Science.gov

Sample records for identify reaction intermediate

  1. 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.

  2. 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

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

    ERIC Educational Resources Information Center

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

    2009-01-01

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

  4. 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

  5. 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.

  6. (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)

  7. 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.

  8. Cryospectrokinetic characterization of intermediates in biochemical reactions: carboxypeptidase A.

    PubMed Central

    Auld, D S; Galdes, A; Geoghegan, K F; Holmquist, B; Martinelli, R A; Vallee, B L

    1984-01-01

    Cryospectrokinetic studies provide concurrent structural, kinetic, and chemical data on short-lived intermediates in the course of the interactions of enzymes with their substrates and of other, similar pairs of biomolecules. Subzero temperatures extend the lifetimes of these intermediates and, combined with rapid-mixing and rapid-scanning instrumentation, allow simultaneous measurement of both their physical-chemical and kinetic characteristics. For carboxypeptidase A, the spectra of a chromophoric, enzymatically functional cobalt atom at the active site signal the structure of the coordination complex during catalysis, while radiationless energy transfer between enzyme tryptophans and the fluorescent dansyl blocking group of rapidly hydrolyzed peptide and ester substrates provides the basis for measurement of the rates of formation and breakdown of intermediates. Subzero radiationless energy transfer kinetic studies of the zinc and cobalt enzymes disclose two intermediates in the hydrolysis of both peptides and esters and furnish all the rate and equilibrium constants for the reaction scheme E + S in equilibrium ES1 in equilibrium ES2----E + P. The chemical and kinetic data indicate that neither of these is an acylenzyme intermediate. Both absorption and EPR spectra of the ES2 reaction intermediates consistently demonstrate the formation of transient metal complexes, differences between the effects induced by peptides and esters, and strong similarities between those induced by all peptides on the one hand and all esters on the other. The marked alterations of the cobalt spectra likely reflect the coordination of a substrate carboxyl and/or carbonyl group to the metal at a critical step in the course of catalysis. The cryospectrokinetic approach developed here in the mechanistic study of this metalloenzyme is applicable to the examination of transients of biochemical reactions in general. It will allow molecular characterization of previously elusive intermediates and greatly magnify the range of mechanistic questions that can be answered. Images PMID:6591178

  9. Recent results on intermediate-energy nucleon knockout reactions

    SciTech Connect

    Wimmer, K.

    2013-04-19

    Nucleon knockout reactions using fast rare isotope beams are a well-suited tool to study single-particle properties of exotic nuclei and the evolution of nuclear shell structure towards the drip-lines. In particular the sudden removal of two protons from an intermediate-energy neutron-rich projectile has been shown to proceed as a direct reaction. In addition to giving spectroscopic information, this type of reaction promises a rather unique tool assign spins by measuring the momentum distributions of the heavy reaction residues. In the present experiment, the heavy reaction residues were measured in coincidence with the removed. These more final-state-exclusive measurements are key for further validation of this direct reaction and its use for quantitative spectroscopy of highly neutron-rich nuclei.

  10. 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

  11. 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; Hernández-Laguna, Alfonso; Sainz-Díaz, 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

  12. 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

  13. 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

  14. Characterization of Anionic Cluster Nucleophilic Substitution Reaction Intermediates

    NASA Astrophysics Data System (ADS)

    Cyr, Donna Marie

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

  15. 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.

  16. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  18. 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.

  19. 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

  20. 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

  1. Structural characterization of the reaction pathway in phosphoserine phosphatase: crystallographic "snapshots" of intermediate states.

    PubMed

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

    2002-05-31

    Phosphoserine phosphatase (PSP) is a member of a large class of enzymes that catalyze phosphoester hydrolysis using a phosphoaspartate-enzyme intermediate. PSP is a likely regulator of the steady-state d-serine level in the brain, which is a critical co-agonist of the N-methyl-d-aspartate type of glutamate receptors. Here, we present high-resolution (1.5-1.9 A) structures of PSP from Methanococcus jannaschii, which define the open state prior to substrate binding, the complex with phosphoserine substrate bound (with a D to N mutation in the active site), and the complex with AlF3, a transition-state analog for the phospho-transfer steps in the reaction. These structures, together with those described for the BeF3- complex (mimicking the phospho-enzyme) and the enzyme with phosphate product in the active site, provide a detailed structural picture of the full reaction cycle. The structure of the apo state indicates partial unfolding of the enzyme to allow substrate binding, with refolding in the presence of substrate to provide specificity. Interdomain and active-site conformational changes are identified. The structure with the transition state analog bound indicates a "tight" intermediate. A striking structure homology, with significant sequence conservation, among PSP, P-type ATPases and response regulators suggests that the knowledge of the PSP reaction mechanism from the structures determined will provide insights into the reaction mechanisms of the other enzymes in this family. PMID:12051918

  2. 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

  3. 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

  4. 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.

  5. 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

  6. Metabolic-intermediate complex formation with cytochrome P450: theoretical studies in elucidating the reaction pathway for the generation of reactive nitroso intermediate.

    PubMed

    Taxak, Nikhil; Desai, Prashant V; Patel, Bhargav; Mohutsky, Michael; Klimkowski, Valentine J; Gombar, Vijay; Bharatam, Prasad V

    2012-08-01

    Mechanism-based inhibition (MBI) of cytochrome P450 (CYP) can lead to drug-drug interactions and often to toxicity. Some aliphatic and aromatic amines can undergo biotransformation reactions to form reactive metabolites such as nitrosoalkanes, leading to MBI of CYPs. It has been proposed that the nitrosoalkanes coordinate with the heme iron, forming metabolic-intermediate complex (MIC), resulting in the quasi-irreversible inhibition of CYPs. Limited mechanistic details regarding the formation of reactive nitroso intermediate and its coordination with heme-iron have been reported. A quantum chemical analysis was performed to elucidate potential reaction pathways for the generation of nitroso intermediate and the formation of MIC. Elucidation of the energy profile along the reaction path, identification of three-dimensional structures of reactive intermediates and transition states, as well as charge and spin density analyses, were performed using the density functional B3LYP method. The study was performed using Cpd I [iron (IV-oxo] heme porphine with SH(-) as the axial ligand) to represent the catalytic domain of CYP, simulating the biotransformation process. Three pathways: (i) N-oxidation followed by proton shuttle, (ii) N-oxidation followed by 1,2-H shift, and (iii) H-abstraction followed by rebound mechanism, were studied. It was observed that the proton shuttle pathway was more favorable over the whole reaction leading to reactive nitroso intermediate. This study revealed that the MIC formation from a primary amine is a favorable exothermic process, involving eight different steps and preferably takes place on the doublet spin surface of Cpd I. The rate-determining step was identified to be the first N-oxidation of primary amine. PMID:22610824

  7. 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

  8. CONSIDERATION OF REACTION INTERMEDIATES IN STRUCTURE-ACTIVITY RELATIONSHIPS: A KEY TO UNDERSTANDING AND PREDICTION

    EPA Science Inventory

    Consideration of Reaction Intermediates in Structure- Activity Relationships: A Key to Understanding and Prediction

    A structure-activity relationship (SAR) represents an empirical means for generalizing chemical information relative to biological activity, and is frequent...

  9. Kinetics and intermediates of the reaction of fully reduced Escherichia coli bo₃ ubiquinol oxidase with O₂.

    PubMed

    Szundi, Istvan; Kittredge, Clive; Choi, Sylvia K; McDonald, William; Ray, Jayashree; Gennis, Robert B; Einarsdóttir, Ólöf

    2014-08-26

    Cytochrome bo₃ ubiquinol oxidase from Escherichia coli catalyzes the reduction of O₂ to water by ubiquinol. The reaction mechanism and the role of ubiquinol continue to be a subject of discussion. In this study, we report a detailed kinetic scheme of the reaction of cytochrome bo₃ with O₂ with steps specific to ubiquinol. The reaction was investigated using the CO flow-flash method, and time-resolved optical absorption difference spectra were collected from 1 μs to 20 ms after photolysis. Singular value decomposition-based global exponential fitting resolved five apparent lifetimes, 22 μs, 30 μs, 42 μs, 470 μs, and 2.0 ms. The reaction mechanism was derived by an algebraic kinetic analysis method using frequency-shifted spectra of known bovine states to identify the bo3 intermediates. It shows 42 μs O₂ binding (3.8 × 10(7) M(-1) s(-1)), producing compound A, followed by faster (22 μs) heme b oxidation, yielding a mixture of PR and F, and rapid heme b rereduction by ubiquinol (30 μs), producing the F intermediate and semiquinone. In the 470 μs step, the o₃ F state is converted into the o₃(3+) oxidized state, presumably by semiquinone/ubiquinol, without the concomitant oxidation of heme b. The final 2 ms step shows heme b reoxidation and the partial rereduction of the binuclear center and, following O₂ binding, the formation of a mixture of P and F during a second turnover cycle. The results show that ubiquinol/semiquinone plays a complex role in the mechanism of O₂ reduction by bo₃, displaying kinetic steps that have no analogy in the CuA-containing heme-copper oxidases. PMID:25076393

  10. Reactions of iodine intermediates in iodate-hydrogen peroxide oscillators

    SciTech Connect

    Furrow, S.

    1987-04-09

    Reaction rates have been measured in acid solution at 25 /sup 0/C for several reactions of iodine species and hydrogen peroxide. The reactions are all subsystems of reactions which occur in iodate-hydrogen peroxide oscillators. Reactions discussed are the following: HOI + HOI ..-->.. HOIO + H/sup +/ + I/sup -/, -1/2d(HOI)dt = 25 +/- 5 M/sup -1/ s/sup -1/(HOI)/sup 2/; HOI + HOIO ..-->.. 2H..mu.. + I/sup -/ + IO/sub 3//sup -/, -d(HOI)/dt = 230 +/- 20 M/sup -1/ s/sup -1/(HOI)(HOIO); HOIO + HOIO ..-->.. H/sup +/ + IO/sub 3//sup -/ + HOI, -1/2d(HOIO)lt. slashdt = 0.3 +/- 0.2 s/sup -1/(HOIO)/sup 2//(H/sup +/); HOI + H/sub 2/O/sub 2/..-->.. H/sup +/ + I/sup -/ + O/sub 2/ + H/sub 2/O, -d(HOI)dt = 5 +/- 3 M/sup -1/ s/sup -1/(HOI)(H/sub 2/O/sub 2/). In addition reaction products have been studied for reaction of H/sub 2/O/sub 2/ with HOI and HOIO. In both cases, at (H/sup +/) approx.0.1 M, oxidation to IO/sub 3//sup -/ is predominant at low (H/sub 2/O/sub 2/). Rates are too fast to establish rate laws by using manual mixing techniques. Calculations for a skeleton model of the Briggs-Rauscher oscillator, using the above rate constants, reproduce basic experimentally observed features.

  11. 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

  12. 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

  13. 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

  14. 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…

  15. 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.

  16. 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.

  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. 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.

  19. 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)

  20. Population of bound excited states in intermediate-energy fragmentation reactions

    SciTech Connect

    Obertelli, A.; Gade, A.; Bazin, D.; Hansen, P.G.; Hoagland, T.; Lecouey, J.-L.; Mueller, W.F.; Yoneda, K.; Campbell, C.M.; Cook, J.M.; Davies, A.D.; Dinca, D.-C.; Glasmacher, T.; Terry, J.R.; Zwahlen, H.; Cottle, P.D.; Kemper, K.W.; Reynolds, R.R.; Roeder, B.T.; Tostevin, J.A.

    2006-04-15

    Fragmentation reactions with intermediate-energy heavy-ion beams exhibit a wide range of reaction mechanisms, ranging from direct reactions to statistical processes. We examine this transition by measuring the relative population of excited states in several sd-shell nuclei produced by fragmentation with the number of removed nucleons ranging from two to sixteen. The two-nucleon removal is consistent with a non-dissipative process, whereas the removal of more than five nucleons appears to be mainly statistical.

  1. 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

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

    NASA Astrophysics Data System (ADS)

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

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

  3. 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

  4. Identification of fleeting electrochemical reaction intermediates using desorption electrospray ionization mass spectrometry.

    PubMed

    Brown, Timothy A; Chen, Hao; Zare, Richard N

    2015-06-17

    We report a new method for the mass spectrometric detection of fleeting reaction intermediates in electrochemical reactions utilizing a "waterwheel" working electrode setup. This setup takes inspiration from desorption electrospray ionization (DESI) mass spectrometry, where the sampling time is on the order of milliseconds, to sample directly from the surface of a working electrode for mass spectrometric analysis. We present data that show the formation of a diimine intermediate of the electrochemical oxidation of uric acid that has a lifetime in solution of 23 ms as well as data that provide evidence for the formation of a similar diimine species from the electrooxidation of xanthine, which has not been previously observed. PMID:26030136

  5. 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.

  6. 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

  7. On the nature of the reaction intermediate in the HIV-1 protease: a quantum chemical study

    NASA Astrophysics Data System (ADS)

    Carnevale, V.; Raugei, S.; Piana, S.; Carloni, P.

    2008-07-01

    Several mechanistic aspects of Aspartic Proteases' enzymatic reaction are currently highly controversial. There is general consensus that the first step of the reaction involves a nucleophilic attack of a water molecule to the substrate carbonyl carbon with subsequent formation of a metastable intermediate (INT). However, the exact nature of this intermediate is subject of debate. While ab initio and QM/MM calculations predict that INT is a neutral gem-diol specie, empirical valence bond calculations suggest that the protein frame can stabilize a charged oxyanion intermediate. Here the relative stability of the gem diol and oxyanion intermediate is calculated by performing density functional and post-Hartree-Fock calculations. The robustness of the results is assessed by increasing the size of the system and of the basis set and by performing QM/MM calculations that explicitly include protein/solvent electrostatic effects. Our results suggest that the neutral gem-diol intermediate is 20-30 kcal/mol more stable than the charged oxyanion. It is therefore concluded that only the neutral specie is populated during the enzymatic reaction.

  8. /sup 12/C+/sup 12/C intermediate structures correlated among elastic and reaction channels

    SciTech Connect

    Cosman, E.R.; Ledoux, R.; Lazzarini, A.J.

    1980-05-01

    Prominent intermediate structure correlations are suggested between /sup 12/C+/sup 12/C elastic and reaction channel excitation functions over a wide range of energies above the Coulomb barrier. The associated resonant states in /sup 24/Mg would have large partial widths to elastic, inelastic, and ..cap alpha..+/sup 20/Ne* channels.

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  17. New observations concerning the chloroacetaldehyde reaction with some tRNA constituents. Stable intermediates, kinetics and selectivity of the reaction.

    PubMed Central

    Biernat, J; Ciesiołka, J; Górnicki, P; Adamiak, R W; Kryzosiak, W J; Wiewiórowski, M

    1978-01-01

    The stable intermediates formed in the reaction of cytosine, cytidine and adenosine with chloracetaldehyde were isolated. The -CH2CH/OH/- bridge between the exo and endo nitrogen atoms of the parent base was found in these compounds by means of PMR spectroscopy. Their acid-induced dehydration resulted in formation of appropriate ethenoderivatives. The rate constants of the intermediate formation and its dehydration were found to be 38x10(-4) and 47x10(-4) /min-1/ for adenosine, and 33x10(-4) and 10x10(-4) /min-1/ for cytidine. The PH range of 4.5--5.0 was found to be optimum for both adenosine and cytidine reactions. The quantitative modification of these two nucleosides in the presence of guanosine may be achieved with high selectivity only at a low pH of 3.0--4.0 N6-methyladenosine and N4-methylcytidine react quantitatively with chloroacetaldehyde and the reaction rate is higher than in the case of the parent nucleosides. The structure of the reaction products was assigned on the basis of PMR spectroscopy. PMID:25420

  18. 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.

  19. 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.

  20. 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)...

  1. Identifying the major intermediate species by combining time-resolved X-ray solution scattering and X-ray absorption spectroscopy.

    PubMed

    Kim, Kyung Hwan; Kim, Jeongho; Oang, Key Young; Lee, Jae Hyuk; Grolimund, Daniel; Milne, Christopher J; Penfold, Thomas J; Johnson, Steven L; Galler, Andreas; Kim, Tae Wu; Kim, Jong Goo; Suh, Deokbeom; Moon, Jiwon; Kim, Joonghan; Hong, Kiryong; Guérin, Laurent; Kim, Tae Kyu; Wulff, Michael; Bressler, Christian; Ihee, Hyotcherl

    2015-09-28

    Identifying the intermediate species along a reaction pathway is a first step towards a complete understanding of the reaction mechanism, but often this task is not trivial. There has been a strong on-going debate: which of the three intermediates, the CHI2 radical, the CHI2-I isomer, and the CHI2(+) ion, is the dominant intermediate species formed in the photolysis of iodoform (CHI3)? Herein, by combining time-resolved X-ray liquidography (TRXL) and time-resolved X-ray absorption spectroscopy (TR-XAS), we present strong evidence that the CHI2 radical is dominantly formed from the photolysis of CHI3 in methanol at 267 nm within the available time resolution of the techniques (∼20 ps for TRXL and ∼100 ps for TR-XAS). The TRXL measurement, conducted using the time-slicing scheme, detected no CHI2-I isomer within our signal-to-noise ratio, indicating that, if formed, the CHI2-I isomer must be a minor intermediate. The TR-XAS transient spectra measured at the iodine L1 and L3 edges support the same conclusion. The present work demonstrates that the application of these two complementary time-resolved X-ray methods to the same system can provide a detailed understanding of the reaction mechanism. PMID:26300122

  2. Identification of reaction intermediates/products from the photocatalytic degradation of trichloroethylene on illuminated titanium dioxide surfaces

    SciTech Connect

    Hung, C.H.; Marinas, B.J.

    1996-11-01

    The objective of this study was to identify reaction intermediates/products from the gas-phase photocatalytic degradation of trichloroethylene (TCE) on anatase titanium dioxide (TiO{sub 2}) surfaces illuminated with near-ultraviolet light (360 nm wavelength). A Pyrex glass annular photocatalytic reactor fabricated with turbulence promoters was used for this purpose. The inner surface of the outside tube forming the annular reactor was coated with TiO{sub 2} prepared by vapor phase hydrolysis of titanium isopropoxide. Reaction intermediates/products were concentrated by passing the photocatalytic reactor off-gas through a stainless steel tube immersed in liquid nitrogen. Compounds deposited were allowed to revolatilize or were washed with deionized water and analyzed by gas chromatography with a mass spectrum selective detector (GC/MS), or by ion chromatography (IC), respectively. Preliminary results revealed the presence of many halogenated organic compounds, including phosgene, 1,2-dichloroethylene, chloroform, carbon tetrachloride, dichloroacetyl chloride, 1,1,2-trichloroethane, tetrachloroethylene, 1,1,2,2-tetrachloroethane, pentchloroethane, and hexachloroethane, as well as hydrochloric acid. The abundance of most of these compounds except phosgene and hydrochloric acid was observed to diminish with increasing oxygen concentrations. Possible reaction mechanisms and pathways for the photocatalytic degradation of TCE will be presented.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. Well-Defined Models for the Elusive Dinuclear Intermediates of the Pauson-Khand Reaction.

    PubMed

    Hartline, Douglas R; Zeller, Matthias; Uyeda, Christopher

    2016-05-10

    The mechanism of the Pauson-Khand reaction has attracted significant interest due to the unusual dinuclear nature of the Co2 (CO)x active site. Experimental and computational data have indicated that the intermediates following the initial Co2 (CO)6 (alkyne) complex are thermodynamically unstable and do not build up in appreciable concentrations during the course of the reaction. As a consequence, the key steps that control the scope of viable substrates and various aspects of selectivity have remained largely uncharacterized. Herein, a direct experimental investigation of the dinuclear metallacycle-forming step of the Pauson-Khand reaction is reported. These studies capitalize on well-defined d(9) -d(9) dinickel complexes supported by a naphthyridine-diimine (NDI) pincer ligand as functional surrogates of Co2 (CO)8 . PMID:27062313

  9. Atomistic Description of Reaction Intermediates for Supported Metathesis Catalysts Enabled by DNP SENS.

    PubMed

    Ong, Ta-Chung; Liao, Wei-Chih; Mougel, Victor; Gajan, David; Lesage, Anne; Emsley, Lyndon; Copéret, Christophe

    2016-04-01

    Obtaining detailed structural information of reaction intermediates remains a key challenge in heterogeneous catalysis because of the amorphous nature of the support and/or the support interface that prohibits the use of diffraction-based techniques. Combining isotopic labeling and dynamic nuclear polarization (DNP) increases the sensitivity of surface enhanced solid-state NMR spectroscopy (SENS) towards surface species in heterogeneous alkene metathesis catalysts; this in turn allows direct determination of the bond connectivity and measurement of the carbon-carbon bond distance in metallacycles, which are the cycloaddition intermediates in the alkene metathesis catalytic cycle. Furthermore, this approach makes possible the understanding of the slow initiation and deactivation steps in these heterogeneous metathesis catalysts. PMID:26953812

  10. 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

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

    PubMed Central

    Shiota, Atsushi; Malinakova, Helena C.

    2012-01-01

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

  12. The Nature of the Reaction Intermediates in the FAD-Dependent Epoxidation Mechanism of Styrene Monooxygenase*

    PubMed Central

    Kantz, Auric; Gassner, George T.

    2010-01-01

    Styrene monooxygenase (SMO) is a two-component flavoenzyme composed of an NADH-specific flavin reductase (SMOB) and FAD-specific styrene epoxidase (NSMOA). NSMOA binds tightly to reduced FAD and catalyzes the stereospecific addition of one atom of molecular oxygen to the vinyl side chain of styrene in the enantioselective synthesis of S-styrene oxide. In this mechanism, molecular oxygen first reacts with NSMOA(FADred) to yield an FAD C(4a)- peroxide intermediate. This species is non-fluorescent and has an absorbance maximum of 382 nm. Styrene then reacts with the peroxide intermediate with a second order rate constant of 2.6 × 106 ± 0.1 × 106 M−1 s−1 to yield a fluorescent intermediate with an absorbance maximum of 368 nm. We compute an activation free energy of 8.7 kcal.mol∙−1 for the oxygenation step in good agreement with that expected for a peroxide-catalyzed epoxidation, and acid-quenched samples recovered at defined time points in the single-turnover reaction indicate that styrene oxide synthesis is coincident with the formation phase of the fluorescent intermediate. These findings support FAD C(4a)-peroxide as the oxygen atom donor and identity of the fluorescent intermediate as an FAD C(4a)-hydroxide product of the styrene epoxidation. Overall, four pH-dependent rate constants corresponding to peroxyflavin formation (pKa = 7.2), styrene epoxidation (pKa = 7.7), styrene oxide dissociation (pKa = 8.3), and hydroxyflavin dehydration (pKa 7.6) are needed to fit the single-turnover kinetics. PMID:21166448

  13. 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

  14. Regioselective, Transition Metal-Free C-O Coupling Reactions Involving Aryne Intermediates.

    PubMed

    Dong, Yuyang; Lipschutz, Michael I; Tilley, T Don

    2016-04-01

    A new transition-metal-free synthetic method for C-O coupling between various aryl halides and alkoxides is described. This type of transformation is typically accomplished using palladium catalysts containing a specialized phosphine ligand. The reactions reported here can be performed under mild, ambient conditions using certain potassium alkoxides and a range of aryl halides, with iodide and bromide derivatives giving the best results. A likely mechanistic pathway involves the in situ generation of an aryne intermediate, and directing groups on the aryl ring inductively control regioselectivity. PMID:27010921

  15. Intramolecular Schmidt reaction of acyl chlorides with alkyl azides: capture of N-acyliminium ion intermediates with aromatic rings.

    PubMed

    Li, Xiao-Jing; Qiao, Jin-Bao; Sun, Jian; Li, Xue-Qiang; Gu, Peiming

    2014-06-01

    Intramolecular Schmidt reaction of acyl chlorides with alkyl azides through N-acyliminium ion intermediates is designed and realized. The intramolecular capture of the intermediates with aromatic rings affords several nitrogen-containing tricyclic skeletons. The important feature of the domino process is the efficiency in bond reorganization and ring formation. PMID:24820453

  16. 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

  17. 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.

  18. 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 α,α-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 α-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

  19. 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.

  20. 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.

  1. 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.

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

    PubMed

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

    2013-10-21

    Reactions of the Criegee intermediate (CI, ˙CH2OO˙) are important in atmospheric ozonolysis models. In this work, we compute the rates for reactions between ˙CH2OO˙ and HCHO, CH3CHO and CH3COCH3 leading to the formation of secondary ozonides (SOZ) and organic acids. Relative to infinitely separated reactants, the SOZ in all three cases is found to be 48-51 kcal mol(-1) lower in energy, formed via 1,3-cycloaddition of ˙CH2OO˙ across the C=O bond. The lowest energy pathway found for SOZ decomposition is intramolecular disproportionation of the singlet biradical intermediate formed from cleavage of the O-O bond to form hydroxyalkyl esters. These hydroxyalkyl esters undergo concerted decomposition providing a low energy pathway from SOZ to acids. Geometries and frequencies of all stationary points were obtained using the B3LYP/MG3S DFT model chemistry, and energies were refined using RCCSD(T)-F12a/cc-pVTZ-F12 single-point calculations. RRKM calculations were used to obtain microcanonical rate coefficients (k(E)) and the reservoir state method was used to obtain temperature and pressure dependent rate coefficients (k(T, P)) and product branching ratios. At atmospheric pressure, the yield of collisionally stabilized SOZ was found to increase in the order HCHO < CH3CHO < CH3COCH3 (the highest yield being 10(-4) times lower than the initial ˙CH2OO˙ concentration). At low pressures, chemically activated formation of organic acids (formic acid in the case of HCHO and CH3COCH3, formic and acetic acid in the case of CH3CHO) was found to be the major product channel in agreement with recent direct measurements. Collisional energy transfer parameters and the barrier heights for SOZ reactions were found to be the most sensitive parameters determining SOZ and organic acid yield. PMID:23958859

  3. 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.

