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Sample records for identify reaction intermediate

  1. Cryogenic Trapping and Isotope Editing Identify a Protonated Water Cluster as an Intermediate in the Photosynthetic Oxygen-Evolving Reaction.

    PubMed

    Guo, Zhanjun; Barry, Bridgette A

    2016-09-01

    Internal water is known to play a catalytic role in several enzymes. In photosystem II (PSII), water is the substrate. To oxidize water, the PSII Mn4CaO5 cluster or oxygen evolving center (OEC) cycles through five oxidation states, termed Sn states. As reaction products, molecular oxygen is released, and protons are transferred through a ∼25 Å hydrogen-bonded network from the OEC to the thylakoid lumen. Previously, it was reported that a broad infrared band at 2880 cm(-1) is produced during the S1-to-S2 transition and accompanies flash-induced, S state cycling at pH 7.5. Here, we report that when the S2 state is trapped by continuous illumination under cryogenic conditions (190 K), an analogous 2740/2900 cm(-1) band is observed. The frequency depended on the sodium chloride concentration. This band is unambiguously assigned to a normal mode of water by D2(16)O and H2(18)O solvent exchange. Its large, apparent H2(18)O isotope shift, ammonia sensitivity, frequency, and intensity support assignment to a stretching vibration of a hydronium cation, H3O(+), in a small, protonated internal water cluster, nH2O(H3O(+)). Water OH stretching bands, which may be derived from the hydration shell of the hydronium ion, are also identified. Using the 2740 cm(-1) infrared marker, the results of calcium depletion and strontium reconstitution on the protonated water cluster are found to be pH dependent. This change is attributed to protonation of an amino acid side chain and a possible change in nH2O(H3O)(+) localization in the hydrogen-bonding network. These results are consistent with an internal water cluster functioning as a proton acceptor and an intermediate during the S1-to-S2 transition. Our experiments demonstrate the utility of this infrared signal as a novel functional probe in PSII. PMID:27491625

  2. Nuclear reactions at intermediate energies

    NASA Astrophysics Data System (ADS)

    Shyam, Radhey

    2016-05-01

    In the domain of Nuclear reactions at intermediate energies, the QCD coupling constant αs is large enough (~ 0.3 - 0.5) to render the perturbative calculational techniques inapplicable. In this regime the quarks are confined into colorless hadrons and it is expected that effective field theories of hadron interactions via exchange of hadrons, provide useful tools to describe such reactions. In this contribution we discuss the application of one such theory, the effective Lagrangian model, in describing the hadronic reactions at intermediate energies whose measurements are the focus of a vast international experimental program.

  3. Fission in intermediate energy heavy ion reactions

    SciTech Connect

    Wilhelmy, J.B.; Begemann-Blaich, M.; Blaich, T.; Boissevain, J.; Fowler, M.M.; Gavron, A.; Jacak, B.V.; Lysaght, P.S.; Britt, H.C.; Fields, D.J.

    1989-04-01

    A systematic study of reaction mechanisms at intermediate energies (50--100 MeV/A) has been performed at the Lawrence Berkeley Laboratory's BeValac using medium weight projectiles on medium and heavy element targets. A gas and plastic phoswich detector system was employed which gave large geometric coverage and a wide dynamic response. The particles identified with the gas detectors could be characterized into three components--intermediate mass fragments (IMF), fission fragments (FF) and heavy residues (HR). Major observed features are: the reaction yields are similar in the 50 to 100 MeV/A range, central collisions have high multiplicity of IMF's with broad angular correlations consistent with a large participant region, effects of final state Coulomb interactions are observed and give information on the size and temporal behavior of the source, true fission yields are dependent on target fissility and correlated with relatively peripheral collisions. Analysis of fission and evaporation yields implies limiting conditions for which fission decay remains a viable deexcitation channel. 15 refs., 7 figs.

  4. Studying Reaction Intermediates Formed at Graphenic Surfaces

    NASA Astrophysics Data System (ADS)

    Sarkar, Depanjan; Sen Gupta, Soujit; Narayanan, Rahul; Pradeep, Thalappil

    2014-03-01

    We report in-situ production and detection of intermediates at graphenic surfaces, especially during alcohol oxidation. Alcohol oxidation to acid occurs on graphene oxide-coated paper surface, driven by an electrical potential, in a paper spray mass spectrometry experiment. As paper spray ionization is a fast process and the time scale matches with the reaction time scale, we were able to detect the intermediate, acetal. This is the first observation of acetal formed in surface oxidation. The process is not limited to alcohols and the reaction has been extended to aldehydes, amines, phosphenes, sugars, etc., where reaction products were detected instantaneously. By combining surface reactions with ambient ionization and mass spectrometry, we show that new insights into chemical reactions become feasible. We suggest that several other chemical transformations may be studied this way. This work opens up a new pathway for different industrially and energetically important reactions using different metal catalysts and modified substrate.

