the 8a band is shifted to an appreciably lower frequency (1587 cm/sup -1/). While the absorption spectra of these latter radicals are very similar and do not allow ready examination of their interconversion by absorption spectrophotometry, the difference between these 8a frequencies is sufficiently great that the Raman method can be used to examine the acid-base equilibrium between the two forms of the radical and to follow the deprotonation kinetics. It is shown that even at high pH the radical monoanion is initially formed on oxidation by N/sub 3/ and that deprotonation subsequently occurs by its reaction with base with a rate constant of (9.6 +/- 1.5) x 10/sup 9/ M/sup -1/ d/sup -1/. These studies illustrate very well the application of time-resolved resonance Raman spectroscopy as a complement to kinetic spectrophotometry in sorting out the details of secondary processes in pulse radiolysis studies.

  13. Unimolecular dissociation of the propargyl radical intermediate of the CH+C{sub 2}H{sub 2} and C+C{sub 2}H{sub 3} reactions

    SciTech Connect

    McCunn, Laura R.; FitzPatrick, Benjamin L.; Krisch, Maria J.; Butler, Laurie J.; Liang, C.-W.; Lin, Jim J.

    2006-10-07

    This paper examines the unimolecular dissociation of propargyl (HCCCH{sub 2}) radicals over a range of internal energies to probe the CH+HCCH and C+C{sub 2}H{sub 3} bimolecular reactions from the radical intermediate to products. The propargyl radical was produced by 157 nm photolysis of propargyl chloride in crossed laser-molecular beam scattering experiments. The H-loss and H{sub 2} elimination channels of the nascent propargyl radicals were observed. Detection of stable propargyl radicals gave an experimental determination of 71.5 (+5/-10) kcal/mol as the lowest barrier to dissociation of the radical. This barrier is significantly lower than predictions for the lowest barrier to the radical's dissociation and also lower than calculated overall reaction enthalpies. Products from both H{sub 2}+HCCC and H+C{sub 3}H{sub 2} channels were detected at energies lower than what has been theoretically predicted. An HCl elimination channel and a minor C-H fission channel were also observed in the photolysis of propargyl chloride.

  14. Intramolecular charge transfer of 4-(dimethylamino)benzonitrile probed by time-resolved fluorescence and transient absorption: No evidence for two ICT states and a {pi}{sigma}{sup *} reaction intermediate

    SciTech Connect

    Zachariasse, Klaas A.; Druzhinin, Sergey I.; Senyushkina, Tamara; Kovalenko, Sergey A.

    2009-12-14

    For the double exponential fluorescence decays of the locally excited (LE) and intramolecular charge transfer (ICT) states of 4-(dimethylamino)benzonitrile (DMABN) in acetonitrile (MeCN) the same times {tau}{sub 1} and {tau}{sub 2} are observed. This means that the reversible LE<-->ICT reaction, starting from the initially excited LE state, can be adequately described by a two state mechanism. The most important factor responsible for the sometimes experimentally observed differences in the nanosecond decay time, with {tau}{sub 1}(LE)<{tau}{sub 1}(ICT), is photoproduct formation. By employing a global analysis of the LE and ICT fluorescence response functions with a time resolution of 0.5 ps/channel in 1200 channels reliable kinetic and thermodynamic data can be obtained. The arguments presented in the literature in favor of a {pi}{sigma}* state with a bent CN group as an intermediate in the ICT reaction of DMABN are discussed. From the appearance of an excited state absorption (ESA) band in the spectral region between 700 and 800 nm in MeCN for N,N-dimethylanilines with CN, Br, F, CF{sub 3}, and C(=O)OC{sub 2}H{sub 2} p-substituents, it is concluded that this ESA band cannot be attributed to a {pi}{sigma}{sup *} state, as only the C-C{identical_to}N group can undergo the required 120 deg. bending.

  15. Acid-catalyzed carboxylic acid esterification and ester hydrolysis mechanism: acylium ion as a sharing active intermediate via a spontaneous trimolecular reaction based on density functional theory calculation and supported by electrospray ionization-mass spectrometry.

    PubMed

    Shi, Hongchang; Wang, Yilei; Hua, Ruimao

    2015-11-11

    By DFT calculation, we found that acid-catalyzed carboxylic acid esterification and ester hydrolysis are brief two-step reactions. First, the carboxylic acid hydroxyl-oxygen or ester alkyl-oxygen is protonated, which generates a highly active acylium ion. The protonation requires an activation energy (Ea) of 4-10 kcal mol(-1), and is the rate-controlling step of the esterification or hydrolysis. Sequentially, the acylium ion spontaneously reacts with two alcohol or two water molecules to form a neutral product molecule; this is a trimolecular reaction. The acylium ion is the highly active intermediate shared by esterification and hydrolysis. ESI-MS data for several typical carboxylic acids confirmed that their acylium ions are easily generated. For 2,4,6-trialkylbenzoic acid and its ester, the two unsubstituted carbons in the benzene ring are very easily protonated, and we have thus revealed the root of the success of Newman's method. Based on these results, the popular esterification and hydrolysis mechanism in organic chemistry textbooks is incorrect. PMID:26445892

  16. Diverse modes of reactivity of dialkyl azodicarboxylates with P(III) compounds: synthesis, structure, and reactivity of products other than the Morrison-Brunn-Huisgen intermediate in a Mitsunobu-type reaction.

    PubMed

    Satish Kumar, N; Praveen Kumar, K; Pavan Kumar, K V P; Kommana, Praveen; Vittal, Jagadese J; Kumara Swamy, K C

    2004-03-19

    The reactivity of diethyl azodicarboxylate (DEAD)/diisopropyl azodicarboxylate (DIAD) with P(III) compounds bearing oxygen or nitrogen substituents is explored. Compounds with structures quite different from that of Morrison-Brunn-Huisgen intermediate R'(3)P(+)N(CO(2)R)N(-)(CO(2)R) (1), observed in the Mitsunobu reaction, have been established by using X-ray crystallography and NMR spectroscopy. Thus reactions with X(6-t-Bu-4-Me-C(6)H(2)O)(2)P-NH-t-Bu [X = S (8), CH(2) (9)] or XP(mu-N-t-Bu)(2)P-NH-t-Bu [X = Cl (14) or NH-t-Bu (15)] and DEAD/DIAD lead to phosphinimine-carbamate-type of products X[6-t-Bu-4-Me-C(6)H(2)O](2)P[N-t-Bu][N(CO(2)R)NH(CO(2)R)] [X = S, R = Et (16); X = CH(2), R = Et (17); X = CH(2), R = i-Pr (18)] or XP(mu-N-t-Bu)(2)P(N-t-Bu)[N-(CO(2)-i-Pr)-N(H)(CO(2)-i-Pr) [X = Cl (19), NH-t-Bu (20)]. Treatment of 19 with 2,2,2-trifluoroethanol afforded the product [(CF(3)CH(2)O)P(mu-N-t-Bu)(2)P(+)(NH-t-Bu)[N(CO(2)-i-Pr)(HNCO(2)-i-Pr)

  17. Synthesis of β-lactams by transition metal promoted Staudinger reactions: alternative synthetic approaches from transition metal enhanced organocatalysis to in situ, highly reactive intermediate synthesis and catalytic tandem reactions.

    PubMed

    Tuba, Robert

    2013-09-28

    The development of new types of β-lactam antibiotics is a relevant field of contemporary pharmaceutical research. Although many types of antibiotics are available on the market and widely used, β-lactam antibiotics are considered to be one of the best choice as they are highly effective while having reasonable safety profiles. The wide application however has led to the appearance of resistant bacteria suppressing their efficacy. In the last decade fewer and fewer new antibiotics have been launched into the market, however more and more multiresistant germs have appeared posing significant threats especially to patients who are suffering from chronic diseases and have weakened immune systems. The development of new, highly efficient antibiotics is now direly needed. One of the options to accelerate β-lactam antibiotic research is the development of alternative robust, convenient, versatile and cheap synthetic procedures in which the β-lactam molecules can be easily synthesized with the desired diastereoselectivity. The most general way to introduce diastereoselectivity in the chemical reactions is the application of chiral catalyst systems. While there are several systems for the synthesis of β-lactams the transition metal assisted Staudinger reaction--[2 + 2] cycloaddition between a ketene and an imine--remained the most simple and most versatile methodology. The motivation behind this brief review is to draw the chemical community's attention to the relevance and applicability of transition metal promoted Staudinger reactions in β-lactam based antibiotic development. This article summarizes the most relevant pioneer works completed on this field in order to open new ideas for the forthcoming organometallic systems based bioactive material development. PMID:23925443

  18. 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.

  19. In Situ Reverse Transcriptase-Nested Polymerase Chain Reaction to Identify Intracellular Nucleic Acids without the Necessity of Dnase Pretreatment and Hybridisation

    PubMed Central

    Menschikowski, Mario; Vogel, Margot; Eckey, Rolf; Dinnebier, Gerd; Jaross, Werner

    2001-01-01

    In the present study a protocol of in situ reverse transcriptase?nested polymerase chain reaction (in situ RT?nested PCR) was examined based on the following modifications. (i) To exclude false positive signals caused by DNA repair mechanisms and endogenous priming, a two?step PCR was applied after reverse transcription. The first step was performed in the presence of extrinsic primers and unlabeled nucleotides with a maximum of PCR cycles possible without destroying the cell morphology. The second step consisted of only one annealing/elongation reaction, the target sequence marked by addition of digoxigenin?labeled nucleotides and intrinsic primers. (ii) In order to prevent amplifications of genomic DNA nested primer pairs were applied crossing intron sequences. (iii) To minimize the diffusion of PCR products in cells, the extrinsic primers were extended with complementary 5??tails. This approach results in the generation of high molecular weight concatamers during PCR cycles. By applying this protocol, immunostainings specific for phospholipase A2 of type IIA mRNA were exclusively detectable in the cytoplasm of HepG2 hepatoma cells, which were used as a model system, whereas the nuclei were unstained. Multiple control experiments yielded completely negative results. These data suggest that the in situ RT?nested PCR, which in comparison to the method of in situ RT?PCR?in situ?hybridisation is simpler and less time?consuming, can be used as an alternative approach to identify intracellular nucleic acids. PMID:11455034

  20. False positive reaction of the immunohistochemistry technique using anti-BCG polyclonal antibodies to identify Mycobacterium leprae in wild nine-banded armadillos.

    PubMed

    Deps, Patrcia D; Michalany, Nilceo S; Tomimori-Yamashita, Jane

    2004-09-01

    The authors studied 66 wild nine-banded armadillos from Brazil. The ear samples were collected and Ziehl-Neelsen or Fite-Faraco stains were performed, as well as immunostaining using polyclonal BCG antibody, to avaluate the presence of the Mycobacterium leprae. The AFB were not detected by the Ziehl-Neelsen or Fite-Faraco staining, neither immunoexpression of the BCG marker. However, many normal structures from the ears of the nine-banded armadillos, such as condrocytes, condroblasts, fibroblasts and endothelial cells, and Gram positive bacteria cocci, showed false positive reaction by the BCG marker. The authors discuss the use of the immunohistochemical studies with the polyclonal BCG antibody to identify M. leprae antigens in wild armadillos. PMID:15485291

  1. 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)].

  2. Catalytic mechanism of ?-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling

    PubMed Central

    Barabs, Orsolya; Nmeth, Veronika; Bodor, Andrea; Perczel, Andrs; Rosta, Edina; Kele, Zoltn; Zagyva, Imre; Szabadka, Zoltn; Grolmusz, Vince I.; Wilmanns, Matthias; Vrtessy, Beta G.

    2013-01-01

    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 MasonPfizer 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 ?-phosphate site. Phosphorus-31 NMR spectroscopy (31P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue ?,?-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 enzymeproduct complex structure. PMID:23982515

  3. Effect of Bonding Time on Interfacial Reaction and Mechanical Properties of Diffusion-Bonded Joint Between Ti-6Al-4V and 304 Stainless Steel Using Nickel as an Intermediate Material

    NASA Astrophysics Data System (ADS)

    Thirunavukarasu, Gopinath; Kundu, Sukumar; Mishra, Brajendra; Chatterjee, Subrata

    2014-04-01

    In the current study, solid-state diffusion bonding between Ti-6Al-4V (TiA) and 304 stainless steel (SS) using pure nickel (Ni) of 200- ?m thickness as an intermediate material was carried out in vacuum. Uniaxial compressive pressure and temperature were kept at 4 MPa and 1023 K (750 C), respectively, and the bonding time was varied from 30 to 120 minutes in steps of 15 minutes. Scanning electron microscopy images, in backscattered electron mode, revealed the layerwise Ti-Ni-based intermetallics like either Ni3Ti or both Ni3Ti and NiTi at titanium alloy-nickel (TiA/Ni) interface, whereas nickel-stainless steel (Ni/SS) interface was free from intermetallic phases for all the joints. Chemical composition of the reaction layers was determined by energy dispersive spectroscopy (SEM-EDS) and confirmed by X-ray diffraction study. Maximum tensile strength of ~382 MPa along with ~3.7 pct ductility was observed for the joints processed for 60 minutes. It was found that the extent of diffusion zone at Ni/SS interface was greater than that of TiA/Ni interface. From the microhardness profile, fractured surfaces, and fracture path, it was demonstrated that the failure of the joints was initiated and propagated apparently at TiA/Ni interface near Ni3Ti intermetallic for bonding time less than 90 minutes, and through Ni for bonding time 90 minutes and greater.

  4. 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. PMID:26178593

  5. Effects of Low to Intermediate Water Concentrations on Proton-Coupled Electron Transfer (PCET) Reactions of Flavins in Aprotic Solvents and a Comparison with the PCET Reactions of Quinones.

    PubMed

    Tan, Serena L J; Novianti, Maria L; Webster, Richard D

    2015-11-01

    The electrochemical reduction mechanisms of 2 synthesized flavins (Flox) were examined in detail in deoxygenated solutions of DMSO containing varying amounts of water, utilizing variable scan rate cyclic voltammetry (? = 0.1-20 V s(-1)), controlled-potential bulk electrolysis, and UV-vis spectroscopy. Flavin 1, which contains a hydrogen atom at N(3), is capable of donating its proton to other reduced flavin species. After 1e(-) reduction, the initially formed Fl(-) receives a proton from another Flox to form FlH() (and concomitantly produce the deprotonated flavin, Fl(-)), although the equilibrium constant for this process favors the back reaction. Any FlH() formed at the electrode surface immediately undergoes another 1e(-) reduction to form FlH(-), which reacts with Fl(-) to form 2 molecules of Fl(-). Further 1e(-) reduction of Fl(-) at more negative potentials produces the dianion, Fl(2-), which can also be protonated by another Flox to form FlH(-) and Fl(-). Flavin 2, which is methylated at N(3) (and therefore has no acidic proton), undergoes a simple chemically reversible 1e(-) reduction process in DMSO provided the water content is low (<100 mM). Further 1e(-) reduction of Fl(-) (from flavin 2) at more negative potentials leads to the dianion, Fl(2-), which is protonated by trace water in solution to form FlH(-), similar to the mechanism of flavin 1 at high scan rates. Addition of sufficient amounts of water to nonaqueous solvents results in protonation of the anion radical species, Fl(-), for both flavins, causing an increase in the amount of FlH(-) in solution. This behavior contrasts with what is observed for quinones, which are also reduced in two 1e(-) steps in aprotic organic solvents to form the radical anions and dianions, but are able to exist in hydrogen-bonded forms (with trace or added water) without undergoing protonation. PMID:26447846

  6. The aromatic ene reaction

    NASA Astrophysics Data System (ADS)

    Niu, Dawen; Hoye, Thomas R.

    2014-01-01

    The ene reaction is a pericyclic process in which an alkene with 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 intermediate 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: (1) hexadehydro-Diels-Alder (for aryne generation), (2) intramolecular aromatic ene and (3) 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 multistage, reagent- and by-product-free, single-pot transformations.

  7. A Label-free Selected Reaction Monitoring Workflow Identifies a Subset of Pregnancy Specific Glycoproteins as Potential Predictive Markers of Early-onset Pre-eclampsia*

    PubMed Central

    Blankley, Richard T.; Fisher, Christal; Westwood, Melissa; North, Robyn; Baker, Philip N.; Walker, Michael J.; Williamson, Andrew; Whetton, Anthony D.; Lin, Wanchang; McCowan, Lesley; Roberts, Claire T.; Cooper, Garth J. S.; Unwin, Richard D.; Myers, Jenny E.

    2013-01-01

    Pre-eclampsia (PE) is a serious complication of pregnancy with potentially life threatening consequences for both mother and baby. Presently there is no test with the required performance to predict which healthy first-time mothers will go on to develop PE. The high specificity, sensitivity, and multiplexed nature of selected reaction monitoring holds great potential as a tool for the verification and validation of putative candidate biomarkersfor disease states. Realization of this potential involves establishing a high throughput, cost effective, reproducible sample preparation workflow. We have developed a semi-automated HPLC-based sample preparation workflow before a label-free selected reaction monitoring approach. This workflow has been applied to the search for novel predictive biomarkers for PE. To discover novel candidate biomarkers for PE, we used isobaric tagging to identify several potential biomarker proteins in plasma obtained at 15 weeks gestation from nulliparous women who later developed PE compared with pregnant women who remained healthy. Such a study generates a number of candidate biomarkers that require further testing in larger patient cohorts. As proof-of-principle, two of these proteins were taken forward for verification in a 100 women (58 PE, 42 controls) using label-free SRM. We obtained reproducible protein quantitation across the 100 samples and demonstrated significant changes in protein levels, even with as little as 20% change in protein concentration. The SRM data correlated with a commercial ELISA, suggesting that this is a robust workflow suitable for rapid, affordable, label-free verification of which candidate biomarkers should be taken forward for thorough investigation. A subset of pregnancy-specific glycoproteins (PSGs) had value as novel predictive markers for PE. PMID:23897580

  8. 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

  9. Multiplex polymerase chain reaction to identify and determine the toxigenicity of Corynebacterium spp with zoonotic potential and an overview of human and animal infections

    PubMed Central

    Torres, Luciene de Ftima Costa; Ribeiro, Dayana; Hirata, Raphael; Pacheco, Luis Gustavo Carvalho; Souza, Monica Cristina; dos Santos, Louisy Sanches; dos Santos, Cntia Silva; Salah, Mohammad; da Costa, Mateus Matiuzzi; Ribeiro, Marcio Garcia; Selim, Salah A; Azevedo, Vasco Ariston de Carvalho; Mattos-Guaraldi, Ana Luiza

    2013-01-01

    Corynebacterium diphtheriae, Corynebacterium ulcerans and Corynebacterium pseudotuberculosis constitute a group of potentially toxigenic microorganisms that are related to different infectious processes in animal and human hosts. Currently, there is a lack of information on the prevalence of disease caused by these pathogens, which is partially due to a reduction in the frequency of routine laboratory testing. In this study, a multiplex polymerase chain reaction (mPCR) assay that can simultaneously identify and determine the toxigenicity of these corynebacterial species with zoonotic potential was developed. This assay uses five primer pairs targeting the following genes: rpoB (Corynebacterium spp), 16S rRNA (C. ulcerans and C. pseudotuberculosis), pld (C. pseudotuberculosis), dtxR (C. diphtheriae) and tox [diphtheria toxin (DT) ]. In addition to describing this assay, we review the literature regarding the diseases caused by these pathogens. Of the 213 coryneform strains tested, the mPCR results for all toxigenic and non-toxigenic strains of C . diphtheriae, C. ulcerans and C. pseudotuberculosis were in 100% agreement with the results of standard biochemical tests and PCR-DT. As an alternative to conventional methods, due to its advantages of specificity and speed, the mPCR assay used in this study may successfully be applied for the diagnosis of human and/or animal diseases caused by potentially toxigenic corynebacterial species. PMID:23778659

  10. Effect of Bonding Temperature on Interfacial Reaction and Mechanical Properties of Diffusion-Bonded Joint Between Ti-6Al-4V and 304 Stainless Steel Using Nickel as an Intermediate Material

    NASA Astrophysics Data System (ADS)

    Thirunavukarasu, Gopinath; Kundu, Sukumar; Mishra, Brajendra; Chatterjee, Subrata

    2014-04-01

    An investigation was carried out on the solid-state diffusion bonding between Ti-6Al-4V (TiA) and 304 stainless steel (SS) using pure nickel (Ni) of 200- ?m thickness as an intermediate material prepared in vacuum in the temperature range from 973 K to 1073 K (700 C to 800 C) in steps of 298 K (25 C) using uniaxial compressive pressure of 3 MPa and 60 minutes as bonding time. Scanning electron microscopy images, in backscattered electron mode, had revealed existence of layerwise Ti-Ni-based intermetallics such as either Ni3Ti or both Ni3Ti and NiTi at titanium alloy-nickel (TiA/Ni) interface, whereas nickel-stainless steel (Ni/SS) diffusion zone was free from intermetallic phases for all joints processed. Chemical composition of the reaction layers was determined in atomic percentage by energy dispersive spectroscopy and confirmed by X-ray diffraction study. Room-temperature properties of the bonded joints were characterized using microhardness evaluation and tensile testing. The maximum hardness value of ~800 HV was observed at TiA/Ni interface for the bond processed at 1073 K (800 C). The hardness value at Ni/SS interface for all the bonds was found to be ~330 HV. Maximum tensile strength of ~206 MPa along with ~2.9 pct ductility was obtained for the joint processed at 1023 K (750 C). It was observed from the activation study that the diffusion rate at TiA/Ni interface is lesser than that at the Ni/SS interface. From microhardness profile, fractured surfaces and fracture path, it was demonstrated that failure of the joints was initiated and propagated apparently at the TiA/Ni interface near Ni3Ti intermetallic phase.