  4. 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.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-08-01

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

  7. 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.

  8. In Crystallo Capture of a Covalent Intermediate in the UDP-Galactopyranose Mutase Reaction.

    PubMed

    Mehra-Chaudhary, Ritcha; Dai, Yumin; Sobrado, Pablo; Tanner, John J

    2016-02-16

    UDP-galactopyranose mutase (UGM) plays an essential role in galactofuranose biosynthesis in pathogens by catalyzing the conversion of UDP-galactopyranose to UDP-galactofuranose. Here we report the first crystal structure of a covalent intermediate in the UGM reaction. The 2.3 Å resolution structure reveals UDP bound in the active site and galactopyranose linked to the FAD through a covalent bond between the anomeric C of galactopyranose and N5 of the FAD. The structure confirms the role of the flavin as nucleophile and supports the hypothesis that the proton destined for O5 of galactofuranose is shuttled from N5 of the FAD via O4 of the FAD. PMID:26836146

  9. 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 μM (9.6 μg/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 μM (76.8 μg/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

  10. 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.

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

    Carraher, Jack McCaslin

    2014-01-01

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

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

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

    PubMed

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

    2014-04-22

    The intramolecular aryl-phenyl scrambling reaction within palladium-DPPP-aryl complex (DPPP=1,3-bis(diphenylphosphino)propane) ions was analyzed by state-of-the-art tandem MS, including gas-phase ion/molecule reactions. The Mizoroki-Heck cross-coupling reaction was performed in the gas phase, and the intrinsic reactivity of important intermediates could be examined. Moreover, linear free-energy correlations were applied, and a mechanism for the scrambling reaction proceeding via phosphonium cations was assumed. PMID:24633762

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

    PubMed Central

    Mavridou, Despoina A. I.; Stevens, Julie M.; Mönkemeyer, 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

  1. 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.

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

    PubMed Central

    Mavian, Carla; López-Bueno, Alberto; Balseiro, Ana; Casais, Rosa; Alcamí, 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

  3. 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

  4. Vibrational characterization of NH and NH 2 reaction intermediates on the Ru(1 1 2¯ 0) surface

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Jacobi, K.

    2002-07-01

    NH and NH 2 reaction intermediates were prepared on the Ru(1 1 2¯ 0) surface by thermal dehydrogenation of NH 3 and studied using high-resolution electron energy-loss spectroscopy. NH 2 and NH were isolated to a high degree, which allows to unambiguously identify their vibrational modes. From isotope experiments with 15ND3, frustrated translational and rotational (bending, rocking) modes were differentiated. NH 2 exhibits a scissoring mode at 189.7 meV, a rocking mode at 165.4 meV and translational modes at 62.2 and 44.3 meV. NH 2 is tilted relative to the surface normal within an adsorbate complex of C s symmetry. For NH two rather low-lying bending modes at 83.2 and 88.2 meV were identified due to NH species presumably adsorbed in the two different threefold-hollow sites within the Ru(1 1 2¯ 0)(1×1) unit cell, also in a tilted geometry. A long-standing wrong assignment of the NH bending mode could be corrected.

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

    PubMed

    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

  6. 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.

  7. 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

  8. ENDOR studies of the intermediate electron acceptor radical anion I-. in Photosystem II reaction centers.

    PubMed

    Lubitz, W; Isaacson, R A; Okamura, M Y; Abresch, E C; Plato, M; Feher, G

    1989-11-23

    The EPR and ENDOR characteristics of the intermediate electron acceptor radical anion I-. in Photosystem II (PS II) are shown to be identical in membrane particles and in the D1D2 cytochrome b-559 complex (Nanba, O. and Satoh, K. (1987) Proc. Natl. Acad. Sci. USA 84, 109-112). These findings provide further evidence that the D1D2 complex is the reaction center of PS II and show that the pheophytin binding site is intact. A hydrogen bond between I-. and the protein (GLU D1-130) is postulated on the basis of D2O exchange experiments. The ENDOR data of I-. and of the pheophytin a radical anion in different organic solvents are compared and the observed differences are related to structural changes of the molecule on the basis of molecular orbital calculations (RHF-INDO/SP). The importance of the orientation of the vinyl group (attached to ring I) on electron transfer is discussed. PMID:2553112

  9. Identifying Predictors of Negative Psychological Reactions to Stalking Victimization

    ERIC Educational Resources Information Center

    Johnson, Matthew C.; Kercher, Glen A.

    2009-01-01

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

  10. Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations

    PubMed Central

    2009-01-01

    Background Genetic studies have often produced conflicting results on the question of whether distant Jewish populations in different geographic locations share greater genetic similarity to each other or instead, to nearby non-Jewish populations. We perform a genome-wide population-genetic study of Jewish populations, analyzing 678 autosomal microsatellite loci in 78 individuals from four Jewish groups together with similar data on 321 individuals from 12 non-Jewish Middle Eastern and European populations. Results We find that the Jewish populations show a high level of genetic similarity to each other, clustering together in several types of analysis of population structure. Further, Bayesian clustering, neighbor-joining trees, and multidimensional scaling place the Jewish populations as intermediate between the non-Jewish Middle Eastern and European populations. Conclusion These results support the view that the Jewish populations largely share a common Middle Eastern ancestry and that over their history they have undergone varying degrees of admixture with non-Jewish populations of European descent. PMID:19995433

  11. LC/MS/MS structure elucidation of reaction intermediates formed during the TiO(2) photocatalysis of microcystin-LR.

    PubMed

    Antoniou, Maria G; Shoemaker, Jody A; de la Cruz, Armah A; Dionysiou, Dionysios D

    2008-05-01

    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) at pH of Milli-Q water (pH(sq)=5.7). Eleven new [M+H](+) were observed in the liquid chromatography mass spectrometry (LC/MS) chromatogram with some of them giving multiple peaks. Most of these reaction intermediates have not been reported from previous studies employing TiO(2) nanoparticles at acidic conditions (pH=4.0). Investigating the effects of pH (for 3.0intermediate steps were identified. Possible structures of the intermediates (formed at neutral pH) after analyzing the corresponding MS/MS spectra are reported. The collision-induced dissociation of the [M+H](+) of MC-LR and the intermediates 1011.5 and 1029.5 are discussed and possible fragmentation pathways and mechanisms are also proposed. Analysis of the MS/MS spectra indicates that the fragmentation of some amino acids is less favorable because of internal interaction with free groups of adjacent amino acids. The MS/MS spectra assisted in determining hydroxylation sites, by the formation or alteration of specific product ions such as m/z 599. PMID:18377943

  12. Organic chemistry on cold molecular films: kinetic stabilization of SN1 and SN2 intermediates in the reactions of ethanol and 2-methylpropan-2-ol with hydrogen bromide.

    PubMed

    Park, Seong-Chan; Maeng, Kye-Won; Kang, Heon

    2003-04-14

    We prepared thin molecular films of ethanol and 2-methylpropan-2-ol on Ru(001) substrates at temperature of 100-150 K and examined their reactivity toward HBr. The reaction intermediates and products formed at the surfaces were unambiguously identified by the techniques of Cs(+) reactive ion scattering (RIS) and low-energy sputtering. The reaction on the ethanol surface produced protonated ethanol, which is stabilized on the surface and does not proceed to further reactions. On the 2-methylpropan-2-ol surface, protonated alcohol [(CH(3))(3)COH(2) (+)] and carbocation [(CH(3))(3)C(+)] were formed with the respective yield of 20 and 78 %. Alkyl bromides, which are the final products of the corresponding reactions in liquid solvents, have extremely small yields on these surfaces (< 0.3 % for ethyl bromide and 2 % for tert-butyl bromide). The results indicate that the reactions on frozen films are characterized by kinetic control, stabilization of ionic intermediates (protonated alcohols and tert-butyl cation), and effective blocking of the charge recombination steps in S(N)1 and S(N)2 paths. The implication of these findings for the molecular evolution process in interstellar medium is also discussed. PMID:12698428

  13. 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.

  14. 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.

  15. 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.

  16. Radical intermediates and their subsequent reaction pathways in salt-catalyzed coal gasification. Topical report, January 1985-January 1986

    SciTech Connect

    White, S.H.; Twardoch, U.M.

    1986-03-01

    The objective of the project was to determine the rates and mechanisms by which electron transfer (radical formation) reactions take place at carbonaceous surfaces contacted with molten (liquid) alkali metal salts and the effects of steam, carbon oxides, and hydrogen on the reactivity of and product formation from the radical intermediates. The carbon-carbon bond network in coal macromolecules might be activated toward fragmentation as a result of oxidative or reductive changes leading to the formation of intermediate charged radicals (radical ions). The project addresses the question of how alkali metal salts can promote (catalyze) the radical ion-mediated chemistry.

  17. 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…

  18. Methanol synthesis on ZnO({{000overline{1}}}). II. Structure, energetics, and vibrational signature of reaction intermediates

    NASA Astrophysics Data System (ADS)

    Kiss, Janos; Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

    2013-07-01

    A rigorous characterization of a wealth of molecular species adsorbed at oxygen defects on ZnO(000overline{1}) is given. These defects represent the putative active sites in methanol synthesis from CO and H2. The oxidation state of the ZnO catalyst and thus the preferred charge state and the reactivity of the oxygen vacancies depend on the gas phase temperature and pressure conditions. Considering charge states of oxygen vacancies relevant at the reducing conditions of the industrial process, i.e., F++/H2, F0, F0/H2, and F-, as well as the F++ center which is abundant at UHV conditions and therefore important to allow for comparison with surface science experiments, we have investigated the structure, energetics, and vibrational frequencies of an exhaustive catalog of reaction intermediates using electronic structure calculations. After having identified the characteristic adsorption modes of CO, formate, formic acid, hydroxymethylene, formyl, formaldehyde, dioxomethylene, hydroxymethyl, hydroxymethoxide, methoxide, as well as methanol itself, the thermodynamic stability of all species with respect to the charge state of the oxygen vacancy and their electronic stabilization is discussed in detail and summarized in an energy level diagram.

  19. High-resolution array CGH identifies novel regions of genomic alteration in intermediate-risk prostate cancer.

    PubMed

    Ishkanian, Adrian S; Mallof, Chad A; Ho, James; Meng, Alice; Albert, Monique; Syed, Amena; van der Kwast, Theodorus; Milosevic, Michael; Yoshimoto, Maisa; Squire, Jeremy A; Lam, Wan L; Bristow, Robert G

    2009-07-01

    Approximately one-third of prostate cancer patients present with intermediate risk disease. Interestingly, while this risk group is clinically well defined, it demonstrates the most significant heterogeneity in PSA-based biochemical outcome. Further, the majority of candidate genes associated with prostate cancer progression have been identified using cell lines, xenograft models, and high-risk androgen-independent or metastatic patient samples. We used a global high-resolution array comparative genomic hybridization (CGH) assay to characterize copy number alterations (CNAs) in intermediate risk prostate cancer. Herein, we show this risk group contains a number of alterations previously associated with high-risk disease: (1) deletions at 21q22.2 (TMPRSS2:ERG), 16q22-24 (containing CDH1), 13q14.2 (RB1), 10q23.31 (PTEN), 8p21 (NKX3.1); and, (2) amplification at 8q21.3-24.3 (containing c-MYC). In addition, we identified six novel microdeletions at high frequency: 1q42.12-q42.3 (33.3%), 5q12.3-13.3 (21%), 20q13.32-13.33 (29.2%), 22q11.21 (25%), 22q12.1 (29.2%), and 22q13.31 (33.3%). Further, we show there is little concordance between CNAs from these clinical samples and those found in commonly used prostate cancer cell models. These unexpected findings suggest that the intermediate-risk category is a crucial cohort warranting further study to determine if a unique molecular fingerprint can predict aggressive versus indolent phenotypes. PMID:19350549

  20. Active site conformational changes upon reaction intermediate biotinyl-5'-AMP binding in biotin protein ligase from Mycobacterium tuberculosis

    PubMed Central

    Ma, Qingjun; Akhter, Yusuf; Wilmanns, Matthias; Ehebauer, Matthias T

    2014-01-01

    Protein biotinylation, a rare form of post-translational modification, is found in enzymes required for lipid biosynthesis. In mycobacteria, this process is essential for the formation of their complex and distinct cell wall and has become a focal point of drug discovery approaches. The enzyme responsible for this process, biotin protein ligase, substantially varies in different species in terms of overall structural organization, regulation of function and substrate specificity. To advance the understanding of the molecular mechanism of biotinylation in Mycobacterium tuberculosis we have biochemically and structurally characterized the corresponding enzyme. We report the high-resolution crystal structures of the apo-form and reaction intermediate biotinyl-5'-AMP-bound form of M. tuberculosis biotin protein ligase. Binding of the reaction intermediate leads to clear disorder-to-order transitions. We show that a conserved lysine, Lys138, in the active site is essential for biotinylation. PMID:24723382

  1. 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

  2. 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.

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

    PubMed

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

    2015-02-28

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

  4. The reaction mechanism of copper amine oxidase: detection of intermediates by the use of substrates and inhibitors.

    PubMed

    Medda, R; Padiglia, A; Pedersen, J Z; Rotilio, G; Finazzi Agrò, A; Floris, G

    1995-12-19

    Intermediate states in the catalytic mechanism of lentil copper amine oxidase have been investigated by ESR and optical spectroscopy. Using highly purified apo- and holoenzyme in combination with a poor substrate and a range of inhibitors, under both aerobic and anaerobic conditions, the single steps of the reaction mechanism can be slowed down or 'frozen' completely. In this way, a sequence of six intermediate species in the catalytic cycle has been established. Oxidative deamination of p-(dimethylamino)benzylamine is 5 x 10(5) times slower than for putrescine; the rate-limiting step is shown to be release of the aldehyde product. This process is not affected in the apoenzyme, but subsequent intramolecular electron transfer to form the characteristic free radical intermediate is completely blocked, and the apoenzyme is trapped as an aminoresorcinol species. Classic hydrazine and hydrazide inhibitors bind to the 6-hydroxydopa cofactor in the same way as active substrates, but rearrangements lead to formation of stable intermediate adducts at the step preceding release of aldehyde. The semicarbazide-6-hydroxydopa adduct is shown to bind simultaneously to Cu(II), providing the first direct evidence for localization of 6-hydroxydopa close to the copper site. PMID:8845363

  5. 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

  6. 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 μM) were also investigated, and then the Hill coefficient (n = 2.6 ± 0.4) and the microscopic dissociation constant (K(m) = 77 ± 5 μM) 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

  7. Liquid-phase hydrogenation of citral over Pt/SiO{sub 2} catalysts. 2. Hydrogenation of reaction intermediate compounds

    SciTech Connect

    Singh, U.K.; Sysak, M.N.; Vannice, M.A.

    2000-04-01

    Liquid-phase hydrogenation of the four principal reaction intermediates formed during citral hydrogenation, i.e., nerol, geraniol, citronellal, and citronellol, was studied at 298 and 373 K under 20 atm H{sub 2} at concentrations of 0.5 to 1.0 M in hexane. A decrease in the initial reaction rate as temperature increased from 298 to 373 K was exhibited during the hydrogenation of all four compounds, just as reported earlier for citral; however, the decrease in rate at 373 K was only one-half for citronellal whereas it was orders of magnitude greater for nerol and geraniol. Furthermore, simultaneous hydrogenation of citronellal and geraniol at 298 K resulted in a continuous decrease in the rate of citronellal disappearance in contrast to the nearly constant rate of disappearance observed during hydrogenation of citronellal alone. Competitive hydrogenation of citral with either geraniol or citronellal showed that geraniol hydrogenation to citronellol is kinetically insignificant during citral hydrogenation at 373 K. The initial activity for hydrogenation of the intermediates at 298 K follows the following trend: geraniol > nerol < citronellol < E-citral, citronellal > Z-citral. Based on the relative hydrogenation rates of the intermediate alone versus its hydrogenation in the presence of other reactants, the relative size of the adsorption equilibrium constants for the various organic compounds appears to be as follows: citral > citronellal > geraniol, nerol > citronellol > 3,7-dimethyloctanol. This study indicates that activation of the C{double_bond}O bond should be performed at higher reaction temperatures to maximize selectivity to the unsaturated alcohols.

  8. 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

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

    DOEpatents

    Maya, Leon

    1991-01-01

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

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

    DOEpatents

    Maya, Leon

    1988-05-24

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

  11. 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.

  12. 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

  13. 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.

  14. Copper(I)-catalyzed substitution reactions of propargylic amines: importance of C(sp)-C(sp3) bond cleavage in generation of iminium intermediates.

    PubMed

    Sugiishi, Tsuyuka; Kimura, Akifumi; Nakamura, Hiroyuki

    2010-04-21

    Substitution reactions of propargylic amines proceed in the presence of copper(I) catalysts. Mechanistic studies showed that C(sp)-C(sp(3)) bond cleavage assisted by nitrogen lone-pair electrons is essential for the reaction, and the resulting iminium intermediates undergo amine exchange, aldehyde exchange, and alkyne addition reactions. Because iminium intermediates are key to aldehyde-alkyne-amine (A(3)) coupling reactions, this transformation is effective not only for reconstruction of propargylic amines but also for chiral induction of racemic compounds in the presence of chiral catalysts. PMID:20353176

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

    PubMed

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

    2007-03-28

    Hydrides of period 2 and 3 elements are promising candidates for hydrogen storage, but typically have heats of reaction that are too high to be of use for fuel cell vehicles. Recent experimental work has focused on destabilizing metal hydrides through mixing metal hydrides with other compounds. A very large number of possible destabilized metal hydride reaction schemes exist, but the thermodynamic data required to assess the enthalpies of these reactions are not available in many cases. We have used density functional theory calculations to predict the reaction enthalpies for more than 300 destabilization reactions that have not previously been reported. The large majority of these reactions are predicted not to be useful for reversible hydrogen storage, having calculated reaction enthalpies that are either too high or too low, and hence these reactions need not be investigated experimentally. Our calculations also identify multiple promising reactions that have large enough hydrogen storage capacities to be useful in practical applications and have reaction thermodynamics that appear to be suitable for use in fuel cell vehicles and are therefore promising candidates for experimental work. PMID:17356751

  16. 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.

  17. 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

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

    PubMed

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

    2016-07-01

    A previous work showed that the night period is important for the occurrence of Fenton-like oxidation of small aromatic acids from biomass burning in atmospheric waters, which originate new chromophoric compounds apparently more complex than the precursors, although the chemical transformations involved in the process are still unknown. In this work were identified by gas chromatography-mass spectrometry (GC-MS) and by electrospray mass spectrometry (ESI-MS) the organic intermediate compounds formed during the Fenton-like oxidation of three aromatic acids from biomass burning (benzoic, 4-hydroxybenzoic and 3,5-dihydroxybenzoic acids), the same compounds evaluated in the previous study, in water and in the absence of light, which in turns allows to disclose the chemical reaction pathways involved. The oxidation intermediate compounds found for benzoic acid were 2-hydroxybenzoic, 3-hydroxybenzoic, 4-hydroxybenzoic, 2,3-dihydroxybenzoic, 2,5-dihydroxybenzoic, 2,6-dihydroxybenzoic and 3,4-dihydroxybenzoic acids. The oxidation intermediates for 4-hydroxybenzoic acid were 3,4-hydroxybenzoic acid and hydroquinone, while for 3,5-dihydroxybenzoic acid were 2,4,6-trihydroxybenzoic and 3,4,5-trihydroxybenzoic acids, and tetrahydroxybenzene. The results suggested that the hydroxylation of the three small aromatic acids is the main step of Fenton-like oxidation in atmospheric waters during the night, and that the occurrence of decarboxylation is also an important step during the oxidation of the 4-dihydroxybenzoic and 3,5-dihydroxybenzoic acids. In addition, it is important to highlight that the compounds produced are also small aromatic compounds with potential adverse effects on the environment, besides becoming available for further chemical reactions in atmospheric waters. PMID:27088537

  19. 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

  20. 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.

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

    PubMed Central

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

    2013-01-01

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

  2. 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

  3. Neutral Current Neutrino-{sup 116}Cd Reaction Cross Sections at Low and Intermediate Energies

    SciTech Connect

    Balasi, K. G.; Kosmas, T. S.; Divari, P. C.; Chasioti, V. C.

    2008-01-24

    Differential and integrated cross sections for inelastic scattering of electron neutrinos from a {sup 116}Cd target at low and intermediate neutrino energies ({epsilon}{sub i}{<=}100 MeV) are presented. The nuclear wave functions for the initial and final nuclear states are constructed in the context of quasiparticle random phase approximation (QRPA). By exploiting the results of these cross sections, we study the response of {sup 116}Cd to supernova neutrino spectra by utilizing the folding procedure and employing a two-parameter Fermi-Dirac distribution for the supernova neutrino spectra. Our results show that, this isotope may play a significant role in supernova neutrino detection, in addition to its use in double-beta-decay experiments (COBRA, etc)

  4. Astrophysically Important Reaction Rates For Novae And X-ray Bursts From Proton Breakup At Intermediate Energies

    SciTech Connect

    Banu, A.; Trache, L.; Carstoiu, F.; Negoita, F.; Rotaru, F.; Orr, N. A.; Achouri, N. L.; Laurent, B.; Bonaccorso, A.; Catford, W. N.; Patterson, N.; Thomas, J. S.; Chartier, M.; Fernandez-Dominguez, B.; Paschalis, S.; Pietras, B.; Freer, M.; Gaudefroy, L.; Roussel-Chomaz, P.; Horoi, M.

    2010-11-24

    We discuss the use of one-nucleon removal reactions of loosely bound nuclei at intermediate energies as an indirect method in nuclear astrophysics. The breakup reactions are proved to be good spectroscopic tools and can be used to study a large number of loosely bound proton- or neutron-rich nuclei over a wide range of beam energies. As peripheral processes, they can be used to extract asymptotic normalization coefficients (ANCs) from which non-resonant capture reaction rates of astrophysical interest can be calculated parameter free. In this talk, we present results of a proton-breakup experiment carried out at GANIL (France) with a cocktail beam centered around {sup 23}Al at 50 MeV/nucleon. Momentum distributions of the breakup fragments, inclusive and in coincidence with gamma rays detected by EXOGAM Germanium clover array, were measured in the focal plan of SPEG energy-loss spectrometer. We present in particular the investigations of reaction rates for {sup 22}Mg(p,{gamma}){sup 23}Al and {sup 23}Al(p,{gamma}){sup 24}Si important for novae and X-ray bursts, respectively.

  5. Reactions of water radiolysis intermediates with pyrimidine and purine bases in aqueous BeF2 glasses: an EPR study.

    PubMed

    Ohlmann, J; Hüttermann, J

    1993-04-01

    Free radical formation by reaction of water radiolysis intermediates produced by X-irradiation in aqueous glasses containing 7 M BeF2 at 77 K with pyrimidine and purine constituents of DNA (10 mM) was studied by electron paramagnetic resonance (EPR) spectroscopy. Reactions of electrons and .OH radicals were observed; H. form a minority and their contribution was difficult to establish. The electrons form substrate radicals at 77 K, while .OH radicals, stabilized in the matrix at 77 K, become mobile at about 140K and in part react with solute molecules. The radicals formed by both reactions were characterized after isolation of the corresponding components by thermal annealing up to about 190 K and spectra simulation using literature parameters whenever possible. The spectra from cytosine gave strong evidence for heteroatom protonation following electron addition while those from adenine were somewhat less clear. The spectra of uracil and all methylated pyrimidines gave no evidence for the protonation state of the electron adduct. For the .OH radical, the reaction with uracil and cytosine was found to be addition to the 5,6-double bond, in line with studies using aqueous solutions. For all methylated pyrimidines, however, H-abstraction from the methyl group was dominant. .OH addition to adenine was found to take place at C2. PMID:8096855

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

    NASA Astrophysics Data System (ADS)

    Halabi, Ghina M.; El Eid, Mounib

    2012-11-01

    We investigate the effects of a modification of the 14N(p,γ)15O 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⊙ to 12M⊙. We show that the blue loops of stars in the mass range 5M⊙ to 8M⊙, that is the range of super ABG stars, are severely affected by a modification of the important 14N(p,γ)15O 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.

  7. 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.