  5. A new intermediate in the Prins reaction

    PubMed Central

    Fukuda, Takeshi; Yamazaki, Shoko

    2013-01-01

    Summary Two Prins reactions were investigated by the use of DFT calculations. A model composed of R–CH=CH2 + H3O+(H2O)13 + (H2C=O)2, R = Me and Ph, was adopted to trace reaction paths. For both alkenes, the concerted path forming 1,3-diols was obtained as the rate determining step (TS1). TS stands for a transition state. From the 1,3-diol, a bimolecular elimination (TS2) leads to the allylic alcohol as the first channel. In the second channel, the 1,3-diol was converted via TS3 into an unprecedented hemiacetal intermediate, HO–CH2–O–CH(R)–CH2–CH2–OH. This intermediate undergoes ring closure (TS4), affording the 1,3-dioxane product. The intermediate is of almost the same stability as the product, and two species were suggested to be in a state of equilibrium. While the geometry of TS1 appears to be forwarded to that of a carbocation intermediate, the cation disappeared through the enlargement of the water cluster. Dynamical calculations of a classical trajectory using the atom-centered density matrix propagation molecular dynamics model on the four TSs were carried out, and results of IRC calculations were confirmed by them. PMID:23532354

  6. A new intermediate in the Prins reaction.

    PubMed

    Yamabe, Shinichi; Fukuda, Takeshi; Yamazaki, Shoko

    2013-01-01

    Two Prins reactions were investigated by the use of DFT calculations. A model composed of R-CH=CH2 + H3O(+)(H2O)13 + (H2C=O)2, R = Me and Ph, was adopted to trace reaction paths. For both alkenes, the concerted path forming 1,3-diols was obtained as the rate determining step (TS1). TS stands for a transition state. From the 1,3-diol, a bimolecular elimination (TS2) leads to the allylic alcohol as the first channel. In the second channel, the 1,3-diol was converted via TS3 into an unprecedented hemiacetal intermediate, HO-CH2-O-CH(R)-CH2-CH2-OH. This intermediate undergoes ring closure (TS4), affording the 1,3-dioxane product. The intermediate is of almost the same stability as the product, and two species were suggested to be in a state of equilibrium. While the geometry of TS1 appears to be forwarded to that of a carbocation intermediate, the cation disappeared through the enlargement of the water cluster. Dynamical calculations of a classical trajectory using the atom-centered density matrix propagation molecular dynamics model on the four TSs were carried out, and results of IRC calculations were confirmed by them. PMID:23532354

  7. Solvent effects on ozonolysis reaction intermediates

    NASA Astrophysics Data System (ADS)

    del Rio, Emma; Aplincourt, Philippe; Ruiz-López, Manuel F.

    1997-12-01

    Solvent effects on relative stability, electronic and molecular structure of ozonolysis reaction intermediates are analyzed with the help of ab initio MP2/6-31+G ** calculations. A continuum model is employed to account for solute-solvent electrostatic interactions. The results show that there are large effects on the structure and relative stability of carbonyl oxide by substantially favoring its zwitterionic character. A complex formed by carbonyl oxide and formaldehyde is shown to be stable in the gas phase and in solution. This complex can be involved in solvent cage reactions leading to secondary ozonides. Thermodynamically, primary ozonide decomposition is favored by the solvent.

  8. Reactions and reaction intermediates on iron surfaces. III. Reactions of aldehydes and ketones on Fe(100)

    SciTech Connect

    Benziger, J.B.; Madix, R.J.

    1982-01-01

    The reactions of formaldehyde, acetaldehyde, and acetone on Fe(100) were studied by temperature-programmed reaction spectroscopy and X-ray photoelectron spectroscopy (XPS). Formaldehyde and acetaldehyde were observed to react with adsorbed hydrogen to form adsorbed alkoxy intermediates. These reactions occurred at low temperature (ca. 200 K). In the absence of adsorbed hydrogen, formaldehyde and acetaldehyde decomposed to adsorbed CO and hydrogen. This reaction was also observed at low temperatures. On an initially clean surface the aldehydes first decomposed, forming adsorbed hydrogen which subsequently reacted with adsorbed aldehyde to form an alkoxy intermediate. The alkoxy intermediates reacted to form CO and H/sub 2/ primarily, with lesser amounts of alcohol, aldehyde, and hydrocarbon products. Acetone reacted differently from the aldehydes and did not appear to form an alkoxy intermediate. XPS results suggested that acetone and acetaldehyde did not adsorb in their keto form on the surface and it is suggested that they adsorbed as enol intermediates. The distinct reaction behavior of acetone may be due to these enol intermediates.

  9. 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…

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

    NASA Astrophysics Data System (ADS)

    Orr-Ewing, Andrew

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

  11. (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)

  12. Electronic energy levels of intermediates in the nickel carbonylation reaction

    NASA Astrophysics Data System (ADS)

    Howard, I. A.; Pratt, G. W.; Johnson, K. H.; Dresselhaus, G.

    1981-03-01

    Using the multiple scattering Xa method, electronic energy levels have been found self-consistently for the intermediates Ni(CO)n, n = 1,2,3 in the formation of nickel tetracarbonyl via the Ni-CO surface reaction. Linear geometries have been assumed for NiCO and Ni(CO)2, and a trigonal planar conformation for Ni(CO)3, in accordance with previously published IR spectra. The intermediates were assumed to be in the gas phase, free of surface interaction. From the energy level structure found, all three of the intermediates were determined to be diamagnetic, as Ni(CO)4 is known to be.