  11. 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.

  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

    NASA Astrophysics Data System (ADS)

    Miller, Laurence G.; Warner, Karen L.; Baesman, Shaun M.; Oremland, Ronald S.; McDonald, Ian R.; Radajewski, Stefan; Murrell, J. Colin

    2004-08-01

    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.

  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)

    Mickler, P. J.; Lu, J.; Nicot, J.

    2013-12-01

    An important side effect of hydraulic fracturing (HF) in shale gas wells is the production of saline flow-back water. This water often contains total dissolved soil (TDS) concentrations greater than 100,000 ppm which requires expensive treatment and disposal of the produced water. Possible origins of the high TDS content include: 1. Mixing of fresh HF-fluids with highly saline pore fluids in the targeted shale. 2. Migration and mixing of saline brines by newly-formed fractures into the HF-water from neighboring formations. 3. Water rock interactions between the targeted shale and HF-water that include mineral dissolution, pyrite oxidation buffered by carbonate dissolution and cation exchange in newly hydrated clay minerals.. These possibilities are not mutually exclusive and all may be operating to alter flow-back water chemistry. This study will examine geochemical reactions between a productive Gulf Coast shale and manufactured HF-waters using sealed bench top experiments and high temperature/high pressure autoclave experiments. The samples of the shale were collected from core material housed at The Bureau of Economic Geology collected from two wells. The manufactured HF-waters were produced by mixing NaCl, KCl and CaCl2 salts with De-ionized water at approximately 0, 2000 and 20,000 ppm. During experiments, elements that show large increases in aqueous concentrations are Na, Cl, Ca and SO4. Simultaneous increases in Na and Cl, coupled with high Cl/Br ratios, suggest halite dissolution rather than pore space brine is responsible for Na and Cl concentrations. Simultaneous increase in Ca and SO4 suggest anhydrite dissolution. (SEM imaging shows that anhydrite crystals are usually embedded with the framework mineral grains, rather than precipitated in pores during sample drying, which suggests mineral source of Ca and SO4, possibly for Na and Cl as well). Pyrite oxidation and calcium carbonate dissolution were not significant due to no decrease in pH and no 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)

    Molnar, I. L.; O'Carroll, D. M.; Willson, C. S.; Gerhard, J.

    2011-12-01

    An important side effect of hydraulic fracturing (HF) in shale gas wells is the production of saline flow-back water. This water often contains total dissolved soil (TDS) concentrations greater than 100,000 ppm which requires expensive treatment and disposal of the produced water. Possible origins of the high TDS content include: 1. Mixing of fresh HF-fluids with highly saline pore fluids in the targeted shale. 2. Migration and mixing of saline brines by newly-formed fractures into the HF-water from neighboring formations. 3. Water rock interactions between the targeted shale and HF-water that include mineral dissolution, pyrite oxidation buffered by carbonate dissolution and cation exchange in newly hydrated clay minerals.. These possibilities are not mutually exclusive and all may be operating to alter flow-back water chemistry. This study will examine geochemical reactions between a productive Gulf Coast shale and manufactured HF-waters using sealed bench top experiments and high temperature/high pressure autoclave experiments. The samples of the shale were collected from core material housed at The Bureau of Economic Geology collected from two wells. The manufactured HF-waters were produced by mixing NaCl, KCl and CaCl2 salts with De-ionized water at approximately 0, 2000 and 20,000 ppm. During experiments, elements that show large increases in aqueous concentrations are Na, Cl, Ca and SO4. Simultaneous increases in Na and Cl, coupled with high Cl/Br ratios, suggest halite dissolution rather than pore space brine is responsible for Na and Cl concentrations. Simultaneous increase in Ca and SO4 suggest anhydrite dissolution. (SEM imaging shows that anhydrite crystals are usually embedded with the framework mineral grains, rather than precipitated in pores during sample drying, which suggests mineral source of Ca and SO4, possibly for Na and Cl as well). Pyrite oxidation and calcium carbonate dissolution were not significant due to no decrease in pH and no 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. 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,

  16. 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.

  17. 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. PMID:25501114

  18. 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.

  19. 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

    The occurrence of high nitrite concentrations as a result of anthropogenic activities is an important water quality concern as it is highly toxic to human and fauna, and it is used as a nitrogen source for the assimilation process. The toxicity of nitrite is related to its transformation into carcinogenic N-nitroso compounds, which are suspected to be responsible for some gastric cancers, and to its ability to convert the hemoglobin to methaemoglobin what is then unable to fix oxygen and to transport it to the tissues, involving hypoxia and the blue-baby syndrome [1]. To reduce the adverse effect of nitrite on human health and on macroalgal blooms, any process enhancing the transformation of nitrite ions to nitrogen gas is of interest for the remediation of natural environments. To achieve this purpose the use of processes involving Fe(II)-containing minerals could be considered as one of the best options. Green-rusts are mixed Fe(II-III) layered double hydroxides commonly found in anoxic zones of natural environments such as sediments and hydromorphic soils. In such anoxic environments, green rust minerals play an important role in the biogeochemical redox cycling of iron and nitrogen, and can affect the speciation and mobility of many organic and inorganic contaminants. The present study investigates the reduction of nitrite by two synthetic and two biogenic green rusts. On the one hand, Fe(II-III) hydroxychloride and Fe(II-III) hydroxycarbonate green rusts were used as synthetic interlayer forms of GR, which are referred to as ';syn-GR(CO3)' and ';syn-GR(Cl)', respectively. On the other hand, the study was performed with biogenic Fe(II-III) hydroxycarbonate green rusts obtained from the bioreduction of two ferric precursors, either Fe(III)-oxyhydroxycarbonate or lepidocrocite; these biogenic green rusts are referred to as ';bio-GR(CO3)F' and ';bio-GR(CO3)L', respectively. For synthetic green rusts, results showed that the oxidation of both syn-GR(CO3) and syn-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.

  20. 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

    NASA Astrophysics Data System (ADS)

    Miller, L. G.; Warner, K. L.; Baesman, S. M.; Oremland, R. S.; McDonald, I. R.; Radajewski, S.; Murrell, J. C.

    2003-12-01

    Methyl bromide (MeBr) and methyl chloride (MeCl) are important atmospheric trace gases that contribute directly to stratospheric ozone depletion. These compounds have natural and anthropogenic sources and sinks in both aquatic and terrestrial environments. Soils comprise the largest known sink for MeBr on the Earth's surface and are also a large sink for MeCl. However, the processes that influence the flux of these compounds from air to soil or soil to air are poorly understood at present. Bacteria in soil microcosm experiments oxidized both MeCl and MeBr, the former compound more rapidly than the latter. MeBr was also removed by chemical reactions while MeCl was not. Chemical degradation of MeBr accounted for more than half of its total loss. We applied new techniques to determine if different bacteria were responsible for degrading MeBr and MeCl. Stable isotope probing revealed that different populations of soil bacteria assimilated added 13C-labeled MeBr and MeCl. Soil bacterial oxidation of MeBr and MeCl was characterized by different kinetic isotope effects (KIEs). The KIE for MeBr oxidation by bacteria was 22 +/- 5 \\permil and the KIE for MeCl oxidation was 56 +/- 3 \\permil, suggesting that different bacteria were responsible for degrading each compound. The identity of the active MeBr and MeCl degrading bacteria in soil was determined by analysis of 16S rDNA sequences amplified from 13C-DNA fractions. The diverse population of active bacteria was reflected by the range of sequences found for the cmuA gene, which codes for the enzyme that catalyzes the initial step in the oxidation of MeBr and MeCl. The diversity and number of different bacteria actively degrading MeBr and MeCl in the soil and the number of bacteria identified that contain the enzyme capable of degrading methyl halides were in contrast to the limited number of methyl halide degrading bacteria that have been isolated thus far from soil and aquatic environments; thus suggesting that the extant degraders represent only a subset of the natural diversity of methyl halide degrading bacteria.

  1. Identification of combustion intermediates in a low-pressure premixed laminar 2,5-dimethylfuran/oxygen/argon flame with tunable synchrotron photoionization

    SciTech Connect

    Wu, Xuesong; Huang, Zuohua; Wei, Lixia; Yuan, Tao; Zhang, Kuiwen

    2009-07-15

    Low-pressure (4.0 kPa) premixed laminar 2,5-dimethylfuran (DMF)/oxygen/argon flame with an equivalence ratio of 2.0 was studied with tunable vacuum ultraviolet (VUV) synchrotron radiation photoionization and molecular-beam mass spectrometry. Photoionization mass spectra of DMF/O{sub 2}/Ar flame were recorded and the photoionization efficiency curves of the combustion intermediates were measured. Flame species, including isomeric intermediates, are identified by comparing the measured ionization energies with those reported in literatures or those calculated with Gaussian-3 procedure. More than 70 species have been detected, including furan and its derivatives, aromatics, and free radicals. Possible reaction pathways of DMF, 2-methylfuran, and furan are proposed based on the intermediates identified. DMF can be consumed by H-abstraction and pyrolysis reactions. 2-Methylfuran and furan can be consumed by H-abstraction, H-addition and pyrolysis reactions. (author)

  2. 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 DOEs Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US DOE by Battelle Memorial Institute.

  3. MHD intermediate shock discontinuities. I - Rankine-Hugoniot conditions

    NASA Technical Reports Server (NTRS)

    Kennel, C. F.; Blandford, R. D.; Coppi, P.

    1989-01-01

    Recent numerical investigations have focused attention once more on the role of intermediate shocks in MHD. Four types of intermediate shock are identified using a graphical representation of the MHD Rankine-Hugoniot conditions. This same representation can be used to exhibit the close relationship of intermediate shocks to switch-on shocks and rotational discontinuities. The conditions under which intermediate discontinuities can be found are elucidated. The variations in velocity, pressure, entropy and magnetic-field jumps with upstream parameters in intermediate shocks are exhibited graphically. The evolutionary arguments traditionally advanced against intermediate shocks may fail because the equations of classical MHD are not strictly hyperbolic.

  4. Teaching about "Intermediate Forms."

    ERIC Educational Resources Information Center

    Hazard, Evan B.

    1998-01-01

    Argues that the common assumption about the lack of intermediate forms in evolutionary history is inaccurate and misleading. Points out that there are many transitional forms, although special creationists refuse to recognize them as such. (DDR)

  5. 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.

  6. Exchange reactions catalyzed by group-transferring enzymes oppose the quantitation and the unravelling of the identify of the pentose pathway.

    PubMed

    Flanigan, I; Collins, J G; Arora, K K; MacLeod, J K; Williams, J F

    1993-04-01

    1. The distributions and rates of transfer of carbon isotopes from a selection of specifically labelled ketosugar-phosphate substrates by exchange reactions catalyzed by the pentose and photosynthetic carbon-reduction-pathway group-transferring enzymes transketolase, transaldolase and aldolase have been measured using 13C-NMR spectroscopy. 2. The rates of these exchange reactions were 5, 4 and 1.5 mumol min-1 mg-1 for transketolase exchange, transaldolase exchange and aldolase exchange, respectively. 3. A comparison of the exchange capacities contributed by the activities of these enzymes in three in vitro liver preparations with the maximum non-oxidative pentose pathway flux rates of the preparations shows that transketolase and aldolase exchanges exceeded flux by 9-19 times in liver cytosol and acetone powder enzyme preparations and by 5 times in hepatocytes. Transaldolase was less effective in the comparison of exchange versus flux rates: transaldolase exchange exceeded flux by 1.6 and 5 in catalysis by liver cytosol and acetone powder preparations, respectively, but was only 0.6 times the flux in hepatocytes. 4. Values of group enzyme exchange and pathway flux rates in the above three preparations are important because of the feature role of liver and of these particular preparations in the establishment, elucidation and measurement of a proposed reaction scheme for the fat-cell-type pentose pathway in biochemistry. 5. It is the claim of this paper that the excess of exchange rate activity (particularly transketolase exchange) over pathway flux will overturn attempts to unravel, using isotopically labelled sugar substrates, the identity, reaction sequence and quantitative contribution of the pentose pathway to glucose metabolism. 6. The transketolase exchange reactions relative to the pentose pathway flux rates in normal, regenerating and foetal liver, Morris hepatomas, mammary carcinoma, melanoma, colonic epithelium, spinach chloroplasts and epididymal fat tissue show that transketolase exchange may exceed flux in these tissues by factors ranging over 5-600 times. 7. The confusion of pentose pathway theory by the effects of transketolase exchange action is illustrated by the 13C-NMR spectrum of the hexose 6-phosphate products of ribose 5-phosphate dissimilation, formed after 30 min of liver enzyme action, and shows 13C-labelling in carbons 1 and 3 of glucose 6-phosphate with ratios which range over 2.1-6.4 rather than the mandatory value of 2 which is imposed by the theoretical mechanism of the pathway. PMID:8477719

  7. Structure and Mechanistic Implications of a Tryptophan Synthase Quinonoid Intermediate

    SciTech Connect

    Barends,T.; Domratcheva, T.; Kulik, V.; Blumenstein, L.; Niks, D.; Dunn, M.; Schlichting, I.

    2008-01-01

    Quinonoid intermediates play a key role in the catalytic mechanism of pyridoxal 5'-phosphate (PLP)-dependent enzymes. Whereas structures of other PLP-bound reaction intermediates have been determined, a high-quality structure of a quinonoid species has not been reported. We present the crystal structure of the indoline quinonoid intermediate of tryptophan synthase (see figure) and discuss its implications for the enzymatic mechanism and allosteric regulation.

  8. Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase.

    PubMed

    Bolduc, J M; Dyer, D H; Scott, W G; Singer, P; Sweet, R M; Koshland, D E; Stoddard, B L

    1995-06-01

    Site-directed mutagenesis and Laue diffraction data to 2.5 A resolution were used to solve the structures of two sequential intermediates formed during the catalytic actions of isocitrate dehydrogenase. Both intermediates are distinct from the enzyme-substrate and enzyme-product complexes. Mutation of key catalytic residues changed the rate determining steps so that protein and substrate intermediates within the overall reaction pathway could be visualized. PMID:7761851

  9. 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

  10. 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. PMID:22258665

  11. Multifragmentation in intermediate energy heavy ion collisions

    SciTech Connect

    Jacak, B.V.; Britt, H.C.; Claesson, G.; Doss, K.G.R.; Ferguosn, R.; Gavron, A.I.; Gustafsson, H.A.; Gutbrod, H.; Harris, J.W.; Kampert, K.H.

    1986-04-14

    The GSL/LBL plastic ball/wall detector system was used to gain insight into the fragment production mechanism in Au + Au and Au + Fe reactions. Full azimuthal coverage for light particles (p,d,t,/sup 3/He,/sup 4/He) and intermediate mass fragments (z greater than 10) is achieved in the forward hemisphere in the center of mass system. The complete measurement of light particles allowed a global analysis of the events and a search for collective effects in fragment emission by comparing to flow effects seen in the light particles. The large acceptance for intermediate mass fragments allowed a measurements of their multiplicities event-by-event.

  12. Intermediates in the Formation of Aromatics in Hydrocarbon Combustion

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

    1994-01-01

    The formation of the first benzene ring is believed to be the rate limiting step in soot formation. Two different mechanisms have been proposed for formation of cyclic C6 species. The first involves the reaction of two acetylenes to give CH2CHCCH (vinyl acetylene), the loss of a H to give CHCHCCH (n-C41-13) or CH2CCCH (iso-C4H3), and addition of another acetylene to n-C4H3, followed by ring closure to give phenyl radical. Miller and Melius argue that only n-C4H3 leads to phenyl radical and since iso-C4H3 is more stable than n-C4H3 this mechanism is unlikely. An alternative mechanism proposed by them is formation of benzene from the dimerization of two CH2CCH (propargyl) radicals (formed by the reaction of singlet methylene with C2H2). We report reaction pathways and accurate energetics (from CASSCF/internally contracted CI calculations) for the reactions of CH(pi-2) and CH2-1 with acetylene, the reaction of vinylidene with acetylene, and the reaction of n-C4H3 and iso-C4H3 with acetylene. These calculations identify two new reactive intermediates CHCHCH ( a A"-2 ground state in Cs symmetry; spin coupling is a doublet from three singly occupied orbitals) and CHCCH (B-3 ground state in C2 symmetry) from the reaction of CH with acetylene. These species dimerize with no barrier to form benzene and para-benzyne, respectively. CHCCH is proposed as a reactive intermediate which can add to benzene to give higher polynuclear aromatic hydrocarbons or fullerenes. The addition of a C3H2 unit releases two C-C bond energies and thus the resulting addition product contains sufficient energy to break several CH bonds leading to a reduction in the H to C ratio as the cluster size increases. It is found that iso-C4H3 adds to acetylene to initially give a fulvene radical but that this species rearranges to phenyl radical. Thus, the reaction of acetylene with iso-C4H3 does lead to phenyl radical and the cyclization pathway may also contribute to formation of the initial benzene ring.