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

    SciTech Connect

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

    1981-01-01

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

  9. Spectral and Kinetic Characterization of Intermediates in the Aromatization Reaction Catalyzed by NikD, an Unusual Amino Acid Oxidase†

    PubMed Central

    Bruckner, Robert C.; Jorns, Marilyn Schuman

    2009-01-01

    The flavoenzyme nikD, a 2-electron acceptor, catalyzes a remarkable aromatization of piperideine-2-carboxylate (P2C) to picolinate, an essential component of nikkomycin antibiotics. Steady-state kinetic data are indicative of a sequential mechanism where oxygen reacts with a reduced enzyme•dihydropicolinate (DHP) complex. The kinetics observed for complex formation with competitive inhibitors are consistent with a one-step binding mechanism. The anaerobic reaction with P2C involves three steps. The first step yields an enzyme•substrate charge transfer complex likely to contain the electron-rich P2C enamine. Calculated rates of formation and dissociation of the nikD•P2C complex are similar to those observed for the enzyme•1-cyclohexenoate complex. Formation of a reduced enzyme•DHP complex, (EH2•DHP)ini, occurs in a second step that exhibits a hyperbolic dependence on substrate concentration. The limiting rate of nikD reduction is at least 10-fold faster than the turnover rate observed with unlabeled or [4, 4, 5, 5, 6, 6-D6]-P2C and exhibits a kinetic isotope effect (KIE = 6.4). The observed KIE on Kd apparent (4.7) indicates that P2C is a sticky substrate. Formation of a final reduced species, (EH2•DHP)fin, occurs in a third step that is independent of P2C concentration and equal to the observed turnover rate. The observed KIE (3.3) indicates that the final step involves cleavage of at least one C-H bond. Tautomerization, followed by isomerization, of the initial DHP intermediate can produce an isomer that could be oxidized to picolinate in a reaction that satisfies known steric constraints of flavoenzyme reactions without the need to reposition a covalently tethered flavin or tightly bound intermediate. PMID:19354202

  10. Solvent dependent structural perturbations of chemical reaction intermediates visualized by time-resolved x-ray diffraction

    SciTech Connect

    Vincent, Jonathan; Eklund, Mattias; Davidsson, Jan; Andersson, Magnus; Woehri, Annemarie B.; Odelius, Michael; Malmerberg, Erik; Neutze, Richard; Kong, Qingyu; Wulff, Michael

    2009-04-21

    Ultrafast time-resolved wide angle x-ray scattering from chemical reactions in solution has recently emerged as a powerful technique for determining the structural dynamics of transient photochemical species. Here we examine the structural evolution of photoexcited CH{sub 2}I{sub 2} in the nonpolar solvent cyclohexane and draw comparisons with a similar study in the polar solvent methanol. As with earlier spectroscopic studies, our data confirm a common initial reaction pathway in both solvents. After photoexcitation, CH{sub 2}I{sub 2} dissociates to form CH{sub 2}I{center_dot}+I{center_dot}. Iodine radicals remaining within the solvent cage recombine with a nascent CH{sub 2}I{center_dot} radical to form the transient isomer CH{sub 2}I-I, whereas those which escape the solvent cage ultimately combine to form I{sub 2} in cyclohexane. Moreover, the transient isomer has a lifetime approximately 30 times longer in the nonpolar solvent. Of greater chemical significance is the property of time-resolved wide angle x-ray diffraction to accurately determine the structure of the of CH{sub 2}I-I reaction intermediate. Thus we observe that the transient iodine-iodine bond is 0.07 A {+-}0.04 A shorter in cyclohexane than in methanol. A longer iodine-iodine bond length for the intermediate arises in methanol due to favorable H-bond interaction with the polar solvent. These findings establish that time-resolved x-ray diffraction has sufficient sensitivity to enable solvent dependent structural perturbations of transient chemical species to be accurately resolved.

  11. CO2 activation and carbonate intermediates: an operando AP-XPS study of CO2 electrolysis reactions on solid oxide electrochemical cells.

    PubMed

    Yu, Yi; Mao, Baohua; Geller, Aaron; Chang, Rui; Gaskell, Karen; Liu, Zhi; Eichhorn, Bryan W

    2014-06-21

    Through the use of ambient pressure X-ray photoelectron spectroscopy and specially designed ceria-based solid oxide electrochemical cells, carbon dioxide (CO2) electrolysis reactions (CO2 + 2e(-)→ CO + O(2-)) and carbon monoxide (CO) electro-oxidation reactions (CO + O(2-)→ CO2 + 2e(-)) over cerium oxide electrodes have been investigated in the presence of 0.5 Torr CO-CO2 gas mixtures at ∼600 °C. Carbonate species (CO3(2-)) are identified on the ceria surface as reaction intermediates. When CO2 electrolysis is promoted on ceria electrodes at +2.0 V applied bias, we observe a higher concentration of CO3(2-) over a 400 μm-wide active region on the ceria surface, accompanied by Ce(3+)/Ce(4+) redox changes. This increase in the CO3(2-) steady-state concentration suggests that the process of pre-coordination of CO2 to the ceria surface to form a CO3(2-) intermediate (CO2(g) + O(2-)(surface)→ CO3(2-)(surface)) precedes a rate-limiting electron transfer process involving CO3(2-) reduction to give CO and oxide ions (CO3(2-)(surface) + 2Ce(3+)→ CO(g) + 2O(2-)(surface) + 2Ce(4+)). When the applied bias is switched to -1.5 V to promote CO electro-oxidation on ceria, the surface CO3(2-) concentration slightly decreases from the equilibrium value, suggesting that the electron transfer process is also a rate-limiting process in the reverse direction. PMID:24806971

  12. [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)

  13. 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)

  14. 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

  15. 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

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

    PubMed

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

  17. 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

  18. 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.

  19. Design Factors Affecting the Reaction Time for Identifying Toilet Signs: A Preliminary Study.

    PubMed

    Chen, Yi-Lang; Sie, Cai-Cin

    2016-04-01

    This study focused on the manner in which design factors affect the reaction time for identifying toilet signs. Taiwanese university students and staff members (50 men, 50 women; M age = 23.5 year, SD = 5.7) participated in the study. The 36 toilet signs were modified on three factors (six presenting styles, two figure-ground exchanges, and three colors), and the reaction time data of all participants were collected when the signs were presented in a simulation onscreen. Participants were quickest when reading Chinese text, followed by graphics and English texts. The findings also showed that men and women had different reaction times across various design combinations. These findings can serve as a reference for practically designing toilet signs, since design factors can lead to difficulties with comprehension based on reaction time measurements. PMID:27166339

  20. A crystallographic description of experimentally identified formation reactions of Cu(In,Ga)Se 2

    NASA Astrophysics Data System (ADS)

    Hergert, F.; Jost, S.; Hock, R.; Purwins, M.

    2006-08-01

    This work describes solid-state reactions for the formation of the chalcopyrite compounds CuInSe 2, CuGaSe 2 and Cu(In,Ga)Se 2 on atomic scale. The most important chalcopyrite formation reactions which were identified by the authors by real-time in situ X-ray diffraction in preceding experiments are (A) CuSe+InSe→CuInSe 2, (B) Cu 2Se+2 InSe+Se→2 CuInSe 2 and (C) Cu 2Se+In 2Se 3→2 CuInSe 2. During the selenistaion of a metallic precursor containing gallium a separate fourth reaction occurs: (D) Cu 2Se+Ga 2Se 3→2 CuGaSe 2. The quaternary compound is finally formed by interdiffusion of CuInSe 2 with CuGaSe 2 (E). These five reactions differ in their activation energy and reaction speed. We explain these differences qualitatively by analysing the involved crystal structures for each reaction. It turns out that all reactions involved in the formation of Cu(In,Ga)Se 2 are promoted by epitaxial relations, which facilitates the formation of polycrystalline thin films at temperatures much below those necessary for single crystal growth. Recommendations for the growth of larger grains of Cu(In,Ga)Se 2 containing fewer defects are given.

  1. 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.

  2. 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.

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

    DOE PAGESBeta

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

    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.more » DFT and RAIRS show that below 500 K, bridge bondedacetate coexists with a moiety formed by adsorption of an acetate at an oxygen vacancy, formed bywater desorption.« less

  4. 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

  5. Bremsstrahlung in intermediate-energy nucleon reactions within an effective one-boson exchange model

    NASA Astrophysics Data System (ADS)

    Shklyar, V. V.; Kämpfer, B.; Reznik, B. L.; Titov, A. I.

    1998-01-01

    Within a covariant effective one-boson exchange model for the T matrix of NN interactions we present detailed calculations of bremsstrahlung cross sections for proton-proton and proton-neutron reactions at beam energies in the 1 GeV region. Besides pure bremsstrahlung processes we consider photons from Λ decays and contributions from the η → γγ process. At beam energies above 700 MeV the Λ decay channel dominates the spectra at large photon energies, where the interference between non-resonance processes and the Λ decay channel becomes also important. Low energy photons stem from pure bremsstrahlung processes. The available experimental data at 730 MeV beam energy is well described. We extrapolate the model down to 280 MeV, where more detailed experimental data exist, and find agreement with angular distributions.

  6. 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.

  7. 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

  8. Identifying Stressors and Reactions to Stressors in Gifted and Non-Gifted Students

    ERIC Educational Resources Information Center

    Amini, Marzieh

    2005-01-01

    Using the Student Life Stress Inventory and the Coopersmith Self-Esteem Inventory, stressors and reactions to stressors were identified in gifted high school students and compared with non-gifted students. Altogether, 340 boys and girls (156 gifted and 184 non-gifted students) from four high schools in Shiraz (two high schools for gifted and two…

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

    SciTech Connect

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

    1996-06-14

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

  10. A Mechanistic Investigation into the Zinc Carbenoid-Mediated Homologation Reaction by DFT Methods: Is a Classical Donor–Acceptor Cyclopropane Intermediate Involved?

    PubMed Central

    Eger, Wilhelm A.; Zercher, Charles K.; Williams, Craig M.

    2011-01-01

    An extensive density functional theory (DFT, M05-2X) investigation has been performed on the zinc carbenoid-mediated homologation reaction of β-keto esters. The mechanistic existence of a classical donor–acceptor cyclopropane intermediate was probed to test the traditional school of thought regarding these systems. Calculations of the carbenoid insertion step, following enolate formation, unmasked two possible pathways. Pathway B was shown to explain the proposed, but spectroscopically unobservable donor–acceptor cyclopropane intermediate, while the second (pathway A) reveals an alternative to the classical intermediate in that a cyclopropane transition state leads to product. PMID:20879758

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

    SciTech Connect

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

    2015-03-28

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

  12. 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

  13. 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

  14. Reaction Intermediates of Quinol Oxidation in a Photoactivatable System that Mimics Electron Transfer in the Cytochrome bc1 Complex

    SciTech Connect

    Cape, Jonathan L.; Bowman, Michael K.; Kramer, David M.

    2005-03-30

    Current competing models for the two-electron oxidation of quinol (QH{sub 2}) at the cytochrome bc{sub 1} complex and related complexes have different requirements for the reaction intermediate. At present, the intermediate species of the enzymatic oxidation process have not been observed or characterized, probably due to their transient nature. Here, we use a biomimetic oxidant, Ru(bpy){sub 2}(pbim)(PF6)2 (bpy = 2,2'-dipyridyl, pbim = 2-(2-benzimidazolate)pyridine) in an aprotic medium to probe the oxidation of the ubiquinol analogue, 2,3-dimethoxy-5-methyl-1,4-benzoquinol (UQH{sub 2}-0), an the plastoquinol analogue, trimethyl-1,4-benzoquinol (TMQH{sub 2}-0), using time-resolved and steady state spectroscopic techniques. This system qualitatively reproduces key features observed during ubiquinol oxidation by the mitochondrial cytochrome bc1 complex. Comparison of isotope dependent activation properties in the native and synthetic systems, as well as, analysis of the time-resolved direct-detection electron para magnetic resonance signals in the synthetic system allows us to conclude that: (1) the initial and rate-limiting step in quinol oxidation, both in the biological and biomimetic systems, involves electron and proton transfer, probably via a proton coupled electron transfer mechanism; (2) a neutral semiquinone intermediate is formed in the biomimetic system; and (3) oxidation of the QH*/QH{sub 2} couple for UQH{sub 2}-0, but not TMQH{sub 2}-0, exhibits a non-classical primary deuterium kinetic isotope effect on its Arrhenius activation energy ({Delta}G{sup TS}), where {Delta}G{sup TS} for the protiated form is larger than for the deuterated form. The same behavior is observed during steady state turnover of the cyt bc{sub 1} complex using ubiquinol, but not plastoquinol, as a substrate, leading to the conclusion that similar chemical pathways are involved in both systems. The synthetic system is an unambiguous n=1 electron acceptor and it is thus inferred that sequential oxidation of ubiquinol (by two sequential n=1 processes) is more rapid than a truly concerted (n=2) oxidation in the cyt bc{sub 1} complex.

  15. Mechanistic studies on Lewis acid catalyzed Biginelli reactions in ionic liquids: evidence for the reactive intermediates and the role of the reagents.

    PubMed

    Ramos, Luciana M; Ponce de Leon y Tobio, Adrian Y; dos Santos, Marcelo R; de Oliveira, Heibbe C B; Gomes, Alexandre F; Gozzo, Fabio C; de Oliveira, Aline L; Neto, Brenno A D

    2012-11-16

    This paper describes the use of common Lewis acids supported in imidazolium-based ionic liquids as the catalysts to promote the Biginelli reaction. The ionic liquid effect and the reaction mechanism are discussed on the basis of nuclear magnetic resonance (NMR), electrospray ionization mass spectrometry (ESI-MS), and theoretical calculations. Indeed, the results showed that the ionic medium plays a fundamental role in the synthesis of biologically active dihydropyrimidinones due to the stabilization of the charged intermediates proposed in the mechanism. When conducted in an ionic liquid as solvent, the reaction mechanism is more complex than in other Lewis acid catalyzed Biginelli reactions. PMID:23101501

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. Dependence and Influence of Projectile Energy and Target Mass on the Production of Light Charged Particles and Intermediate Mass Fragments in Proton Induced Reactions

    NASA Astrophysics Data System (ADS)

    Sharma, S. K.; Filges, D.; Goldenbaum, F.; Kamys, B.

    2014-05-01

    Calculations were performed for proton induced spallation reactions over a wide range of atomic masses on the targets: 12C, 27Al, natNi, 108Ag and 197Au using an Intra-nuclear Cascade Model (INCL4.6) with coalescence which includes the emission of protons, light clusters (d-4He), and intermediate mass fragments (up to A=8) formed by the nucleons during the first stage of the reaction. The emission of particles from excited cascade residua are described using three different theoretical models SMM, ABLA07, and GEMINI++. A comparison of calculations with experimental double differential cross-sections d2σ/dΩdE for light charged particles and selected intermediate mass fragments was studied at proton beam energies from 1.2-2.5 GeV. Systematic deviations of the simulated cross sections from the experimental data were found for both light charged particles and intermediate mass fragments.

  1. 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.

  2. 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

    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

  3. Intramolecular Schmidt reaction of acyl chlorides with alkyl azides: preparation of pyrrolizine by intramolecular capture of intermediates with alkenes or alkynes.

    PubMed

    Wang, Bao-Juan; Xue, Ping; Gu, Peiming

    2015-02-11

    The preparation of substituted pyrrolizines through the Schmidt reaction of acyl chlorides with alkyl azides has been realized. Intramolecular capture of the isocyanate ion and N-acyliminium ion intermediates from the Schmidt process with alkene or alkyne units was achieved, and the efficiency of the conversion with respect to ring construction and bond formation was demonstrated. PMID:25558477

  4. 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.

  5. 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.

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

    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

  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

    2009-03-25

    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.

  8. 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.

  9. 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.

  10. 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

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

    PubMed

    Skerry, Amy E; Spelke, Elizabeth S

    2014-02-01

    Identifying the goal of another agent's action allows an observer to make inferences not only about the outcomes the agent will pursue in the future and the means to be deployed in a given context, but also about the emotional consequences of goal-related outcomes. While numerous studies have characterized the former abilities in infancy, expectations about emotions have gone relatively unexplored. Using a violation of expectation paradigm, we present infants with an agent who attains or fails to attain a demonstrated goal, and reacts with positive or negative affect. Across several studies, we find that infants' attention to a given emotional display differs depending on whether that reaction is congruent with the preceding goal outcome. Specifically, infants look longer at a negative emotional display when it follows a completed goal compared to when it follows a failed goal. The present results suggest that infants' goal representations support expectations not only about future actions but also about emotional reactions, and that infants in the first year of life can relate different emotional reactions to conditions that elicit them. PMID:24321623

  12. 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

  13. Identifiability for the pointwise source detection in Fisher’s reaction-diffusion equation

    NASA Astrophysics Data System (ADS)

    Ben Belgacem, Faker

    2012-06-01

    We are interested in the detection of a pointwise source in a class of semi-linear advection-diffusion-reaction equations of Fisher type. The source is determined by its location, which may be steady or unsteady, and its time-dependent intensity. Observations recorded at a couple of points are the available data. One observing station is located upstream of the source and the other downstream. This is a severely ill-posed nonlinear inverse problem. In this paper, we pursue an identifiability result. The process we follow has been developed earlier for the linear model and may be sharpened to operate for the semi-linear equation. It is based on the uniqueness for a parabolic (semi-linear) sideways problem, which is obtained by a suitable unique continuation theorem. We state a maximum principle that turns out to be necessary for our proof. The identifiability is finally obtained for a stationary or a moving source. Many applications may be found in biology, chemical physiology or environmental science. The problem we deal with is the detection of pointwise organic pollution sources in rivers and channels. The basic equation to consider is the one-dimensional biochemical oxygen demand equation, with a nonlinear power growth inhibitor and/or the Michaelis-Menten reaction coefficient.

  14. Interaction of Gd-DTPA with phosphate and phosphite: toward the reaction intermediate in nephrogenic systemic fibrosis.

    PubMed

    Gao, Song; George, Simon J; Zhou, Zhao-Hui

    2016-03-15

    Direct reactions of the MRI contrast agent K2[Gd(DTPA)(H2O)]·5H2O () (H5DTPA = diethylenetriaminepentaacetic acid) with dipotassium hydrogen phosphate (K2HPO4) or phosphite (K2HPO3) result in the isolation of well-defined Gd-DTPA phosphite K6[Gd2(DTPA)2(HPO3)]·7H2O () or phosphate K6[Gd2(DTPA)2(HPO4)]·10H2O (), respectively. Their lanthanum analogs K4[La2(DTPA)2(H2O)]·8H2O (), K6[La2(DTPA)2(HPO3)]·7H2O () and K6[La2(DTPA)2(HPO4)]·10H2O () are used for comparison. The phosphate and phosphite groups are able to substitute the coordinated water molecules in and in a close physiological aqueous solution, and act as bridging ligands to link adjacent Ln(DTPA)(2-) (Ln = Gd and La) into dimeric structures. Solid state and solution (13)C NMR spectra of dimer show complete dissociation into its monomeric species in solution, while no dissociation is observed for lanthanum phosphite and phosphate in solution, which show only one set of (13)C spectra with the largest downfield shifts at 182.0 and 182.3 ppm respectively. Comparisons of the bond distances and spectral data indicate that the interaction between DTPA and central Ln(3+) cations are weakened after the substitutions, which support phosphate substituted Gd-DTPA as an initial intermediate in nephrogenic systemic fibrosis. PMID:26906409

  15. Metabolic modeling of muscle metabolism identifies key reactions linked to insulin resistance phenotypes

    PubMed Central

    Nogiec, Christopher; Burkart, Alison; Dreyfuss, Jonathan M.; Lerin, Carles; Kasif, Simon; Patti, Mary-Elizabeth

    2015-01-01

    Objective Dysregulated muscle metabolism is a cardinal feature of human insulin resistance (IR) and associated diseases, including type 2 diabetes (T2D). However, specific reactions contributing to abnormal energetics and metabolic inflexibility in IR are unknown. Methods We utilize flux balance computational modeling to develop the first systems-level analysis of IR metabolism in fasted and fed states, and varying nutrient conditions. We systematically perturb the metabolic network to identify reactions that reproduce key features of IR-linked metabolism. Results While reduced glucose uptake is a major hallmark of IR, model-based reductions in either extracellular glucose availability or uptake do not alter metabolic flexibility, and thus are not sufficient to fully recapitulate IR-linked metabolism. Moreover, experimentally-reduced flux through single reactions does not reproduce key features of IR-linked metabolism. However, dual knockdowns of pyruvate dehydrogenase (PDH), in combination with reduced lipid uptake or lipid/amino acid oxidation (ETFDH), does reduce ATP synthesis, TCA cycle flux, and metabolic flexibility. Experimental validation demonstrates robust impact of dual knockdowns in PDH/ETFDH on cellular energetics and TCA cycle flux in cultured myocytes. Parallel analysis of transcriptomic and metabolomics data in humans with IR and T2D demonstrates downregulation of PDH subunits and upregulation of its inhibitory kinase PDK4, both of which would be predicted to decrease PDH flux, concordant with the model. Conclusions Our results indicate that complex interactions between multiple biochemical reactions contribute to metabolic perturbations observed in human IR, and that the PDH complex plays a key role in these metabolic phenotypes. PMID:25737951

  16. 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).

  17. 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

  18. 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%.

  19. Enantioselective ring-opening reactions of racemic ethynyl epoxides via copper-allenylidene intermediates: efficient approach to chiral beta-amino alcohols.

    PubMed

    Hattori, Gaku; Yoshida, Akiko; Miyake, Yoshihiro; Nishibayashi, Yoshiaki

    2009-10-16

    Enantioselective copper-catalyzed ring-opening reactions of racemic ethynyl epoxides with amines using (R)-DTBM-MeO-BIPHEP as a chiral ligand have been found to give the corresponding amino alcohols in high yields with up to 94% ee. The reaction is considered to proceed via copper-allenylidene complexes as key intermediates. This methodology may provide a novel synthetic approach to optically active amino alcohols, the structures of which are widely found in many natural products, biologically active compounds, and chiral ligands. PMID:19575533

  20. 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

  1. Composition of reaction intermediates for stoichiometric and fuel-rich dimethyl ether flames: flame-sampling mass spectrometry and modeling studies.

    PubMed

    Wang, Juan; Chaos, Marcos; Yang, Bin; Cool, Terrill A; Dryer, Fred L; Kasper, Tina; Hansen, Nils; Osswald, Patrick; Kohse-Höinghaus, Katharina; Westmoreland, Phillip R

    2009-03-01

    Molecular-beam synchrotron photoionization mass spectrometry and electron-ionization mass spectrometry are used for measurements of species mole fraction profiles for low-pressure premixed dimethyl ether (DME) flames with equivalence ratios ranging from near-stoichiometric conditions (Phi = 0.93) to fuel-rich flames near the limits of flat-flame stability (Phi = 1.86). The results are compared with predictions of a recently modified kinetic model for DME combustion [Zhao et al., Int. J. Chem. Kinet., 2008, 40, 1-18] that has been extensively tested against laminar flame speed measurements, jet-stirred reactor experiments, pyrolysis and oxidation experiments in flow reactors, species measurements for burner-stabilized flames and ignition delay measurements in shock tubes. The present comprehensive measurements of the composition of reaction intermediates over a broad range of equivalence ratios considerably extends the range of the previous experiments used for validation of this model and allows for an accurate determination of contributions of individual reactions to the formation or destruction of any given flame species. The excellent agreement between measurements and predictions found for all major and most intermediate species over the entire range of equivalence ratios provides a uniquely sensitive test of details of the kinetic model. The dependence on equivalence ratio of the characteristic reaction paths in DME flames is examined within the framework of reaction path analyses. PMID:19224033

  2. Two putative protein-tyrosine kinases identified by application of the polymerase chain reaction.

    PubMed Central

    Wilks, A F

    1989-01-01

    The pivotal role that protein-tyrosine kinases (PTKs) play in the growth regulation of eukaryotic cells is manifest in the frequent appearance of members of the PTK family as growth factor receptors or as the transforming agents of acutely transforming retroviruses. A feature common to all members of the PTK family is a highly conserved catalytic domain which is characteristic of the group as a whole and whose activity appears to be tightly regulated within the cell by other domains of the PTK. Degenerate oligonucleotide probes corresponding to two invariant amino acid sequence motifs within the catalytic domains of all PTK family members were synthesized and employed in the polymerase chain reaction (PCR) to amplify cDNA sequences between them. An M13 PCR library was produced in this way from cDNA prepared against mRNA from the murine hemopoietic cell line FDC-P1. The PCR library was then screened by DNA sequencing for PTK-related sequences. Two sequences were identified that, on the basis of sequence comparison with known PTKs, may encode representatives of a new class of PTK. Images PMID:2466296

  3. 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.

  4. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect

    Zheng, Zhongzhou; Sosnick, Tobin R.

    2010-05-25

    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 {yields} Glu{sup -}) to destabilize and unfold a specific region of the protein. We applied this strategy to ubiquitin, reversibly trapping a folding intermediate in which the {beta}5-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.