  13. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  15. 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

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

    PubMed

    Kraka, Elfi; Cremer, Dieter

    2010-05-18

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

  17. Accomplishing structural change: Identifying intermediate indicators of success

    PubMed Central

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

    2012-01-01

    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

  18. 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

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

    PubMed

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

    2012-08-14

    Criegee biradicals, i.e., carbonyl oxides, are critical intermediates in ozonolysis and have been implicated in autoignition chemistry and other hydrocarbon oxidation systems, but until recently the direct measurement of their gas-phase kinetics has not been feasible. Indirect determinations of Criegee intermediate kinetics often rely on the introduction of a scavenger molecule into an ozonolysis system and analysis of the effects of the scavenger on yields of products associated with Criegee intermediate reactions. Carbonyl species, in particular hexafluoroacetone (CF(3)COCF(3)), have often been used as scavengers. In this work, the reactions of the simplest Criegee intermediate, CH(2)OO (formaldehyde oxide), with three carbonyl species have been measured by laser photolysis/tunable synchrotron photoionization mass spectrometry. Diiodomethane photolysis produces CH(2)I radicals, which react with O(2) to yield CH(2)OO + I. The formaldehyde oxide is reacted with a large excess of a carbonyl reactant and both the disappearance of CH(2)OO and the formation of reaction products are monitored. The rate coefficient for CH(2)OO + hexafluoroacetone is k(1) = (3.0 ± 0.3) × 10(-11) cm(3) molecule(-1) s(-1), supporting the use of hexafluoroacetone as a Criegee-intermediate scavenger. The reactions with acetaldehyde, k(2) = (9.5 ± 0.7) × 10(-13) cm(3) molecule(-1) s(-1), and with acetone, k(3) = (2.3 ± 0.3) × 10(-13) cm(3) molecule(-1) s(-1), are substantially slower. Secondary ozonides and products of ozonide isomerization are observed from the reactions of CH(2)OO with acetone and hexafluoroacetone. Their photoionization spectra are interpreted with the aid of quantum-chemical and Franck-Condon-factor calculations. No secondary ozonide was observable in the reaction of CH(2)OO with acetaldehyde, but acetic acid was identified as a product under the conditions used (4 Torr and 293 K). PMID:22481381

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

    PubMed

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

    2013-10-14

    Periodic density functional theory (DFT) calculations have been performed to systematically investigate the effect of reaction intermediate on catalytic activity for hydrazine (N2H4) decomposition on Rh(111). Reaction mechanisms via intramolecular and NH2-assisted N2H4 decompositions are comparatively analyzed, including adsorption configuration, reaction energy and barrier of elementary step, and reaction network. Our results show that the most favorable N2H4 decomposition pathway starts with the initial N-N bond scission to the NH2 intermediate, followed by stepwise H stripping from adsorbed N2Hx (x = 1-4) species, and finally forms the N2 and NH3 products. Comparatively, the stepwise intramolecular dehydrogenation via N2H4→ N2H3→ N2H2→ N2H → N2, and N2H4→ NH2→ NH → N with or without NH2 promotion effect, are unfavorable due to higher energy barriers encountered. Energy barrier analysis, reaction rate constants, and electronic structures are used to identify the crucial competitive route. The promotion effect of the NH2 intermediate is structurally reflected in the weakening of the N-H bond and strengthening of the N-N bond in N2Hx in the coadsorption system; it results intrinsically from the less structural deformation of the adsorbate, and weakening of the interaction between dehydrogenated fragment and departing H in transition state. Our results highlight the crucial effect of reaction intermediate on catalytic activity and provide a theoretical approach to analyze the effect. PMID:23990024

  1. 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.

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

    PubMed

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

    2009-04-21

    The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 A resolution or better of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct are described. The D402N enzyme has no detectable activity with neutral nitroalkanes [Valley, M. P., and Fitzpatrick, P. F. (2003) J. Am. Chem. Soc. 125, 8738-8739]. The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped [Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062-2066]. The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2'-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle. PMID:19265437

  3. Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction

    SciTech Connect

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

    2009-01-01

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

  4. 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.

  5. 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

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

    SciTech Connect

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

    2004-04-12

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

  7. 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.