  13. Intermediate DNA methylation is a conserved signature of genome regulation

    PubMed Central

    Elliott, GiNell; Hong, Chibo; Xing, Xiaoyun; Zhou, Xin; Li, Daofeng; Coarfa, Cristian; Bell, Robert J.A.; Maire, Cecile L.; Ligon, Keith L.; Sigaroudinia, Mahvash; Gascard, Philippe; Tlsty, Thea D.; Harris, R. Alan; Schalkwyk, Leonard C.; Bilenky, Misha; Mill, Jonathan; Farnham, Peggy J.; Kellis, Manolis; Marra, Marco A.; Milosavljevic, Aleksandar; Hirst, Martin; Stormo, Gary D.; Wang, Ting; Costello, Joseph F.

    2015-01-01

    The role of intermediate methylation states in DNA is unclear. Here, to comprehensively identify regions of intermediate methylation and their quantitative relationship with gene activity, we apply integrative and comparative epigenomics to 25 human primary cell and tissue samples. We report 18,452 intermediate methylation regions located near 36% of genes and enriched at enhancers, exons and DNase I hypersensitivity sites. Intermediate methylation regions average 57% methylation, are predominantly allele-independent and are conserved across individuals and between mouse and human, suggesting a conserved function. These regions have an intermediate level of active chromatin marks and their associated genes have intermediate transcriptional activity. Exonic intermediate methylation correlates with exon inclusion at a level between that of fully methylated and unmethylated exons, highlighting gene context-dependent functions. We conclude that intermediate DNA methylation is a conserved signature of gene regulation and exon usage. PMID:25691127

  14. Structure-property relationship of bifunctional MnO2 nanostructures: highly efficient, ultra-stable electrochemical water oxidation and oxygen reduction reaction catalysts identified in alkaline media.

    PubMed

    Meng, Yongtao; Song, Wenqiao; Huang, Hui; Ren, Zheng; Chen, Sheng-Yu; Suib, Steven L

    2014-08-13

    Manganese oxides of various structures (?-, ?-, and ?-MnO2 and amorphous) were synthesized by facile methods. The electrocatalytic properties of these materials were systematically investigated for catalyzing both oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) in alkaline media. Extensive characterization was correlated with the activity study by investigating the crystal structures (XRD, HRTEM), morphologies (SEM), porosities (BET), surfaces (XPS, O2-TPD/MS), and electrochemical properties (Tafel analysis, Koutechy-Levich plots, and constant-current electrolysis). These combined results show that the electrocatalytic activities are strongly dependent on the crystallographic structures, and follow an order of ?-MnO2 > AMO > ?-MnO2 > ?-MnO2. Both OER studies and ORR studies reveal similar structure-determined activity trends in alkaline media. In the OER studies, ?-MnO2 displays an overpotential of 490 mV compared to 380 mV shown by an Ir/C catalyst in reaching 10 mA cm(-2). Meanwhile, ?-MnO2 also exhibits stability for 3 h when supplying a constant current density of 5 mA cm(-2). This was further improved by adding Ni(2+) dopants (ca. 8 h). The superior OER activity was attributed to several factors, including abundant di-?-oxo bridges existing in ?-MnO2 as the protonation sites, analogous to the OEC in PS-II of the natural water oxidation system; the mixed valencies (AOS = 3.7); and the lowest charge transfer resistances (91.8 ?, ? = 430 mV) as revealed from in situ electrochemical impedance spectroscopy (EIS). In the ORR studies, when reaching 3 mA cm(-2), ?-MnO2 shows 760 mV close to 860 mV for the best ORR catalyst (20% Pt/C). The outstanding ORR activity was due to the strongest O2 adsorption capability of ?-MnO2 suggested by temperature-programmed desorption. As a result, this discovery of the structure-related electrocatalytic activities could provide guidance in the further development of easily prepared, scalable, and low-cost catalysts based on metal oxides and their derivatives. PMID:25058174

  15. The Shopping Center. Intermediate.

    ERIC Educational Resources Information Center

    Timmons, Darrell; And Others

    This teaching guide is designed to develop thinking skills of intermediate elementary school children by using the concept of a shopping center. Thinking skills defined in the guide are observing, recalling, noticing differences and similarities, ordering, grouping, concept labeling, classifying, concept testing, inferring causes and effects,

  16. 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

  17. Intermediate Mathematics Study Guide.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. School Mathematics Study Group.

    This SMSG study guide is intended to provide teachers who use "Intermediate Mathematics," as a textbook with references to materials which will help them to gain a better understanding of the mathematics contained in the text. For each chapter of the text a brief resume of its content is followed by a list of annotated references which are…

  18. 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. PMID:22232460

  19. Appropriate chicken sample size for identifying the composition of broiler intestinal microbiota affected by dietary antibiotics, using the polymerase chain reaction-denaturing gradient gel electrophoresis technique.

    PubMed

    Zhou, H; Gong, J; Brisbin, J T; Yu, H; Sanei, B; Sabour, P; Sharif, S

    2007-12-01

    The bacterial microbiota in the broiler gastrointestinal tract are crucial for chicken health and growth. Their composition can vary among individual birds. To evaluate the composition of chicken microbiota in response to environmental disruption accurately, 4 different pools made up of 2, 5, 10, and 15 individuals were used to determine how many individuals in each pool were required to assess the degree of variation when using the PCR-denaturing gradient gel electrophoresis (DGGE) profiling technique. The correlation coefficients among 3 replicates within each pool group indicated that the optimal sample size for comparing PCR-DGGE bacterial profiles and downstream applications (such as identifying treatment effects) was 5 birds per pool for cecal microbiota. Subsequently, digesta from 5 birds was pooled to investigate the effects on the microbiota composition of the 2 most commonly used dietary antibiotics (virginiamycin and bacitracin methylene disalicylate) at 2 different doses by using PCR-DGGE, DNA sequencing, and quantitative PCR techniques. Thirteen DGGE DNA bands were identified, representing bacterial groups that had been affected by the antibiotics. Nine of them were validated. The effect of dietary antibiotics on the microbiota composition appeared to be dose and age dependent. These findings provide a working model for elucidating the mechanisms of antibiotic effects on the chicken intestinal microbiota and for developing alternatives to dietary antibiotics. PMID:18029800

  20. Criegee intermediates in the indoor environment. New insights

    DOE PAGESBeta

    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.

  1. Experimental and Theoretical Study on the OH-Reaction Kinetics and Photochemistry of Acetyl Fluoride (CH3C(O)F), an Atmospheric Degradation Intermediate of HFC-161 (C2H5F).

    PubMed

    Song, Xinli; Zgner, Gbor L; Farkas, Mria; Ills, dm; Sarzy?ski, Dariusz; Rozgonyi, Tams; Wang, Baoshan; Db, Sndor

    2015-07-16

    The direct reaction kinetic method of low pressure fast discharge flow (DF) with resonance fluorescence monitoring of OH (RF) has been applied to determine rate coefficients for the overall reactions OH + C2H5F (EtF) (1) and OH + CH3C(O)F (AcF) (2). Acetyl fluoride reacts slowly with the hydroxyl radical, the rate coefficient at laboratory temperature is k2(300 K) = (0.74 0.05) 10(-14) cm(3) molecule(-1) s(-1) (given with 2? statistical uncertainty). The temperature dependence of the reaction does not obey the Arrhenius law and it is described well by the two-exponential rate expression of k2(300-410 K) = 3.60 10(-3)?exp(-10500/T) + 1.56 10(-13)?exp(-910/T) cm(3) molecule(-1) s(-1). The rate coefficient of k1 = (1.90 0.19) 10(-13) cm(3) molecule(-1) s(-1) has been determined for the EtF-reaction at room temperature (T = 298 K). Microscopic mechanisms for the OH + CH3C(O)F reaction have also been studied theoretically using the ab initio CBS-QB3 and G4 methods. Variational transition state theory was employed to obtain rate coefficients for the OH + CH3C(O)F reaction as a function of temperature on the basis of the ab initio data. The calculated rate coefficients are in good agreement with the experimental data. It is revealed that the reaction takes place predominantly via the indirect H-abstraction mechanism involving H-bonded prereactive complexes and forming the nascent products of H2O and the CH2CFO radical. The non-Arrhenius behavior of the rate coefficient at temperatures below 500 K is ascribed to the significant tunneling effect of the in-the-plane H-abstraction dynamic bottleneck. The production of FC(O)OH + CH3 via the addition/elimination mechanism is hardly competitive due to the significant barriers along the reaction routes. Photochemical experiments of AcF were performed at 248 nm by using exciplex lasers. The total photodissociation quantum yield for CH3C(O)F has been found significantly less than unity; among the primary photochemical processes, C-C bond cleavage is by far dominating compared with CO-elimination. The absorption spectrum of AcF has also been determined by displaying a strong blue shift compared with the spectra of aliphatic carbonyls. Consequences of the results on atmospheric chemistry have been discussed. PMID:25859909

  2. Carbonylation as a Key Reaction in Anaerobic Acetone Activation by Desulfococcus biacutus

    PubMed Central

    Gutiérrez Acosta, Olga B.; Hardt, Norman

    2013-01-01

    Acetone is activated by aerobic and nitrate-reducing bacteria via an ATP-dependent carboxylation reaction to form acetoacetate as the first reaction product. In the activation of acetone by sulfate-reducing bacteria, acetoacetate has not been found to be an intermediate. Here, we present evidence of a carbonylation reaction as the initial step in the activation of acetone by the strictly anaerobic sulfate reducer Desulfococcus biacutus. In cell suspension experiments, CO was found to be a far better cosubstrate for acetone activation than CO2. The hypothetical reaction product, acetoacetaldehyde, is extremely reactive and could not be identified as a free intermediate. However, acetoacetaldehyde dinitrophenylhydrazone was detected by mass spectrometry in cell extract experiments as a reaction product of acetone, CO, and dinitrophenylhydrazine. In a similar assay, 2-amino-4-methylpyrimidine was formed as the product of a reaction between acetoacetaldehyde and guanidine. The reaction depended on ATP as a cosubstrate. Moreover, the specific activity of aldehyde dehydrogenase (coenzyme A [CoA] acylating) tested with the putative physiological substrate was found to be 153 ± 36 mU mg−1 protein, and its activity was specifically induced in extracts of acetone-grown cells. Moreover, acetoacetyl-CoA was detected (by mass spectrometry) after the carbonylation reaction as the subsequent intermediate after acetoacetaldehyde was formed. These results together provide evidence that acetoacetaldehyde is an intermediate in the activation of acetone by sulfate-reducing bacteria. PMID:23913429

  3. Unveiling the crucial intermediates in androgen production.

    PubMed

    Mak, Piotr J; Gregory, Michael C; Denisov, Ilia G; Sligar, Stephen G; Kincaid, James R

    2015-12-29

    Ablation of androgen production through surgery is one strategy against prostate cancer, with the current focus placed on pharmaceutical intervention to restrict androgen synthesis selectively, an endeavor that could benefit from the enhanced understanding of enzymatic mechanisms that derives from characterization of key reaction intermediates. The multifunctional cytochrome P450 17A1 (CYP17A1) first catalyzes the typical hydroxylation of its primary substrate, pregnenolone (PREG) and then also orchestrates a remarkable C17-C20 bond cleavage (lyase) reaction, converting the 17-hydroxypregnenolone initial product to dehydroepiandrosterone, a process representing the first committed step in the biosynthesis of androgens. Now, we report the capture and structural characterization of intermediates produced during this lyase step: an initial peroxo-anion intermediate, poised for nucleophilic attack on the C20 position by a substrate-associated H-bond, and the crucial ferric peroxo-hemiacetal intermediate that precedes carbon-carbon (C-C) bond cleavage. These studies provide a rare glimpse at the actual structural determinants of a chemical transformation that carries profound physiological consequences. PMID:26668369

  4. Highly enantioselective trapping of zwitterionic intermediates by imines

    NASA Astrophysics Data System (ADS)

    Qiu, Huang; Li, Ming; Jiang, Li-Qin; Lv, Feng-Ping; Zan, Li; Zhai, Chang-Wei; Doyle, Michael P.; Hu, Wen-Hao

    2012-09-01

    Reactions with the unstable and highly reactive zwitterionic intermediates generated in processes catalysed by transition metals are providing new opportunities for molecular constructions. Insertion reactions involve the collapse of zwitterionic intermediates, but trapping them would allow structural elaborations that are not currently available. To synthesize complex molecules in this manner, reactive electrophiles can be used to trap the zwitterionic intermediates. Here, we describe the use of imines, activated by chiral organocatalysts, and a highly efficient integrated rhodium and chiral Brnsted acid co-catalysed process to trap zwitterionic intermediates that have been proposed previously to undergo a formal C-H insertion reaction, allowing us to obtain polyfunctionalized indole and oxindole derivatives in a single step with excellent diastereoselectivity and enantioselectivity.

  5. 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.

  6. 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.

  7. Activity and stability of the luciferase--flavin intermediate.

    PubMed

    Becvar, J E; Tu, S C; Hastings, J W

    1978-05-01

    A luciferase intermediate in the bacterial bioluminescence system, which is formed by reaction of enzyme with reduced flavin mononucleotide (FMNH2) and oxygen, is shown to emit light with added aldehyde under anaerobic conditions. The reaction with oxygen is thus effectively irreversible under the conditions used. The flavin chromophore has an absorption maximum at about 370 nm and the potential activity (bioluminescence yield) in the further reaction of the isolated intermediate with aldehyde is strictly proportional to the amount of this flavin chromophore. PMID:306832

  8. On the role of the R configuration of the reaction-intermediate isostere in HIV-1 protease-inhibitor binding: X-ray structure at 2.0 A resolution.

    PubMed

    Duskov, Jarmila; Dohnlek, Jan; Sklov, Tereza; Petrokov, Hana; Vondrckov, Eva; Hradlek, Martin; Konvalinka, Jan; Soucek, Milan; Brynda, Jir; Fbry, Milan; Sedlcek, Juraj; Hasek, Jindrich

    2006-05-01

    Peptidomimetic inhibitors of human immunodeficiency virus-1 protease are successful lead substances for the development of virostatic drugs against HIV as the causative agent of acquired immunodeficiency syndrome (AIDS). The hydroxyethylamine isostere of the proteolytic cleavage intermediate provides a suitable replacement for the peptide bond. A series of acyclic pseudopeptide inhibitors with the hydroxyethylamine isostere varying in chiral carbon configuration and P'2 residue type were structurally analysed by single-crystal X-ray crystallography. The compounds inhibit HIV protease with subnanomolar inhibition constants and block viral replication in tissue cultures. Here, the structure of such a complex with the R configuration of the isosteric group (PDB code 1zsf) is presented together with newly available synchrotron data for a complex with the S stereoisomer of the inhibitor (PDB code 1zsr). Comparison of the structure and binding with other complexes of HIV-1 protease and similar inhibitors contributes to the understanding of how these molecules bind to the wild-type form of this enzyme. The hydroxy group of the R stereoisomer interacts with one of the catalytic aspartic acids by a short hydrogen bond with rather extreme geometry. The change of configuration of the chiral carbon bearing the hydroxyl from S to R does not influence the inhibition efficiency in this case. PMID:16627941

  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. 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

  11. Intermediates of stigmasterol metabolism in Spodoptera littoralis

    SciTech Connect

    Svoboda, J.A.; Rees, H.H.; Thompson, M.J.; Hoggard, N. )

    1989-03-01

    Stigmasterol-24,28-epoxide, 22E-stigmasta-5,22,24(28E)-trien-3 beta-ol, and 22E-cholesta-5,22,24-trien-3 beta-ol were identified as normal metabolites of (3H)stigmasterol in Spodoptera littoralis larvae. Relative concentrations of all three of these metabolites increased when a diazasterol inhibitor was fed in combination with stigmasterol in the artificial diet. Identification of these sterols as intermediates in the conversion of stigmasterol to cholesterol in this insect indicates that intermediates analogous to fucosterol and fucosterol-24,28-epoxide in the conversion of sitosterol to cholesterol are produced in the metabolism of stigmasterol. This is the first published identification of stigmasterol-24,28-epoxide and 22E-stigmasta-5,22,24(28E)-trien-3 beta-ol as intermediates in this pathway in an insect.

  12. Incoherence in the South African Labour Market for Intermediate Skills

    ERIC Educational Resources Information Center

    Kraak, Andre

    2008-01-01

    This article is concerned with the production and employment of technically skilled labour at the intermediate level in South Africa. Three differing labour market pathways to intermediate skilling are identified. These are: the traditional apprenticeship route, the new "Learnerships" pathway (similar to the "modern apprenticeship" schemes adopted

  13. 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

  14. 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.

  15. Photoelectron-photoion coincidence spectroscopy for multiplexed detection of intermediate species in a flame.

    PubMed

    Krger, Julia; Garcia, Gustavo A; Felsmann, Daniel; Moshammer, Kai; Lackner, Alexander; Brockhinke, Andreas; Nahon, Laurent; Kohse-Hinghaus, Katharina

    2014-11-01

    Complex reactive processes in the gas phase often proceed via numerous reaction steps and intermediate species that must be identified and quantified to develop an understanding of the reaction pathways and establish suitable reaction mechanisms. Here, photoelectron-photoion coincidence (PEPICO) spectroscopy has been applied to analyse combustion intermediates present in a premixed fuel-rich (? = 1.7) ethene-oxygen flame diluted with 25% argon, burning at a reduced pressure of 40 mbar. For the first time, multiplexing fixed-photon-energy PEPICO measurements were demonstrated in a chemically complex reactive system such as a flame in comparison with the scanning "threshold" TPEPICO approach used in recent pioneering combustion investigations. The technique presented here is capable of detecting and identifying multiple species by their cations' vibronic fingerprints, including radicals and pairs or triplets of isomers, from a single time-efficient measurement at a selected fixed photon energy. Vibrational structures for these species have been obtained in very good agreement with scanning-mode threshold photoelectron spectra taken under the same conditions. From such spectra, the temperature in the ionisation volume was determined. Exemplary analysis of species profiles and mole fraction ratios for isomers shows favourable agreement with results obtained by more common electron ionisation and photoionisation mass spectrometry experiments. It is expected that the multiplexing fixed-photon-energy PEPICO technique can contribute effectively to the analysis of chemical reactivity and kinetics in and beyond combustion. PMID:25237782

  16. Reaction mechanism of the reverse water-gas shift reaction using first-row middle transition metal catalysts L'M (M = Fe, Mn, Co): a computational study.