  5. 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

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

    PubMed

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

    2016-04-21

    Current microscale tracking of chemical kinetics is limited to destructive ex situ methods. Here we utilize Ag nanocube-based plasmonic liquid marble (PLM) microreactor for in situ molecular-level identification of reaction dynamics. We exploit the ultrasensitive surface-enhanced Raman scattering (SERS) capability imparted by the plasmonic shell to unravel the mechanism and kinetics of aryl-diazonium surface grafting reaction in situ, using just a 2-μL reaction droplet. This reaction is a robust approach to generate covalently functionalized metallic surfaces, yet its kinetics remain unknown to date. Experiments and simulations jointly uncover a two-step sequential grafting process. An initial Langmuir chemisorption of sulfonicbenzene diazonium (dSB) salt onto Ag surfaces forms an intermediate sulfonicbenzene monolayer (Ag-SB), followed by subsequent autocatalytic multilayer growth of Ag-SB3. Kinetic rate constants reveal 19-fold faster chemisorption than multilayer growth. Our ability to precisely decipher molecular-level reaction dynamics creates opportunities to develop more efficient processes in synthetic chemistry and nanotechnology. PMID:27050645

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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

  13. Isolation, Characterization of an Intermediate in an Oxygen Atom-Transfer Reaction, and the Determination of the Bond Dissociation Energy

    SciTech Connect

    Nemykin, Victor N.; Laskin, Julia; Basu, Partha

    2004-07-19

    Redox reactions coupled with the formal loss or gain of an oxygen atom are ubiquitous in chemical processes. Such reactions proceed through the reduction of the donor center (XO) and the oxidation of the acceptor (Y) molecule. Among many examples of the metal centered oxygen atom transfer (OAT) reactivity, those involving molybdenum complexes have been widely investigated due to their involvement in mononuclear molybdenum enzymes. The heat of reaction of the overall atom transfer process can be expressed as a difference between the bond dissociation energies (BDEs) of the oxygen-donor(X) and oxygen-acceptor(Y) bond, i.e., H=DX=o-DY=O.

  14. Ruthenium-catalyzed reactions of 1-cyclopropyl-2-propyn-1-ols with anilines and water via allenylidene intermediates: selective preparation of tri- and tetrasubstituted conjugated enynes.

    PubMed

    Yamauchi, Yoshihiro; Onodera, Gen; Sakata, Ken; Yuki, Masahiro; Miyake, Yoshihiro; Uemura, Sakae; Nishibayashi, Yoshiaki

    2007-04-25

    Ruthenium-catalyzed efficient preparation of the conjugated enynes can be carried out in the reactions of 1-cyclopropyl-2-propyn-1-ols with nitrogen- and oxygen-centered nucleophiles such as anilines and water in the presence of a catalytic amount of sulfur-bridged diruthenium complexes. The use of such complexes as catalysts realizes the completely stereoselective preparation of tri- and tetrasubstituted conjugated enynes, where ruthenium-allenylidene complexes work as key intermediates. The direct attack of nucleophiles on a cyclopropane ring connected to an allenylidene ligand is a key step to obtain the enynes stereoselectively. PMID:17391034

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

    PubMed

    Jacob, Sharon E; Breithaupt, Andrew D

    2009-09-01

    This article presents the case of a patient with rheumatoid arthritis who was referred to dermatology for what was suspected to be a photosensitivity reaction to hydroxychloroquine, a common culprit in photodrug reactions. Despite the patient's insistence to the contrary, the cause of her eruption was an airborne allergic contact dermatitis to chemicals she was exposed to during her longtime hobby of soap-making. This case serves as an important illustration of the anatomical differences between eruptions occurring in exposed and photodistributed areas. This article also discusses the causes of dermatitis that may mimic photodrug reactions. PMID:20729959

  16. Isoindolinone compounds active as Kv1.5 blockers identified using a multicomponent reaction approach.

    PubMed

    Kajanus, Johan; Jacobson, Ingemar; Åstrand, Annika; Olsson, Roine I; Gran, Ulrik; Björe, Annika; Fjellström, Ola; Davidsson, Öjvind; Emtenäs, Hans; Dahlén, Anders; Löfberg, Boel; Yuan, Zhong-Qing; Sundell, Johan; Cassel, Johan; Gyll, Jonna; Iliefski, Tommy; Högberg, Ågot; Lindhardt, Emma; Malmberg, Jesper

    2016-04-15

    A series of isoindolinone compounds have been developed showing good in vitro potency on the Kv1.5 ion channel. By modification of two side chains on the isoindolinone scaffold, metabolically stable compounds with good in vivo PK profile could be obtained leaving the core structure unsubstituted. In this way, low microsomal intrinsic clearance (CLint) could be achieved despite a relatively high logD. The compounds were synthesized using the Ugi reaction, in some cases followed by Suzuki and Diels-Alder reactions, giving a diverse set of compounds in a small number of reaction steps. PMID:26965854

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. Origin of Product Selectivity in a Prenyl Transfer Reaction from the Same Intermediate: Exploration of Multiple FtmPT1-Catalyzed Prenyl Transfer Pathways

    PubMed Central

    2015-01-01

    FtmPT1 is a fungal indole prenyltransferase that catalyzes the reaction of tryptophan derivatives with dimethylallyl pyrophosphate to form various biologically active compounds. Herein, we describe detailed studies of FtmPT1 catalysis involving dimethylallyl pyrophosphate and Brevianamide F following the native pathway (yielding Tryprostatin B) and an alternate pathway observed in the Gly115Thr mutant of FtmPT1 yielding a novel cyclized product. Importantly, these two products arise from the same intermediate state, meaning that a step other than the cleavage of the dimethylallyl pyrophosphate (DMAPP; C–O) bond is differentiating between the two product reaction channels. From detailed potential of mean force (PMF) and two-dimensional PMF analyses, we conclude that the rate-limiting step is the cleavage of the C–O bond in DMAPP, while the deprotonation/cyclization step determines the final product distribution. Hence, in the case of FtmPT1, the optimization of the necessary catalytic machinery guides the generation of the final product after formation of the intermediate carbocation. PMID:25188320

  3. 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

  4. 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

  5. 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.

  6. A two-hybrid screen identifies an unconventional role for the intermediate filament peripherin in regulating the subcellular distribution of the SNAP25-interacting protein, SIP30.

    PubMed

    Gentil, Benoit J; McLean, Jesse R; Xiao, Shangxi; Zhao, Beibei; Durham, Heather D; Robertson, Janice

    2014-12-01

    Peripherin is a type III intermediate filament protein, the expression of which is associated with the acquisition and maintenance of a terminally differentiated neuronal phenotype. Peripherin up-regulation occurs during acute neuronal injury and in degenerating motor neurons of amyotrophic lateral sclerosis. The functional role(s) of peripherin during normal, injurious, and disease conditions remains unknown, but may be related to differential expression of spliced isoforms. To better understand peripherin function, we performed a yeast two-hybrid screen on a mouse brain cDNA library using an assembly incompetent peripherin isoform, Per-61, as bait. We identified new peripherin interactors with roles in vesicular trafficking, signal transduction, DNA/RNA processing, protein folding, and mitochondrial metabolism. We focused on the interaction of Per-61 and the constitutive isoform, Per-58, with SNAP25 interacting protein 30 (SIP30), a neuronal protein involved in SNAP receptor-dependent exocytosis. We found that peripherin and SIP30 interacted through coiled-coil domains and colocalized in cytoplasmic aggregates in SW13vim(-) cells. Interestingly, Per-61 and Per-58 differentially altered the subcellular distribution of SIP30 and SNAP25 in primary motor neurons. Our findings suggest a novel role of peripherin in vesicle trafficking. PMID:25113441

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

    PubMed

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

    2013-04-01

    Nickel dithiolene complexes have been proposed as electrocatalysts for alkene purification. Recent studies of the ligand-based reactions of Ni(tfd)2 (tfd = S2C2(CF3)2) and its anion [Ni(tfd)2](-) with alkenes (ethylene and 1-hexene) showed that in the absence of the anion, the reaction proceeds most rapidly to form the intraligand adduct, which decomposes by releasing a substituted dihydrodithiin. However, the presence of the anion increases the rate of formation of the stable cis-interligand adduct, and decreases the rate of dihydrodithiin formation and decomposition. In spite of both computational and experimental studies, the mechanism, especially the role of the anion, remained somewhat elusive. We are now providing a combined experimental and computational study that addresses the mechanism and explains the role of the anion. A kinetic study (global analysis) for the reaction of 1-hexene is reported, which supports the following mechanism: (1) reversible intraligand addition, (2) oxidation of the intraligand addition product prior to decomposition, and (3) interligand adduct formation catalyzed by Ni(tfd)2(-). Density functional theory (DFT) calculations were performed on the Ni(tfd)2/Ni(tfd)2(-)/ethylene system to shed light on the selectivity of adduct formation in the absence of anion and on the mechanism in which Ni(tfd)2(-) shifts the reaction from intraligand addition to interligand addition. Computational results show that in the neutral system the free energy of activation for intraligand addition is lower than that for interligand addition, in agreement with the experimental results. The computations predict that the anion enhances the rate of the cis-interligand adduct formation by forming a dimetallic complex with the neutral complex. The [(Ni(tfd)2)2](-) dimetallic complex then coordinates ethylene and isomerizes to form a Ni,S-bound ethylene complex, which then rapidly isomerizes to the stable interligand adduct but not to the intraligand adduct. Thus, the anion catalyzes the formation of the interligand adduct. Significant experimental evidence for dimetallic species derived from nickel bis(dithiolene) complexes has been found. ESI-MS data indicate the presence of a [(Ni(tfd)2)2](-) dimetallic complex as the acetonitrile adduct. A charge-neutral association complex of Ni(tfd)2 with the ethylene adduct of Ni(tfd)2 has been crystallographically characterized. Despite the small driving force for the reversible association, very major structural reorganization (square-planar → octahedral) occurs. PMID:23484481

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods.

    PubMed

    Dong, Geng; Ryde, Ulf

    2016-06-01

    The [NiFe] hydrogenases catalyse the reversible conversion of H2 to protons and electrons. The active site consists of a Fe ion with one carbon monoxide, two cyanide, and two cysteine (Cys) ligands. The latter two bridge to a Ni ion, which has two additional terminal Cys ligands. It has been suggested that one of the Cys residues is protonated during the reaction mechanism. We have used combined quantum mechanical and molecular mechanics (QM/MM) geometry optimisations, large QM calculations with 817 atoms, and QM/MM free energy simulations, using the TPSS and B3LYP methods with basis sets extrapolated to the quadruple zeta level to determine which of the four Cys residues is more favourable to protonate for four putative states in the reaction mechanism, Ni-SIa, Ni-R, Ni-C, and Ni-L. The calculations show that for all states, the terminal Cys-546 residue is most easily protonated by 14-51 kJ/mol, owing to a more favourable hydrogen-bond pattern around this residue in the protein. PMID:26940957

  13. 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

  14. 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

  15. Radical intermediates and their subsequent reaction pathways in salt-catalyzed coal gasification. Final report, January 1985-January 1988

    SciTech Connect

    White, S.H.; Twardoch, U.M.

    1988-09-01

    The purpose of the study has been to seek evidence for the occurrence of both anodic and cathodic radical forming processes in catalytically inert metal chloride containing solvents using model arene compounds with and without additions of catalysts such as alkali carbonates and bicarbonates at temperatures in excess of ambient. Spectroscopic studies of perylene in the ternary zinc chloride-alkali metal chloride mixture demonstrate the stability of the arene to temperatures in excess of 400/sup 0/C, although the vapor pressure is considerably higher than expected from literature data. The results of these studies show that the treatment of the melts with hydrogen chloride does not lead to significant residual HCl in the melt with the resultant formation of perylinium ions. Electrochemical studies have shown that arenes undergo redox reactions in the alkali metal chloride and zinc chloride based melts. The oxidative reaction of perylene in melts of low nucleophilicity leads to polymerization. In the case of the vitreous-carbon surface, polymeric films are formed and are chlorinated at high anodic potentials to produce another polymeric film with quite different electrochemical characteristics.

  16. Multipulse spectroscopy on the wild-type and YM210W Bacterial Reaction Centre uncovers a new intermediate state in the special pair excited state

    NASA Astrophysics Data System (ADS)

    Cohen Stuart, T. A.; van Grondelle, R.

    2009-06-01

    The Bacterial Reaction Centre (BRC) has a complex electronic excited state, P ∗, that evolves into subsequent charge separated product states P +H - and P +B -. Pump-dump-probe spectroscopy on the wild-type BRC and on YM210W, a mutant with a stabilized, long-lived P ∗ excited state, has uncovered a new charge-separated state in both BRC's. When P ∗ is dumped, a fraction of its population is transferred to this state that has a strong Stark shift in the accessory bacteriochlorophyll (B M) region which serves as a signature for P + and a lifetime highly comparable to the slow phase of P ∗ decay. This lead us propose this intermediate to be P +/P -.

  17. 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.

  18. 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…

  19. 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

  20. 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.

  1. Quasielastic charge-exchange reaction p/sup 3/ He. -->. n/sub F/ ppp at intermediate energies

    SciTech Connect

    Blinov, A.V.; Vanyushin, I.A.; Grechko, V.E.; Zombkovskii, S.M.; Kondratyuk, L.A.; Korolev, Y.V.; Selektor, Y.M.; Solov'ev, V.V.; Turov, V.F.; Chuvilo, I.V.; and others

    1988-04-01

    The principal characteristics of the quasielastic-charge-exchange reaction p/sup 3/He..-->..n/sub F/ppp are investigated by means of the liquid-hydrogen bubble chamber at our institute of diameter 80 cm, exposed in beams of /sup 3/He nuclei with momenta 2.5 and 5 GeV/c (the kinetic energy of the primary protons T/sub p/ in the rest system of the nucleus is respectively 0.318 and 0.978 GeV). The experimental data are compared with the predictions of the Glauber-Sitenko multiple-scattering theory and with the pole model taking into account the interaction of spectator nucleons in the final state. In the mass spectrum of the 3p system at 3.05 GeV a well expressed structure is observed which is not described in the framework of the pole model. A possible resonance occurrence of this structure is discussed.

  2. 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.

  3. 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

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

    PubMed

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

    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(1) and tau(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(1)(LE)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(3), and C(=O)OC(2)H(2) p-substituents, it is concluded that this ESA band cannot be attributed to a pisigma( *) state, as only the C-C[Triple Bond]N group can undergo the required 120 degrees bending. PMID:20001042

  5. 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

  6. 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

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

    NASA Astrophysics Data System (ADS)

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

    The reaction of gaseous NO 2 with alkali halides is of significant interest for its potential to occur in polluted marine atmospheres ((Finlayson-Pitts, 1993), Res. Chem. Int.19, 235-249). We report here a new paramagnetic signal in NaBr and NaCl formed upon reaction with gaseous NO 2 and assigned to a radical anion intermediate of the type [X… NO 2] - where X = Br, Cl. This is a new type of V k center (Castner and Känzig, 1957, J. Phys. Chem. Solids3, 178-195; Fowler, 1968; Seidel, 1969, in Magnetic Resonance and Radiofrequency Spectroscopy (edited by Averbuch P.), North Holland, Amsterdam, pp. 141-156), which is remarkably stable. Indeed, with NaCl it can be observed for several days following the reaction after handling the sample in room light and ambient air. This intermediate may be responsible at least in part for synergistic effects observed in the deep lung in rats exposed simultaneously to gaseous NO 2 and NaCl aerosol (Last and Warren, 1987, Toxicol. Appl. Pharmacol.90, 34-42). While the gaseous product ClNO was suggested earlier as the causative agent (Last and Warren, 1987, Toxicol. Appl. Pharmacol.90, 34-42), it is highly reactive with liquid water and will be removed largely in the upper respiratory tract, while small particles are able to penetrate into the deep lung. Given the ubiquitous occurrence (Finlayson-Pitts and Pitts, 1986, Atmospheric Chemistry: Fundamentals and Experimental Techniques, Wiley, New York), of NO 2 and airborne salt particles, which occur not only in marine areas but also significant distances inland (Shaw, 1991, J. geophys. Res.96, 22,369-22,372) as well as in the plumes from oil well burning (Lowenthal et al., 1993, Geophys. Res. Lett.20, 691-693; Stevens et al., 1993, Wat. Sci. Technol.27, 223-233; Sheridan et al., 1992, Geophys. Res. Lett.19, 389-392; Parungo et al., 1992, J. geophys. Res. 97, 15,867-15,882; Cahill et al., 1992, J. geophys. Res.97, 14,513-14,520) this radical anion could provide a vehicle for delivery of reactive species into the deep lung. These observations are discussed in the context of the mechanism of action of PM 10 which has been associated recently with increased mortality (Dockery et al., 1993, New Eng. J. Med.329, 1753-1759).

  8. Model reduction and a priori kinetic parameter identifiability analysis using metabolome time series for metabolic reaction networks with linlog kinetics.

    PubMed

    Nikerel, I Emrah; van Winden, Wouter A; Verheijen, Peter J T; Heijnen, Joseph J

    2009-01-01

    In this work, we present a time-scale analysis based model reduction and parameter identifiability analysis method for metabolic reaction networks. The method uses the information obtained from short term chemostat perturbation experiments. We approximate the time constant of each metabolite pool by their turn-over time and classify the pools accordingly into two groups: fast and slow pools. We performed a priori model reduction, neglecting the dynamic term of the fast pools. By making use of the linlog approximative kinetics, we obtained a general explicit solution for the fast pools in terms of the slow pools by elaborating the degenerate algebraic system resulting from model reduction. The obtained relations yielded also analytical relations between a subset of kinetic parameters. These relations also allow to realize an analytical model reduction using lumped reaction kinetics. After solving these theoretical identifiability problems and performing model reduction, we carried out a Monte Carlo approach to study the practical identifiability problems. We illustrated the methodology on model reduction and theoretical/practical identifiability analysis on an example system representing the glycolysis in Saccharomyces cerevisiae cells. PMID:18718548

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

    DOEpatents

    Holzrichter, John F.; Siekhaus, Wigbert J.

    1997-01-01

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

  10. 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.

  11. Wildtype and Engineered Monomeric Triosephosphate Isomerase from Trypanosoma brucei: Partitioning of Reaction Intermediates in D2O and Activation by Phosphite Dianion‡

    PubMed Central

    Malabanan, M. Merced; Go, Maybelle K.; Amyes, Tina L.; Richard, John P.

    2011-01-01

    Product yields for the reactions of (R)-glyceraldehyde 3-phosphate (GAP) in D2O at pD 7.9 catalyzed by wildtype triosephosphate isomerase from Trypanosoma brucei brucei (Tbb TIM) and a monomeric variant (monoTIM) of this wildtype enzyme were determined by 1H NMR spectroscopy, and were compared with the yields determined in earlier work for the reactions catalyzed by TIM from rabbit and chicken muscle [O’Donoghue, A. C, Amyes, T. L. and Richard J.P. (2005), Biochemistry 44, 2610–2621]. Three products were observed from the reactions catalyzed by TIM: dihydroxyacetone phosphate (DHAP) from isomerization with intramolecular transfer of hydrogen, d-DHAP from isomerization with incorporation of deuterium from D2O into C-1 of DHAP, and d-GAP from incorporation of deuterium from D2O into C-2 of GAP. The yield of DHAP formed by intramolecular transfer of hydrogen decreases from 49% for the muscle enzymes to 40% for wildtype Tbb TIM to 34% for monoTIM. There is no significant difference in the ratio of the yields of d-DHAP and d-GAP for wildtype TIM from muscle sources and Trypanosoma brucei brucei, but partitioning of the enediolate intermediate of the monoTIM reaction to form d-DHAP is less favorable ((kC1)D/(kC2)D = 1.1) than for the wildtype enzyme ((kC1)D/(kC2)D = 1.7). Product yields for the wildtype Tbb TIM and monoTIM-catalyzed reactions of glycolaldehyde labeled with carbon-13 at the carbonyl carbon ([1-13C]-GA) at pD 7.0 in the presence of phosphite dianion and in its absence were determined by 1H NMR spectroscopy [Go, M. K., Amyes, T. L., and Richard, J. P. (2009) Biochemistry 48, 5769–5778]. There is no detectable difference in the yields of the products of wildtype muscle and Tbb TIM-catalyzed reactions of [1-13C]-GA in D2O. The kinetic parameters for phosphite dianion activation of the reactions of [1-13C]-GA catalyzed by wildtype Tbb TIM are similar to those reported for the enzyme from rabbit muscle TIM [Amyes, T. L., and Richard, J. P. (2007), Biochemistry 46, 5841–5854], but there is no detectable dianion activation of the reaction catalyzed by monoTIM. The engineered disruption of subunit contacts at monoTIM causes movement of the essential side chains of Lys-13 and His-95 away from the catalytic active positions. We suggest that this places an increased demand that the intrinsic binding energy of phosphite dianion be utilized to drive the change in the conformation of monoTIM back to the active structure for wildtype TIM, with the result that there is insufficient binding energy remaining to give a detectable stabilization of the transition state for the monoTIM-catalyzed reaction of [1-13C]-GA. PMID:21553855

  12. 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

  13. Remote substituent effects on the photooxygenation of 9,10-diarylanthracenes: strong evidence for polar intermediates.

    PubMed

    Fudickar, Werner; Linker, Torsten

    2008-04-21

    Two different reaction pathways in the photooxygenation of 9,10-diarylanthracenes are identified, with strong evidence for polar (forward, singlet oxygen addition) and radical (backward, thermolysis) intermediates. PMID:18379688

  14. Imino-Oxy Acetic Acid Dealkylation as Evidence for an Inner-Sphere Alcohol Intermediate in the Reaction Catalyzed by Peptidylglycine α-Hydroxylating Monooxygenase (PHM)

    PubMed Central

    McIntyre, Neil R.; Lowe, Edward W.; Merkler, David J.

    2009-01-01

    Peptidylglycine α-hydroxylating monooxygenase (PHM, EC 1.14.17.3) catalyzes the stereospecific hydroxylation of a glycyl α-carbon in a reaction that requires O2 and ascorbate. Subsequent dealkylation of the α-hydroxyglycine by another enzyme, peptidylamidoglycolate lyase (PAL. EC 4.3.2.5), yields a bioactive amide and glyoxylate. PHM is a non-coupled, type II dicopper monooxygenase which activates O2 at only a single copper atom, CuM. In this study, the PHM mechanism was probed using a non-natural substrate, benzaldehyde imino-oxy acetic acid (BIAA). PHM catalyzes the O-oxidative dealkylation of BIAA to benzaldoxime and glyoxylate with no involvement of PAL. The minimal kinetic mechanism for BIAA was shown to be steady-state ordered using primary deuterium kinetic isotope effects. The D(V/K)APPARENT, BIAA decreased from 14.7 ± 1.0 as [O2] → 0 to 1.0 ± 0.2 as [O2] → ∞ suggesting the dissociation rate constant from the PHM·BIAA complex decreases as [O2] increases; thereby, reducing the steady-state concentration of [PHM]free. BIAA was further used to differentiate between potential oxidative Cu/O species using a QM/MM reaction coordinate simulation to determine which species could yield product O-dealkylation that matched our experimental data. The results of this study provided compelling evidence for the presence of a covalently linked CuII-alkoxide intermediate with a quartet spin state responsible BIAA oxidation. PMID:19569683

  15. Utility of reaction intermediate monitoring with photodissociation multi-stage (MSn) time-of-flight mass spectrometry for mechanistic and structural studies: Phosphopeptides

    NASA Astrophysics Data System (ADS)

    Moon, Jeong Hee; Shin, Young Sik; Kim, Myung Soo

    2009-12-01

    In tandem mass spectra of phosphopeptides, intact sequence ions are often missing or appear weakly. Instead, dephosphorylated sequence ions appear prominently. In this work, we used photodissociation (PD) multi-stage (MSn) time-of-flight mass spectrometry that can monitor reaction intermediates with lifetime as short as 100 ns to study the formation of dephosphorylated sequence ions such as yn-H3PO4. yn-H3PO4 was found to be formed mainly by H3PO4 loss from yn. For doubly phosphorylated peptides, yn seemed to lose H3PO4 stepwise and form yn-H3PO4 and yn-2H3PO4. Even when yn was absent in PD-MS2 spectrum, its m/z could be predicted from those of yn-H3PO4 and/or yn-2H3PO4. Complete sequence coverage was possible when the data from PD-MS2 and PD-MS3 were combined, demonstrating the utility of transient ion detection by PD-MS3 for structure analysis.

  16. Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway

    SciTech Connect

    Moure, Carmen M.; Gimble, Frederick S.; Quiocho, Florante A.

    2008-07-28

    I-SceI is a homing endonuclease that specifically cleaves an 18-bp double-stranded DNA. I-SceI exhibits a strong preference for cleaving the bottom strand DNA. The published structure of I-SceI bound to an uncleaved DNA substrate provided a mechanism for bottom strand cleavage but not for top strand cleavage. To more fully elucidate the I-SceI catalytic mechanism, we determined the X-ray structures of I-SceI in complex with DNA substrates that are nicked in either the top or bottom strands. The structures resemble intermediates along the DNA cleavage reaction. In a structure containing a nick in the top strand, the spatial arrangement of metal ions is similar to that observed in the structure that contains uncleaved DNA, suggesting that cleavage of the bottom strand occurs by a common mechanism regardless of whether this strand is cleaved first or second. In the structure containing a nick in the bottom strand, a new metal binding site is present in the active site that cleaves the top strand. This new metal and a candidate nucleophilic water molecule are correctly positioned to cleave the top strand following bottom strand cleavage, providing a plausible mechanism for top strand cleavage.

  17. 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.