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

    PubMed

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

    2015-01-23

    The ozonation of 1H-benzotriazole (BZ) and 3-methylindole (ML), two emerging contaminants that are frequently present in aquatic environments, was investigated. The experiments were performed with the contaminants (1μM) dissolved in ultrapure water. The kinetic study led to the determination of the apparent rate constants for the ozonation reactions. In the case of 1H-benzotriazole, these rate constants varied from 20.1 ± 0.4M(-1)s(-1) at pH=3 to 2143 ± 23 M(-1)s(-1) at pH=10. Due to its acidic nature (pKa=8.2), the degree of dissociation of this pollutant was determined at every pH of work, and the specific rate constants of the un-dissociated and dissociated species were evaluated, being the values of these rate constants 20.1 ± 2.0 and 2.0 ± 0.3 × 10(3)M(-1)s(-1), respectively. On the contrary, 3-methylindole does not present acidic nature, and therefore, it can be proposed an average value for its rate constant of 4.90 ± 0.7 × 10(5)M(-1)s(-1) in the whole pH range 3-10. Further experiments were performed to identify the main degradation byproducts (10 mg L(-1) of contaminants, 0.023 gh(-1) of ozone). Up to 8 intermediates formed in the ozonation of 3-methylindole were identified by LC-TOFMS, while 6 intermediates were identified in the ozonation of 1H-benzotriazole. By considering these intermediate compounds, the reaction mechanisms were proposed and discussed. Finally, evaluated rate constants allowed to predict and modeling the oxidation of these micropollutants in general aquatic systems. PMID:24953706

  9. 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

  10. Role of compound nuclei in intermediate-energy heavy-ion reactions

    SciTech Connect

    Moretto, L.G.; Wozniak, G.J.

    1988-05-01

    Hot compound nuclei are frequently produced in intermediate-energy reactions through a variety of processes. Their decay is shown to be an important and at times dominant source of complex fragments, high energy-gamma rays, and even pions.

  11. 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...

  12. 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

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

    SciTech Connect

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

    1999-11-16

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

  14. 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

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

    PubMed

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

    2016-02-24

    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

  16. Incomplete Combustion of Hydrogen: Trapping a Reaction Intermediate

    ERIC Educational Resources Information Center

    Mattson, Bruce; Hoette, Trisha

    2007-01-01

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

  17. 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.

  18. 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.

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

    PubMed

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

    2015-02-13

    Carbonyl oxides, or Criegee intermediates, are important transient species formed in the reactions of unsaturated hydrocarbons with ozone. Although direct detection of Criegee intermediates has recently been realized, the main atmospheric sink of Criegee intermediates remains unclear. We report ultraviolet absorption spectroscopic measurements of the lifetime of the simplest Criegee intermediate, CH2OO, at various relative humidity levels up to 85% at 298 kelvin. An extremely fast decay rate of CH2OO was observed at high humidity. The observed quadratic dependence of the decay rate on water concentration implied a predominant reaction with water dimer. On the basis of the water dimer equilibrium constant, the effective rate coefficient of the CH2OO + (H2O)2 reaction was determined to be 6.5 (±0.8) × 10(-12) cubic centimeters per second. This work would help modelers to better constrain the atmospheric concentrations of CH2OO. PMID:25569112

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

    PubMed

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

    2015-06-15

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

  1. 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)

  2. Mössbauer and EPR Study of Reaction Intermediates of Cytochrome P450

    NASA Astrophysics Data System (ADS)

    Schünemann, V.; Trautwein, A. X.; Jung, C.; Terner, J.

    2002-06-01

    We present a complementary Mössbauer and EPR study on reaction intermediates of substrate-free and substrate-bound cytochrome P450cam from Pseudomonas putida prepared by the freeze-quench method from 57Fe-labeled P450cam using peroxy acetic acid as oxidizing agent. When reacting the substrate-free P450cam for 8 ms reaction time the reaction mixture consists of ˜85% of ferric low-spin iron (Fe(III)) with g-factors and hyperfine parameters of the starting material; the remaining ˜15% are identified as ferryl iron (Fe(IV); S Fe=1) by its Mössbauer signature. Parallel to the ferryl iron a tyrosine radical ( S rad=1/2) is formed. The two paramagnetic species are not exchange-coupled; however, they are close enough to significantly influence the (EPR) relaxation behavior of the radical spin. In the case of substrate-bound P450cam only trace amounts of the tyrosine radical are formed within 8 ms (<3%); within the accuracy of Mössbauer spectroscopy (5%) iron(IV) can not be detected. The results point to Tyr-96, which is hydrogen-bonded to the substrate camphor, as the candidate for the observed tyrosine radical.

  3. Clustering recognition model for intermediate energy heavy ion reactions

    SciTech Connect

    Garcia-Solis, E.J.; Mignerey, A.C.

    1996-07-01

    A clustering model which allows the recognition of mass fragments from dynamical simulations has been developed. Studying the evolution of a microscopic computation based on the nuclear Boltzman equation, a suitable time is chosen to define bound clusters. At this stopping time the cluster cores for each member of the distribution are defined as a function of the overall density. Then an iterative routine is applied to estimate the coalescence of the surrounding nucleons. Once the fragment formation has been established, a statistical decay code is used to generate the final fragment distributions. Applications are shown to the reactions {sup 129}Xe + {sup nat}Cu at 50 MeV/nucleon and {sup 139}La on {sup 27}Al and {sup nat}Cu at 45 MeV/nucleon. A general improvement in cluster identification is found over approaches where a standard cluster separation algorithm has been used. {copyright} {ital 1996 The American Physical Society.}

  4. Multidimensional least-squares resolution of Raman spectra from intermediates in sensitized photochemical reactions

    SciTech Connect

    Fister, J.C. III; Harris, J.M.