    PubMed

    Liu, Cong; Cundari, Thomas R; Wilson, Angela K

    2011-09-19

    The mechanism of the reverse water-gas shift reaction (CO(2) + H(2) ? CO + H(2)O) was investigated using the 3d transition metal complexes L'M (M = Fe, Mn, and Co, L' = parent ?-diketiminate). The thermodynamics and reaction barriers of the elementary reaction pathways were studied with the B3LYP density functional and two different basis sets: 6-311+G(d) and aug-cc-pVTZ. Plausible reactants, intermediates, transition states, and products were modeled, with different conformers and multiplicities for each identified. Different reaction pathways and side reactions were also considered. Reaction Gibbs free energies and activation energies for all steps were determined for each transition metal. Calculations indicate that the most desirable mechanism involves mostly monometallic complexes. Among the three catalysts modeled, the Mn complex shows the most favorable catalytic properties. Considering the individual reaction barriers, the Fe complex shows the lowest barrier for activation of CO(2). PMID:21838224

  17. A Putative Fe2+-Bound Persulfenate Intermediate in Cysteine Dioxygenase

    SciTech Connect

    Simmons, C.; Krishnamoorthy, K; Granett, S; Schuller, D; Dominy, Jr. , J; Begley, T; Stipanuk, M; Karplus, P

    2008-01-01

    The common reactions of dioxygen, superoxide, and hydroperoxides with thiolates are thought to proceed via persulfenate intermediates, yet these have never been visualized. Here we report a 1.4 {angstrom} resolution crystal structure of the Fe{sup 2+}-dependent enzyme cysteine dioxygenase (CDO) containing this putative intermediate trapped in its active site pocket. The complex raises the possibility that, distinct from known dioxygenases and proposed CDO mechanisms, the Fe-proximal oxygen atom may be involved in the primary oxidation event yielding a unique three-membered Fe-S-O cyclic intermediate. A nonpolar environment of the distal oxygen would facilitate isomerization of the persulfenate to the sulfinate product.

  18. Non-Heme Fe(IV)-Oxo Intermediates

    PubMed Central

    Krebs, Carsten; Galoni?-Fujimori, Danica P.; Walsh, Christopher T.; Bollinger, J. Martin

    2012-01-01

    High-valent non-heme iron-oxo intermediates have been proposed for decades as the key intermediates in numerous biological oxidation reactions. In the last three years, the first direct characterization of such intermediates has been provided by studies of several ?KG-dependent oxygenases that catalyze either hydroxylation or halogenation of their substrates. In each case, the Fe(IV)-oxo intermediate is implicated in cleavage of the aliphatic C-H bond to initiate hydroxylation or halogenation. The observation of non-heme Fe(IV)-oxo intermediates and Fe(II)-containing product(s) complexes with almost identical spectroscopic parameters in the reactions of two distantly related ?KG-dependent hydroxylases suggests that members of this sub-family follow a conserved mechanism for substrate hydroxylation. In contrast, for the ?KG-dependent non-heme-iron halogenase, CytC3, two distinct Fe(IV) complexes form and decay together, suggesting that they are in rapid equilibrium. The existence of two distinct conformers of the Fe site may be the key factor accounting for the divergence of the halogenase reaction from the more usual hydroxylation pathway after C-H cleavage. Distinct transformations catalyzed by other mononuclear non-heme enzymes are likely also to involve initial C-H-cleavage by Fe(IV)-oxo complexes, followed by diverging reactivities of the resulting Fe(III)-hydroxo/substrate radical intermediates. PMID:17542550

  19. Investigation of the reactions of small neutral iron oxide clusters with methanol.

    PubMed

    Xie, Yan; Dong, Feng; Heinbuch, Scott; Rocca, Jorge J; Bernstein, Elliot R

    2009-03-21

    Reactions of neutral iron oxide clusters (Fe(m)O(n), m=1-2, n=0-5) with methanol (CH(3)OH) in a fast flow reactor are investigated by time of flight mass spectrometry. Detection of the neutral iron oxide cluster distribution and reaction intermediates and products is accomplished through single photon ionization by a 118 nm (10.5 eV) VUV laser. Partially deuterated methanol (CD(3)OH) is employed to distinguish reaction products and reaction mechanisms. Three major reactions are identified experimentally: CH(3)OH association with FeO; methanol dehydrogenation on FeO(1,2) and Fe(2)O(2-5); and (CH(2)O)Fe formation. Density functional theory calculations are carried out to identify reaction products, and to explore the geometric and electronic structures of the iron oxide clusters, reaction intermediates, and transition states, and to evaluate reaction pathways. Neutral formaldehyde is calculated to be formed on FeO(1,2) and Fe(2)O(2-5) clusters. Hydrogen transfer from methanol to iron oxide clusters occurs first from the O-H moiety of methanol, and is followed by a hydrogen transfer from the C-H moiety of methanol. Computational results are in good agreement with experimental observations and reveal reaction mechanisms for neutral iron oxide clusters taking methanol to formaldehyde through various reaction intermediates. Based on the experimental results and the calculated reaction mechanisms and pathways, complete catalytic cycles are suggested for the heterogeneous reaction of CH(3)OH to CH(2)O facilitated by an iron oxide catalyst. PMID:19317538

  20. Mixed reactant photocatalysis: Intermediates and mutual rate inhibition

    SciTech Connect

    Turchi, C.S.; Ollis, D.F. )

    1989-10-01

    Near UV-illuminated slurries of titanium dioxide were used to study the photocatalyzed degradation kinetics of benzene and perchloroethylene (PCE) as water contaminants. In all runs, the concentration(s) of reactant(s) (initially 15-500 {mu}M) as well as the evolution of CO{sub 2} final product were monitored. The single component initial rate data were well described by Langmuir-Hinshelwood rate forms, and integration of these rate equations provided simulations of the entire time course of each reaction. Perchloroethylene degraded completely without any evidence of kinetically significant chemical intermediates; however, adequate simulation of the benzene time course data required the incorporation in the model of at least two reaction intermediates. Subsequent GC/MS analysis of a benzene reaction slurry revealed several intermediate species, with positive identification of phenol and quinone. Using the kinetic rate parameters obtained from the single component initial rate data and including competitive intermediate terms, the Langmuir-Hinshelwood rate form was able to simulate the results of several binary reactant experiments. The data showed that the effect of PCE concentration on benzene reaction rate was negligible, while benzene and its intermediates significantly inhibited PCE degradation. Simulations with this simple model for diminution of both reactants as well as CO{sub 2} product evolution were quite good for low initial reactant concentrations, but overestimated the competitive inhibitory effect of high ({approx} 300 {mu}M) initial PCE concentrations.

  1. [Fever of intermediate duration].

    PubMed

    Rivero, Antonio; Zambrana, Jos Luis; Pachn, Jernimo

    2003-03-01

    Fever of intermediate duration (FID) is defined as non-localized fever occurring in the community, lasting from one to four weeks, and having no diagnostic orientation after basic clinical, analytical and radiological evaluations are completed. These may include careful recording of clinical history, physical examination, hemogram, plasma creatinine determination, urinalysis, and chest radiography. The etiology of FID is still not completely defined. In our country, 70% of cases are caused by systemic infectious diseases (rickettsiosis, brucellosis, and mononucleosis syndrome) and 7.7% by localized infections; vasculitis and neoplasms account for less than 2%. In most cases FID can be attended on an outpatient basis, with the guarantee of the easy accessibility. In cases without social support or when there is digestive intolerance or criteria of severe disease, hospital care is required. For the diagnostic approach, it is useful to establish basic rules and to organize the study in several stages, taking into account the most frequent etiologies. The first visit would include elaboration of the clinical history, a hemogram, biochemistry analyses, blood cultures, urine culture, serological studies for the most frequent etiologies, a chest radiograph, and other examinations, as indicated by the clinical history data. The care provided and subsequent diagnostic studies performed will depend on the patient's progression and findings from additional studies. Further works conducted in various geographic settings are necessary to define the complete etiological spectrum of FID. PMID:12586020

  2. Isoporphyrin intermediate in heme oxygenase catalysis. Oxidation of alpha-meso-phenylheme.

    PubMed

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

    2008-07-11

    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 alpha-meso carbon by a ferric hydroperoxide and is predicted to proceed via an isoporphyrin pi-cation intermediate. Here we report spectroscopic detection of a transient intermediate during oxidation by hHO-1 of alpha-meso-phenylheme-IX, alpha-meso-(p-methylphenyl)-mesoheme-III, and alpha-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 alpha-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 alpha-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

  3. 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.

  4. A Fluorogenic Aromatic Nucleophilic Substitution Reaction for Demonstrating Normal-Phase Chromatography and Isolation of Nitrobenzoxadiazole Chromophores

    ERIC Educational Resources Information Center

    Key, Jessie A.; Li, Matthew D.; Cairo, Christopher W.

    2011-01-01

    Normal-phase chromatography is an essential technique for monitoring chemical reactions, identifying the presence of specific components, as well as the purification of organic compounds. An experiment to facilitate the instruction and understanding of the concepts behind normal-phase chromatography at the introductory and intermediate

  5. 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

  6. 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)…

  7. Genetic resources for intermediate wheatgrass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Intermediate wheatgrass (Thinopyrum intermedium) is a perennial Triticeae species, closely related to wheat, barley, and rye. Intermediate wheatgrass is a highly productive and palatable forage grass, which is also a potentially useful source of resistance genes for important plant diseases such as...

  8. Detection of dideoxyosone intermediates of glycation using a monoclonal antibody: characterization of major epitope structures.

    PubMed

    Puttaiah, Shivaprakash; Zhang, Yuming; Pilch, Heather A; Pfahler, Christoph; Oya-Ito, Tomoko; Sayre, Lawrence M; Nagaraj, Ram H

    2006-02-15

    Glycation or the Maillard reaction in proteins forms advanced glycation end products (AGEs) that contribute to age- and diabetes-associated changes in tissues. Dideoxyosones, which are formed by the long-range carbonyl shift of the Amadori product, are newly discovered intermediates in the process of AGE formation in proteins. They react with o-phenylenediamine (OPD) to produce quinoxalines. We developed a monoclonal antibody against 2-methylquinoxaline-6-carboxylate coupled to keyhole limpet hemocyanin. The antibody reacted strongly with ribose and fructose (+OPD)-modified RNase A and weakly with glucose and ascorbate (+OPD)-modified RNase A. Reaction with substituted quinoxalines indicated that this antibody favored the 2-methyl group on the quinoxaline ring. We used high performance liquid chromatography to isolate and purify three antibody-reactive products from a reaction mixture of N alpha-hippuryl-L-lysine+ribose+OPD. The two most reactive products were identified as diastereoisomers of N1-benzoylglycyl-N6-(2-hydroxy-3-quinoxalin-2-ylpropyl)lysine and the other less reactive product as N1-benzoylglycyl-N6-[2-hydroxy-2-(3-methylquinoxalin-2-yl)ethyl]lysine. Our study confirms that dideoxyosone intermediates form during glycation and offers a new tool for the study of this important pathway in diabetes and aging. PMID:16406213

  9. 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

  10. Intermediate neutron spectrum problems and the intermediate neutron spectrum experiment

    SciTech Connect

    Jaegers, P.J.; Sanchez, R.G.

    1996-06-01

    Criticality benchmark data for intermediate energy spectrum systems does not exist. These systems are dominated by scattering and fission events induced by neutrons with energies between 1 eV and 1 MeV. Nuclear data uncertainties have been reported for such systems which can not be resolved without benchmark critical experiments. Intermediate energy spectrum systems have been proposed for the geological disposition of surplus fissile materials. Without the proper benchmarking of the nuclear data in the intermediate energy spectrum, adequate criticality safety margins can not be guaranteed. The Zeus critical experiment now under construction will provide this necessary benchmark data.

  11. Probing Hydrothermal Organic Reaction Mechanisms with Hydrothermal Photochemistry

    NASA Astrophysics Data System (ADS)

    Yang, Z.; Gould, I.; Shock, E.

    2013-12-01

    In most hydrothermal organic experiments the emphasis is on reaction product distributions and kinetic measurements, with mechanistic information or the direct evidence of proposed reaction intermediates rare or lacking. We believe that greater mechanistic insight will yield greater predictive power. Previously, we studied the reactions of a model ketone, dibenzylketone (DBK) in aqueous media at 300C and 700 bars for durations up to several days [1], and found that many of the reaction products arise from coupling of benzyl and related radicals generated through homolytic bond cleavage of DBK. In the present work, we find that in situ photochemical generation of the radicals can provide independent evidence for radical intermediates in the hydrothermal reaction of DBK, yielding valuable insights into the thermal reactions. Hydrothermal photochemical experiments of DBK were conducted in water in sealed fused silica glass tubes at 300C and 86 bars under UV irradiation for minutes. The short timescale of the experiments allows the primary radical coupling products of DBK to be generated and identified, and their follow-up reactions to be monitored directly. The primary hydrothermal photolysis products include toluene, bibenzyl, a three-benzene-ring product (with isomers), and two four-benzene-ring products (with isomers), which represent a much simpler version of the products obtained through thermal reactions under similar conversions. Most of the observed photolysis products were identical to the ones in the thermal reactions, and those not observed in thermal reactions were found to be the short-lived precursors of the thermal products. As an example, the transformation of one four-ring product to the other was attained and monitored by experiments in which hydrothermal photolysis of DBK was followed by thermolysis at 300C for a further few hours. The transformation steps included dehydration and isomerization, which were known to be thermodynamically favorable and rapid at hydrothermal conditions [1]. These results show that several relatively stable hydrothermal products from DBK are derived from the radical-coupled intermediates, and that these intermediates can be successfully captured using the tool of hydrothermal photolysis. Analysis of the product distributions and the quantum yields for the hydrothermal photolysis also provides convincing evidence for the previously proposed radical cleavage mechanism for the thermal reactions of DBK. [1] Yang et al. (2012) Geochim. Cosmochim. Acta 98, 48-65.

  12. 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. PMID:12950733

  13. Photocatalytic mineralization of codeine by UV-A/TiO?--Kinetics, intermediates, and pathways.

    PubMed

    Kuo, Chin-Sheng; Lin, Cheng-Fang; Hong, Pui-Kwan Andy

    2016-01-15

    This study investigated the photocatalytic degradation of codeine by UV-irradiated TiO2. The degradation kinetics was determined under varied conditions including the TiO2 loading, codeine concentration, and pH. Codeine and several reaction intermediates including morphine were identified and tracked during degradation using HPLC/MS-MS technique, along with TOC and IC measurements. Specifically, removal of 100 ?g/L of spike codeine was complete in 3 min by contact with a 0.1 g/L suspension of TiO2 under UV irradiation at pH 7. The degradation kinetics of codeine was first-order with respect to both the catalyst TiO2 and the reactant codeine, with enhanced reaction rates with increasing pH up to pH 9. Mineralization of codeine was possible upon prolonged contact; near complete mineralization of 10 mg/L of codeine was achieved in 90 min with 0.1 g/L TiO2 under irradiation at pH 5, during which the organic nitrogen was converted to NH3-N (74%) and NO3-N (22%). Based on the identified intermediates, two degradation pathways were proposed of which one involved ipso-substitution followed by cleavage of the aromatic ring and another involved repeated hydroxylation of the codeine molecule followed by its fragmentation. PMID:26348146

  14. Kinetics and product studies of the reaction ClO + BrO using discharge-flow mass spectrometry

    NASA Technical Reports Server (NTRS)

    Friedl, Randall R.; Sander, Stanley P.

    1989-01-01

    The kinetics and product branching ratios of the reaction between ClO and BrO were studied at 1 torr pressure over the temperature range 220-400 K, using the method of discharge-flow mass spectrometry. Three product channels were identified and quantified: Br + ClOO, Br + OClO, and BrCl + O2, indicating that the reaction mechanism of ClO + BrO involves metastable intermediates. The overall reaction rate coefficient and the rate coefficients for the three channel reactions are given.

  15. Kinetics, intermediates and acute toxicity of arsanilic acid photolysis.

    PubMed

    Zhu, Xiang-Dong; Wang, Yu-Jun; Liu, Cun; Qin, Wen-Xiu; Zhou, Dong-Mei

    2014-07-01

    Arsanilic acid (4-amino phenyl arsenic acid, ASA) is widely used in poultry production as feed additives, while most of ASA in the feed is excreted in the animal manure and released into the environment. However, the environmental behaviors of ASA were not well understood. In the present study, the photolysis behaviors of ASA and the toxicity of its metabolites to luminescent bacterium were studied. The results showed that ASA could be photodegraded and this process was strongly affected by solution pH, humic acid and dissolved oxygen. Upon UV irradiation for 360 min, ASA could be completely eliminated, but the reduction of total organic carbon (TOC) was not significant. In addition, NH4(+) ions and inorganic arsenic including arsenite and arsenate were identified as the predominant end-products. The conversion of ASA included both direct and indirect photolysis involving radicals, and its possible photolysis pathways were proposed on the basis of the identified intermediates. Unfortunately, higher adverse effects of the conversion products of ASA on bacteria were observed during the photolysis reaction. The results of present study might be helpful for assessing the environmental persistence and risks of ASA. PMID:24405966

  16. Structure and Electronic Configurations of the Intermediates of Water Oxidation in Blue Ruthenium Dimer Catalysis

    SciTech Connect

    Moonshiram, Dooshaye; Jurss, Jonah W.; Concepcion, Javier J.; Zakharova, Taisiya; Alperovich, Igor; Meyer, Thomas J.; Pushkar, Yulia

    2013-04-08

    Catalytic O{sub 2} evolution with cis,cis-[(bpy){sub 2}(H{sub 2}O)Ru{sup III}ORu{sup III}(OH{sub 2})(bpy){sub 2}]{sup 4+} (bpy is 2,2-bipyridine), the so-called blue dimer, the first designed water oxidation catalyst, was monitored by UV-vis, EPR, and X-ray absorption spectroscopy (XAS) with ms time resolution. Two processes were identified, one of which occurs on a time scale of 100 ms to a few seconds and results in oxidation of the catalyst with the formation of an intermediate, here termed [3,4]'. A slower process occurring on the time scale of minutes results in the decay of this intermediate and O{sub 2} evolution. Spectroscopic data suggest that within the fast process there is a short-lived transient intermediate, which is a precursor of [3,4]'. When excess oxidant was used, a highly oxidized form of the blue dimer [4,5] was spectroscopically resolved within the time frame of the fast process. Its structure and electronic state were confirmed by EPR and XAS. As reported earlier, the [3,4]' intermediate likely results from reaction of [4,5] with water. While it is generated under strongly oxidizing conditions, it does not display oxidation of the Ru centers past [3,4] according to EPR and XAS. EXAFS analysis demonstrates a considerably modified ligand environment in [3,4]'. Raman measurements confirmed the presence of the O-O fragment by detecting a new vibration band in [3,4]' that undergoes a 46 cm{sup -1} shift to lower energy upon {sup 16}O/{sup 18}O exchange. Under the conditions of the experiment at pH 1, the [3,4]' intermediate is the catalytic steady state form of the blue dimer catalyst, suggesting that its oxidation is the rate-limiting step.

  17. Intermediate depth seismicity - a reflection seismic approach

    NASA Astrophysics Data System (ADS)

    Haberland, C.; Rietbrock, A.