  18. 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.

  19. C(aryl)-C(alkyl) bond formation from Cu(ClO4)2-mediated oxidative cross coupling reaction between arenes and alkyllithium reagents through structurally well-defined Ar-Cu(III) intermediates.

    PubMed

    Wang, Zu-Li; Zhao, Liang; Wang, Mei-Xiang

    2012-09-28

    The stable and structurally well-defined Ar-Cu(III) intermediates, that are prepared almost quantitatively from the reaction of azacalix[1]arene[3]pyridines with Cu(ClO(4))(2)·6H(2)O under aerobic conditions, reacted smoothly with a number of alkyllithium reagents under mild conditions to form C(aryl)-C(alkyl) bonds. PMID:22892907

  20. Combining real-time polymerase chain reaction using SYBR Green I detection and sequencing to identify vertebrate bloodmeals in fleas.

    PubMed

    Graham, Christine B; Black, William C; Boegler, Karen A; Montenieri, John A; Holmes, Jennifer L; Gage, Kenneth L; Eisen, Rebecca J

    2012-11-01

    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 Bouché) 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

  1. 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.

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  5. 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.

  6. 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

  7. 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

  8. The synthesis, testing and use of 5-fluoro-alpha-D-galactosyl fluoride to trap an intermediate on green coffee bean alpha-galactosidase and identify the catalytic nucleophile.

    PubMed

    Ly, H D; Howard, S; Shum, K; He, S; Zhu, A; Withers, S G

    2000-11-17

    5-Fluoro-alpha-D-galactopyranosyl fluoride was synthesized and its interaction with the active site of an alpha-galactosidase from green coffee bean (Coffea arabica), a retaining glycosidase, characterized kinetically and structurally. The compound behaves as an apparently tight binding (Ki = 600 nM) competitive inhibitor, achieving this high affinity through reaction as a slow substrate that accumulates a high steady-state concentration of the glycosyl-enzyme intermediate, as evidenced by ESiMS. Proteolysis of the trapped enzyme coupled with HPLC/MS analysis allowed the localization of a labeled peptide that was subsequently sequenced. Comparison of this sequence information to that of other members of the same glycosidase family revealed the active site nucleophile to be Asp145 within the sequence LKYDNCNNN. The importance of this residue to catalysis has been confirmed by mutagenesis studies. PMID:11128583

  9. 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.

  10. Using postural reactions as a screening test to identify high-risk infants for cerebral palsy: a prospective study.

    PubMed

    Zafeiriou, D I; Tsikoulas, I G; Kremenopoulos, G M; Kontopoulos, E E

    1998-08-01

    To clarify the predictive value of the seven more commonly used postural reactions (PR) in the 1st year of life regarding the diagnosis of cerebral palsy (CP), we prospectively examined 204 high-risk infants of whom 58 developed CP, 22 had developmental retardation (DR) and 124 were normal at follow-up at 3 years of age. Abnormalities of five or more PR from the 1st month of life were correlated with spastic CP, while five or six abnormal PR were also correlated with athetoid CP. Three or less abnormal PR correlated with a normal outcome. All seven PR tested were significantly abnormal in children with spastic CP from the 1st month compared to normal children. Athetoid children demonstrated abnormalities of the Peiper-Isbert (P-I) reaction and Vojta reaction from the 1st month and of the vertical, horizontal and Collis vertical suspension from the 3rd month. Children with DR had significantly abnormal Collis horizontal and Collis vertical suspension, Vojta reaction and traction response from the 1st month and Peiper-Isbert reaction from the 3rd month. Ataxic children demonstrated significantly abnormal traction response from the 1st month, Collis horizontal reaction from the 7th month and Peiper-Isbert reaction from the 11th month. We conclude that the examination of PR is a useful quantitative and qualitative diagnostic screening tool for high-risk infants from the 1st month of life. PMID:9761000

  11. 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

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

    PubMed Central

    2014-01-01

    Background Identifying the relevant environmental variables that cause GxE interaction is often difficult when they cannot be experimentally manipulated. Two statistical approaches can be applied to address this question. When data on candidate environmental variables are available, GxE interaction can be quantified as a function of specific environmental variables using a reaction norm model. Alternatively, a factor analytic model can be used to identify the latent common factor that explains GxE interaction. This factor can be correlated with known environmental variables to identify those that are relevant. Previously, we reported a significant GxE interaction for body weight at harvest in rainbow trout reared on three continents. Here we explore their possible causes. Methods Reaction norm and factor analytic models were used to identify which environmental variables (age at harvest, water temperature, oxygen, and photoperiod) may have caused the observed GxE interaction. Data on body weight at harvest was recorded on 8976 offspring reared in various locations: (1) a breeding environment in the USA (nucleus), (2) a recirculating aquaculture system in the Freshwater Institute in West Virginia, USA, (3) a high-altitude farm in Peru, and (4) a low-water temperature farm in Germany. Akaike and Bayesian information criteria were used to compare models. Results The combination of days to harvest multiplied with daily temperature (Day*Degree) and photoperiod were identified by the reaction norm model as the environmental variables responsible for the GxE interaction. The latent common factor that was identified by the factor analytic model showed the highest correlation with Day*Degree. Day*Degree and photoperiod were the environmental variables that differed most between Peru and other environments. Akaike and Bayesian information criteria indicated that the factor analytical model was more parsimonious than the reaction norm model. Conclusions Day*Degree and photoperiod were identified as environmental variables responsible for the strong GxE interaction for body weight at harvest in rainbow trout across four environments. Both the reaction norm and the factor analytic models can help identify the environmental variables responsible for GxE interaction. A factor analytic model is preferred over a reaction norm model when limited information on differences in environmental variables between farms is available. PMID:24571451

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

    PubMed Central

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

    2012-01-01

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

  14. 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

  15. Oxidative hemoglobin reactions: Applications to drug metabolism.

    PubMed

    Spolitak, Tatyana; Hollenberg, Paul F; Ballou, David P

    2016-06-15

    Hb is a protein with multiple functions, acting as an O2 transport protein, and having peroxidase and oxidase activities with xenobiotics that lead to substrate radicals. However, there is a lack of evidence for intermediates involved in these reactions of Hb with redox-active compounds, including those with xenobiotics such as drugs, chemical carcinogens, and sulfides. In particular, questions exist as to what intermediates participate in reactions of either metHb or oxyHb with sulfides. The studies presented here elaborate kinetics and intermediates involved in the reactions of Hb with oxidants (H2O2 and mCPBA), and they demonstrate the formation of high valent intermediates, providing insights into mechanistic issues of sulfur and drug oxidations. Overall, we propose generalized mechanisms that include peroxidatic reactions using H2O2 generated from the autooxidation of oxyHb, with involvement of substrate radicals in reactions of Hb with oxidizable drugs such as metyrapone or 2,4-dinitrophenylhydrazine and with sulfides. We identify ferryl intermediates (with a Soret band at 407 nm) in oxidative reactions with all of the above-mentioned reactions. These spectral properties are consistent with a protonated ferryl heme, such as Cpd II or Cpd ES-like species (Spolitak et al., JIB, 2006, 100, 2034-2044). Mechanism(s) of Hb oxidative reactions are discussed. PMID:27091316

  16. 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

  17. "Pump-probe" atom-centered density matrix propagation studies to gauge anharmonicity and energy repartitioning in atmospheric reactive adducts: case study of the OH + isoprene and OH + butadiene reaction intermediates.

    PubMed

    Pacheco, Alexander B; Dietrick, Scott M; Stevens, Philip S; Iyengar, Srinivasan S

    2012-04-26

    Time-resolved "pump-probe" ab initio molecular dynamics studies are constructed to probe the stability of reaction intermediates, the mechanism of energy transfer, and energy repartitioning, for moieties involved during the interaction of volatile organic compunds with hydroxyl radical. These systems are of prime importance in the atmosphere. Specifically, the stability of reaction intermediates of hydroxyl radical adducts to isoprene and butadiene molecules is used as a case study to develop novel computational techniques involving "pump-probe" ab initio molecular dynamics. Starting with the various possible hydroxyl radical adducts to isoprene and butadiene, select vibrational modes of each of the adducts are populated with excess energy to mimic the initial conditions of an experiment. The flow of energy into the remaining modes is then probed by subjecting the excited adducts to ab initio molecular dynamics simulations. It is found that the stability of the adducts arises directly due to the anhormonically driven coupling of the modes to facilitate repartitioning of the excess vibrational energy. This kind of vibrational repartitioning has a critical influence on the energy density. PMID:22401490

  18. A Closer Look at the Spectroscopic Properties of Possible Reaction Intermediates in WT and Mutant (E)-4-hydroxy-3-methyl-but-2-enyl Diphosphate Reductase (IspH/LytB)†

    PubMed Central

    Xu, Weiya; Lees, Nicholas S.; Hall, Dominique; Welideniya, Dhanushi; Hoffman, Brian M.; Duin, Evert C.

    2012-01-01

    (E)-4-Hydroxy-3-methyl-but-2-enyl diphosphate reductase (IspH or LytB) catalyzes the terminal step of the MEP/DOXP pathway where it converts (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) into the two products isopentenyl diphosphate and dimethylallyl diphosphate. The reaction involves the reductive elimination of the C4 hydroxyl group, using a total of two electrons. Here we show that the active form of IspH contains a [4Fe-4S] cluster and not the [3Fe-4S] form. Our studies show that the cluster is not only the direct electron source for the reaction but that a reaction intermediate is bound directly to the cluster. This active form, has been trapped in a state, dubbed FeSA, that was detected in EPR spectroscopy when one-electron-reduced IspH was incubated with HMBPP. In addition, three mutants of IspH protein have been prepared and studied, His42, His124 and Glu126 (Aquifex aeolicus numbering), with particular attention to the effects on the cluster properties and possible reaction intermediates. None of the mutants affected the properties of the [4Fe-4S]+ cluster significantly, but different effects were observed when one-electron-reduced forms were incubated with HMBPP. Replacing the His42 led to an increased Km value and much lower catalytic efficiency, confirming the role of this residue in substrate binding. Replacing the His124 also resulted in lower catalytic efficiency. In this case, however, enzyme showed the loss of the [4Fe-4S]+ EPR signal upon addition of HMBPP without the subsequent formation of the FeSA signal. Instead, a radical-type signal was observed in some of the samples indicating that this residue plays a role in the correct positioning of the substrate. The incorrect orientation in the mutant leads to the formation of substrate-based radicals instead of the cluster-bound-intermediate complex FeSA. Replacing the Glu126 also resulted in lower catalytic efficiency, with yet a third type of EPR signal being detected upon incubation with HMBPP. 31P- and 2H-ENDOR measurements on the FeSA species incubated with regular and 2H-C4-labeled HMBPP reveal that the substrate binds to the enzyme in close proximity of the active-site cluster with the C4 adjacent to the site of linkage between the FeS cluster and HMBPP. Comparison of the spectroscopic properties of this intermediate to those of intermediates detected in (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase and ferredoxin:thioredoxin reductase suggest that HMBPP binds to the FeS cluster via its hydroxyl group instead of a side-on binding as previously proposed for the species detected in the inactive Glu126 variant. Consequences for the IspH reaction mechanism are discussed. PMID:22646150

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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≅2-5×10 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≅5.7×10 9 dm 3mol -1s -1 at pH 7. They show λmax 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.

  4. 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

  5. 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

  6. Role of a Guanidinium Cation-Phosphodianion Pair in Stabilizing the Vinyl Carbanion Intermediate of Orotidine 5'-Phosphate Decarboxylase-Catalyzed Reactions.†

    PubMed Central

    Goryanova, Bogdana; Goldman, Lawrence M.; Amyes, Tina L.; Gerlt, John A; Richard, John P.

    2013-01-01

    The side chain cation of Arg235 provides a 5.6 and 2.6 kcal/mol stabilization of the transition states for orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae (OMPDC) catalyzed reactions of OMP and 5-fluoroorotidine 5'-monophosphate (FOMP), respectively, a 7.2 kcal/mol stabilization of the vinyl carbanion-like transition state for enzyme-catalyzed exchange of the C-6 proton of 5-fluorouridine 5'-monophosphate (FUMP), but no stabilization of the transition states for enzyme-catalyzed decarboxylation of truncated substrates 1-(β-d-erythrofuranosyl)orotic acid and 1-(β-d-erythrofuranosyl) 5-fluorouracil. These observations show that the transition state stabilization results from formation of a protein cation-phosphodianion pair, and that there is no detectable stabilization from an interaction between the side chain and the pyrimidine ring of substrate. The 5.6 kcal/mol side chain interaction with the transition state for the decarboxylation reaction is 50% of the total 11.2 kcal/mol transition state stabilization by interactions with the phosphodianion of OMP, while the 7.2 kcal/mol side-chain interaction with the transition state for the deuterium exchange reaction is a larger 78% of the total 9.2 kcal/mol transition state stabilization by interactions with the phosphodianion of FUMP. The effect of the R235A mutation on the enzyme-catalyzed deuterium exchange is expressed predominantly as a change in the turnover number kex while the effect on the enzyme-catalyzed decarboxylation of OMP is expressed predominantly as a change in the Michaelis constant Km. These results are rationalized by a mechanism in which the binding of OMP, compared with FUMP, provides a larger driving force for conversion of OMPDC from an inactive open conformation to a productive, active, closed conformation. PMID:24053466

  7. 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.

  8. 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).

  9. Gas-phase hydrodenitrogenation reactions of polynuclear heteroaromatic nitrogen compounds and selected intermediates with a 50% nickel oxide/aluminate supported on silica-alumina catalyst

    SciTech Connect

    Fish, R.H.; Heinemann, H. ); Michaels, J.N.; Moore, R.S. )

    1990-05-01

    The gas-phase hydrodenitrogenation (HDN) of quinoline, 1,2,3,4-tetrahydroquinoline, 2-propylaniline, and propylbenzene with a 50% nickel oxide/aluminate on SiO{sub 2}-Al{sub 2}O{sub 3} catalyst has been studied at 250{degree}C under 1 atm of hydrogen gas. Under these mild conditions, alkylaromatics are the predominant HDN products. In the reaction network of this catalytic process, quinoline is hydrogenated to 1,2,3,4-tetrahydroquinoline, which subsequently undergoes C-N bond hydrogenolysis to form 2-propylaniline and then propylbenzene. Significant alkyl side-chain hydrogenolysis occurs in parallel to these reactions, producing a mixture of alkylanilines and alkylbenzenes. Small amounts of alkylcyclohexanes are produced by hydrogenation of the alkylbenzenes. This network differs significantly from that of commercial HDN processes in which quinoline is hydrogenated fully to decahydroquinoline prior to C-H bond cleavage. Pseudo-first-order rate constants have been estimated for quinoline hydrogenation, alkylaniline formation, alkylaniline HDN, and alkylbenzene hydrogenation and compared to analogous data for commercial HDN. This comparison indicates that the activity of the nickel oxide/aluminate on SiO{sub 2}-Al{sub 2}O{sub 3} catalyst is within an order of magnitude of the activity of commercial HDN catalysts. The nickel oxide catalyst is irreversibly poisoned by sulfur and slowly deactivates during HDN due to coke formation; the coked catalyst can be regenerated by oxidation in air and subsequent reduction in hydrogen.

  10. Reactions to Participating in Intimate Partner Violence and Minority Stress Research: A Mixed Methodological Study of Self-Identified Lesbian and Gay Emerging Adults.

    PubMed

    Edwards, Katie M; Sylaska, Kateryna M

    2016-01-01

    The purpose of this study was to examine lesbian and gay (LG) young adults' reactions to participating in intimate partner violence (IPV) and minority stress research using a mixed methodological design. Participants were 277 U.S. college students currently involved in same-sex relationships and self-identified cisgender LG who completed an online questionnaire that included closed- and open-ended questions. Results suggested that IPV research was well tolerated by the vast majority of participants; close to one in 10 participants reported being upset by the study questions, yet 75% of upset individuals reported some level of personal benefit. Reasons for upset as identified in the open-ended responses included thinking about personal experiences with IPV, as the perpetrator or friend of a victim, as well as thinking about the uncertainty of their future with their current partner. The correlates of emotional reactions and personal benefits to research participation were also examined, and these varied among gay men and lesbian women. Implications of these findings underscore the importance of accurate reflection of risk and benefits in informed consent documents as well as systematic evaluation of sexual minority participants' reactions to research participation in an effort to conduct ethically sound sexual science research. PMID:26421906

  11. 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

  12. LiCuS, an intermediate phase in the electrochemical conversion reaction of CuS with Li: A potential environment-friendly battery and solar cell material

    NASA Astrophysics Data System (ADS)

    Beleanu, Andreea; Kiss, Janos; Baenitz, Michael; Majumder, Mayukh; Senyshyn, Anatoliy; Kreiner, Guido; Felser, Claudia

    2016-05-01

    The crystal structure of a ternary sulfide with the approximate composition LiCuS, which is a promising candidate for environment-friendly battery and solar cell materials is reported. The crystal structure was solved by a combination of neutron and X-ray powder diffraction data, and 7Li solid-state NMR analysis. A yellow powder, Li1.1Cu0.9S, was obtained by the reaction of CuS with a slight excess of Li metal. The compound crystallizes in the Na3AgO2 structure type in the space group Ibam. An idealized crystal structure of Li1.1Cu0.9S can be derived from the cubic Li2S structure by moving a part of the Li along the c axis so that these Li atoms become linearly coordinated by S. All the metal sites are occupied by randomly mixed Li and Cu atoms; however, there is a strong preference for linear coordination by Cu. The density functional theory calculations show that Li1.1Cu0.9S is a direct band-gap semiconductor with an energy gap of 1.95 eV in agreement with experimental data.

  13. 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 (ΔA) 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) (γ, xn) products by giant-resonance and/or quasi-deuteron resonance absorption, (2) (γ, xnyp) products by mainly (3, 3) resonance absorption. Slightly rapid increase of T was found around ΔA=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.

  14. 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 (ΔA) 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) (γ, xn) products by giant-resonance and/or quasi-deuteron resonance absorption, (2) (γ, xnyp) products by mainly (3, 3) resonance absorption. Slightly rapid increase of T was found around ΔA=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.

  15. 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.

  16. 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.

  17. 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.

  18. 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)

  19. Charge dependence of identified two-hadron correlation relative to the reaction plane in Pb-Pb collisions measured with ALICE

    NASA Astrophysics Data System (ADS)

    Onderwaater, Jacobus; ALICE Collaboration

    2015-05-01

    Recently a non-zero charge dependence of two-particle correlation relative to the reaction plane in relativistic heavy-ion collisions was observed by RHIC and LHC experiments. The interpretation of these results is a hot topic of debate in the heavy-ion community because of its possible implication for our understanding of parity violation in strong interactions. We extend the ALICE measurement of the charge dependent two-particle correlation in Pb-Pb collisions at \\sqrt{sNN} = 2.76 TeV with one identified hadron (pion, kaon, or proton). Correlations are reported as a function of the identified hadron transverse momentum. These new results are important for disentangling contributions from a number of competing physics effects, such as local charge conservation coupled with strong anisotropic flow, flow fluctuations, and possible contribution from parity violation coupled with strong magnetic fields, the so-called chiral magnetic effect.

  20. 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

  1. 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.

  2. Mechanism of HDS/HDN reactions

    SciTech Connect

    Mullins, D.R.; Lyman, P.F.

    1993-06-01

    One method for exploring the mechanisms involved in HDS/HDN reactions is to study the elementary reaction steps that occur for model systems using UHV surface science techniques. Our approach has been to examine reactions involving a prototypical organosulfur molecule, methanethiol, adsorbed on different clean and modified metal surfaces. In general, as the surface is heated, this molecule follows two principle reaction pathways on most transition metal surfaces. At low coverages, the molecule undergoes total decomposition producing adsorbed atomic sulfur and carbon and gaseous H{sub 2}. At higher coverages a competing pathway results in adsorbed sulfur and gaseous methane. In order to understand these reactions, the different chemical intermediates are identified, and the differences in reactivity for these intermediates are studied as a function of adsorbate coverage, surface composition and sample temperature. Several analytical techniques are employed in these experiments. Temperature programmed desorption, TPD, is used to identify the desorbed reaction products, their desorption temperature and the branching ratio as the system is modified. Auger electron spectroscopy, AES, is used to determine the amount of adsorbed atomic species that result from the reaction. The reaction intermediates are studied by high resolution soft x-ray photoelectron spectroscopy.

  3. Mechanism of HDS/HDN reactions

    SciTech Connect

    Mullins, D.R.; Lyman, P.F.

    1993-01-01

    One method for exploring the mechanisms involved in HDS/HDN reactions is to study the elementary reaction steps that occur for model systems using UHV surface science techniques. Our approach has been to examine reactions involving a prototypical organosulfur molecule, methanethiol, adsorbed on different clean and modified metal surfaces. In general, as the surface is heated, this molecule follows two principle reaction pathways on most transition metal surfaces. At low coverages, the molecule undergoes total decomposition producing adsorbed atomic sulfur and carbon and gaseous H[sub 2]. At higher coverages a competing pathway results in adsorbed sulfur and gaseous methane. In order to understand these reactions, the different chemical intermediates are identified, and the differences in reactivity for these intermediates are studied as a function of adsorbate coverage, surface composition and sample temperature. Several analytical techniques are employed in these experiments. Temperature programmed desorption, TPD, is used to identify the desorbed reaction products, their desorption temperature and the branching ratio as the system is modified. Auger electron spectroscopy, AES, is used to determine the amount of adsorbed atomic species that result from the reaction. The reaction intermediates are studied by high resolution soft x-ray photoelectron spectroscopy.

  4. tRNAGlu Increases the Affinity of Glutamyl-tRNA Synthetase for Its Inhibitor Glutamyl-Sulfamoyl-Adenosine, an Analogue of the Aminoacylation Reaction Intermediate Glutamyl-AMP: Mechanistic and Evolutionary Implications

    PubMed Central

    Blais, Sébastien P.; Kornblatt, Jack A.; Barbeau, Xavier; Bonnaure, Guillaume; Lagüe, Patrick; Chênevert, Robert; Lapointe, Jacques

    2015-01-01

    For tRNA-dependent protein biosynthesis, amino acids are first activated by aminoacyl-tRNA synthetases (aaRSs) yielding the reaction intermediates aminoacyl-AMP (aa-AMP). Stable analogues of aa-AMP, such as aminoacyl-sulfamoyl-adenosines, inhibit their cognate aaRSs. Glutamyl-sulfamoyl-adenosine (Glu-AMS) is the best known inhibitor of Escherichia coli glutamyl-tRNA synthetase (GluRS). Thermodynamic parameters of the interactions between Glu-AMS and E. coli GluRS were measured in the presence and in the absence of tRNA by isothermal titration microcalorimetry. A significant entropic contribution for the interactions between Glu-AMS and GluRS in the absence of tRNA or in the presence of the cognate tRNAGlu or of the non-cognate tRNAPhe is indicated by the negative values of –TΔSb, and by the negative value of ΔCp. On the other hand, the large negative enthalpy is the dominant contribution to ΔGb in the absence of tRNA. The affinity of GluRS for Glu-AMS is not altered in the presence of the non-cognate tRNAPhe, but the dissociation constant Kd is decreased 50-fold in the presence of tRNAGlu; this result is consistent with molecular dynamics results indicating the presence of an H-bond between Glu-AMS and the 3’-OH oxygen of the 3’-terminal ribose of tRNAGlu in the Glu-AMS•GluRS•tRNAGlu complex. Glu-AMS being a very close structural analogue of Glu-AMP, its weak binding to free GluRS suggests that the unstable Glu-AMP reaction intermediate binds weakly to GluRS; these results could explain why all the known GluRSs evolved to activate glutamate only in the presence of tRNAGlu, the coupling of glutamate activation to its transfer to tRNA preventing unproductive cleavage of ATP. PMID:25860020

  5. 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)].

  6. 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

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

    PubMed Central

    Barabás, Orsolya; Németh, Veronika; Bodor, Andrea; Perczel, András; Rosta, Edina; Kele, Zoltán; Zagyva, Imre; Szabadka, Zoltán; Grolmusz, Vince I.; Wilmanns, Matthias; Vértessy, Beáta G.

    2013-01-01

    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 Mason–Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the α-phosphate site. Phosphorus-31 NMR spectroscopy (31P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue α,β-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme–product complex structure. PMID:23982515

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

    PubMed

    Barabás, Orsolya; Németh, Veronika; Bodor, Andrea; Perczel, András; Rosta, Edina; Kele, Zoltán; Zagyva, Imre; Szabadka, Zoltán; Grolmusz, Vince I; Wilmanns, Matthias; Vértessy, Beáta G

    2013-12-01

    Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason-Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the α-phosphate site. Phosphorus-31 NMR spectroscopy ((31)P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue α,β-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme-product complex structure. PMID:23982515

  9. 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- μm 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.

  10. 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

  11. 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.

  12. Establishing the Intermediate Unit.

    ERIC Educational Resources Information Center

    Pennsylvania State Dept. of Education, Harrisburg.

    The State of Pennsylvania Act 102 establishes a system of 29 intermediate units, creates intermediate unit boards of directors, spells out their duties and functions, and provides a system of financing their operations. This handbook has been prepared by the Pennsylvania Department of Education to provide intermediate unit boards of directors,…

  13. Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds.