    1995-12-01

    Transient resonance Raman spectroscopy is used to elicit reaction kinetics and intermediate spectra from sensitized photochemical reactions. Nonlinear least-squares analysis of Raman spectra of a triplet-state photosensitizer (benzophenone), acquired as a function of laser intensity and/or quencher concentration allow the Raman spectra of the sensitizer excited state and intermediate photoproducts to be resolved from the spectra of the ground state and solvent. In cases where physical models describing the system kinetics cannot be found, factor analysis techniques are used to obtain the intermediate spectra. Raman spectra of triplet state benzophenone and acetophenone, obtained as a function of laser excitation kinetics, and the Raman spectra of intermediates formed by energy transfer (triplet-state biacetyl) and hydrogen abstraction (benzhydrol radical) are discussed.

  5. Glutathione peroxidase's reaction intermediate selenenic acid is stabilized by the protein microenvironment.

    PubMed

    Li, Fei; Liu, Jun; Rozovsky, Sharon

    2014-11-01

    Selenenic acids are highly reactive intermediates of selenoproteins' enzymatic reactions. Knowledge of how the protein environment protects and stabilizes them is fundamental not only to descriptions of selenoproteins' reactivity but also potentially for proteomics and therapeutics. However, selenenic acids are considered particularly short-lived and are not yet identified in wild-type selenoproteins. Here, we report trapping the selenenic acid in glutathione peroxidase, an antioxidant enzyme that efficiently eliminates hydroperoxides. It has long been thought that selenium-containing glutathione peroxidases form a selenenic acid intermediate. However, this putative species has eluded detection. Here, we report its identification. The selenenic acid in bovine glutathione peroxidase 1 was chemically trapped using dimedone, an alkylating agent specific to sulfenic and selenenic acids. The alkylation of the catalytic selenocysteine was verified by electrospray ionization mass spectrometry. In the presence of glutathione, the selenocysteine was not alkylated because the selenenic acid condenses faster with glutathione than the alkylation reaction. In the absence of thiols, the selenenic acid was surprisingly long-lived with 95% of the protein still able to react with dimedone 10 min after hydrogen peroxide was removed, indicating that the protein environment stabilizes the selenenic acid by shielding it from reactive groups in the protein. After 30 min, the selenocysteine was no longer modified but became accessible once the protein was exposed to reducing agents. This suggests that the selenenic acid reacted with a protein's amide or amine to form a selenylamide bond. Such a modification may play a role in protecting glutathione peroxidase׳' reactivity. PMID:25124921

  6. Glutathione Peroxidase’s Reaction Intermediate Selenenic Acid is Stabilized by the Protein Microenvironment

    PubMed Central

    Li, Fei; Liu, Jun; Rozovsky, Sharon

    2014-01-01

    Selenenic acids are highly reactive intermediates of selenoproteins’ enzymatic reactions. Knowledge of how the protein environment protects and stabilizes them is fundamental not only to descriptions of selenoproteins’ reactivity but also potentially for proteomics and therapeutics. However, selenenic acids are considered particularly short-lived and were not yet identified in wild-type selenoproteins. Here, we report trapping the selenenic acid in glutathione peroxidase, an anti-oxidant enzyme that efficiently eliminates hydroperoxides. It has long been thought that selenium-containing glutathione peroxidases form a selenenic acid intermediate. However, this putative species has eluded detection. Here, we report its identification. The selenenic acid in bovine glutathione peroxidase 1 was chemically trapped using dimedone, an alkylating agent specific to sulfenic and selenenic acids. The alkylation of the catalytic selenocysteine was verified by electrospray ionization mass spectrometry. In the presence of glutathione, the selenocysteine was not alkylated because the selenenic acid condenses faster with glutathione than the alkylation reaction. In the absence of thiols, the selenenic acid was surprisingly long-lived with 95% of the protein still able to react with dimedone 10 min after hydrogen peroxide was removed, indicating that the protein environment stabilizes the selenenic acid by shielding it from reactive groups in the protein. After 30 min, the selenocysteine was no longer modified but became accessible once the protein was exposed to reducing agents. This suggests that the selenenic acid reacted with a protein’s amide or amine to form a selenylamide bond. Such a modification may play a role in protecting glutathione peroxidase’s reactivity. PMID:25124921

  7. 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.

  8. 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

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

    PubMed

    Cai, Yujuan; Tang, Xinjun; Ma, Shengming

    2016-02-12

    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

  10. Intermediates Formed in the Reactions of Organocuprates with α,β-Unsaturated Nitriles.

    PubMed

    Putau, Aliaksei; Brand, Harald; Koszinowski, Konrad

    2016-08-26

    Conjugate additions of organocuprates are of outstanding importance for organic synthesis. To improve our mechanistic understanding of these reactions, we have used electrospray ionization mass spectrometry for the identification of the ionic intermediates formed upon the treatment of LiCuR2 ⋅LiCN (R=Me, Bu, Ph) with a series of α,β-unsaturated nitriles. Acrylonitrile, the weakest Michael acceptor included, did not afford any detectable intermediates. Fumaronitrile (FN) yielded adducts of the type Lin-1 Cun R2n (FN)n (-) , n=1-3. When subjected to fragmentation in the gas phase, these adducts were not converted into the conjugate addition products, but re-dissociated into the reactants. In contrast, the reaction with 1,1-dicyanoethylene furnished the products of the conjugate addition without any observable intermediates. Tri- and tetracyanoethylene proved to be quite reactive as well. The presence of several cyano groups in these substrates opened up reaction pathways different from simple conjugate additions, however, and led to dimerization and substitution reactions. Moreover, the gas-phase fragmentation behavior of the species formed from these substrates indicated the occurrence of single-electron transfer processes. Additional quantum-chemical calculations provided insight into the structures and stabilities of the observed intermediates and their consecutive reactions. PMID:27461093

  11. 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.