    2004-12-01

    During subduction the descending oceanic lithosphere is subject to metamorphic reactions, some of them associated with the release of fluids. It is now widely accepted, that these reactions and associated dehydration processes are directly related with the generation of intermediate depth earthquakes (dehydration embrittlement). However, the structure of the layered oceanic plate at depth and the location of the earthquakes relative to structural units of the subducting plate (sources within the oceanic crust and/or in the upper oceanic mantle lithosphere?) are still not resolved yet. This is in mainly due to the fact that the observational resolution needed to address these topics (in the range of only a few kilometers) is hardly achieved in field experiments and related studies. Here we study the wavefields of intermediate depth earthquakes typically observed by temporary networks in order to assess their high-resolution potential in resolving structure of the down going slab and locus of seismicity. In particular we study whether the subducted oceanic Moho can be detected by the analysis of secondary phases of local earthquakes (near vertical reflection). Due to the irregular geometry of sources and receivers we apply an imaging technique similar to diffraction stack migration. The method is tested using synthetic data both based on 2-D finite difference simulations and 3-D kinematic ray tracing. The accuracy of the hypocenter location and onset times crucial for the successful application of stacking techniques (coherency) was achieved by the use of relatively relocated intermediate depth seismicity. Additionally, we simulate the propagation of the wavefields at larger distance (wide angle) indicating the development of guided waves traveling in the low-velocity waveguide associated with the modeled oceanic crust. We also present application on local earthquake data from the South American subduction zone.

  18. 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.

  19. Virtual Screening for Transition State Analogue Inhibitors of IRAP Based on Quantum Mechanically Derived Reaction Coordinates.

    PubMed

    Svensson, Fredrik; Engen, Karin; Lundbck, Thomas; Larhed, Mats; Skld, Christian

    2015-09-28

    Transition state and high energy intermediate mimetics have the potential to be very potent enzyme inhibitors. In this study, a model of peptide hydrolysis in the active site of insulin-regulated aminopeptidase (IRAP) was developed using density functional theory calculations and the cluster approach. The 3D structure models of the reaction coordinates were used for virtual screening to obtain new chemical starting points for IRAP inhibitors. This mechanism-based virtual screening process managed to identify several known peptidase inhibitors from a library of over 5 million compounds, and biological testing identified one compound not previously reported as an IRAP inhibitor. This novel methodology for virtual screening is a promising approach to identify new inhibitors mimicking key transition states or intermediates of an enzymatic reaction. PMID:26252078

  20. Incomplete and complete fusion in intermediate energy heavy ion reactions

    SciTech Connect

    Aleklett, K.; Loveland, W.; Sugihara, T.T.; Morrissey, D.J.; Wenxin, L.; Kot, W.; Seaborg, G.T.

    1984-03-01

    The yields, angular distributions and differential range spectra have been measured for individual target residues from the interaction of 8.5 MeV/A /sup 16/O, 19 MeV/A /sup 16/O, 35 MeV/A /sup 12/C and 86 MeV/A /sup 12/C with /sup 154/Sm. From the measured data, fragment isobaric yields and velocity spectra were deduced. The results are compared to the sum rule model of Wilczyski et al. and the nuclear firestreak model. 18 references.

  1. 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.

  2. Reaction products of gas-phase photocatalytic degradation of perchloroethylene over titanium dioxide (UV/TiO{sub 2})

    SciTech Connect

    Yuan, C.S.; Hsu, B.C.; Wu, J.F.; Hung, C.H.

    1999-07-01

    This study investigated the reaction intermediates/products from heterogeneous photocatalysis of perchloroethylene (PCE) by near-UV/TiO{sub 2}. Glass beads coated with Degussa P-25 anatase TiO{sub 2} were packed in a Pyrex glass tubular reactor. Four 10W near-UV lamps (main wavelength = 365 nm) provided the required the light source. The varying experimental parameters including PCE concentration (7.7 {approximately} 45.3 ppmv), relative humidity (0 {approximately} 70 %), oxygen content (0 {approximately} 21%), and retention time (0.5 {approximately} 2.0 seconds). The formation concentrations of these reaction intermediates for different experimental parameters were discussed in this paper. Experimental results were demonstrated that fast decomposition of PCE in the established photocatalytic reactor was observed. The identified reaction intermediates included CHCl{sub 3}, CCl{sub 4}, C{sub 2}HCl{sub 5}, C{sub 2}Cl{sub 6}, COCl{sub 2}, CCl{sub 3}CClO, Cl{sub 2}, HCl, CO, and CO{sub 2} and good mass balance relationships were achieved in the study. Competitive reactions between Cl radical chlorinating and oxygen oxidation affect the formation concentrations of chlorinated reaction intermediates. Among the quantified reaction products, couple products including Cl{sub 2}, HCl, CO, and CO{sub 2} were the main products with higher formation concentrations.

  3. Learning to predict chemical reactions.

    PubMed

    Kayala, Matthew A; Azencott, Chlo-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 is generalizable, making reasonable predictions over reactants and conditions which the rule-based expert does not handle. A web interface to the machine learning based mechanistic reaction predictor is accessible through our chemoinformatics portal ( http://cdb.ics.uci.edu) under the Toolkits section. PMID:21819139

  4. Learning to Predict Chemical Reactions

    PubMed Central

    Kayala, Matthew A.; Azencott, Chlo-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 is generalizable, making reasonable predictions over reactants and conditions which the rule-based expert does not handle. A web interface to the machine learning based mechanistic reaction predictor is accessible through our chemoinformatics portal (http://cdb.ics.uci.edu) under the Toolkits section. PMID:21819139

  5. Intermediate ions in the atmosphere

    NASA Astrophysics Data System (ADS)

    Tammet, Hannes; Komsaare, Kaupo; Hõrrak, Urmas

    2014-01-01

    Intermediate air ions are charged nanometer-sized aerosol particles with an electric mobility of about 0.03-0.5 cm2 V- 1 s- 1 and a diameter of about 1.5-7.5 nm. Intensive studies of new particle formation provided good knowledge about intermediate ions during burst events of atmospheric aerosol nucleation. Information about intermediate ions during quiet periods between the bursts remained poor. The new mobility analyzer SIGMA can detect air ions at concentrations of mobility fractions of about 1 cm- 3 and enables studying intermediate ions during quiet periods. It became evident that intermediate ions always exist in atmospheric air and should be considered an indicator and a mediator of aerosol nucleation. The annual average concentration of intermediate ions of one polarity in Tartu, Estonia, was about 40 cm- 3 while 5% of the measurements showed a concentration of less than 10 cm- 3. The fraction concentrations in logarithmic 1/8-decade mobility bins between 0.1 and 0.4 cm2 V- 1 s- 1 often dropped below 1 cm- 3. The bursts of intermediate ions at stations separated by around 100 km appeared to be correlated. The lifespan of intermediate ions in the atmosphere is a few minutes, and they cannot be carried by wind over long distances. Thus the observed long-range correlation of intermediate ions is explained by simultaneous changes in air composition in widely spaced stations. A certain amount of intermediate ion bursts, predominantly of negative polarity, are produced by the balloelectric effect at the splashing of water drops during rain. These bursts are usually excluded when speaking about new particle formation because the balloelectric particles are assumed not to grow to the size of the Aitken mode. The mobility distribution of balloelectric ions is uniform in shape in all measurements. The maximum is located at a mobility of about 0.2 cm2 V- 1 s- 1, which corresponds to the diameter of particles of about 2.5 nm.

  6. BB Seminar: Prediction of Survival Incorporating Intermediate Event Info

    Cancer.gov

    In recent years, an increasing number of predictive markers have been identified as useful for risk prediction. When interest lies in predicting long term survival, it has often been argued that intermediate event information may be very helpful in improving the prediction. Most existing methods for incorporating potentially censored intermediate event information in predicting long term survival focus on modeling the disease process and are derived under restrictive parametric models in a multi-state survival setting.

  7. Detecting Folding Intermediates of a Protein as It Passes Through the Bacterial Translocation Channel

    PubMed Central

    Kadokura, Hiroshi; Beckwith, Jon

    2009-01-01

    Summary Most bacterial exported proteins cross the cytoplasmic membrane as unfolded polypeptides. However, little is known about how they fold during or after this process due to the difficulty in detecting folding intermediates. Here we identify co-translational and post-translational folding intermediates of a periplasmic protein in which the protein and DsbA, a periplasmic disulfide bond-forming enzyme, are covalently-linked by a disulfide bond. The co-translational mixed-disulfide intermediate is, upon further chain elongation, resolved, releasing the oxidized polypeptide, thus allowing us to follow the folding process. This analysis reveals that two cysteines that are joined to form a structural disulfide can play different roles during the folding reaction and that the mode of translocation (co-translational verse post-translational) can affect the folding process of a protein in the periplasm. The latter finding leads us to propose that the activity of the ribosome (translation) can modulate protein folding even in an extra-cytosolic compartment. PMID:19766568

  8. Photolysis pathway of imazapic in aqueous solution: ultrahigh resolution mass spectrometry analysis of intermediates.

    PubMed

    Harir, M; Gaspar, A; Frommberger, M; Lucio, M; El Azzouzi, M; Martens, D; Kettrup, A; Schmitt-Kopplin, Ph

    2007-11-28

    Direct degradation of imazapic, an herbicide of the imidazoline family, has been investigated in aqueous solution at different concentrations, pH values, and temperatures. The efficiency of the photodegradation process has been evaluated through degradation rate constants that could be fitted best with pseudo-first-order kinetics ( Ct = C0 e(- kt )). Ultrahigh resolution mass spectrometry (FTICR/MS) was used in electrospray ionization mode as a tool to study the photolysis process on a molecular level, whereas UV-vis and high-performance liquid chromatography/mass spectrometry analysis were used to follow, by time, the evolution of the intermediates. Taking advantage of the high resolving power of FTICR/MS to perform precise formula assignments taking account of the natural abundance of isotopes, we herein propose and demonstrate an approach using 2D-derived van Krevelen visualization (O/C, H/C, m/z) to confirm the formation of imazapic intermediates. Such an approach allows a qualitative analysis of intermediates and elucidates the plausible reaction pathways of the photolysis process. More than eight photoproducts were separated and identified as a phototransformation of the imidazole ring. A mechanistical pathway was proposed. PMID:17960882

  9. Hydroxo-Bridged Dicopper(II,III) and -(III,III) Complexes: Models for Putative Intermediates in Oxidation Catalysis

    PubMed Central

    2015-01-01

    A macrocyclic ligand (L4) comprising two pyridine(dicarboxamide) donors was used to target reactive copper species relevant to proposed intermediates in catalytic hydrocarbon oxidations by particulate methane monooxygenase and heterogeneous zeolite systems. Treatment of LH4 with base and Cu(OAc)2H2O yielded (Me4N)2[L2Cu4(?4-O)] (1) or (Me4N)[LCu2(?-OH)] (2), depending on conditions. Complex 2 was found to undergo two reversible 1-electron oxidations via cyclic voltammetry and low-temperature chemical reactions. On the basis of spectroscopy and theory, the oxidation products were identified as novel hydroxo-bridged mixed-valent Cu(II)Cu(III) and symmetric Cu(III)2 species, respectively, that provide the first precedence for such moieties as oxidation catalysis intermediates. PMID:24821432

  10. Hydroxo-bridged dicopper(II,III) and -(III,III) complexes: models for putative intermediates in oxidation catalysis.

    PubMed

    Halvagar, Mohammad Reza; Solntsev, Pavlo V; Lim, Hyeongtaek; Hedman, Britt; Hodgson, Keith O; Solomon, Edward I; Cramer, Christopher J; Tolman, William B

    2014-05-21

    A macrocyclic ligand (L(4-)) comprising two pyridine(dicarboxamide) donors was used to target reactive copper species relevant to proposed intermediates in catalytic hydrocarbon oxidations by particulate methane monooxygenase and heterogeneous zeolite systems. Treatment of LH4 with base and Cu(OAc)2H2O yielded (Me4N)2[L2Cu4(?4-O)] (1) or (Me4N)[LCu2(?-OH)] (2), depending on conditions. Complex 2 was found to undergo two reversible 1-electron oxidations via cyclic voltammetry and low-temperature chemical reactions. On the basis of spectroscopy and theory, the oxidation products were identified as novel hydroxo-bridged mixed-valent Cu(II)Cu(III) and symmetric Cu(III)2 species, respectively, that provide the first precedence for such moieties as oxidation catalysis intermediates. PMID:24821432

  11. The critical iron-oxygen intermediate in human aromatase

    SciTech Connect

    Gantt, Stephanie L.; Denisov, Ilia G.; Grinkova, Yelena V.; Sligar, Stephen G.

    2009-09-11

    Aromatase (CYP19) is the target of several therapeutics used for breast cancer treatment and catalyzes the three-step conversion of androgens to estrogens, with an unusual C-C cleavage reaction in the third step. To better understand the CYP19 reaction, the oxy-ferrous complex of CYP19 with androstenedione substrate was cryotrapped, characterized by UV-vis spectroscopy, and cryoreduced to generate the next reaction cycle intermediate. EPR analysis revealed that the initial intermediate observed following cryoreduction is the unprotonated g{sub 1} = 2.254 peroxo-ferric intermediate, which is stable up to 180 K. Upon gradual cryoannealing, the low-spin (g{sub 1} = 2.39) product complex is formed, with no evidence for accumulation of the g{sub 1} = 2.30 hydroperoxo-ferric intermediate. The relative stabilization of the peroxo-ferric heme and the lack of observed hydroperoxo-ferric heme distinguish CYP19 from other P450s, suggesting that the proton delivery pathway is more hindered in CYP19 than in most other P450s.

  12. 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.

  13. Intermediate-sized filaments of human endothelial cells

    PubMed Central

    1979-01-01

    Human endothelial cells prepared from unbilical cords are characterized in parallel by electron microscopy and indirect immunofluorescence microscopy using specific antibodies against different classes of intermediate-sized filaments. The strongly developed, loose bundles of intermediate-sized filaments typically found in these cells are not decorated by antibodies against prekeratin or antibodies against smooth muscle desmin. They are, however, strongly decorated by antibodies directed against murine "vimentin," i.e., the 57,000 mol wt polypeptide which is the major protein of the intermediate-sized filaments predominant in various cells of mesenchymal origin. Cytoskeletal preparations greatly enriched in intermediate-sized filaments show the enrichment of a polypeptide band comigrating with murine vimentin. This shows that the intermediate-sized filaments that are abundant in human endothelial cells are predominantly of the vimentin type and can be demonstrated by their cross-reaction with the vimentin of rodents. These data also strengthen the evidence for several subclasses of intermediate-sized filaments, which can be distinguished by immunological procedures. PMID:379021

  14. Fenton Oxidation Kinetics and Intermediates of Nonylphenol Ethoxylates.

    PubMed

    Cui, Kai; Yi, Hao; Zhou, Zi-Jian; Zhuo, Qiong-Fang; Bing, Yong-Xin; Guo, Qing-Wei; Xu, Zhen-Cheng

    2014-05-01

    Removal of nonylphenol ethoxylates (NPEOs) in aqueous solution by Fenton oxidation process was studied in a laboratory-scale batch reactor. Operating parameters, including initial pH temperature, hydrogen peroxide, and ferrous ion dosage, were thoroughly investigated. Maximum NPEOs reduction of 84% was achieved within 6?min, under an initial pH of 3.0, 25C, an H2O2 dosage of 9.7410(-3) M, and a molar ratio of [H2O2]/[Fe(2+)] of 3. A modified pseudo-first-order kinetic model was found to well represent experimental results. Correlations of reaction rate constants and operational parameters were established based on experimental data. Results indicated that the Fenton oxidation rate and removal efficiency were more dependent on the dosage of H2O2 than Fe(2+), and the apparent activation energy (?E) was 17.5?kJ/mol. High-performance liquid chromatography and gas chromatograph mass spectrometer analytical results indicated degradation of NPEOs obtained within the first 2?min stepwise occurred by ethoxyl (EO) unit shortening. Long-chain NPEOs mixture demonstrated a higher degradation rate than shorter-chain ones. Nonylphenol (NP), short-chain NPEOs, and NP carboxyethoxylates were identified as the primary intermediates, which were mostly further degraded. PMID:24868141

  15. Intermediates in the Formation of the Chlorophyll Isocyclic Ring 1

    PubMed Central

    Wong, Yum-Shing; Castelfranco, Paul A.; Goff, Dane A.; Smith, Kevin M.

    1985-01-01

    Cell-free, organelle-free synthesis of Mg-2,4-divinylpheoporphyrin a5 (MgDVP) from Mg-protoporphyrin IX monomethyl ester (Mg-Proto Me) has been described (Wong and Castelfranco 1984 Plant Physiol 75: 658-661). This system consists of plastid membrane and stromal fractions and requires O2, NAD(P)H and S-adenosylmethionine (SAM). The synthetic 6-methyl-?-ketopropionate analog of Mg-Proto Me was converted to MgDVP by the same catalytic system in the presence of O2 and NADPH. SAM was not required. A compound (X) displaying the kinetic behavior of an intermediate was isolated from reaction mixtures with Mg-Proto Me as the substrate, but not with the 6-methyl-?-ketopropionate analog as the substrate. X was identified as the 6-methyl-?-hydroxypropionate analog of Mg-Proto Me by conversion to the dimethyl ester with CH2N2 and comparison with authentic 6-?-hydroxydimethyl ester. X was converted to MgDVP by the same catalytic system in the presence of O2 and NADPH. We conclude that the conversion of Mg-Proto Me to MgDVP proceeds through the 6-?-hydroxy and the 6-?-ketopropionate esters in agreement with earlier suggestions. PMID:16664481

  16. Fenton Oxidation Kinetics and Intermediates of Nonylphenol Ethoxylates

    PubMed Central

    Cui, Kai; Yi, Hao; Zhou, Zi-jian; Zhuo, Qiong-fang; Bing, Yong-xin; Guo, Qing-wei; Xu, Zhen-cheng

    2014-01-01

    Abstract Removal of nonylphenol ethoxylates (NPEOs) in aqueous solution by Fenton oxidation process was studied in a laboratory-scale batch reactor. Operating parameters, including initial pH temperature, hydrogen peroxide, and ferrous ion dosage, were thoroughly investigated. Maximum NPEOs reduction of 84% was achieved within 6?min, under an initial pH of 3.0, 25C, an H2O2 dosage of 9.7410?3 M, and a molar ratio of [H2O2]/[Fe2+] of 3. A modified pseudo-first-order kinetic model was found to well represent experimental results. Correlations of reaction rate constants and operational parameters were established based on experimental data. Results indicated that the Fenton oxidation rate and removal efficiency were more dependent on the dosage of H2O2 than Fe2+, and the apparent activation energy (?E) was 17.5?kJ/mol. High-performance liquid chromatography and gas chromatograph mass spectrometer analytical results indicated degradation of NPEOs obtained within the first 2?min stepwise occurred by ethoxyl (EO) unit shortening. Long-chain NPEOs mixture demonstrated a higher degradation rate than shorter-chain ones. Nonylphenol (NP), short-chain NPEOs, and NP carboxyethoxylates were identified as the primary intermediates, which were mostly further degraded. PMID:24868141

  17. 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.