    PubMed

    Alves, Vinicius M; Muratov, Eugene; Fourches, Denis; Strickland, Judy; Kleinstreuer, Nicole; Andrade, Carolina H; Tropsha, Alexander

    2015-04-15

    Repetitive exposure to a chemical agent can induce an immune reaction in inherently susceptible individuals that leads to skin sensitization. Although many chemicals have been reported as skin sensitizers, there have been very few rigorously validated QSAR models with defined applicability domains (AD) that were developed using a large group of chemically diverse compounds. In this study, we have aimed to compile, curate, and integrate the largest publicly available dataset related to chemically-induced skin sensitization, use this data to generate rigorously validated and QSAR models for skin sensitization, and employ these models as a virtual screening tool for identifying putative sensitizers among environmental chemicals. We followed best practices for model building and validation implemented with our predictive QSAR workflow using Random Forest modeling technique in combination with SiRMS and Dragon descriptors. The Correct Classification Rate (CCR) for QSAR models discriminating sensitizers from non-sensitizers was 71-88% when evaluated on several external validation sets, within a broad AD, with positive (for sensitizers) and negative (for non-sensitizers) predicted rates of 85% and 79% respectively. When compared to the skin sensitization module included in the OECD QSAR Toolbox as well as to the skin sensitization model in publicly available VEGA software, our models showed a significantly higher prediction accuracy for the same sets of external compounds as evaluated by Positive Predicted Rate, Negative Predicted Rate, and CCR. These models were applied to identify putative chemical hazards in the Scorecard database of possible skin or sense organ toxicants as primary candidates for experimental validation. PMID:25560674

  14. Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds

    SciTech Connect

    Alves, Vinicius M.; Muratov, Eugene; Fourches, Denis; Strickland, Judy; Kleinstreuer, Nicole; Tropsha, Alexander

    2015-04-15

    Repetitive exposure to a chemical agent can induce an immune reaction in inherently susceptible individuals that leads to skin sensitization. Although many chemicals have been reported as skin sensitizers, there have been very few rigorously validated QSAR models with defined applicability domains (AD) that were developed using a large group of chemically diverse compounds. In this study, we have aimed to compile, curate, and integrate the largest publicly available dataset related to chemically-induced skin sensitization, use this data to generate rigorously validated and QSAR models for skin sensitization, and employ these models as a virtual screening tool for identifying putative sensitizers among environmental chemicals. We followed best practices for model building and validation implemented with our predictive QSAR workflow using Random Forest modeling technique in combination with SiRMS and Dragon descriptors. The Correct Classification Rate (CCR) for QSAR models discriminating sensitizers from non-sensitizers was 71–88% when evaluated on several external validation sets, within a broad AD, with positive (for sensitizers) and negative (for non-sensitizers) predicted rates of 85% and 79% respectively. When compared to the skin sensitization module included in the OECD QSAR Toolbox as well as to the skin sensitization model in publicly available VEGA software, our models showed a significantly higher prediction accuracy for the same sets of external compounds as evaluated by Positive Predicted Rate, Negative Predicted Rate, and CCR. These models were applied to identify putative chemical hazards in the Scorecard database of possible skin or sense organ toxicants as primary candidates for experimental validation. - Highlights: • It was compiled the largest publicly-available skin sensitization dataset. • Predictive QSAR models were developed for skin sensitization. • Developed models have higher prediction accuracy than OECD QSAR Toolbox. • Putative chemical hazards in the Scorecard database were found using our models.

  15. 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

  16. 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- μm 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.

  17. 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

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

    2013-05-01

    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

  18. 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 Fátima Costa; Ribeiro, Dayana; Hirata, Raphael; Pacheco, Luis Gustavo Carvalho; Souza, Monica Cristina; dos Santos, Louisy Sanches; dos Santos, Cíntia 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

  19. 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.

  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, 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.

  1. 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.

  2. 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.

  3. 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,…

  4. 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.

  5. Genome-wide association study identifies HLA-A*3101 allele as a genetic risk factor for carbamazepine-induced cutaneous adverse drug reactions in Japanese population.

    PubMed

    Ozeki, Takeshi; Mushiroda, Taisei; Yowang, Amara; Takahashi, Atsushi; Kubo, Michiaki; Shirakata, Yuji; Ikezawa, Zenro; Iijima, Masafumi; Shiohara, Tetsuo; Hashimoto, Koji; Kamatani, Naoyuki; Nakamura, Yusuke

    2011-03-01

    An anticonvulsant, carbamazepine (CBZ), is known to show incidences of cutaneous adverse drug reactions (cADRs) including Stevens-Johnson syndrome (SJS), toxic epidermal necrolysis (TEN) and drug-induced hypersensitivity syndrome (DIHS). To identify a gene(s) susceptible to CBZ-induced cADRs, we conducted a genome-wide association study (GWAS) in 53 subjects with the CBZ-induced cADRs, including SJS, TEN and DIHS, and 882 subjects of a general population in Japan. Among the single nucleotide polymorphisms (SNPs) analyzed in the GWAS, 12 SNPs showed significant association with CBZ-induced cADRs, and rs1633021 showed the smallest P-value for association with CBZ-induced cADRs (P = 1.18 × 10⁻¹³). These SNPs were located within a 430 kb linkage disequilibrium block on chromosome 6p21.33, including the HLA-A locus. Thus, we genotyped the individual HLA-A alleles in 61 cases and 376 patients who showed no cADRs by administration of CBZ (CBZ-tolerant controls) and found that HLA-A*3101 was present in 60.7% (37/61) of the patients with CBZ-induced cADRs, but in only 12.5% (47/376) of the CBZ-tolerant controls (odds ratio = 10.8, 95% confidence interval 5.9-19.6, P = 3.64 × 10⁻¹⁵), implying that this allele has the 60.7% sensitivity and 87.5% specificity when we apply HLA-A*3101 as a risk predictor for CBZ-induced cADRs. Although DIHS is clinically distinguished from SJS and TEN, our data presented here have indicated that they share a common genetic factor as well as a common pathophysiological mechanism. Our findings should provide useful information for making a decision of individualized medication of anticonvulsants. PMID:21149285

  6. 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.

  7. 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.

  8. Intermediate vector bosons

    NASA Astrophysics Data System (ADS)

    Smondyrev, M. A.

    1983-12-01

    Physical discoveries underlying the theory of intermediate vector bosons are reviewed, with emphasis on the work of Fermi. The mass, generation, and decay of these particles are considered in the framework of Weinberg-Salam theory. Experiments aimed at the study of intermediate vector bosons are briefly discussed, with particular attention given to the LEP project.

  9. [Intermediate phenotype studies in psychiatric disorder].

    PubMed

    Hashimoto, Ryota

    2016-02-01

    The concept of intermediate phenotype was proposed by Dr. Weinberger of the National Institute of Mental Health (NIMH). The risk genes for mental disorders define intermediate phenotypes, neurobiological characteristics observed in psychiatric disorders, and intermediate phenotypes increase the risk of mental disorders. The author worked at Dr. Weinberger's laboratory, and after returning home, introduced the concept to Japan, creating a term "Chukanhyogengata" to translate "intermediate phenotype". Intermediate phenotype has been proposed as a tool for the identification of risk genes for mental disorders, spreading the concept as a biomarker for the bridging between genes and behaviors. Intermediate phenotype studies later became one of the main pillars of psychiatric research. As a large number of data and samples are needed for intermediate phenotype research, we built a research resource database that combines the brain phenotype and bioresources. We performed genome-wide association analysis of cognitive decline in schizophrenia and identified the DEGS2 gene using this sample. This research resource database was developed for a multicenter study by COCORO (Cognitive Genetics Collaborative Research Organization). COCORO carried out genome-wide association analysis of the gray matter volume of the superior temporal gyrus and identified genome-wide significant loci. In this paper, we introduce the concept and history of intermediate phenotype study of mental illness and the latest trends. We hope to contribute to the future development of mental illness research through translational research. PMID:27044135

  10. 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)

  11. A common intermediate for N2 formation in enzymes and zeolites: side-on Cu-nitrosyl complexes

    SciTech Connect

    Kwak, Ja Hun; Lee, Jong H.; Burton, Sarah D.; Lipton, Andrew S.; Peden, Charles HF; Szanyi, Janos

    2013-09-16

    Understanding the mechanisms of catalytic processes requires the identification of reaction centers and key intermediates, both of which are often achieved by the use of spectroscopic characterization tools. Due to the heterogeneity of active centers in heterogeneous catalysts, it is frequently difficult to identify the specific sites that are responsible for the overall activity. Furthermore, the simultaneous presence of a large number of surface species on the catalyst surface often poses a great challenge for the unambiguous determination of the relevant species in the reaction mechanism. In contrast, enzymes possess catalytically active centers with precisely defined coordination environments that are only able to accommodate intermediates relevant to the specific catalytic process. Here we show that side-on Cu+-NO+ complexes characterized by high magnetic field solid state magic angle spinning nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR) spectroscopies are the key intermediates in the selective catalytic reduction of NO over Cu-SSZ-13 zeolite catalysts. Analogous intermediates have been observed and characterized in nitrite reductase enzymes, and shown to be the critical intermediates in the formation of N2 for anaerobic ammonium oxidation reactions.[1] The identification of this key reaction intermediate, combined with the results of our prior kinetic studies, allows us to propose a new reaction mechanism for the selective catalytic reduction of NO with NH3 under oxygen-rich environments over Cu-SSZ-13 zeolites, a key reaction in automotive emission control. The authors acknowledge the US Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy/Vehicle Technologies Program for the support of this work. The research described in this paper was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US DOE by Battelle Memorial Institute.

  12. 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.

  13. Branching of keratin intermediate filaments.

    PubMed

    Nafeey, Soufi; Martin, Ines; Felder, Tatiana; Walther, Paul; Felder, Edward

    2016-06-01

    Keratin intermediate filaments (IFs) are crucial to maintain mechanical stability in epithelial cells. Since little is known about the network architecture that provides this stiffness and especially about branching properties of filaments, we addressed this question with different electron microscopic (EM) methods. Using EM tomography of high pressure frozen keratinocytes, we investigated the course of several filaments in a branching of a filament bundle. Moreover we found several putative bifurcations in individual filaments. To verify our observation we also visualized the keratin network in detergent extracted keratinocytes with scanning EM. Here bifurcations of individual filaments could unambiguously be identified additionally to bundle branchings. Interestingly, identical filament bifurcations were also found in purified keratin 8/18 filaments expressed in Escherichia coli which were reassembled in vitro. This excludes that an accessory protein contributes to the branch formation. Measurements of the filament cross sectional areas showed various ratios between the three bifurcation arms. This demonstrates that intermediate filament furcation is very different from actin furcation where an entire new filament is attached to an existing filament. Instead, the architecture of intermediate filament bifurcations is less predetermined and hence consistent with the general concept of IF formation. PMID:27039023

  14. Identifying Reactive Sites and Transport Limitations of Oxygen Reactions in Aprotic Lithium-O2 Batteries at the Stage of Sudden Death.

    PubMed

    Wang, Jiawei; Zhang, Yelong; Guo, Limin; Wang, Erkang; Peng, Zhangquan

    2016-04-18

    Discharging of the aprotic Li-O2 battery relies on the O2 reduction reaction (ORR) forming solid Li2 O2 in the positive electrode, which is often characterized by a sharp voltage drop (that is, sudden death) at the end of discharge, delivering a capacity far below its theoretical promise. Toward unlocking the energy capabilities of Li-O2 batteries, it is crucial to have a fundamental understanding of the origin of sudden death in terms of reactive sites and transport limitations. Herein, a mechanistic study is presented on a model system of Au|Li2 O2 |Li(+) electrolyte, in which the Au electrode was passivated with a thin Li2 O2 film by discharging to the state of sudden death. Direct conductivity measurement of the Li2 O2 film and in situ spectroscopic study of ORR using (18) O2 for passivation and (16) O2 for further discharging provide compelling evidence that ORR (and O2 evolution reaction as well) occurs at the buried interface of Au|Li2 O2 and is limited by electron instead of Li(+) and O2 transport. PMID:26970228

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. Identifying the major bacteria causing intramammary infections in individual milk samples of sheep and goats using traditional bacteria culturing and real-time polymerase chain reaction.

    PubMed

    Rovai, M; Caja, G; Salama, A A K; Jubert, A; Lázaro, B; Lázaro, M; Leitner, G

    2014-09-01

    Use of DNA-based methods, such as real-time PCR, has increased the sensitivity and shortened the time for bacterial identification, compared with traditional bacteriology; however, results should be interpreted carefully because a positive PCR result does not necessarily mean that an infection exists. One hundred eight lactating dairy ewes (56 Manchega and 52 Lacaune) and 24 Murciano-Granadina dairy goats were used for identifying the main bacteria causing intramammary infections (IMI) using traditional bacterial culturing and real-time PCR and their effects on milk performance. Udder-half milk samples were taken for bacterial culturing and somatic cell count (SCC) 3 times throughout lactation. Intramammary infections were assessed based on bacteria isolated in ≥2 samplings accompanied by increased SCC. Prevalence of subclinical IMI was 42.9% in Manchega and 50.0% in Lacaune ewes and 41.7% in goats, with the estimated milk yield loss being 13.1, 17.9, and 18.0%, respectively. According to bacteriology results, 87% of the identified single bacteria species (with more than 3 colonies/plate) or culture-negative growth were identical throughout samplings, which agreed 98.9% with the PCR results. Nevertheless, the study emphasized that 1 sampling may not be sufficient to determine IMI and, therefore, other inflammatory responses such as increased SCC should be monitored to identify true infections. Moreover, when PCR methodology is used, aseptic and precise milk sampling procedures are key for avoiding false-positive amplifications. In conclusion, both PCR and bacterial culture methods proved to have similar accuracy for identifying infective bacteria in sheep and goats. The final choice will depend on their response time and cost analysis, according to the requirements and farm management strategy. PMID:24996276

  20. THE EVOLVING INTERMEDIATE UNIT.

    ERIC Educational Resources Information Center

    ISENBERG, ROBERT M.

    THE TRADITIONAL CONCEPT OF THE INTERMEDIATE ADMINISTRATIVE SCHOOL UNIT IS THAT OF THE COUNTY SUPERINTENDENT OF SCHOOLS OPERATING AS AN ARM OF THE STATE, WITH REGULATORY POWERS AND RECORD KEEPING DUTIES AS WELL AS EDUCATIONAL LEADERSHIP FUNCTIONS. THE NEW TYPE OF UNIT THAT IS EVOLVING IS LARGELY SERVICE ORIENTED (I.E., SPECIAL EDUCATION, DATA…

  1. 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…

  2. 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…

  3. 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

  4. 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.

  5. 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; Zügner, Gábor L; Farkas, Mária; Illés, Ádám; Sarzyński, Dariusz; Rozgonyi, Tamás; Wang, Baoshan; Dóbé, Sándor

    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 2σ 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

  6. 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

  7. 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

  8. 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

  9. GFP's Mechanical Intermediate States

    PubMed Central

    Saeger, John; Hytönen, Vesa P.; Klotzsch, Enrico; Vogel, Viola

    2012-01-01

    Green fluorescent protein (GFP) mutants have become the most widely used fluorescence markers in the life sciences, and although they are becoming increasingly popular as mechanical force or strain probes, there is little direct information on how their fluorescence changes when mechanically stretched. Here we derive high-resolution structural models of the mechanical intermediate states of stretched GFP using steered molecular dynamics (SMD) simulations. These structures were used to produce mutants of EGFP and EYFP that mimic GFP's different mechanical intermediates. A spectroscopic analysis revealed that a population of EGFP molecules with a missing N-terminal α-helix was significantly dimmed, while the fluorescence lifetime characteristic of the anionic chromophore state remained unaffected. This suggests a mechanism how N-terminal deletions can switch the protonation state of the chromophore, and how the fluorescence of GFP molecules in response to mechanical disturbance might be turned off. PMID:23118864

  10. 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.

  11. 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.

  12. Statistical properties of multistep enzyme-mediated reactions

    SciTech Connect

    Nemenman, Ilya; Sinitsyn, Nikolai A; De Ronde, Wiet H; Daniels, Bryan C; Mugler, Andrew

    2008-01-01

    Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In this paper, we address this problem by solving the chemical master equations for various enzymatic reactions. We devise a perturbation theory analogous to that used in quantum mechanics that allows us to determine the first () and the second (variance) cumulants of the distribution of created product molecules as a function of the substrate concentration and the kinetic rates of the intermediate processes. The mean product flux V=d/dt (or 'dose-response' curve) and the Fano factor F=variance/ are both realistically measurable quantities, and while the mean flux can often appear the same for different reaction types, the Fano factor can be quite different. This suggests both qualitative and quantitative ways to discriminate between different reaction schemes, and we explore this possibility in the context of four sample multistep enzymatic reactions. We argue that measuring both the mean flux and the Fano factor can not only discriminate between reaction types, but can also provide some detailed information about the internal, unobserved kinetic rates, and this can be done without measuring single-molecule transition events.

  13. 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...

  14. The intermediate endpoint effect in logistic and probit regression

    PubMed Central

    MacKinnon, DP; Lockwood, CM; Brown, CH; Wang, W; Hoffman, JM

    2010-01-01

    Background An intermediate endpoint is hypothesized to be in the middle of the causal sequence relating an independent variable to a dependent variable. The intermediate variable is also called a surrogate or mediating variable and the corresponding effect is called the mediated, surrogate endpoint, or intermediate endpoint effect. Clinical studies are often designed to change an intermediate or surrogate endpoint and through this intermediate change influence the ultimate endpoint. In many intermediate endpoint clinical studies the dependent variable is binary, and logistic or probit regression is used. Purpose The purpose of this study is to describe a limitation of a widely used approach to assessing intermediate endpoint effects and to propose an alternative method, based on products of coefficients, that yields more accurate results. Methods The intermediate endpoint model for a binary outcome is described for a true binary outcome and for a dichotomization of a latent continuous outcome. Plots of true values and a simulation study are used to evaluate the different methods. Results Distorted estimates of the intermediate endpoint effect and incorrect conclusions can result from the application of widely used methods to assess the intermediate endpoint effect. The same problem occurs for the proportion of an effect explained by an intermediate endpoint, which has been suggested as a useful measure for identifying intermediate endpoints. A solution to this problem is given based on the relationship between latent variable modeling and logistic or probit regression. Limitations More complicated intermediate variable models are not addressed in the study, although the methods described in the article can be extended to these more complicated models. Conclusions Researchers are encouraged to use an intermediate endpoint method based on the product of regression coefficients. A common method based on difference in coefficient methods can lead to distorted conclusions regarding the intermediate effect. PMID:17942466

  15. Oxidation of sulfoxides and arsenic(III) in corrosion of nanoscale zero valent iron by oxygen: evidence against ferryl ions (Fe(IV)) as active intermediates in Fenton reaction.

    PubMed

    Pang, Su-Yan; Jiang, Jin; Ma, Jun

    2011-01-01

    Previous studies have shown that the corrosion of zerovalent iron (ZVI) by oxygen (O(2)) via the Fenton reaction can lead to the oxidation of various organic and inorganic compounds. However, the nature of the oxidants involved (i.e., ferryl ion (Fe(IV)) versus hydroxyl radical (HO(•))) is still a controversial issue. In this work, we reevaluated the relative importance of these oxidants and their role in As(III) oxidation during the corrosion of nanoscale ZVI (nZVI) in air-saturated water. It was shown that Fe(IV) species could react with sulfoxides (e.g., dimethyl sulfoxide, methyl phenyl sulfoxide, and methyl p-tolyl sulfoxide) through a 2-electron transfer step producing corresponding sulfones, which markedly differed from their HO(•)-involved products. When using these sulfoxides as probe compounds, the formation of oxidation products indicative of HO(•) but no generation of sulfone products supporting Fe(IV) participation were observed in the nZVI/O(2) system over a wide pH range. As(III) could be completely or partially oxidized by nZVI in air-saturated water. Addition of scavengers for solution-phase HO(•) and/or Fe(IV) quenched As(III) oxidation at acidic pH but had little effect as solution pH increased, highlighting the importance of the heterogeneous iron surface reactions for As(III) oxidation at circumneutral pH. PMID:21133375

  16. 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.

  17. 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…

  18. 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

  19. 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…

  20. 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.

  1. Conformational dynamics through an intermediate

    NASA Astrophysics Data System (ADS)

    Garai, Ashok; Zhang, Yaojun; Dudko, Olga K.

    2014-04-01

    The self-assembly of biological and synthetic nanostructures commonly proceeds via intermediate states. In living systems in particular, the intermediates have the capacity to tilt the balance between functional and potentially fatal behavior. This work develops a statistical mechanical treatment of conformational dynamics through an intermediate under a variable force. An analytical solution is derived for the key experimentally measurable quantity—the distribution of forces at which a conformational transition occurs. The solution reveals rich kinetics over a broad range of parameters and enables one to locate the intermediate and extract the activation barriers and rate constants.

  2. 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.

  3. 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

  4. Masonry. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Thompson, Moses

    Several intermediate performance objectives and corresponding criterion measures are listed for each of 13 terminal objectives for an intermediate masonry course. These materials, developed for a two-semester (3 hours daily) course, are designed to provide the student with the skills and knowledge necessary for entry level employment in the field…

  5. 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)…

  6. 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

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

    PubMed

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

    2007-09-01

    Aromatic compounds such as toluene and xylene are major components of many fuels. Accurate kinetic mechanisms for the combustion of toluene are, however, incomplete, as they do not accurately model experimental results such as strain rates and ignition times and consistently underpredict conversion. Current kinetic mechanisms for toluene combustion neglect the reactions of the methylphenyl radicals, and we believe that this is responsible, in part, for the shortcomings of these models. We also demonstrate how methylphenyl radical formation is important in the combustion and pyrolysis of other alkyl-substituted aromatic compounds such as xylene and trimethylbenzene. We have studied the oxidation reactions of the methylphenyl radicals with O2 using computational ab initio and density functional theory methods. A detailed reaction submechanism is presented for the 2-methylphenyl radical + O2 system, with 16 intermediates and products. For each species, enthalpies of formation are calculated using the computational methods G3 and G3B3, with isodesmic work reactions used to minimize computational errors. Transition states are calculated at the G3B3 level, yielding high-pressure limit elementary rate constants as a function of temperature. For the barrierless methylphenyl + O2 and methylphenoxy + O association reactions, rate constants are determined from variational transition state theory. Multichannel, multifrequency quantum Rice-Ramsperger-Kassel (qRRK) theory, with master equation analysis for falloff, provides rate constants as a function of temperature and pressure from 800 to 2400 K and 1 x 10(-4) to 1 x 10(3) atm. Analysis of our results shows that the dominant pathways for reaction of the three isomeric methylphenyl radicals is formation of methyloxepinoxy radicals and subsequent ring opening to methyl-dioxo-hexadienyl radicals. The next most important reaction pathway involves formation of methylphenoxy radicals + O in a chain branching process. At lower temperatures, the formation of stabilized methylphenylperoxy radicals becomes significant. A further important reaction channel is available only to the 2-methylphenyl isomer, where 6-methylene-2,4-cyclohexadiene-1-one (ortho-quinone methide, o-QM) is produced via an intramolecular hydrogen transfer from the methyl group to the peroxy radical in 2-methylphenylperoxy, with subsequent loss of OH. The decomposition of o-QM to benzene + CO reveals a potentially important new pathway for the conversion of toluene to benzene during combustion. A number of the important products of toluene combustion proposed in this study are known to be precursors of polyaromatic hydrocarbons that are involved in soot formation. Reactions leading to the important unsaturated oxygenated intermediates identified in this study, and the further reactions of these intermediates, are not included in current aromatic oxidation mechanisms. PMID:17696501

  8. 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

  9. Modeling the Reaction of Fe Atoms with CCl4

    SciTech Connect

    Camaioni, Donald M.; Ginovska, Bojana; Dupuis, Michel

    2009-01-05

    The reaction of zero-valent iron with carbon tetrachloride (CCl4) in gas phase was studied using density functional theory. Temperature programmed desorption experiments over a range of Fe and CCl4 coverages on a FeO(111) surface, demonstrate a rich surface chemistry with several reaction products (C2Cl4, C2Cl6, OCCl2, CO, FeCl2, FeCl3) observed. The reactivity of Fe and CCl4 was studied under three stoichiometries, one Fe with one CCl4, one Fe with two CCl4 molecules and two Fe with one CCl4, modeling the environment of the experimental work. The electronic structure calculations give insight into the reactions leading to the experimentally observed products and suggest that novel Fe-C-Cl containing species are important intermediates in these reactions. The intermediate complexes are formed in highly exothermic reactions, in agreement with the experimentally observed reactivity with the surface at low temperature (30 K). This initial survey of the reactivity of Fe with CCl4 identifies some potential reaction pathways that are important in the effort to use Fe nano-particles to differentiate harmful pathways that lead to the formation of contaminants like chloroform (CHCl3) from harmless pathways that lead to products such as formate (HCO2-) or carbon oxides in water and soil. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  10. Photocatalytic mineralization of codeine by UV-A/TiO₂--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 μg/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

  11. Surface intermediates in selective olefin oxidation and ammoxidation

    SciTech Connect

    Burrington, J.D.; Kartisek, C.T.; Grasselli, R.K.