  12. A Major Intermediate Component in Drawn High-Density Polyethylene Identified by Solid-State NMR

    NASA Astrophysics Data System (ADS)

    Mowery, Daniel; Schmidt-Rohr, Klaus

    2001-03-01

    In a commercial polyethylene (HDPE) highly drawn at 295 K, a distinct morphological component intermediate to the crystalline and the almost isotropic amorphous phases has been identified by solid-state nuclear magnetic resonance (NMR). This intermediate component accounts for nearly 25% of the material bulk, exceeding the amorphous fraction at the highest draw ratios. In the neat isotropic material examined for reference, the NMR-derived composition shows excellent agreement with other techniques. 13C NMR isotropic chemical shifts of the intermediate component, whose signal was selected using an “inverse T1,C filter”, prove chains of nearly all-trans conformations; the line width indicates significant disorder. Reduction of dipolar couplings and the chemical-shift anisotropy show fast rotations of 30 50 deg. amplitude around the chain axes. The degree of orientation of the chain axes is high. Spin diffusion experiments suggest that the intermediate component consists mostly of extended chain bundles closely associated with the amorphous phase (tie-molecule bundles ?).

  13. Acetic anhydride: an intermediate analogue in the acyl-exchange reaction of citramalate lyase.

    PubMed

    Buckel, W

    1976-04-15

    1. Reactivation of deacetyl citramalate lyase by acetic anhydride proceeds through an enzyme-anhydride complex prior to actual acetylation. The reaction is inhibited by citramalate which is competitive with acetic anhydride. 2. A corresponding complex is an intermediate in the carboxymethylation of deacetyl enzyme by iodoacetate. However, the inhibition of this reaction by S-citramalate appears to be non-competitive with iodoacetate. 3. The results lead to the conclusion that acetic anhydride can be regarded as a structural analogue of citramalic acetic anhydride, the proposed intermediate in the acyl exchange reaction on citramalate lyase. 4. The formation of 6-citryl thiolester from the 1-thiolester via the cyclic citric anhydride provides a chemicla model for enzymic acyl exchange. 5. The data suggest that anhydrides are of general importance in acyl exchange reactions of thiolesters. PMID:1278157

  14. 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.

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

    PubMed

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

    2013-09-01

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

  16. International chemical identifier for reactions (RInChI)

    PubMed Central

    2013-01-01

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

  17. Recent developments in methods for identifying reaction coordinates

    PubMed Central

    Li, Wenjin; Ma, Ao

    2014-01-01

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

  18. Arylpalladium Phosphonate Complexes as Reactive Intermediates in Phosphorus-Carbon Bond Forming Reactions

    SciTech Connect

    Kohler, Mark C.; Grimes, Thomas V.; Wang, Xiaoping; Cundari, Thomas R.; Stockland, Robert A. Jr.

    2009-01-01

    Phosphorus-carbon bond formation from discrete transition metal complexes have been investigated through a combination of synthetic, spectroscopic, crystallographic, and computational methods. Reactive intermediates of the type (diphosphine)Pd(aryl)(P(O)(OEt)(2)) have been prepared, characterized, and studied as possible intermediates in metal-mediated coupling reactions. Several of the reactive intermediates were characterized crystallographicaliy, and a discussion of the solid state structures is presented. In contrast to other carbon-heteroelement bond forming reactions, palladium complexes containing electron-donating substituents on the aromatic fragment exhibited faster rates of reductive elimination. Large bite angle diphosphine ligands induced rapid rates of elimination, while bipyridine and small bite angle diphosphine ligands resulted in much slower rates of elimination. An investigation of the effect of typical impurities on the elimination reaction was carried out. While excess diphosphine, pyridine, and acetonitrile had little effect on the observed rate, the addition of water slowed the phosphorus-carbon bond forming reaction. Coordination of water to the complex was observed spectroscopically and crystallographically. Computational studies were utilized to probe the reaction pathways for P-C bond formation via Pd catalysis.

  19. Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates

    PubMed Central

    Radisky, Evette S.; Lee, Justin M.; Lu, Chia-Jung Karen; Koshland, Daniel E.

    2006-01-01

    Atomic resolution structures of trypsin acyl-enzymes and a tetrahedral intermediate analog, along with previously solved structures representing the Michaelis complex, are used to reconstruct events in the catalytic cycle of this classic serine protease. Structural comparisons provide insight into active site adjustments involved in catalysis. Subtle motions of the catalytic serine and histidine residues coordinated with translation of the substrate reaction center are seen to favor the forward progress of the acylation reaction. The structures also clarify the attack trajectory of the hydrolytic water in the deacylation reaction. PMID:16636277

  20. 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.