  18. Identification of an Active Site-bound Nitrile Hydratase Intermediate through Single Turnover Stopped-flow Spectroscopy*

    PubMed Central

    Gumataotao, Natalie; Kuhn, Misty L.; Hajnas, Natalia; Holz, Richard C.

    2013-01-01

    Stopped-flow kinetic data were obtained for the iron-type nitrile hydratase from Rhodococcus equi TG328-2 (ReNHase) using methacrylonitrile as the substrate. Multiple turnover experiments suggest a three-step kinetic model that allows for the reversible binding of substrate, the presence of an intermediate, and the formation of product. Microscopic rate constants determined from these data are in good agreement with steady state data confirming that the stopped-flow method used was appropriate for the reaction. Single turnover stopped-flow experiments were used to identify catalytic intermediates. These data were globally fit confirming a three-step kinetic model. Independent absorption spectra acquired between 0.005 and 0.5 s of the reaction reveal a significant increase in absorbance at 375, 460, and 550 nm along with the hypsochromic shift of an Fe3+?S ligand-to-metal charge transfer band from 700 to 650 nm. The observed UV-visible absorption bands for the Fe3+-nitrile intermediate species are similar to low spin Fe3+-enzyme and model complexes bound by NO or N3?. These data provide spectroscopic evidence for the direct coordination of the nitrile substrate to the nitrile hydratase active site low spin Fe3+ center. PMID:23589282

  19. Cryogenic Ion Vibrational Spectroscopy of - CH Activation Intermediates

    NASA Astrophysics Data System (ADS)

    Marsh, Brett; Garand, Etienne

    2013-06-01

    Despite the rather simple composition of alkanes the strength of their C-C and C-H bonds has made controlled, selective reaction of these compounds an unrealized goal of synthetic chemistry. The field was pioneered by Shilov and coworkers in 1969 when they observed the exchange of H and D in methane that was bubbled into an acidic solution of K_2PtCl_4. The Shilov reaction has since been extended to induce oxidation of methane selectively to methanol and has become the standard bearer of CH activation despite its limitations. The mechanism for the reaction, while inferred from kinetics studies, is still largely uncharacterized. Here, we present our work towards applying cryogenic ion vibrational spectroscopy (CIVS) to capture the intermediate species of this reaction with a focus on the σ-CH adduct formed between methane and Pt(II) complexes that is believed to be crucial to the selectivity and rate of this reaction.

  20. Controlling reaction specificity in pyridoxal phosphate enzymes

    PubMed Central

    Toney, Michael D.

    2012-01-01

    Pyridoxal 5'-phosphate enzymes are ubiquitous in the nitrogen metabolism of all organisms. They catalyze a wide variety of reactions including racemization, transamination, decarboxylation, elimination, retro-aldol cleavage, Claisen condensation, and others on substrates containing an amino group, most commonly ?-amino acids. The wide variety of reactions catalyzed by PLP enzymes is enabled by the ability of the covalent aldimine intermediate formed between substrate and PLP to stabilize carbanionic intermediates at C? of the substrate. This review attempts to summarize the mechanisms by which reaction specificity can be achieved in PLP enzymes by focusing on three aspects of these reactions: stereoelectronic effects, protonation state of the external aldimine intermediate, and interaction of the carbanionic intermediate with the protein side chains present in the active site. PMID:21664990

  1. 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.

  2. Photosensitized reduction of DDT using visible light: the intermediates and pathways of dechlorination.

    PubMed

    Lin, Chitsan; Chang, Tien-Chin

    2007-01-01

    A reaction mixture containing DDT (1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane), methylene green (as the photosensitizer), and triethylamine (as the electron donor) in acetonitrile:water (1:1) was irradiated by an ordinary 150-W GE-Miser spotlight to facilitate visible-light photosensitized DDT dehalogenation. The intermediates and reaction products were identified by GC/MS (gas chromatography/mass spectrometer) and NMR (nuclear magnetic resonance). The photosensitized dehalogenation method partially degraded DDT via an electron transfer relay mechanism. Results indicate that DDT lost about three chlorines after a total of 19 days of irradiation. Aliphatic chlorines were found to be removed easier than aromatic chlorines. Various types of reductants were compared for electron donation efficiency, and photosensitizer concentration was optimized for our reaction system. In most cases, clean and simple dechlorinated products were observed. The proposed photosensitized reduction was coexisted with a thermal elimination effect for the first chlorine removal of DDT, and the photosensitized electron transfer reduction was shown to be the dominating mechanism responsible for further dechlorination after the initial stage. A sequential dechlorination pathway was proposed, with each successive dehalogenation, the reaction proceeds more slowly. The results have shown the feasibility of utilizing visible light, nontoxic dyes and electron donors to render a toxic compound less toxic and to enhance the natural carbon regeneration rates. PMID:16949127

  3. A polymerase chain reaction strategy to identify and clone cyclic nucleotide phosphodiesterase cDNAs. Molecular cloning of the cDNA encoding the 63-kDa calmodulin-dependent phosphodiesterase.

    PubMed

    Repaske, D R; Swinnen, J V; Jin, S L; Van Wyk, J J; Conti, M

    1992-09-15

    Multiple isozymes of cyclic nucleotide phosphodiesterases (PDEs) are expressed simultaneously in mammalian tissues. To identify and clone these PDEs, a polymerase chain reaction (PCR) strategy was developed using degenerate oligonucleotide primers designed to hybridize with highly conserved PDE DNA domains. Both known and novel PDEs were cloned from rat liver, the mouse K30a-3.3 lymphoma cell line, and a human hypothalamus cDNA library, demonstrating that these PCR primers can be used to amplify the cDNA of multiple PDE isozymes. One unique mouse PDE clone was found to encode a polypeptide identical with the corresponding portion of the bovine brain 63-kDa calmodulin-dependent PDE as reported in the companion article (Bentley, J. K., Kadlecek, A., Sherbert, C. H., Seger, D., Sonnenburg, W. K., Charbonneau, H., Novack, J. P., and Beavo, J. A. (1992) J. Biol. Chem. 267, 18676-18682). This mouse clone was used as a probe to screen a rat brain cDNA library for a full-length clone. The conceptual translation of the nucleotide sequence of the resulting rat clone has an open reading frame of 535 amino acids and maintains a high degree of homology with the bovine 63-kDa calmodulin-dependent PDE, indicating that this protein is likely to be the rat homolog of the 63-kDa calmodulin-dependent PDE. Expression of the full-length clone in Escherichia coli yielded a cGMP hydrolyzing activity that was stimulated severalfold by calmodulin. Northern blot analysis demonstrated that the mRNA encoding this PDE is highly expressed in rat brain and also in the S49.1 T-lymphocyte cell line. These data demonstrate that the PCR method described is a viable strategy to isolate cDNA clones of known and novel members of different families of PDE isozymes. Molecular cloning of these PDEs will provide valuable tools for investigating the roles of these isozymes in regulation of intracellular concentrations of the cyclic nucleotides. PMID:1326532

  4. Cestina pro Pokrocile (Intermediate Czech).

    ERIC Educational Resources Information Center

    Kabat, Grazyna; And Others

    The textbook in intermediate Czech is designed for second-year students of the language and those who already have a basic knowledge of Czech grammar and vocabulary. It is appropriate for use in a traditional college language classroom, the business community, or a government language school. It can be covered in a year-long conventional…

  5. Intermediate Nepali Structure. Volume 1.

    ERIC Educational Resources Information Center

    Verma, M. K.; Sharma, T. N.

    This volume is made up of 20 lessons and is part of a comprehensive course in intermediate Nepali. It explains and illustrates the basic structures of Nepali grammar through lessons which include different tense forms, postpositions, conditionals, comparatives, and other structural elements. The first lesson is devoted specifically to guiding

  6. Intermediate Nepali Reader. Volume II.

    ERIC Educational Resources Information Center

    Verma, M. K.; Sharma, T. N.

    A set of twelve reading lessons is presented as part of a comprehensive intermediate Nepali course. The lessons are graded in terms of language complexity and selected in terms of style. Highly sophisticated and journalistic compositions are included as well as the colloquial and folk styles of the common people. Each reading passage is

  7. 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)…

  8. 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

  9. 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

  10. Modeling the HCOOH/CO2 Electrocatalytic Reaction: When Details Are Key.

    PubMed

    Steinmann, Stephan N; Michel, Carine; Schwiedernoch, Renate; Filhol, Jean-Sebastien; Sautet, Philippe

    2015-08-01

    Our first principles simulations of the electrooxidation of formic acid over nickel identify the reorientation of the formate intermediate and the desorption of CO2 as the rate-limiting steps. Although they are not associated with an electron transfer, these barriers are strongly modified when the electrochemical potential is explicitly accounted for and when modeling the influence of the solvent. Hence, such a level of modeling is key to understand the kinetic limitations that penalize the reaction. PMID:26097137

  11. Insignificant disease among men with intermediate-risk prostate cancer

    PubMed Central

    Hong, Sung Kyu; Vertosick, Emily; Sjoberg, Daniel D.; Scardino, Peter T.; Eastham, James A.

    2015-01-01

    Purpose A paucity of data exists on the insignificant disease potentially suitable for active surveillance among men with intermediate-risk prostate cancer. We tried to identify pathologically insignificant disease and its preoperative predictors in men who underwent radical prostatectomy for intermediate-risk prostate cancer. Methods We analyzed data of 1630 men who underwent radical prostatectomy for intermediate-risk disease. Total tumor volume data were available in 332 men. We examined factors associated with classically-defined pathologically insignificant cancer (organ-confined disease with total tumor volume ? 0.5 ml with no Gleason pattern 4 or 5) and pathologically favorable cancer (organ-confined disease with no Gleason pattern 4 or 5) potentially suitable for active surveillance. Decision curve analysis was used to assess clinical utility of a multivariable model including preoperative variables for predicting pathologically unfavorable cancer. Results In the entire cohort, 221 of 1630 (13.6%) total patients had pathologically favorable cancer. Among 332 patients with total tumor volume data available, 26 (7.8%) had classically-defined pathologically insignificant cancer. Between threshold probabilities of 20% and 40%, decision curve analysis demonstrated that using multivariable model to identify active surveillance candidates would not provide any benefit over simply treating all men who have intermediate-risk disease with radical prostatectomy. Conclusions Although a minority of patients with intermediate risk disease may harbor pathologically favorable or insignificant cancer, currently available conventional tools are not sufficiently able to identify those patients. PMID:25261260

  12. Photocrystallographic Observation of Halide-Bridged Intermediates in Halogen Photoeliminations

    PubMed Central

    2015-01-01

    Polynuclear transition metal complexes, which frequently constitute the active sites of both biological and chemical catalysts, provide access to unique chemical transformations that are derived from metal–metal cooperation. Reductive elimination via ligand-bridged binuclear intermediates from bimetallic cores is one mechanism by which metals may cooperate during catalysis. We have established families of Rh2 complexes that participate in HX-splitting photocatalysis in which metal–metal cooperation is credited with the ability to achieve multielectron photochemical reactions in preference to single-electron transformations. Nanosecond-resolved transient absorption spectroscopy, steady-state photocrystallography, and computational modeling have allowed direct observation and characterization of Cl-bridged intermediates (intramolecular analogues of classical ligand-bridged intermediates in binuclear eliminations) in halogen elimination reactions. On the basis of these observations, a new class of Rh2 complexes, supported by CO ligands, has been prepared, allowing for the isolation and independent characterization of the proposed halide-bridged intermediates. Direct observation of halide-bridged structures establishes binuclear reductive elimination as a viable mechanism for photogenerating energetic bonds. PMID:25264809

  13. Methanogenic toluene metabolism: community structure and intermediates.

    PubMed

    Fowler, S Jane; Dong, Xiaoli; Sensen, Christoph W; Suflita, Joseph M; Gieg, Lisa M

    2012-03-01

    Toluene is a model compound used to study the anaerobic biotransformation of aromatic hydrocarbons. Reports indicate that toluene is transformed via fumarate addition to form benzylsuccinate or by unknown mechanisms to form hydroxylated intermediates under methanogenic conditions. We investigated the mechanism(s) of syntrophic toluene metabolism by a newly described methanogenic enrichment from a gas condensate-contaminated aquifer. Pyrosequencing of 16S rDNA revealed that the culture was comprised mainly of Clostridiales. The predominant methanogens affiliated with the Methanomicrobiales. Methane production from toluene ranged from 72% to 79% of that stoichiometrically predicted. Isotope studies using (13)C(7) toluene showed that benzylsuccinate and benzoate transiently accumulated revealing that members of this consortium can catalyse fumarate addition and subsequent reactions. Detection of a BssA gene fragment in this culture further supported fumarate addition as a mechanism of toluene activation. Transient formation of cresols, benzylalcohol, hydroquinone and methylhydroquinone suggested alternative mechanism(s) for toluene metabolism. However, incubations of the consortium with (18)O-H(2)O showed that the hydroxyl group in these metabolites did not originate from water and abiotic control experiments revealed abiotic formation of hydroxylated species due to reactions of toluene with sulfide and oxygen. Our results suggest that toluene is activated by fumarate addition, presumably by the dominant Clostridiales. PMID:22040260

  14. Chronic candida endophthalmitis as a cause of intermediate uveitis.

    PubMed

    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

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

    PubMed

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

    2015-12-21

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

  16. 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.

  17. 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 C than conventional manganite or cobaltite cathodes.

  18. 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.

  19. A straightforward implementation of in situ solution electrochemical C NMR spectroscopy for studying reactions on commercial electrocatalysts: ethanol oxidation.

    PubMed

    Huang, L; Sorte, E G; Sun, S-G; Tong, Y Y J

    2015-05-11

    Identifying and quantifying electrocatalytic-reaction-generated solution species, be they reaction intermediates or products, are highly desirable in terms of understanding the associated reaction mechanisms. We report herein a straightforward implementation of in situ solution electrochemical (13)C NMR spectroscopy for the first time that enables in situ studies of reactions on commercial fuel-cell electrocatalysts (Pt and PtRu blacks). Using ethanol oxidation reaction (EOR) as a working example, we discovered that (1) the complete oxidation of ethanol to CO2 only took place dominantly at the very beginning of a potentiostatic chronoamperometric (CA) measurement and (2) the PtRu had a much higher activity in catalysing oxygen insertion reaction that leads to acetic acid. PMID:25868425

  20. 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…

  1. 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

  2. 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

  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. 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. PMID:26949842

  5. 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)

  6. 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

  7. The Mechanisms of Oxygen Reduction and Evolution Reactions in Nonaqueous Lithium-Oxygen Batteries

    SciTech Connect

    Cao, Ruiguo; Walter, Eric D.; Xu, Wu; Nasybulin, Eduard N.; Bhattacharya, Priyanka; Bowden, Mark E.; Engelhard, Mark H.; Zhang, Jiguang

    2014-09-01

    The oxygen reduction/evolution reaction (ORR/OER) mechanisms in nonaqueous Li-O2 batteries have been investigated by using electron paramagnetic resonance spectroscopy in this work. We identified the superoxide radical anion (O2•-) as an intermediate in the ORR process using 5,5-dimethyl-pyrroline N-oxide as a spin trap, while no O2•- in OER was detected during the charge process. These findings provide insightful understanding on the fundamental oxygen reaction mechanisms in rechargeable nonaqueous Li-O2 batteries.

  8. The adsorption and reaction of halogenated volatile organic compounds (VOC's) on metal oxides. 1998 annual progress report

    SciTech Connect

    Lunsford, J.; Goodman, D.W.; Haw, J.F.

    1998-06-01

    'The goal of the research is to elucidate the properties of the materials responsible for the activation of halocarbons and the nature of the intermediates formed in the dissociative adsorption of this class of compounds. This information is essential for interpreting and predicting stoichiometric and catalytic pathways for the safe destruction of halocarbon pollutants. The specific objectives are: (1) to study the adsorption and reactivity of chloromethanes and chloroethanes on metal oxides; (2) to identify the reaction intermediates using spectroscopic methods; and (3) to develop kinetic models for the reaction of these halocarbons with oxide surfaces. This report summarizes work after 20 months of a 36-month project. Emphasis has been placed understanding the surfaces phases, as well as the bulk phases that are present during the reactions of chlorinated hydrocarbons with strongly basic metal oxides. Most of the research has been carried out with carbon tetrachloride.'

  9. 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

  10. 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. PMID:24689797

  11. Elucidation of Intermediates and Mechanisms in Heterogeneous Catalysis Using Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Savara, Aditya; Weitz, Eric

    2014-04-01

    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.

  12. 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. PMID:26706928

  13. 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.

  14. Pineal parenchymal tumor of intermediate differentiation.

    PubMed

    Patil, Meena; Karandikar, Manjiri

    2015-01-01

    The 2007 World Health Organization classification of tumors of the central nervous system identified "pineal parenchymal tumor of intermediate differentiation" (PPTID) as a new pineal parenchymal neoplasm, located between pineocytoma and pineoblastoma as grade II or III. Because of the small number of reported cases, the classification of PPT is still a matter of controversy. We report a case of PPTID. A 25-year-old female patient was admitted to hospital with complaints of a headache, nausea, vomiting since 1-year. Computed tomography/magnetic resonance imaging of the brain showed well-defined, mildly enhancing lesion in the region of the pineal gland with areas of calcification. The tumor was excised. After 3 years, she presented with metastasis in thoracic and lumbosacral spinal region. This is a rare event. PMID:26549088

  15. Theoretical investigation of the mechanism of the reaction IO + NO ? I + NO 2

    NASA Astrophysics Data System (ADS)

    Papayannis, Demetrios K.; Kosmas, Agnie M.

    2006-12-01

    The reaction IO + NO ? I + NO 2 has been studied theoretically using DFT and ab initio methods. Six transition state configurations have been characterized in total. Four of them correspond to the conformational and isomerization barriers among the reaction intermediates, namely between cis-and trans-iodine nitrites, IONO c, IONO t and nitryl iodide, INO 2. Interesting features identified in the potential energy surface are the two distinct iodine abstraction transition states that lead to I + NO 2 through each nitrite conformer. The heats of formation for the three bound intermediates are evaluated based on the calculated dissociation energies and are compared to the corresponding properties of the Cl and Br derivatives.

  16. Reaction theory

    NASA Astrophysics Data System (ADS)

    Typel, Stefan

    2016-01-01

    Reactions with atomic nuclei play a pivotal role in the experimental study of nuclei. They are a tool in order to obtain crucial information on nuclear structure of nuclei, in particular for unstable nuclei far off the valley of stability. Besides the investigation of nuclear properties, nuclear reactions can be used as indirect methods to extract cross sections of astrophysical interest that cannot be measured directly in the laboratory. After an overview over the variety of nuclear reactions and their major characteristics, the basic formalism of reaction theory is introduced and essential concepts are presented in order to describe direct reactions. The main challenges in the future development of reaction theory are addressed.

  17. Evidence for an Ionic Intermediate in the Transformation of Fatty Acid Hydroperoxide by a Catalase-related Allene Oxide Synthase from the Cyanobacterium Acaryochloris marina*

    PubMed Central

    Gao, Benlian; Boeglin, William E.; Zheng, Yuxiang; Schneider, Claus; Brash, Alan R.