    1983-02-01

    An investigation of the mechanism of the oxidation and ammoxidation of propylene was made. The products of the above reactions were acrylonitrile and acrolein for ammoxidation and oxidation, respectively. Also, the ammoxidation and oxidation of allyl alcohol, allyl amine, and their allylic deuterium substituted analogues was studied. It was concluded that oxidation and ammoxidation of propylene have the same rate determining step. Other conclusions about the reaction intermediates were also made.

  12. 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.

  13. 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.

  14. 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.

  15. Moving beyond Intermediate English Proficiency

    ERIC Educational Resources Information Center

    Jewell, Mary

    2009-01-01

    Too many English learners get stuck at intermediate levels of English language proficiency. In this article, teacher Mary Jewell describes how she uses literature and scaffolds to ensure that students develop academic language.

  16. Tachyon field in intermediate inflation

    SciTech Connect

    Campo, Sergio del; Herrera, Ramon; Toloza, Adolfo

    2009-04-15

    The tachyonic inflationary universe model in the context of intermediate inflation is studied. General conditions for this model to be realizable are discussed. In the slow-roll approximation, we describe in great detail the characteristics of this model.

  17. Silver-Catalyzed Allylation of Ketones and Intramolecular Cyclization through Carbene Intermediates from Cyclopropenes Under Ambient Conditions.

    PubMed

    Nakano, Takeo; Endo, Kohei; Ukaji, Yutaka

    2016-03-01

    Tandem C-C bond formation was achieved through silver-catalyzed ring-opening of cyclopropenes via carbene intermediates. The reaction of cyclopropenes in the presence of a silver catalyst gave indene derivatives under ambient conditions. In contrast, the insertion of organozinc reagents to silver carbene or allylic cation intermediates afforded allylmetal intermediates for the tandem allylation of carbonyl compounds. PMID:26611195

  18. Identifying harms.

    PubMed

    Harrosh, Shlomit

    2012-11-01

    Moral disagreements often revolve around the issue of harm to others. Identifying harms, however, is a contested enterprise. This paper provides a conceptual toolbox for identifying harms, and so possible wrongdoing, by drawing several distinctions. First, I distinguish between four modes of human vulnerability, forming four ways in which one can be in a harmed state. Second, I argue for the intrinsic disvalue of harm and so distinguish the presence of harm from the fact that it is instrumental to or constitutive of a valued act, practice or way of life. Finally, I distinguish between harm and wrongdoing, arguing that while harm is a normative concept requiring justification, not all harmed states are automatically unjustified. The advantage of this view is that it refocuses the moral debate on the normative issues involved while establishing a common basis to which both sides can agree: the presence of harm to others. PMID:21434956

  19. Learning to Predict Chemical Reactions

    PubMed Central

    Kayala, Matthew A.; Azencott, Chloé-Agathe; Chen, Jonathan H.

    2011-01-01

    Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles respectively are not high-throughput, are not generalizable or scalable, or lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry dataset consisting of 1630 full multi-step reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval, problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of non-productive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system 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

  20. 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

  1. 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.

  2. 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

  3. Suprabasal Overexpression of the hsRPB7 Gene in Psoriatic Epidermis as Identified by a Reverse Transcriptase-Polymerase Chain Reaction Differential Display Model Comparing Psoriasis Plaque Tissue with Peritonsillar Mucosa

    PubMed Central

    Böckelmann, Raik; Neugebauer, Peter; Djahan Paseban, Nuschin; Hüttemann, Martin; Gollnick, Harald; Bonnekoh, Bernd

    2001-01-01

    In psoriasis an etiopathogenetic vicious circle is nowadays hypothesized that the disease is triggered by skin-specific autoantigen structures, the expression and accessibility of which are positively correlated with the intensity of the hyperproliferation and inflammation in the epidermopapillary compartment driven by autoreactive T cells. Despite the close microanatomical relation between skin and mucosa, clinicians have always been intrigued by the observation that psoriatic affection of the mucosa, if at all existing, is only seen as very rare events in the lips and tongue sparing buccopharyngeal sites. This prompted us to establish an experimental model system comparing psoriatic-involved skin and peritonsillar mucosa from tonsillectomies by a reverse transcriptase-polymerase chain reaction/differential display strategy. Among more than 60 cDNA species to be displayed in psoriasis, but missing in peritonsillar mucosa, one species was identified as coding for the RNA polymerase IIA seventh subunit (hsRPB7 gene) as a most critical factor for DNA to RNA transcription. Immunohistochemistry showed a hitherto unknown, distinctive pattern of hsRPB7 expression that was 1) tissue type-dependent with a surplus in skin keratinocytes and a near absence in peritonsillar mucosa, 2) tightly regulated by the keratinocyte differentiation process with a sharp suprabasal up-regulation in contrast to a basal down-regulation, and 3) substantially augmented in psoriatic-involved skin as compared to normal and psoriatic uninvolved skin. Keratinocytes of actinic keratoses also showed a strong hsRPB7 expression that however did not strictly spare the basal cell layer presumably reflecting the disturbed intraepidermal stratification because of the premalignant status of these precancerous lesions. PMID:11159173

  4. 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.

  5. 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.

  6. 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-β-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-β-ketopropionate analog as the substrate. X was identified as the 6-methyl-β-hydroxypropionate analog of Mg-Proto Me by conversion to the dimethyl ester with CH2N2 and comparison with authentic 6-β-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-β-hydroxy and the 6-β-ketopropionate esters in agreement with earlier suggestions. PMID:16664481

  7. 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, 25°C, an H2O2 dosage of 9.74×10−3 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 (ΔE) 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

  8. 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.

  9. Keto-Enol Thermodynamics of Breslow Intermediates.

    PubMed

    Paul, Mathias; Breugst, Martin; Neudörfl, Jörg-Martin; Sunoj, Raghavan B; Berkessel, Albrecht

    2016-04-20

    Breslow intermediates, first postulated in 1958, are pivotal intermediates in carbene-catalyzed umpolung. Attempts to isolate and characterize these fleeting amino enol species first met with success in 2012 when we found that saturated bis-Dipp/Mes imidazolidinylidenes readily form isolable, though reactive diamino enols with aldehydes and enals. In contrast, triazolylidenes, upon stoichiometric reaction with aldehydes, gave exclusively the keto tautomer, and no isolable enol. Herein, we present the synthesis of the "missing" keto tautomers of imidazolidinylidene-derived diamino enols, and computational thermodynamic data for 15 enol-ketone pairs derived from various carbenes/aldehydes. Electron-withdrawing substituents on the aldehyde favor enol formation, the same holds for N,N'-Dipp [2,6-di(2-propyl)phenyl] and N,N'-Mes [2,4,6-trimethylphenyl] substitution on the carbene component. The latter effect rests on stabilization of the diamino enol tautomer by Dipp substitution, and could be attributed to dispersive interaction of the 2-propyl groups with the enol moiety. For three enol-ketone pairs, equilibration of the thermodynamically disfavored tautomer was attempted with acids and bases but could not be effected, indicating kinetic inhibition of proton transfer. PMID:26876370

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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)…

  15. 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…

  16. Music Handbook for Intermediate Grades.

    ERIC Educational Resources Information Center

    Bowman, Doris; And Others

    GRADES OR AGES: Intermediate Grades. SUBJECT MATTER: Music. ORGANIZATION AND PHYSICAL APPEARANCE: This guide has been developed to help the classroom teacher supplement the program of the music specialist. There are three main sections: Section 1 includes general concepts of music that the specialists will cover and has subsections on rhythm,…

  17. 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…

  18. 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

  19. Support workers in intermediate care.

    PubMed

    Nancarrow, Susan A; Shuttleworth, Penny; Tongue, Alison; Brown, Lucy

    2005-07-01

    Despite the proliferation of support worker roles in the UK, little is known about their actual numbers, employment conditions or levels of training. Intermediate care services appear to be an important employer of support workers, but the diversity of intermediate care services makes the task of understanding support worker roles even more complex. This paper presents data from 33 services which were involved in an NHS Modernisation Agency's Changing Workforce Programme project, the Accelerated Development Programme for Support Workers in Intermediate Care in England. Within this project, the main employers of support workers were primary care trusts and/or social services. Participating intermediate care teams were involved in admission avoidance, assisted discharge and reablement, or combinations of these services, and the majority of care was provided in the patient's own home. The 33 services employed 794 support workers and 368 professionally qualified staff. The mean ratio of professionally qualified staff to support workers was 0.95 (range = 0-4.9, SD = 1.05). Support worker roles included multidisciplinary working, meeting rehabilitation needs, providing personal care and enablement. Team leaders included nurses, social workers, physiotherapists, professional managers, home carers and support workers. The most commonly reported sources of support worker training were National Vocational Qualifications and in-house training. In 80% of the services, at least half of the support workers had a qualification. Three models of supervision emerged across the services: the allocation of a mentor; team supervision; and formal and informal line management. These findings illustrate the diversity of employment of support workers in intermediate care. The variations in training, supervision and skill mix have implications for clinical governance and support worker regulation. The employment of support worker staff jointly across health and social care raises cross-boundary issues around employment contracts and pay. PMID:15969705

  20. Reaction Mechanism of Guanosine Triphosphate Hydrolysis by the Vision-Related Protein Complex Arl3-RP2.

    PubMed

    Khrenova, Maria G; Kots, Ekaterina D; Nemukhin, Alexander V

    2016-04-28

    Complexes of small GTPases with GTPase-activating proteins have been intensively studied with the main focus on the complex of H-Ras with p120GAP (Ras-GAP). The detailed mechanism of GTP hydrolysis is still unresolved. To clarify it, we calculated the energy profile of GTP hydrolysis in the active site of a recently characterized vision-related member of this family, the Arl3-RP2 complex. The mechanism suggested in this study retains the main features of GTP hydrolysis by the Ras-GAP complex, but the relative energies of the corresponding intermediates are different and an additional intermediate exists in the Arl3-RP2 complex compared with the Ras-GAP. These differences arise from small deviations in the catalytic arginine conformation of the active site. In the Arl3-RP2 complex, the first two intermediates, corresponding to the Pγ-Oβγ bond cleavage and the glutamine-assisted proton transfer, are almost isoenergetic with the ES complex. Numerical simulations of the kinetic curves demonstrate that the concentrations of these intermediates are comparable with that of ES during the reaction. The calculated IR spectra reveal specific vibrational bands, corresponding to these intermediates. These specific features of the Arl3-RP2 complex open the opportunity to identify spectroscopically two more reaction intermediates in GTP hydrolysis in addition to the ES and EP complexes. PMID:27043216

  1. Intermediate structure in the photoexcitation of 77Sem, 79Brm, and 137Bam

    NASA Astrophysics Data System (ADS)

    Carroll, J. J.; Collins, C. B.; Heyde, K.; Huber, M.; von Neumann-Cosel, P.; Ponomarev, V. Yu.; Richmond, D. G.; Richter, A.; Schlegel, C.; Sinor, T. W.; Taylor, K. N.

    1993-11-01

    Continuing the systematic investigation into the photoexcitation of isomers over wide mass and energy ranges, the production of 77Sem, 79Brm, and 137Bam was studied with the bremsstrahlung facility at the superconducting Darmstadt linear accelerator. These isomers have half-lives on the order of seconds. Excitation functions were measured for the (γ,γ') reactions populating the metastable states for energies of 2-7 MeV and the important intermediate states were identified. Nuclear structure calculations with the quasiparticle-phonon model for 79Br and the particle- (hole-) core coupling approach for 137Ba gave satisfactory descriptions for the strength and position of the dominant mediating levels. Admixtures of fragmented outershell single-particle strength shifted to low energies were identified as essential features of the wave functions of those states. Intermediate states in 77Se displayed very large strengths compared to other isomers in the same mass region, providing further support for the correlation between integrated cross sections and ground state deformations recently discovered in the A=160-200 mass region. Such an enhancement would considerably improve the feasibility of a gamma-ray laser based on the sudden deexcitation of isomeric populations in deformed nuclei.

  2. Ultrasound promoted reaction of Rhodamine B with sodium hypochlorite using sonochemical and dental ultrasonic instruments.

    PubMed

    Tiong, T Joyce; Price, Gareth J

    2012-03-01

    The sonochemical acceleration of bleaching of Rhodamine B by sodium hypochlorite has been studied using ultrasound intensities in the range 0-7 W cm(-2). Using a 20 kHz ultrasonic horn, it was shown that ultrasound could significantly shorten the treatment time and/or the concentration of hypochlorite required for the reaction. A number of intermediate species formed during the reaction have been identified. It was demonstrated that the same sonochemical reactions occur during the use of dental ultrasound instruments of the type used in endodontics where hypochlorite solutions act as disinfectants. Results showed pseudo-first order degradation kinetics for the degradation of Rhodamine B for both types of source. Both the distribution of cavitation and the resulting bleaching reactions were dependent on the design of the tips. The bleaching reaction can therefore be used to characterise the behaviour of dental instruments and aid in the optimisation of their performance. PMID:21868274

  3. 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

  4. 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

  5. Substrate radical intermediates in soluble methane monooxygenase

    SciTech Connect

    Liu Aimin; Jin Yi; Zhang Jingyan; Brazeau, Brian J.; Lipscomb, John D. . E-mail: lipsc001@umn.edu

    2005-12-09

    EPR spin-trapping experiments were carried out using the three-component soluble methane monooxygenase (MMO). Spin-traps 5,5-dimethyl-1-pyrroline N-oxide (DMPO), {alpha}-4-pyridyl-1-oxide N-tert-butylnitrone (POBN), and nitrosobenzene (NOB) were used to investigate the possible formation of substrate radical intermediates during catalysis. In contrast to a previous report, the NADH-coupled oxidations of various substrates did not produce any trapped radical species when DMPO or POBN was present. However, radicals were detected by these traps when only the MMO reductase component and NADH were present. DMPO and POBN were found to be weak inhibitors of the MMO reaction. In contrast, NOB is a strong inhibitor for the MMO-catalyzed nitrobenzene oxidation reaction. When NOB was used as a spin-trap in the complete MMO system with or without substrate, EPR signals from an NOB radical were detected. We propose that a molecule of NOB acts simultaneously as a substrate and a spin-trap for MMO, yielding the long-lived radical and supporting a stepwise mechanism for MMO.

  6. Radical SAM catalysis via an organometallic intermediate with an Fe-[5'-C]-deoxyadenosyl bond.

    PubMed

    Horitani, Masaki; Shisler, Krista; Broderick, William E; Hutcheson, Rachel U; Duschene, Kaitlin S; Marts, Amy R; Hoffman, Brian M; Broderick, Joan B

    2016-05-13

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to cleave SAM to initiate diverse radical reactions. These reactions are thought to involve the 5'-deoxyadenosyl radical intermediate, which has not yet been detected. We used rapid freeze-quenching to trap a catalytically competent intermediate in the reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme. Characterization of the intermediate by electron paramagnetic resonance and (13)C, (57)Fe electron nuclear double-resonance spectroscopies reveals that it contains an organometallic center in which the 5' carbon of a SAM-derived deoxyadenosyl moiety forms a bond with the unique iron site of the [4Fe-4S] cluster. Discovery of this intermediate extends the list of enzymatic bioorganometallic centers to the radical SAM enzymes, the largest enzyme superfamily known, and reveals intriguing parallels to B12 radical enzymes. PMID:27174986

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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…

  13. Transformation and removal of bisphenol A from aqueous phase via peroxidase mediated oxidative coupling reactions: efficacy, products, and pathways.

    PubMed

    Huang, Qingguo; Weber, Walter J

    2005-08-15

    A systematic investigation of the feasibility of and mechanisms for transformation and removal of bisphenol A (BPA) from aqueous phase via oxidative coupling mediated by horseradish peroxidase is described. It is demonstrated that BPA can be effectively transformed into precipitable solid products in HRP-mediated oxidative coupling reactions. A total of 13 reaction intermediates and products are identified using LC/MS and GC/MS techniques, and with the help of ab initio molecular modeling, detailed reaction pathways are proposed. It is postulated that two BPA radicals are coupled primarily by the interaction of an oxygen atom on one radical and propyl-substituted aromatic carbon atom on another, followed by elimination of an isopropylphenol carboncation. All intermediates or products detected can be interpreted as resulting from either coupling or substitution reactions between BPA and other intermediates or products. The efficacy of the reaction at low substrate concentrations is demonstrated using a sensitive analytical procedure involving solid-phase extractions. The results suggest that catalyzed oxidative coupling reactions may be important natural transformation pathways for estrogenic phenolic compounds and indicate their potential use as an efficient means for removal of estrogenicity from waters and wastewaters. PMID:16173560

  14. Study of entropy in intermediate-energy heavy ion collisions

    NASA Astrophysics Data System (ADS)

    Xiao-Ji, Zhang; Wen-Jun, Guo; Xian-Jie, Li; Kuo, Wang

    2016-03-01

    Using the isospin-dependent quantum molecular dynamics model, the entropy of an intermediate-energy heavy ion collision system after the reaction and the number of deuteronlike and protonlike particles produced in the collision is calculated. In the collision, different parameters are used and the mass number used here is from 40 to 93 at incident energy from 150 MeV to 1050 MeV. We build a new model in which the density distribution of the reaction product is used to calculate the size of the entropy. The entropy calculated with this model is in good agreement with experimental values. Our data reveals that with the increase of the neutron-proton ratio and impact parameter, the entropy of the reaction system decreases, and it increases with the increase of system mass and reaction energy.

  15. Detailed Mechanism of the Autoxidation of N-hydroxyurea Catalyzed by a Superoxide Dismutase Mimic Mn(III) Porphyrin: Formation of the Nitrosylated Mn(II) Porphyrin as an Intermediate

    PubMed Central

    Kalmár, József; Biri, Bernadett; Bányai, István; Budimir, Ana; Biruš, Mladen; Batinić-Haberle, Ines; Fábián, István

    2012-01-01

    The in vitro autoxidation of N-hydroxyurea (HU) is catalyzed by MnIIITTEG-2-PyP5+, a synthetic water soluble Mn(III) porphyrin which is also a potent mimic of the enzyme superoxide dismutase. The detailed mechanism of the reaction is deduced from kinetic studies under basic conditions mostly based on data measured at pH = 11.7 but also including some pH-dependent observations in the pH range 9 – 13. The major intermediates were identified by UV-vis spectroscopy and electrospray ionization mass spectrometry. The reaction starts with a fast axial coordination of HU to the metal center of MnIIITTEG-2-PyP5+, which is followed by a ligand-to-metal electron transfer to get MnIITTEG-2-PyP4+ and the free radical derived from HU (HU•). Nitric oxide (NO) and nitroxyl (HNO) are minor intermediates. The major pathway for the formation of the most significant intermediate, the {MnNO} complex of MnIITTEG-2-PyP4+, is the reaction of MnIITTEG-2-PyP4+ with NO. We have confirmed that the autoxidation of the intermediates open alternative reaction channels, and the process finally yields NO2− and the initial MnIIITTEG-2-PyP5+. The photochemical release of NO from the {MnNO} intermediate was also studied. Kinetic simulations were performed to validate the deduced rate constants. The investigated reaction has medical implications: the accelerated production of NO and HNO from HU may be utilized for therapeutic purposes. PMID:22911446

  16. 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.

  17. Superasymmetric fission of heavy nuclei induced by intermediate-energy protons

    NASA Astrophysics Data System (ADS)

    Deppman, A.; Andrade-II, E.; Guimarães, V.; Karapetyan, G. S.; Tavares, O. A. P.; Balabekyan, A. R.; Demekhina, N. A.; Adam, J.; Garcia, F.; Katovsky, K.

    2013-12-01

    In this work we present the results for the investigation of intermediate-mass fragment (IMF) production with the proton-induced reaction at 660 MeV on 238U and 237Np target. The data were obtained with the LNR Phasotron U-400M Cyclotron at Joint Institute for Nuclear Research (JINR), Dubna, Russia. A total of 93 isotopes, in the mass range of 30identified with high precision. The fragment production cross sections were obtained by means of the induced-activation method in an off-line analysis. Mass-yield distributions were derived from the data and compared with the results of the simulation code CRISP for multimodal fission. A discussion of the superasymmetric fragment production mechanism is also given.

  18. 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

  19. 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

  20. 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.

  1. 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)…

  2. 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…

  3. 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.'

  4. Role of Intermediate Filaments in Vesicular Traffic.

    PubMed

    Margiotta, Azzurra; Bucci, Cecilia

    2016-01-01

    Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway. PMID:27120621

  5. 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

  6. 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

  7. 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

  8. 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.

  9. Complexity, universality and intermediate degrees

    NASA Astrophysics Data System (ADS)

    Joosten, Joost J.

    2012-09-01

    This paper is a philosophical account of complexity versus universality. It seems sustainable to equate universal systems to complex systems or at least to potentially complex systems. Post's problem on the existence of (natural) intermediate degrees (between decidable and universal Σ01) then finds its analog in the Principle of Computional Equivalence (PCE). In this abstract we address possible driving forces -if any- behind PCE. Both the natural aspects as well as the cognitive ones are investigated. We postulate a principle GNS that we call the Generalized Natural Selection principle that together with the Church-Turing thesis is seen to be equivalent in a sense to a weak version of PCE.

  10. Intermediate sanctions for healthcare organizations.

    PubMed

    Samuels, David G; Shoretz, Morris

    2002-09-01

    Intermediate sanctions legislation requires that tax-exempt providers take steps to ensure that their senior staff members are compensated at fair-market value. A first-time violation could subject an individual to an excise tax of 25 percent of the compensation amount deemed to be excess benefit. Failure to correct the violation could subject the individual to an excise tax of 200 percent of the excess benefit. Tax-exempt organizations may invoke a rebuttable presumption of reasonableness that compensation levels are appropriate. Tax-exempt providers should refer to IRS guidance regarding steps to ensuring compliance. PMID:12235978

  11. Reactions of orthophthalaldehyde with ammonia and 2-aminoethanol.

    PubMed

    Kulla, Eliona; Zuman, Petr

    2008-10-21

    Reactions of orthophthalaldehyde (OPA) with amines are used in the determination of amino acids and in applications of OPA as a biocide. To contribute to the understanding of processes involved, the reactions of OPA with ammonia, which are conveniently slow, were studied. In a set of rapidly established equilibria, the 1,3-dihydroxyindole and the product of its dehydration are formed (Scheme 1). The individual equilibria were identified and equilibrium constants determined using DC polarography and UV spectra. The ring closure involves the carbinolamine; the imine formation is a side reaction. Both the ring formation and the dehydration of the carbinolamine are generally acid catalyzed. In the finally established overall equilibria between OPA and the isoindole derivative, the concentrations of intermediates are negligible. The same applies to the reaction of OPA with 2-aminoethanol, in which the initial formation of a carbinolamine and of an imine are too fast to be followed. Very slow reactions taking place during periods of hours or days, which probably result in the formation of dimeric species, have also been observed. This contribution demonstrates the advantages of combinations of polarographic and spectrophotometric techniques in the investigation of complex reactions of some organic compounds. PMID:18843407

  12. 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.

  13. White Dwarfs in Intermediate Polars

    NASA Astrophysics Data System (ADS)

    Belle, Kunegunda E.; Sion, E. M.

    2009-01-01

    Intermediate polars (IPs), magnetic cataclysmic variables (CVs) in which the white dwarf (WD) has an intermediate strength magnetic field (B< 5 MG), present an interesting laboratory for the study of the evolution of CVs as they contain elements of both non-magnetic and magnetic systems. Do magnetic CVs and IPs evolve in the same manner as non-magnetic systems? One answer in this puzzle may come from understanding the nature of the white dwarf in a magnetic CV. Standard CV evolution theory predicts a white dwarf temperature for a given CV orbital period and accretion rate. By investigating the temperature of white dwarfs in IPs and comparing the temperatures to those predicted from theory, we can learn where IPs fit into the model of CV evolution. Here we present the results of our continued study of the nature of WDs in IPs. We compare temperatures derived from model fits to UV spectra with temperatures calculated based on the accretion rate and binary orbital period. Our preliminary results indicate that IPs follow the general trend of magnetic CVs containing cooler WDs than non-magnetic CVs.

  14. 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

  15. 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.

  16. 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.

  17. Identification of combustion intermediates in low-pressure premixed pyridine/oxygen/argon flames.

    PubMed

    Tian, Zhenyu; Li, Yuyang; Zhang, Taichang; Zhu, Aiguo; Qi, Fei

    2008-12-25

    Combustion intermediates of two low-pressure premixed pyridine/oxygen flames with respective equivalence ratios of 0.56 (C/O/N = 1:4.83:0.20) and 2.10 (C/O/N = 1:1.29:0.20) have been identified with tunable synchrotron vacuum ultraviolet (VUV) photoionization and molecular-beam mass spectrometry techniques. About 80 intermediates in the rich flame and 60 intermediates in the lean flame, including nitrogenous, oxygenated, and hydrocarbon intermediates, have been identified by measurements of photoionization mass spectra and photoionization efficiency spectra. Some radicals and new nitrogenous intermediates are identified in the present work. The experimental results are useful for studying the conversion of volatile nitrogen compounds and understanding the formation mechanism of NO(x) in flames of nitrogenous fuels. PMID:19053546

  18. Transiting Sub-stellar companions of Intermediate-mass stars

    NASA Astrophysics Data System (ADS)

    Sebastian, Daniel; Guenther, Eike W.; Heber, Ulrich; Geier, Stephan; Grziwa, Sascha

    2015-09-01

    We use the CoRoT-survey to search for transiting close-in planets of intermediate-mass stars (M* = 1.3 - 2.1 M⊙). We present recent results of our survey. RV-surveys and direct imaging campaigns showed, that intermediate-mass main-sequence stars have more massive planets then solar-like stars. Even brown dwarfs have been found. In our study we concentrated on short-period planets for which a mass-determination is possible. The detection of close-in planets of intermediate-mass stars put strong constraints on the timescales of the formation and migration. We already have identified transiting Jupiter-like planet candidates with short orbital periods and observed these candidates with high-resolution echelle-spectrographs at various Telescopes.