  1. Electron nuclear double resonance determined structures of enzyme reaction intermediates: structural evidence for substrate destabilization

    NASA Astrophysics Data System (ADS)

    Makinen, Marvin W.

    1998-12-01

    Angle selective ENDOR of nitroxyl spin-labels is briefly reviewed to illustrate the methodology of structure analysis developed in our laboratory for characterizing catalytically competent intermediates of enzyme catalyzed reactions. ENDOR structure determination of a reaction intermediate of α-chymotrypsin formed with a kinetically specific spin-labeled substrate and of an enzyme-inhibitor complex formed with a spin-labeled transition-state inhibitor analog is briefly described. Both spin-labeled molecules bound in the active site of the enzyme are found in torsionally distorted conformations. It is suggested that this torsionally distorted state in which the bound ligand is of higher potential energy than in the ground state conformation reflects substrate destabilization in the course of the enzyme catalyzed reaction.

  2. Benchmarking of activation reaction distribution in an intermediate energy neutron field.

    PubMed

    Ogawa, Tatsuhiko; Morev, Mikhail N; Hirota, Masahiro; Abe, Takuya; Koike, Yuya; Iwai, Satoshi; Iimoto, Takeshi; Kosako, Toshiso

    2011-07-01

    Neutron-induced reaction rate depth profiles inside concrete shield irradiated by intermediate energy neutron were calculated using a Monte-Carlo code and compared with an experiment. An irradiation field of intermediate neutron produced in the forward direction from a thick (stopping length) target bombarded by 400 MeV nucleon(-1) carbon ions was arranged at the heavy ion medical accelerator in Chiba. Ordinary concrete shield of 90 cm thickness was installed 50 cm downstream the iron target. Activation detectors of aluminum, gold and gold covered with cadmium were inserted at various depths. Irradiated samples were extracted after exposure and gamma-ray spectrometry was performed for each sample. Comparison of experimental and calculated shows good agreement for both low- and high-energy neutron-induced reaction except for (27)Al(n,X)(24)Na reaction at the surface. PMID:21515619

  3. 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 substrate’s nonreacting phosphoryl group to accelerate catalysis. Evidence for the involvement of the phosphodianion in transition state formation has come from reactions of the substrate in pieces, in which reaction of a truncated substrate lacking its phosphorylmethyl group is activated by inorganic phosphite. What has remained unknown until now is how the phosphodianion group influences the reaction energetics at different points along the reaction coordinate. 1-Deoxy-D-xylulose-5-phosphate (DXP) reductoisomerase (DXR), which catalyzes the isomerization of DXP to 2-C-methyl-D-erythrose 4-phosphate (MEsP) and subsequent NADPH-dependent reduction, presents a unique opportunity to address this concern. Previously, we have reported the effect of covalently linked phosphate on the energetics of DXP turnover. Through the use of chemically synthesized MEsP and its phosphate-truncated analogue, 2-C-methyl-D-glyceraldehyde, the current study revealed a loss of 6.1 kcal/mol of kinetic barrier stabilization upon truncation, of which 4.4 kcal/mol was regained in the presence of phosphite dianion. The activating effect of phosphite was accompanied by apparent tightening of its interactions within the active site at the intermediate stage of the reaction, suggesting a role of the phosphodianion in disfavoring intermediate release and in modulation of the on-enzyme isomerization equilibrium. The results of kinetic isotope effect and structural studies indicate rate limitation by physical steps when the covalent linkage is severed. These striking differences in the energetics of the natural reaction and the reactions in pieces provide a deeper insight into the contribution of enzyme–phosphodianion interactions to the reaction coordinate. PMID:25642788

  4. 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.

  5. The Identification of Stable Reaction Intermediates on Aluminum Oxide Surfaces with Inelastic Electron Tunneling Spectroscopy

    NASA Astrophysics Data System (ADS)

    Templeton, Michael Karpovich

    The stable surface intermediates that were formed in several heterogeneous reactions on aluminum oxide films were identified with inelastic electron tunneling spectroscopy. The alumina films were synthesized by the plasma oxidation of aluminum metal films. The temperature and exposure dependent interaction of cyclopropane carboxylic acid with alumina films was studied. Cyclopropane carboxylate and n-butane carboxylate were the only adsorbed species formed. The n-butane carboxylate results from hydrogenolysis of the cyclopropyl ring of the adsorbed cyclopropane carboxylate with hydrogen supplied by surface hydroxyl groups. The relative populations of the two surface species are strongly dependent upon coverage and temperature. The adsorption of gaseous dimethyl methyl phosphonate (DMMP) on alumina films was investigated. Surface temperatures ranged between 200 K and 673 K, and exposures ranged between 3 x 10('-4) and 10 Torr-s. Tunneling spectra of deuterium labeled DMMP, perdeutero methyl alcohol, methyl methyl phosphonic acid, methyl phosphonic acid and trimethyl phosphine oxide, all adsorbed on aluminum oxide surfaces, were used to clarify the structures of the species resulting from the adsorption and decomposition of DMMP. At 200 K, DMMP is adsorbed molecularly with high surface coverages. At surface temperatures above 295 K, DMMP is adsorbed dissociatively in low coverages. Surface temperatures above 473 K lead to the dealkylation of the dissociatively adsorbed adspecies, which results in the formation of adsorbed methyl phosphonate. The adsorption and reaction of three phosphonate esters on alumina films was comparatively examined. The phosphonate esters were diisopropyl methyl phosphonate (DIMP), dimethyl methyl phosphonate (DMMP) and diphenyl methyl phosphonate (DPMP). The adsorption temperatures ranged from 200 to 673 K. At 373 K, DIMP was found to adsorb dissociatively in low coverages as isopropyl methyl phosphonate. Above 373 K the isopropyl methyl