    2009-01-01

    Allene oxides are reactive epoxides biosynthesized from fatty acid hydroperoxides by specialized cytochrome P450s or by catalase-related hemoproteins. Here we cloned, expressed, and characterized a gene encoding a lipoxygenase-catalase/peroxidase fusion protein from Acaryochloris marina. We identified novel allene oxide synthase (AOS) activity and a by-product that provides evidence of the reaction mechanism. The fatty acids 18.4ω3 and 18.3ω3 are oxygenated to the 12R-hydroperoxide by the lipoxygenase domain and converted to the corresponding 12R,13-epoxy allene oxide by the catalase-related domain. Linoleic acid is oxygenated to its 9R-hydroperoxide and then, surprisingly, converted ∼70% to an epoxyalcohol identified spectroscopically and by chemical synthesis as 9R,10S-epoxy-13S-hydroxyoctadeca-11E-enoic acid and only ∼30% to the 9R,10-epoxy allene oxide. Experiments using oxygen-18-labeled 9R-hydroperoxide substrate and enzyme incubations conducted in H218O indicated that ∼72% of the oxygen in the epoxyalcohol 13S-hydroxyl arises from water, a finding that points to an ionic intermediate (epoxy allylic carbocation) during catalysis. AOS and epoxyalcohol synthase activities are mechanistically related, with a reacting intermediate undergoing a net hydrogen abstraction or hydroxylation, respectively. The existence of epoxy allylic carbocations in fatty acid transformations is widely implicated although for AOS reactions, without direct experimental support. Our findings place together in strong association the reactions of allene oxide synthesis and an ionic reaction intermediate in the AOS-catalyzed transformation. PMID:19531485

  18. MCNP6 fragmentation of light nuclei at intermediate energies

    NASA Astrophysics Data System (ADS)

    Mashnik, Stepan G.; Kerby, Leslie M.

    2014-11-01

    Fragmentation reactions induced on light target nuclei by protons and light nuclei of energies around 1 GeV/nucleon and below are studied with the latest Los Alamos Monte Carlo transport code MCNP6 and with its cascade-exciton model (CEM) and Los Alamos version of the quark-gluon string model (LAQGSM) event generators, version 03.03, used as stand-alone codes. Such reactions are involved in different applications, like cosmic-ray-induced single event upsets (SEU's), radiation protection, and cancer therapy with proton and ion beams, among others; therefore, it is important that MCNP6 simulates them as well as possible. CEM and LAQGSM assume that intermediate-energy fragmentation reactions on light nuclei occur generally in two stages. The first stage is the intranuclear cascade (INC), followed by the second, Fermi breakup disintegration of light excited residual nuclei produced after the INC. Both CEM and LAQGSM account also for coalescence of light fragments (complex particles) up to 4He from energetic nucleons emitted during INC. We investigate the validity and performance of MCNP6, CEM, and LAQGSM in simulating fragmentation reactions at intermediate energies and discuss possible ways of further improving these codes.

  19. 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.

  20. Mechanism of Ethane Destruction in Dielectric Barrier Discharge in Air: Detailed Elementary Reaction Model and Experiment

    NASA Astrophysics Data System (ADS)

    Krasnoperov, Lev; Modenese, Camila; Krishtopa, Larisa

    2006-10-01

    Free radical destruction mechanism was extended by inclusion of reactions of excited and ionic species. The mechanism consists of 935 reactions of 85 neutral species, 9 excited states and 38 ions. The reactions include 9 initiation processes in streamers, 66 processes involving excited states and 83 reactions involving ions. The reactant, the final products as well as the major intermediates of the destruction of ethane in air in corona discharge were identified and quantified Carbon dioxide (CO2), water (H2O), formaldehyde (H2CO), acetaldehyde (CH3CHO), methanol (CH3OH), ethanol (C2H5OH), formic acid (HCOOH), acetic acid (CH3COOH), methyl nitrate (CH3ONO2) and ethyl nitrate (C2H5ONO2) were identified among the major destruction products. The destruction efficiency predicted by the mechanism is in good agreement with the experiment, the major contribution is being due to the ionization transfer reactions. Reactions of excited species play but only a minor role. The product spectrum is consistent with the subsequent low temperature free radical reactions complicated by the presence of ozone and nitrogen oxides. The generic reaction mechanism for other organic as well as inorganic compounds is discussed.

  1. Demonstration of HNE-related aldehyde formation via lipoxygenase-catalyzed synthesis of a bis-allylic dihydroperoxide intermediate

    PubMed Central

    Jin, Jing; Zheng, Yuxiang; Brash, Alan R.

    2013-01-01

    One of the proposed pathways to the synthesis of 4-hydroxy-nonenal (HNE) and related aldehydes entails formation of an intermediate bis-allylic fatty acid dihydroperoxide. As a first direct demonstration of such a pathway and proof of principle, herein we show that 8R-lipoxygenase (8R-LOX) catalyzes the enzymatic production of the HNE-like product (11-oxo-8-hydroperoxy-undeca-5,9-dienoic acid) via synthesis of 8,11-dihydroperoxy-eicosa-5,9,12,14-tetraenoic acid intermediate. Incubation of arachidonic acid with 8R-LOX formed initially 8R-hydroperoxyeicosatetraenoic acid (8R-HPETE) which was further converted to a mixture of products including a prominent HPNE-like enone. A new bis-allylic dihydroperoxide was trapped when the incubation was repeated on ice. Re-incubation of this intermediate with 8R-LOX successfully demonstrated its conversion to the enone products, and this reaction was greatly accelerated by co-incubation with NDGA, a reductant of the LOX iron. These findings identify a plausible mechanism that could contribute to the production of 4-hydroxy-alkenals in vivo. PMID:23668325

  2. Reaction mechanism governing formation of 1,3-bis(diphenylphosphino)propane-protected gold nanoclusters.

    PubMed

    Hudgens, Jeffrey W; Pettibone, John M; Senftle, Thomas P; Bratton, Ryan N

    2011-10-17

    This report outlines the determination of a reaction mechanism that can be manipulated to develop directed syntheses of gold monolayer-protected clusters (MPCs) prepared by reduction of solutions containing 1,3-bis(diphenylphosphino)propane (L(3)) ligand and Au(PPh(3))Cl. Nanocluster synthesis was initiated by reduction of two-coordinate phosphine-ligated [Au(I)LL'](+) complexes (L, L' = PPh(3), L(3)), resulting in free radical complexes. The [Au(0)LL'](•) free radicals nucleated, forming a broad size distribution of ligated clusters. Timed UV-vis spectroscopy and electrospray ionization mass spectrometry monitored the ligated Au(x), 6 ≤ x ≤ 13, clusters, which comprise reaction intermediates and final products. By employing different solvents and reducing agents, reaction conditions were varied to highlight the largest portion of the reaction mechanism. We identified several solution-phase reaction classes, including dissolution of the gold precursor, reduction, continuous nucleation/core growth, ligand exchange, ion-molecule reactions, and etching of colloids and larger clusters. Simple theories can account for the reaction intermediates and final products. The initial distribution of the nucleation products contains mainly neutral clusters. However, the rate of reduction controls the amount of reaction overlap occurring in the system, allowing a clear distinction between reduction/nucleation and subsequent solution-phase processing. During solution-phase processing, the complexes undergo core etching and core growth reactions, including reactions that convert neutral clusters to cations, in a cyclic process that promotes formation of stable clusters of specific metal nuclearity. These processes comprise "size-selective" processing that can narrow a broad distribution into specific nuclearities, enabling development of tunable syntheses. PMID:21928777

  3. Activation of the intermediate sum in intentional and automatic calculations

    PubMed Central

    Abramovich, Yael; Goldfarb, Liat

    2015-01-01

    Most research investigating how the cognitive system deals with arithmetic has focused on the processing of two addends. Arithmetic that involves more addends has specific cognitive demands such as the need to compute and hold the intermediate sum. This study examines the intermediate sums activations in intentional and automatic calculations. Experiment 1 included addition problems containing three operands. Participants were asked to calculate the sum and to remember the digits that appeared in the problem. The results revealed an interference effect in which it was hard to identify that the digit representing the intermediate sum was not actually one of the operands. Experiment 2, further examined if the intermediate sum is activated automatically when a task does not require calculation. Here, participants were presented with a prime of an addition problem followed by a target number. The task was to determine whether the target number is odd or even, while ignoring the addition problem in the prime. The results suggested that the intermediate sum of the addition problem in the prime was activated automatically and facilitated the target. Overall, the implications of those findings in the context of theories that relate to cognitive mathematical calculation is further discussed. PMID:26483749

  4. Top predators induce the evolutionary diversification of intermediate predator species.

    PubMed

    Zu, Jian; Yuan, Bo; Du, Jianqiang

    2015-12-21

    We analyze the evolutionary branching phenomenon of intermediate predator species in a tritrophic food chain model by using adaptive dynamics theory. Specifically, we consider the adaptive diversification of an intermediate predator species that feeds on a prey species and is fed upon by a top predator species. We assume that the intermediate predator?s ability to forage on the prey can adaptively improve, but this comes at the cost of decreased defense ability against the top predator. First, we identify the general properties of trade-off relationships that lead to a continuously stable strategy or to evolutionary branching in the intermediate predator species. We find that if there is an accelerating cost near the singular strategy, then that strategy is continuously stable. In contrast, if there is a mildly decelerating cost near the singular strategy, then that strategy may be an evolutionary branching point. Second, we find that after branching has occurred, depending on the specific shape and strength of the trade-off relationship, the intermediate predator species may reach an evolutionarily stable dimorphism or one of the two resultant predator lineages goes extinct. PMID:26431773

  5. Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines)

    PubMed Central

    Klink, Vincent P.; Overall, Christopher C.; Alkharouf, Nadim W.; MacDonald, Margaret H.; Matthews, Benjamin F.

    2010-01-01

    Background. A comparative microarray investigation was done using detection call methodology (DCM) and differential expression analyses. The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods. Laser capture microdissection (LCM) was used to isolate nearly homogeneous populations of plant root cells. Results. The analyses identified the presence of 13,291 transcripts between the 4 different sample types. The transcripts filtered down into a total of 6,267 that were detected as being present in one or more sample types. A comparative analysis of DCM and differential expression methods showed a group of genes that were not differentially expressed, but were expressed at detectable amounts within specific cell types. Conclusion. The DCM has identified patterns of gene expression not shown by differential expression analyses. DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process. PMID:20508855

  6. Diradical intermediate within the context of tryptophan tryptophylquinone biosynthesis

    PubMed Central

    Yukl, Erik T.; Liu, Fange; Krzystek, J.; Shin, Sooim; Jensen, Lyndal M. R.; Davidson, Victor L.; Wilmot, Carrie M.; Liu, Aimin

    2013-01-01

    Despite the importance of tryptophan (Trp) radicals in biology, very few radicals have been trapped and characterized in a physiologically meaningful context. Here we demonstrate that the diheme enzyme MauG uses Trp radical chemistry to catalyze formation of a Trp-derived tryptophan tryptophylquinone cofactor on its substrate protein, premethylamine dehydrogenase. The unusual six-electron oxidation that results in tryptophan tryptophylquinone formation occurs in three discrete two-electron catalytic steps. Here the exact order of these oxidation steps in the processive six-electron biosynthetic reaction is determined, and reaction intermediates are structurally characterized. The intermediates observed in crystal structures are also verified in solution using mass spectrometry. Furthermore, an unprecedented Trp-derived diradical species on premethylamine dehydrogenase, which is an intermediate in the first two-electron step, is characterized using high-frequency and -field electron paramagnetic resonance spectroscopy and UV-visible absorbance spectroscopy. This work defines a unique mechanism for radical-mediated catalysis of a protein substrate, and has broad implications in the areas of applied biocatalysis and understanding of oxidative protein modification during oxidative stress. PMID:23487750

  7. Molecular orbital investigation of various reaction pathways in reaction of ketones with bromoform

    NASA Astrophysics Data System (ADS)

    eljko, J. Vitnik; Kiricojevi?, Vesna D.; Ivanovi?, Milovan D.; Jurani?, Ivan O.

    To elucidate the ring opening, nucleophilic reactions of dihaloepoxides the extensive calculations were done on a model system cyclohexanone-bromoform. In this reaction, the formation of dihaloepoxide is postulated as a key step that determines the distribution and stereochemistry of products. Every reaction scheme involves epoxide as a key intermediate (1). Three major products (2, 3, and 4) can be obtained, in principle, by three different competing reaction pathways. The calculations showed that all the pathways are exothermic. Reaction pathway 1 is most convenient, it does not include any intermediate, and its energy is not much affected by the polarity of the medium. In pathways 2 and 3, the calculations showed the intermediates having a largely carbocationic character on the spiro junction carbon atom. The step in which these intermediates are formed determines the reaction rate. Because of the polarity of intermediates in pathways 2 and 3, the base concentration and polarity of solvent determine the balance of reaction pathways and the product yield.

  8. Kinetic Intermediates in RNA Folding

    NASA Astrophysics Data System (ADS)

    Zarrinkar, Patrick P.; Williamson, James R.

    1994-08-01

    The folding pathways of large, highly structured RNA molecules are largely unexplored. Insight into both the kinetics of folding and the presence of intermediates was provided in a study of the Mg2+-induced folding of the Tetrahymena ribozyme by hybridization of complementary oligodeoxynucleotide probes. This RNA folds via a complex mechanism involving both Mg2+-dependent and Mg2+-independent steps. A hierarchical model for the folding pathway is proposed in which formation of one helical domain (P4-P6) precedes that of a second helical domain (P3-P7). The overall rate-limiting step is formation of P3-P7, and takes place with an observed rate constant of 0.72 ± 0.14 minute-1. The folding mechanism of large RNAs appears similar to that of many multidomain proteins in that formation of independently stable substructures precedes their association into the final conformation.

  9. 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. PMID:26283390

  10. 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

  11. Sub-classification of intermediate-stage (Barcelona Clinic Liver Cancer stage-B) hepatocellular carcinomas

    PubMed Central

    Yamakado, Koichiro; Hirota, Shozo

    2015-01-01

    Hepatocellular carcinoma (HCC), the fifth most common cancer in the world, shows increasing incidence worldwide. Curative treatments such as hepatectomy, liver transplantation, and radiofrequency ablation are applied in only 30%-60% of cases. Most remaining patients receive transarterial chemoembolization (TACE). Patients with intermediate-stage HCCs are regarded as good candidates for TACE. However, the intermediate stage includes non-homogeneous patients. Some movements are underway to stratify patients using prognostic factors to identify patient groups exhibiting greater benefit from TACE than other patient groups. This review describes two substaging systems that subclassify intermediate-stage HCCs and discusses the importance of dividing intermediate-stage patients. PMID:26457020

  12. Intermediate P* from Soluble Methane Monooxygenase Contains a Diferrous Cluster

    PubMed Central

    Banerjee, Rahul; Meier, Katlyn K.; Mnck, 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. Mssbauer spectra of rapid freeze quench samples at these times show that the intermediates are formed at almost exactly the predicted levels. The Mssbauer 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 the electronic structure of the FeIIFeII center rather than oxidation. The similarity of the optical and Mssbauer spectra of Hred, O, and P* suggest that only subtle changes occur in the electronic and physical structure of the diiron cluster as P* forms. Nevertheless, the changes that do occur are necessary for O2 to be activated for hydrocarbon oxidation. PMID:23718184

  13. Intermediate P* from soluble methane monooxygenase contains a diferrous cluster.

    PubMed

    Banerjee, Rahul; Meier, Katlyn K; Mnck, 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)). O? 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. Mssbauer spectra of rapid freeze-quench samples at these times show that the intermediates are formed at almost exactly the predicted levels. The Mssbauer spectra show that the diiron cluster of P*, quite unexpectedly, is in the Fe(II)Fe(II) state. Thus, the loss of the g = 16 EPR signal results from a change in the electronic structure of the Fe(II)Fe(II) center rather than oxidation. The similarity of the optical and Mssbauer spectra of H(red), O, and P* suggests that only subtle changes occur in the electronic and physical structure of the diiron cluster as P* forms. Nevertheless, the changes that do occur are necessary for O? to be activated for hydrocarbon oxidation. PMID:23718184

  14. 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...

  15. 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. PMID:25548185

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Transformation, products, and pathways of chlorophenols via electro-enzymatic catalysis: How to control toxic intermediate products.

    PubMed

    Du, Penghui; Zhao, He; Li, Haitao; Zhang, Di; Huang, Ching-Hua; Deng, Manfeng; Liu, Chenming; Cao, Hongbin

    2016-02-01

    Chlorophenols can be easily oxidized into chlorobenzoquinones (CBQs), which are highly toxic and have been linked to bladder cancer risk. Herein, we report the transformation, products, and pathways of 2,4-dichlorophenol (DCP) by horseradish peroxidase (HRP) and electro-generated hydrogen peroxide (H2O2) and suggest methods to control the formation of toxic intermediate products. After a 10-min electroenzymatic process, 99.7% DCP removal may be achieved under optimal conditions. A total of 16 reaction products, most of which are subsequently verified as DCP polymers and related quinone derivatives, are identified by using ultra-performance liquid chromatography-time-of-flight mass spectrometry (UPLC-TOF-MS). A five-step reaction pathway for DCP transformation, including HRP-driven substrate oxidation, substitution and radical coupling, quick redox equilibrium, nucleophilic reaction and precipitation from aqueous solution, is proposed. Current variations and the presence of CO2 could significantly affect these reaction pathways. In particular, higher currents enhance the hydroxylation process by promoting alkaline conditions and abundant H2O2 formation. As both OH(-) and H2O2 are strong nucleophiles, they easily react with CBQ products to form hydroxylated products, which can significantly reduce solution toxicity. An adequate supply of CO2 can provide favorable pH conditions and facilitate enzymatic steps, such as substrate oxidation and radical coupling, to generate precipitable polymerized products. All of the results suggest that toxic intermediate products can be effectively reduced and controlled during the electro-enzymatic process to remove DCP and other phenolic pollutants from wastewaters. PMID:26519798

  2. Spatially Organized Enzymes Drive Cofactor-Coupled Cascade Reactions.

    PubMed

    Ngo, Tien Anh; Nakata, Eiji; Saimura, Masayuki; Morii, Takashi

    2016-03-01

    We report the construction of an artificial enzyme cascade based on the xylose metabolic pathway. Two enzymes, xylose reductase and xylitol dehydrogenase, were assembled at specific locations on DNA origami by using DNA-binding protein adaptors with systematic variations in the interenzyme distances and defined numbers of enzyme molecules. The reaction system, which localized the two enzymes in close proximity to facilitate transport of reaction intermediates, resulted in significantly higher yields of the conversion of xylose into xylulose through the intermediate xylitol with recycling of the cofactor NADH. Analysis of the initial reaction rate, regenerated amount of NADH, and simulation of the intermediates' diffusion indicated that the intermediates diffused to the second enzyme by Brownian motion. The efficiency of the cascade reaction with the bimolecular transport of xylitol and NAD(+) likely depends more on the interenzyme distance than that of the cascade reaction with unimolecular transport between two enzymes. PMID:26881296

  3. Electrocatalytic oxygen activation by carbanion intermediates of nitrogen-doped graphitic carbon.

    PubMed

    Li, Qiqi; Noffke, Benjamin W; Wang, Yilun; Menezes, Bruna; Peters, Dennis G; Raghavachari, Krishnan; Li, Liang-shi

    2014-03-01

    Nitrogen-doped graphitic carbon has been intensively studied for potential use as an electrocatalyst in fuel cells for the oxygen reduction reaction (ORR). However, the lack of a mechanistic understanding on the carbon catalysis has severely hindered the progress of the catalyst development. Herein we use a well-defined graphene nanostructure as a model system and, for the first time, reveal an oxygen activation mechanism that involves carbanion intermediates in these materials. Our work shows that the overpotential of the electrocatalytic ORR is determined by the generation of the carbanion intermediates, and the current by the rate the intermediates activate oxygen. PMID:24533901

  4. 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

    2016-05-01

    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. PMID:26508263

  5. Theoretical studies on the deacylation step of acylated Candida Antarctica lipase B: structural and reaction pathway analysis.