  19. Caspase cleavage of vimentin disrupts intermediate filaments and promotes apoptosis.

    PubMed

    Byun, Y; Chen, F; Chang, R; Trivedi, M; Green, K J; Cryns, V L

    2001-05-01

    Caspases are key mediators of apoptosis. Using a novel expression cloning strategy we recently developed to identify cDNAs encoding caspase substrates, we isolated the intermediate filament protein vimentin as a caspase substrate. Vimentin is preferentially cleaved by multiple caspases at distinct sites in vitro, including Asp85 by caspases-3 and -7 and Asp259 by caspase-6, to yield multiple proteolytic fragments. Vimentin is rapidly proteolyzed by multiple caspases into similar sized fragments during apoptosis induced by many stimuli. Caspase cleavage of vimentin disrupts its cytoplasmic network of intermediate filaments and coincides temporally with nuclear fragmentation. Moreover, caspase proteolysis of vimentin at Asp85 generates a pro-apoptotic amino-terminal fragment whose ability to induce apoptosis is dependent on caspases. Taken together, our findings suggest that caspase proteolysis of vimentin promotes apoptosis by dismantling intermediate filaments and by amplifying the cell death signal via a pro-apoptotic cleavage product. PMID:11423904

  20. Photo-fenton degradation of diclofenac: identification of main intermediates and degradation pathway.

    PubMed

    Pérez-Estrada, Leónidas A; Malato, Sixto; Gernjak, Wolfgang; Agüera, Ana; Thurman, E Michael; Ferrer, Imma; Fernández-Alba, Amadeo R

    2005-11-01

    In recent years, the presence of pharmaceuticals in the aquatic environment has been of growing interest. These new contaminants are important because many of them are not degraded under the typical biological treatments applied in the wastewater treatment plants and represent a continuous input into the environment. Thus, compounds such as diclofenac are present in surface waters in all Europe and a crucial need for more enhanced technologies that can reduce its presence in the environment has become evident. In this sense, advanced oxidation processes (AOPs) represent a good choice for the treatment of hazardous nonbiodegradable pollutants. This work deals with the solar photodegradation of diclofenac, an antiinflammatory drug, in aqueous solutions by photo-Fenton reaction. A pilot-scale facility using a compound parabolic collector (CPC) reactor was used for this study. Results obtained show rapid and complete oxidation of diclofenac after 60 min, and total mineralization (disappearance of dissolved organic carbon, DOC) after 100 min of exposure to sunlight. Although diclofenac precipitates during the process at low pH, its degradation takes place in the homogeneous phase governed by a precipitation-redissolution-degradation process. Establishment of the reaction pathway was made possible by a thorough analysis of the reaction mixture identifying the main intermediate products generated. Gas chromatography-mass spectrometry (GC/ MS) and liquid chromatography coupled with time-of-flight mass spectrometry (LC/TOF-MS) were used to identify 18 intermediates, in two tentative degradation routes. The main one was based on the initial hydroxylation of the phenylacetic acid moiety in the C-4 position and subsequent formation of a quinone imine derivative that was the starting point for further multistep degradation involving hydroxylation, decarboxylation, and oxidation reactions. An alternative route was based on the transient preservation of the biphenyl amino moiety that underwent a similar oxidative process of C-N bond cleavage. The proposed degradation route differs from those previously reported involving alternative degradation processes (ozonization, UV/H2O2, or photolysis), indicating that diclofenac degradation follows different pathways, depending on the treatment applied. PMID:16294867

  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. Evidence for an intermediate in tau filament formation.

    PubMed

    Chirita, Carmen N; Kuret, Jeff

    2004-02-17

    Alzheimer's disease is defined in part by the intraneuronal accumulation of filaments comprised of the microtubule-associated protein tau. In vitro, fibrillization of full-length, unphosphorylated recombinant tau can be induced under near-physiological conditions by treatment with various agents, including anionic surfactants. Here we examine the pathway through which anionic surfactants promote tau fibrillization using a combination of electron microscopy and fluorescence spectroscopy. Protein and surfactant first interacted in solution to form micelles, which then provided negatively charged surfaces that accumulated tau aggregates. Surface aggregation of tau protein was followed by the time-dependent appearance of a thioflavin S reactive intermediate that accumulated over a period of hours. The intermediate was unstable in the absence of anionic surfaces, suggesting it was not filamentous. Fibrillization proceeded after intermediate formation with classic nucleation-dependent kinetics, consisting of lag phase followed by the exponential increase in filament lengths, followed by an equilibrium phase reached in approximately 24 h. The pathway did not require protein insertion into the micelle hydrophobic core or conformational change arising from mixed micelle formation, because anionic microspheres constructed from impermeable polystyrene were capable of qualitatively reproducing all aspects of the fibrillization reaction. It is proposed that the progression from amorphous aggregation through intermediate formation and fibrillization may underlie the activity of other inducers such as hyperphosphorylation and may be operative in vivo. PMID:14769048

  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. 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

  8. 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

  9. 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.

  10. 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

  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.; Münck, Eckard; Lipscomb, John D.

    2013-01-01

    During a single turnover of the hydroxylase component (MMOH) of soluble methane monooxygenase from Methylosinus trichosporium OB3b, several discrete intermediates are formed. The diiron cluster of MMOH is first reduced to the FeIIFeII state (Hred). O2 binds rapidly at a site away from the cluster to form the FeIIFeII intermediate O, which converts to an FeIIIFeIII-peroxo intermediate P and finally to the FeIVFeIV intermediate Q. Q binds and reacts with methane to yield methanol and water. The rate constants for these steps are increased by a regulatory protein, MMOB. Previously reported transient kinetic studies have suggested that an intermediate P* forms between O and P in which the g = 16 EPR signal characteristic of the reduced diiron cluster of Hred and O is lost. This was interpreted as signaling oxidation of the cluster, but low accumulation of P* prevented further characterization. In this study, three methods to directly detect and trap P* are applied together to allow its spectroscopic and kinetic characterization. First, the MMOB mutant His33Ala is used to specifically slow the decay of P* without affecting its formation rate, leading to its nearly quantitative accumulation. Second, spectra-kinetic data collection is used to provide a sensitive measure of the formation and decay rate constants of intermediates as well as their optical spectra. Finally, the substrate furan is included to react with Q and quench its strong chromophore. The optical spectrum of P* closely mimics those of Hred and O, but it is distinctly different from that of P. The reaction cycle rate constants allowed prediction of the times for maximal accumulation of the intermediates. Mössbauer spectra of rapid freeze quench samples at these times show that the intermediates are formed at almost exactly the predicted levels. The Mössbauer spectra show that the diiron cluster of P*, quite unexpectedly, is in the FeIIFeII state. Thus, the loss of the g = 16 EPR results from a change of the electronic structure of the FeIIFeII center rather than oxidation. The similarity of the optical and Mössbauer 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 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

  16. 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

  17. Direct VUV photodegradation of gaseous α-pinene in a spiral quartz reactor: intermediates, mechanism, and toxicity/biodegradability assessment.

    PubMed

    Chen, Jian-Meng; Cheng, Zhuo-Wei; Jiang, Yi-Feng; Zhang, Li-Li

    2010-11-01

    Photodegradation of gaseous α-pinene by a vacuum ultraviolet (VUV) in a spiral reactor was investigated under various gaseous reaction media and residence time, and their respective effects on types and biodegradability of the intermediates were studied. Analysis of carbon amounts showed that about 33% and 43% of total carbon were converted to soluble organic carbon in the air medium with a relative humidity (RH) of 35-40% at empty bed residence times (EBRTs) of 18 and 45 s. Based on the identified intermediates by GC/MS and IC, a photodegradation pathway was proposed by the combined roles of photolysis, OH. photooxidation and O₃ photooxidation. Biodegradability to active sludge, toxicity to Chlorella vulgaris and 96-well microplates showed that α-pinene could be largely converted to more biodegradable and less toxic compounds through photodegradation in the air reaction medium with a RH of 35-40% at an EBRT of 18s, in which the initial concentration was 600 mg m⁻³. Therefore, VUV photodegradation could be applied as an effective pre-treatment method for detoxification and biodegradability improvement under the optimized photodegradation conditions. Such results supported the potential use of VUV photodegradation to improve the removal capacity of conventional biological treatments for hydrophobic and poorly biodegradable compounds. PMID:20965544

  18. 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.

  19. 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.

  20. Improved evidence for the existence of an intermediate phase during hydration of tricalcium silicate

    SciTech Connect

    Bellmann, Frank; Damidot, Denis; Moeser, Bernd; Skibsted, Jorgen

    2010-06-15

    Tricalcium silicate (Ca{sub 3}SiO{sub 5}) with a very small particle size of approximately 50 nm has been prepared and hydrated for a very short time (5 min) by two different modes in a paste experiment, using a water/solid-ratio of 1.20, and by hydration as a suspension employing a water/solid-ratio of 4000. A phase containing uncondensed silicate monomers close to hydrogen atoms (either hydroxyl groups or water molecules) was formed in both experiments. This phase is distinct from anhydrous tricalcium silicate and from the calcium-silicate-hydrate (C-S-H) phase, commonly identified as the hydration product of tricalcium silicate. In the paste experiment, approximately 79% of silicon atoms were present in the hydrated phase containing silicate monomers as determined from {sup 29}Sileft brace{sup 1}Hright brace CP/MAS NMR. This result is used to show that the hydrated silicate monomers are part of a separate phase and that they cannot be attributed to a hydroxylated surface of tricalcium silicate after contact with water. The phase containing hydrated silicate monomers is metastable with respect to the C-S-H phase since it transforms into the latter in a half saturated calcium hydroxide solution. These data is used to emphasize that the hydration of tricalcium silicate proceeds in two consecutive steps. In the first reaction, an intermediate phase containing hydrated silicate monomers is formed which is subsequently transformed into C-S-H as the final hydration product in the second step. The introduction of an intermediate phase in calculations of the early hydration of tricalcium silicate can explain the presence of the induction period. It is shown that heterogeneous nucleation on appropriate crystal surfaces is able to reduce the length of the induction period and thus to accelerate the reaction of tricalcium silicate with water.

  1. 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

  2. Branched Intermediate Formation Stimulates Peptide Bond Cleavage in Protein Splicing

    PubMed Central

    Frutos, Silvia; Goger, Michael; Giovani, Baldissera; Cowburn, David; Muir, Tom W.

    2010-01-01

    Protein splicing is a posttranslational modification in which an intein domain excises itself out of a host protein. Here, we investigate how the steps in the splicing process are coordinated so as to maximize the production of the final splice products and minimize the generation of undesired cleavage products. Our approach has been to prepare a branched intermediate (and analogs thereof) of the Mxe GyrA intein using protein semi-synthesis. Kinetic analysis of these molecules indicates that the high fidelity of this protein splicing reaction results from the penultimate step in the process (intein-succinimide formation) being rate-limiting. NMR experiments indicate that formation of the branched intermediate affects the local structure around the amide bond cleaved during succinimide formation. We propose that this structural change reflects a re-organization of the catalytic apparatus to accelerate succinimide formation at the C-terminal splice junction. PMID:20495572

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. Intermediate behavior of Kerr tails

    NASA Astrophysics Data System (ADS)

    Zenginoğlu, Anıl; Khanna, Gaurav; Burko, Lior M.

    2014-03-01

    The numerical investigation of wave propagation in the asymptotic domain of Kerr spacetime has only recently been possible thanks to the construction of suitable hyperboloidal coordinates. The asymptotics revealed an apparent puzzle in the decay rates of scalar fields: the late-time rates seemed to depend on whether finite distance observers are in the strong field domain or far away from the rotating black hole, an apparent phenomenon dubbed `splitting.' We discuss far-field `splitting' in the full field and near-horizon `splitting' in certain projected modes using horizon-penetrating, hyperboloidal coordinates. For either case we propose an explanation to the cause of the `splitting' behavior, and we determine uniquely decay rates that previous studies found to be ambiguous or immeasurable. The far-field `splitting' is explained by competition between projected modes. The near-horizon `splitting' is due to excitation of lower multipole modes that back excite the multipole mode for which `splitting' is observed. In both cases `splitting' is an intermediate effect, such that asymptotically in time strong field rates are valid at all finite distances. At any finite time, however, there are three domains with different decay rates whose boundaries move outwards during evolution. We then propose a formula for the decay rate of tails that takes into account the inter-mode excitation effect that we study.

  11. 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.

  12. 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.

  13. 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 analogues—3’-keto-aristeromycin (3KA) and noraristeromycin (NRN)—at resolutions of 1.55, 1.55, and 1.65 Å. 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

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. Degradation of toluene-2,4-diamine by persulphate: kinetics, intermediates and degradation pathway.

    PubMed

    Jiang, Yong-hai; Zhang, Jin-bao; Xi, Bei-dou; An, Da; Yang, Yu; Li, Ming-xiao

    2015-01-01

    In this study, the degradation of toluene-2,4-diamine (TDA) by persulphate (PS) in an aqueous solution at near-neutral pH was examined. The result showed that the degradation rate of TDA increased with increasing PS concentrations. The optimal dosage of PS in the reaction system was determined by efficiency indicator (I) coupling in the consumption of PS and decay half-life of TDA. Calculation showed that 0.74 mM of PS was the most effective dosage for TDA degradation, at that level the maximum I of 24.51 was obtained. PS can oxidize TDA for an extended reaction time period. Under neutral condition without activation, four degradation intermediates, 2,4-diamino-3-hydroxy-5-sulfonicacidtoluene, 2,4-diaminobenzaldehyde, 2,4-bis(vinylamino)benzaldehyde and 3,5-diamino-4-hydroxy-2-pentene, were identified by high-performance liquid chromatography-mass spectrometry. The tentative degradation pathway of TDA was proposed as well. It was found that hydroxyl radical played an important role in degradation of TDA with the activation of Fe2+, whereas PS anion and sulphate radicals were responsible for the degradation without activation of Fe2+. PMID:25442404

  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

  1. Establishment of an intermediate care ward for babies and mothers.

    PubMed Central

    Dear, P R; McLain, B I

    1987-01-01

    This paper describes one year's experience with the running of a special postnatal ward area, established so that babies who needed more treatment and monitoring than is generally undertaken on postnatal wards but who did not need the facilities of the neonatal unit could be kept by their mother's bedside. This 'intermediate care ward' admitted 297 babies with their mothers during its first year of operation. We estimate that the opening of the ward led to a 20% reduction in admissions to the neonatal unit, without disadvantage to any baby. The indications for admission are outlined and the reactions of patients and staff to the innovation discussed. PMID:3619477

  2. Reaction Product Identification in Extreme Chemical Environments by Broadband Rotational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Pate, Brooks

    Molecular rotational spectroscopy has several advantages for detection of reaction intermediates and products under extreme laboratory conditions. Rotational spectroscopy has high sensitivity to the molecular structure and provides high spectral resolution in low pressure environments. Furthermore, quantum chemistry provides accurate estimates of the spectroscopic parameters. As a result, rotational spectroscopy can identify molecular species in complex reaction mixtures without the need for chromatographic separation and without the need for a previously recorded ``library spectrum'' of the molecule. The application of chirped pulse Fourier transform rotational spectroscopy methods for the identification of molecules of astrochemical interest formed in pulsed discharge sources will be described including recent advances for high-throughput mm-wave spectroscopy. The set of reaction products created in the experiment can provide insight into the reaction mechanism. Reactions involving the CN radical will be discussed. These reactions can be barrierless making them candidates for interstellar gas reactions. The possibility that interstellar cyanomethanimine is produced by gas phase radical-neutral reactions instead of surface chemistry on grain-supported ices will be discussed using recent spatially resolved chemical images in Sagittarius B2 observed with the Jansky Very Large Array. This work supported by NSF CHE 1213200.

  3. Nuclear structure at intermediate energies

    SciTech Connect

    Bonner, B.E.; Mutchler, G.S.

    1991-09-30

    The theme that unites the sometimes seemingly disparate experiments undertaken by the Bonner Lab Medium Energy Group is a determination to understand in detail the many facets and manifestations of the strong interaction, that which is now referred to as nonperturbative QCD. Whether we are investigating the question of just what does carry the spin of baryons, or the extent of the validity of the SU(6) wavefunctions for the excited hyperons (as will be measured in their radiative decays in our CEBAF experiment), or questions associated with the formation of a new state of matter predicted by QCD (the subject of our BNL experiments E810, E854, as well as our approved experiment at RHIC), -- all these projects share this common goal. Our other experiments represent different approaches to the same broad undertaking. LAMPF E1097 will provide definitive answers to the question of the spin dependence of the inelastic channel of pion production in the n-p interaction. FNAL E683 may well open a new field of investigation in nuclear physics: that of just how quarks and gluons interact with nuclear matter as they transverse nuclei of different sizes. In most all of the experiments mentioned above, the Bonner Lab Group is playing major leadership roles as well as doing a big fraction of the hard work that such experiments require. We use many of the facilities that are unavailable to the intermediate energy physics community and we use our expertise to design and fabricate the detectors and instrumentation that are required to perform the measurements which we decide to do.

  4. Isospin dependence of fragment spectra in heavy/super-heavy colliding nuclei at intermediate energies

    NASA Astrophysics Data System (ADS)

    Chugh, Rajiv; Kumar, Rohit; Vinayak, Karan Singh

    2016-05-01

    Using isospin-dependent quantum molecular dynamics (IQMD) approach, we performed a theoretical investigation of the evolution of various kinds of fragments in heavy and superheavy-ion reactions in the intermediate/medium energy domain. We demonstrated direct impact of symmetry energy and Coulomb interactions on the evolution of fragments. Final fragment spectra (yields) obtained from the analysis of various heavy/super-heavy ion reactions at different reaction conditions show high sensitivity towards Coulomb interactions and less significant sensitivity to symmetry energy forms. No inconsistent pattern of fragment structure is obtained in case of super-heavy ion involved reactions for all the parameterizations of density dependence of symmetry energy.

  5. Liver resection for intermediate hepatocellular carcinoma.

    PubMed

    Yi, Peng-Sheng; Zhang, Ming; Zhao, Ji-Tong; Xu, Ming-Qing

    2016-05-18

    Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in China. The Barcelona Clinic Liver Cancer (BCLC) staging system is regarded as the gold standard staging system for HCC, classifying HCC as early, intermediate, or advanced. For intermediate HCC, trans-catheter arterial chemoembolization (TACE) is recommended as the optimal strategy by the BCLC guideline. This review investigates whether liver resection is better than TACE for intermediate HCC. Based on published studies, we compare the survival benefits and complications of liver resection and TACE for intermediate HCC. We also compare the survival benefits of liver resection in early and intermediate HCC. We find that liver resection can achieve better or at least comparable survival outcomes compared with TACE for intermediate HCC; however, we do not observe a significant difference between liver resection and TACE in terms of safety and morbidity. We conclude that liver resection may improve the short- and long-term survival of carefully selected intermediate HCC patients, and the procedure may be safely performed in the management of intermediate HCC. PMID:27190577

  6. Gasoline Engine Mechanics. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Jones, Marion

    Several intermediate performance objectives and corresponding criterion measures are listed for each of six terminal objectives presented in this curriculum guide for an intermediate gasoline engine mechanics course at the secondary level. (For the beginning course guide see CE 010 947.) The materials were developed for a two-semester (2 hour…

  7. Diesel Mechanics. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Tidwell, Joseph

    Several intermediate performance objectives and corresponding criterion measures are listed for each of six terminal objectives for an intermediate diesel mechanics course (two semesters, 3 hours daily) designed for high school students who upon completion would be ready for an on-the-job training experience in diesel service and repair. Through…

  8. Appliance Services. Intermediate Course. Career Education.

    ERIC Educational Resources Information Center

    Killough, Joseph

    Several intermediate performance objectives and corresponding criterion measures are listed for each of 16 terminal objectives for an intermediate appliance repair course. The materials were developed for a 36-week course (3 hours daily) covering the areas of refrigeration, maintenance, repair, and troubleshooting of refrigerators and air…

  9. 19 CFR 122.84 - Intermediate airport.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 19 Customs Duties 1 2014-04-01 2014-04-01 false Intermediate airport. 122.84 Section 122.84 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE... Intermediate airport. (a) Application. The provisions of this section apply at any U.S. airport to which...

  10. 19 CFR 122.84 - Intermediate airport.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 19 Customs Duties 1 2012-04-01 2012-04-01 false Intermediate airport. 122.84 Section 122.84 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE... Intermediate airport. (a) Application. The provisions of this section apply at any U.S. airport to which...

  11. 19 CFR 122.84 - Intermediate airport.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 19 Customs Duties 1 2013-04-01 2013-04-01 false Intermediate airport. 122.84 Section 122.84 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE... Intermediate airport. (a) Application. The provisions of this section apply at any U.S. airport to which...

  12. 19 CFR 122.84 - Intermediate airport.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Intermediate airport. 122.84 Section 122.84 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY AIR COMMERCE REGULATIONS Procedures for Residue Cargo and Stopover Passengers § 122.84 Intermediate airport. (a) Application. The provisions...

  13. 19 CFR 122.84 - Intermediate airport.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 19 Customs Duties 1 2011-04-01 2011-04-01 false Intermediate airport. 122.84 Section 122.84 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE... Intermediate airport. (a) Application. The provisions of this section apply at any U.S. airport to which...

  14. 39 CFR 3001.39 - Intermediate decisions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 39 Postal Service 1 2010-07-01 2010-07-01 false Intermediate decisions. 3001.39 Section 3001.39... Applicability § 3001.39 Intermediate decisions. (a) Initial decision by presiding officer. In any proceedings in...) the appropriate recommended decision, advisory opinion or public report pursuant to the Act....

  15. Radio and Television Servicing. Intermediate Course.

    ERIC Educational Resources Information Center

    Campbell, Guy; And Others

    Several intermediate performance objectives and corresponding criterion measures are listed for each of 32 terminal objectives for an intermediate (second year) radio/TV servicing course. This 1-year course (3 hours daily) was designed to provide the student with the basic skills and knowledges necessary for entry level employment in the Radio/TV…

  16. Automotive Body Repair. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Lang, Thomas

    Several intermediate performance objectives and corresponding criterion measures are listed for each of 10 terminal objectives for an intermediate automotive body repair and refinishing course. The materials were developed for a two-semester (3 hours daily) course for specialized classrooms, shop, and practical experiences designed to enable the

  17. Liver resection for intermediate hepatocellular carcinoma

    PubMed Central

    Yi, Peng-Sheng; Zhang, Ming; Zhao, Ji-Tong; Xu, Ming-Qing

    2016-01-01

    Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in China. The Barcelona Clinic Liver Cancer (BCLC) staging system is regarded as the gold standard staging system for HCC, classifying HCC as early, intermediate, or advanced. For intermediate HCC, trans-catheter arterial chemoembolization (TACE) is recommended as the optimal strategy by the BCLC guideline. This review investigates whether liver resection is better than TACE for intermediate HCC. Based on published studies, we compare the survival benefits and complications of liver resection and TACE for intermediate HCC. We also compare the survival benefits of liver resection in early and intermediate HCC. We find that liver resection can achieve better or at least comparable survival outcomes compared with TACE for intermediate HCC; however, we do not observe a significant difference between liver resection and TACE in terms of safety and morbidity. We conclude that liver resection may improve the short- and long-term survival of carefully selected intermediate HCC patients, and the procedure may be safely performed in the management of intermediate HCC. PMID:27190577

  18. 39 CFR 3001.39 - Intermediate decisions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 39 Postal Service 1 2011-07-01 2011-07-01 false Intermediate decisions. 3001.39 Section 3001.39... Applicability § 3001.39 Intermediate decisions. (a) Initial decision by presiding officer. In any proceedings in... certify and file with the Secretary, a copy of the record of the hearing and his/her initial decision...

  19. Marine Engine Mechanics. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Jones, Marion

    Several intermediate performance objectives and corresponding criterion measures are presented for each of ten terminal objectives for a two-semester course (3 hours daily). This 540-hour intermediate course includes advanced troubleshooting techniques on outboard marine engines, inboard-outboard marine engines, inboard marine engines, boat…

  20. Automotive Body Repair. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Lang, Thomas

    Several intermediate performance objectives and corresponding criterion measures are listed for each of 10 terminal objectives for an intermediate automotive body repair and refinishing course. The materials were developed for a two-semester (3 hours daily) course for specialized classrooms, shop, and practical experiences designed to enable the…