    PubMed

    Sadeghi Googheri, Mohammad Sadegh; Housaindokht, Mohammad Reza; Sabzyan, Hassan

    2015-04-01

    The deacylation step of acylated Candida Antarctica lipase B, which was acylated with methylcaprylate (MEC) and acetylcholine (ACh), has been studied by using density functional theory method. Free energies of the entire reaction were calculated for enzyme deacylation by water and hydrogen peroxide that represented hydrolysis and perhydrolysis reactions, respectively. The calculations displayed that a stepwise mechanism there was with the enzyme-product complex being a deep minimum on the free energy surfaces of both of two reactions. The tetrahedral intermediate formation was the rate-determining step of all reactions, which needed 8.1 to 10.5kcalmol(-1) for activation in different reactions. In the second stage of the reaction, fewer free energy barriers, between 4.7 and 5.9kcalmol(-1), were identified to enable the proton transfer from His224 to Ser105 and the breakdown of the tetrahedral intermediate. These calculated activation free energies approved theoretical possibility of both of two reactions for two substrates. Finally, an applied tool examined the interactions role in the stability and energy levels of different chemical species. PMID:25622130

  6. Acyl Silicates and Acyl Aluminates as Activated Intermediates in Peptide Formation on Clays

    NASA Astrophysics Data System (ADS)

    White, David H.; Kennedy, Robert M.; Macklin, John

    1984-12-01

    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 (i.e., the anhydride of a carboxylic acid with Si-OH or Al-OH), analogous to acyl phosphates involved in several biochemical reactions including peptide bond synthesis. We confirmed the proposed mechanism 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 widespread, geologically realistic setting for prebiotic peptide formation via in situ activation.

  7. Intermediate evolution using SNIa, and BAO

    NASA Astrophysics Data System (ADS)

    Cárdenas, Víctor H.; Herrera, O.

    2015-10-01

    We study the intermediate evolution model and show that, compared with the recent study of a power-law evolution, the intermediate evolution is a better description of the low-redshift regime supported by observations from type Ia supernovae and BAO. We found also that recent data suggest that the intermediate evolution is as good a fit to this redshift range as the \\varLambdaCDM model.

  8. 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 Ssmica 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 600-1,000C 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.

  9. Resonant photoemission spectroscopy for intermediate band materials

    NASA Astrophysics Data System (ADS)

    Mazzola, F.; Nematollahi, M.; Li, Z. S.; Cooil, S.; Yang, X.; Reenaas, T. W.; Wells, J. W.

    2015-11-01

    Resonant photoemission spectroscopy is used to study the intermediate-band material Cr doped ZnS. Using resonant photoemission, we show that the intermediate-band can be characterized, revealing the filling and specific orbital character of the states contributing to the resonant photoemission signal. We demonstrate that resonant photoemission spectroscopy is a powerful approach for understanding the origin of intermediate bands in doped ZnS. The methodology can be widely extended to a large variety of materials, providing useful information towards engineering of high efficiency intermediate band solar cells and of other optoelectronic devices.

  10. Modeling of intermediate phase growth

    SciTech Connect

    Umantsev, A.

    2007-01-15

    We introduced a continuum method for modeling of intermediate phase growth and numerically simulated three common experimental situations relevant to the physical metallurgy of soldering: growth of intermetallic compound layer from an unlimited amount of liquid and solid solders and growth of the compound from limited amounts of liquid solder. We found qualitative agreements with the experimental regimes of growth in all cases. For instance, the layer expands in both directions with respect to the base line when it grows from solid solder, and grows into the copper phase when the solder is molten. The quantitative agreement with the sharp-interface approximation was also achieved in these cases. In the cases of limited amounts of liquid solder we found the point of turnaround when the compound/solder boundary changed the direction of its motion. Although such behavior had been previously observed experimentally, the simulations revealed important information: the turnaround occurs approximately at the time of complete saturation of solder with copper. This result allows us to conclude that coarsening of the intermetallic compound structure starts only after the solder is practically saturated with copper.

  11. Characterization of a transient intermediate formed in the liver alcohol dehydrogenase catalyzed reduction of 3-hydroxy-4-nitrobenzaldehyde

    SciTech Connect

    MacGibbon, A.K.H.; Koerber, S.C.; Pease, K.; Dunn, M.F.

    1987-06-02

    The compounds 3-hydroxy-4-nitrobenzaldehyde and 3-hydroxy-4-nitrobenzyl alcohol are introduced as new chromophoric substrates for probing the catalytic mechanism of horse liver alcohol dehydrogenase (LADH). Ionization of the phenolic hydroxyl group shifts the spectrum of the aldehyde from 360 to 433 nm (pK/sub a/ = 6.0), whereas the spectrum of the alcohol shifts from 350 to 417 nm (pK/sub a/ = 6.9). Rapid-scanning, stopped-flow (RSSF) studies at alkaline pH show that the LADH-catalyzed interconversion of these compounds occurs via the formation of an enzyme-bound intermediate with a blue-shifted spectrum. When reaction is limited to a single turnover of enzyme sites, the formation and decay of the intermediate when aldehyde reacts with enzyme-bound reduced nicotinamide adenine dinucleotide E(NADH) are characterized by two relaxations. Detailed stopped-flow kinetic studies were carried out to investigate the disappearance of aldehyde and NADH, the formation and decay of the intermediate, the displacement of Auramine O by substrate, and /sup 2/H kinetic isotope effects. It was found that (1) NADH oxidation takes place at the rate of the slower relaxation (2) when NADD is substituted for NADH, lambda/sub s/ is subject to a small primary isotope effect; and (3) the events that occur in lambda/sub s/ precede lambda/sub f/. These findings identify the intermediate as a ternary complex containing bound oxidized nicotinamide adenine dinucleotide (NAD/sup +/) and some form of 3-hydroxy-4-nitrobenzyl alcohol. The authors conclude that the LADH substrate site can be divided into two subsites: a highly polar, electropositive subsite in the vicinity of the active-site zinc and, just a few angstroms away, a rather nonpolar region.

  12. Mechanistic Insight into the Dehydro-Diels-Alder Reaction of Styrene-Ynes.

    PubMed

    Kocsis, Laura S; Kagalwala, Husain N; Mutto, Sharlene; Godugu, Bhaskar; Bernhard, Stefan; Tantillo, Dean J; Brummond, Kay M

    2015-12-01

    The Diels-Alder reaction represents one of the most thoroughly studied and well-understood synthetic transformations for the assembly of six-membered rings. Although intramolecular dehydro-Diels-Alder (IMDDA) reactions have previously been employed for the preparation of naphthalene and dihydronaphthalene substrates, low yields and product mixtures have reduced the impact and scope of this reaction. Through the mechanistic studies described within, we have confirmed that the thermal IMDDA reaction of styrene-ynes produces a naphthalene product via loss of hydrogen gas from the initially formed cycloadduct, a tetraenyl intermediate. Alternatively, the dihydronaphthalene product is afforded from the same tetraenyl intermediate via a radical isomerization process. Moreover, we have identified conditions that can be used to achieve efficient, high-yielding, and selective IMDDA reactions of styrene-ynes to form either naphthalene or dihydronaphthalene products. The operational simplicity and retrosynthetic orthogonality of this method for the preparation of naphthalenes and dihydronaphthalenes makes this transformation appealing for the synthesis of medicinal and material targets. The mechanistic studies within may impact the development of other thermal transformations. PMID:25671399

  13. Isosynthesis reactions of CO/H/sub 2/ over zirconium dioxide

    SciTech Connect

    Tseng, S.C.

    1987-01-01

    The isosynthesis reactions of an equimolar mixture of carbon monoxide and hydrogen were studied over zirconium dioxide catalysts. The main objectives of this work were: (1) to investigate the reaction pathway, (2) identify the surface intermediates leading to the formation of i-butene, and (3) determine the mechanisms of carbon chain propagation. The reactions were conducted at 250-450/sup 0/C, 35 atm (500 psig) total pressure, and 100-200 cc/min total flow rate in a differential reactor. Oxygenated intermediates are proposed to exist on the zirconia surface. This is supported by the observations that oxygenated products were favored at lower reaction temperatures or at shorter residence times. Propylene, propionaldehyde, acetone, i-propanol, and n-propanol were used as probe molecules to examine the chain growth and branching mechanisms, leading to the formation of i-butene. Reaction schemes are proposed. Carbon-13 labeled acetone and methanol were utilized to examine quantitatively the above two schemes. The labeled acetone studies revealed that both the branched and linear olefins were formed from the acetone added. The presence of carbon-13 carbons in linear olefins indicated that methylation at the acetone methyl occurred. The labeled methanol studies revealed that aldol-type condensation did proceed over zirconia, leading to the formation of branching olefins.

  14. Structural insights into the reaction mechanism of S-adenosyl-L-homocysteine hydrolase

    PubMed Central

    Kusakabe, Yoshio; Ishihara, Masaaki; Umeda, Tomonobu; Kuroda, Daisuke; Nakanishi, Masayuki; Kitade, Yukio; Gouda, Hiroaki; Nakamura, Kazuo T.; Tanaka, Nobutada

    2015-01-01

    S-adenosyl-L-homocysteine hydrolase (SAH hydrolase or SAHH) is a highly conserved enzyme that catalyses the reversible hydrolysis of SAH to L-homocysteine (HCY) and adenosine (ADO). High-resolution crystal structures have been reported for bacterial and plant SAHHs, but not mammalian SAHHs. Here, we report the first high-resolution crystal structure of mammalian SAHH (mouse SAHH) in complex with a reaction product (ADO) and with two reaction intermediate analogues3-keto-aristeromycin (3KA) and noraristeromycin (NRN)at resolutions of 1.55, 1.55, and 1.65?. Each of the three structures constitutes a structural snapshot of one of the last three steps of the five-step process of SAH hydrolysis by SAHH. In the NRN complex, a water molecule, which is an essential substrate for ADO formation, is structurally identified for the first time as the candidate donor in a Michael addition by SAHH to the 3-keto-4,5-didehydroadenosine reaction intermediate. The presence of the water molecule is consistent with the reaction mechanism proposed by Palmer & Abeles in 1979. These results provide insights into the reaction mechanism of the SAHH enzyme. PMID:26573329

  15. Photoaffinity labelling with P3-(4-azidoanilido)uridine 5'-triphosphate identifies gpi3p as the UDP-GlcNAc-binding subunit of the enzyme that catalyses formation of GlcNAc-phosphatidylinositol, the first glycolipid intermediate in glycosylphosphatidylinositol synthesis.

    PubMed Central

    Kostova, Z; Rancour, D M; Menon, A K; Orlean, P

    2000-01-01

    Glycosylphosphatidylinositols (GPIs) are made by all eukaryotes. The first step in their synthesis is the transfer of GlcNAc from UDP-GlcNAc to phosphatidylinositol (PI). Four proteins in mammals and at least three in yeast make up a complex that carries out this reaction. Three of the proteins are highly conserved between yeast and mammals: the Gpi1 protein, the Pig-C/Gpi2 protein and the Pig-A/Gpi3 protein. The function of the individual subunits is not known, but of the three, the Pig-A/Gpi3 proteins resemble members of a large family of nucleotide-sugar-utilizing glycosyltransferases. To establish whether Gpi3p is the UDP-GlcNAc-binding subunit of the yeast GlcNAc-PI synthetic complex, we tested its ability to become cross-linked to the photoactivatable substrate analogue P(3)-(4-azidoanilido)-uridine 5'-triphosphate (AAUTP). We report that Gpi3p bearing the FLAG epitope at its C-terminus becomes cross-linked to AAUTP[alpha-(32)P], but that Gpi2p-FLAG does not. Furthermore, Gpi3p-FLAG expressed in Escherichia coli is also cross-linked. These results indicate that Gpi3p is the UDP-GlcNAc-binding and probable catalytic subunit of the GlcNAc-PI synthetic complex. PMID:10970797

  16. Probing simple patterns in complex nuclei with transfer reactions

    NASA Astrophysics Data System (ADS)

    Cizewski, Jolie

    2011-04-01

    The first observation of the O(6) limit of the Interacting Boson Model provided an unexpected benchmark for nuclear structure. A shape intermediate between a spherical vibrator and deformed rotor was a new simple pattern that described the complex nucleus, 196Pt. Shortly thereafter simple patterns in odd-mass nuclei were recognized as the coupling of a fermion to O(6) structures of the core. In addition to selection rules for electromagnetic transitions, there were now selection rules for single-particle transfer. As the properties of nuclei further from stability are explored, identifying simple patterns in complex nuclei becomes even more important as benchmarks in extrapolations of nuclear models to even more exotic nuclei. Identifying such benchmarks requires a full spectrum of spectroscopic probes, including single-particle transfer reactions. The present talk will provide an overview of how transfer reactions have been used to identify simple patterns in complex nuclei, from proton transfer reactions near 196Pt to recent neutron transfer work near 132Sn, eight neutrons from stability. This work was supported in part by the National Nuclear Security Administration under the Stewardship Science Academic Alliances program and the National Science Foundation.

  17. Chemoenzymatic synthesis of vitamin B5-intermediate (R)-pantolactone via combined asymmetric organo- and biocatalysis.

    PubMed

    Heidlindemann, Marcel; Hammel, Matthias; Scheffler, Ulf; Mahrwald, Rainer; Hummel, Werner; Berkessel, Albrecht; Grger, Harald

    2015-04-01

    The combination of an asymmetric organocatalytic aldol reaction with a subsequent biotransformation toward a "one-pot-like" process for the synthesis of (R)-pantolactone, which to date is industrially produced by a resolution process, is demonstrated. This process consists of an initial aldol reaction catalyzed by readily available l-histidine followed by biotransformation of the aldol adduct by an alcohol dehydrogenase without the need for intermediate isolation. Employing the industrially attractive starting material isobutanal, a chemoenzymatic three-step process without intermediate purification is established allowing the synthesis of (R)-pantolactone in an overall yield of 55% (three steps) and high enantiomeric excess of 95%. PMID:25710713

  18. Direct detection of pyridine formation by the reaction of CH (CD) with pyrrole: a ring expansion reaction

    SciTech Connect

    Soorkia, Satchin; Taatjes, Craig A.; Osborn, David L.; Selby, Talitha M.; Trevitt, Adam J.; Wilson, Kevin R.; Leone, Stephen R.

    2010-03-16

    The reaction of the ground state methylidyne radical CH (X2Pi) with pyrrole (C4H5N) has been studied in a slow flow tube reactor using Multiplexed Photoionization Mass Spectrometry coupled to quasi-continuous tunable VUV synchrotron radiation at room temperature (295 K) and 90 oC (363 K), at 4 Torr (533 Pa). Laser photolysis of bromoform (CHBr3) at 248 nm (KrF excimer laser) is used to produce CH radicals that are free to react with pyrrole molecules in the gaseous mixture. A signal at m/z = 79 (C5H5N) is identified as the product of the reaction and resolved from 79Br atoms, and the result is consistent with CH addition to pyrrole followed by Helimination. The Photoionization Efficiency curve unambiguously identifies m/z = 79 as pyridine. With deuterated methylidyne radicals (CD), the product mass peak is shifted by +1 mass unit, consistent with the formation of C5H4DN and identified as deuterated pyridine (dpyridine). Within detection limits, there is no evidence that the addition intermediate complex undergoes hydrogen scrambling. The results are consistent with a reaction mechanism that proceeds via the direct CH (CD) cycloaddition or insertion into the five-member pyrrole ring, giving rise to ring expansion, followed by H atom elimination from the nitrogen atom in the intermediate to form the resonance stabilized pyridine (d-pyridine) molecule. Implications to interstellar chemistry and planetary atmospheres, in particular Titan, as well as in gas-phase combustion processes, are discussed.

  19. Heuristics-Guided Exploration of Reaction Mechanisms.

    PubMed

    Bergeler, Maike; Simm, Gregor N; Proppe, Jonny; Reiher, Markus

    2015-12-01

    For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive species are involved that might cause a myriad of side reactions. Without automation, a complete investigation of complex reaction mechanisms is tedious and possibly unfeasible. Therefore, only the expected dominant reaction paths of a chemical reaction network (e.g., a catalytic cycle or an enzymatic cascade) are usually explored in practice. Here, we present a computational protocol that constructs such networks in a parallelized and automated manner. Molecular structures of reactive complexes are generated based on heuristic rules derived from conceptual electronic-structure theory and subsequently optimized by quantum-chemical methods to produce stable intermediates of an emerging reaction network. Pairs of intermediates in this network that might be related by an elementary reaction according to some structural similarity measure are then automatically detected and subjected to an automated search for the connecting transition state. The results are visualized as an automatically generated network graph, from which a comprehensive picture of the mechanism of a complex chemical process can be obtained that greatly facilitates the analysis of the whole network. We apply our protocol to the Schrock dinitrogen-fixation catalyst to study alternative pathways of catalytic ammonia production. PMID:26642988

  20. A detailed investigation on electro-Fenton treatment of propachlor: Mineralization kinetic and degradation intermediates.

    PubMed

    Gençten, Metin; Özcan, Ali

    2015-10-01

    In this study, electrochemical removal of propachlor from water has been investigated by electro-Fenton process which provides continuous electrochemical production of hydroxyl radical which is a highly oxidizing agent. This radical can react with propachlor unselectively and can oxidize it into carbon dioxide and water. Effects of applied current, catalyst (Fe2(SO4)3) and supporting electrolyte (Na2SO4) concentrations on the degradation rate of propachlor have been examined and determined as 200 mA, 0.20 mM and 25 mM, respectively. The oxidation reaction showed a second-order reaction kinetic with an absolute rate constant value of (3.6±0.2)×10(9) M(-1) s(-1) which was determined by competition kinetic experiments. Total organic carbon analysis was employed to follow the mineralization of propachlor. The total mineralization was completed in a seven-hour electrolysis at 300 mA indicating that the electro-Fenton process is very effective in the mineralization of propachlor in water. Oxidation of propachlor with hydroxyl radical led to the formation of intermediate species. Some of these species were detected and quantified by chromatographic and spectroscopic methods such as HPLC, GC-MS and IC. A plausible mineralization pathway for the electrochemical removal of propachlor was proposed based on the identified by-products. PMID:25989604