  6. 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.

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

    PubMed

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

    2015-02-01

    Criegee intermediates are important species formed during the ozonolysis of alkenes. Reaction of stabilized Criegee intermediates with various species like SO2 and NO2 may contribute significantly to tropospheric chemistry. In the laboratory, self-reaction can be an important loss pathway for Criegee intermediates and thus needs to be characterized to obtain accurate bimolecular reaction rate coefficients. Cavity ring-down spectroscopy was used to perform kinetic measurements for various reactions of CH2OO at 293 K and under low pressure (7 to 30 Torr) conditions. For the reaction CH2OO + CH2OO (8), a rate coefficient k8 = (7.35 ± 0.63) × 10(-11) cm(3) molecule(-1) s(-1) was derived from the measured CH2OO decay rates, using an absorption cross section value reported previously. A rate coefficient of k4 = (3.80 ± 0.04) × 10(-11) cm(3) molecule(-1) s(-1) was obtained for the CH2OO + SO2 (4) reaction. An upper limit for the unimolecular CH2OO loss rate coefficient of 11.6 ± 8.0 s(-1) was deduced from studies of reaction (4). SO2 catalysed CH2OO isomerization or intersystem crossing is proposed to occur with a rate coefficient of (3.53 ± 0.32) × 10(-11) cm(3) molecule(-1) s(-1). PMID:25553776

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  9. 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.

  10. Holliday intermediates and reaction by-products in FLP protein-promoted site-specific recombination.

    PubMed Central

    Meyer-Leon, L; Huang, L C; Umlauf, S W; Cox, M M; Inman, R B

    1988-01-01

    Holliday structures are formed and resolved by FLP protein during site-specific recombination. These structures have been isolated and are visualized in both native and partially denatured states by electron microscopy. No single-strand breaks are found within the junction, indicating that the structure results from a reciprocal exchange of strands. These structures have properties consistent with being reaction intermediates. Double-strand cleavage products and "Y structures" are also detected and appear to be by-products of the reaction. The Y structures are three-armed branched molecules with a covalently closed junction located at the FLP recombination target site. Models are discussed, suggesting that both of these novel structures are made by aberrant cleavages during formation and resolution of the Holliday intermediate. Images PMID:3065624

  11. Possibility of production of neutron-rich isotopes in transfer-type reactions at intermediate energies

    SciTech Connect

    Adamian, G. G.; Antonenko, N. V.; Lukyanov, S. M.; Penionzhkevich, Yu. E.

    2008-08-15

    The production cross sections of neutron-rich isotopes of Mg, Al, Si, P, S, Cl, Ar, K, Ca, Sc, and Ti in the multinucleon transfer reactions {sup 48}Ca(64 MeV/nucleon, 140 MeV/nucleon) + {sup 181}Ta and {sup 48}Ca(142 MeV/nucleon) + {sup nat}W are estimated. A good agreement of the calculated results with the available experimental data confirms the mechanism of multinucleon transfer at almost peripheral collisions at intermediate energies. The global trend of production cross section with the charge (mass) number of target in reactions with {sup 48}Ca beam is discussed for the future experiments.

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

    SciTech Connect

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

    2013-06-01

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

  13. 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)...

  14. 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.

  15. 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.

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

    PubMed Central

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

    2015-01-01

    Acetyl-CoA carboxylase catalyzes the first and regulated step in fatty acid synthesis. In most Gram-negative and Gram-positive bacteria, the enzyme is composed of three proteins: biotin carboxylase, a biotin carboxyl carrier protein (BCCP), and carboxyltransferase. The reaction mechanism involves two half-reactions with biotin carboxylase catalyzing the ATP-dependent carboxylation of biotin-BCCP in the first reaction. In the second reaction, carboxyltransferase catalyzes the transfer of the carboxyl group from biotin-BCCP to acetyl-CoA to form malonyl-CoA. In this report, high-resolution crystal structures of biotin carboxylase from Haemophilus influenzae were determined with bicarbonate, the ATP analogue AMPPCP; the carboxyphosphate intermediate analogues, phosphonoacetamide and phosphonoformate; the products ADP and phosphate; and the carboxybiotin analogue N1′-methoxycarbonyl biotin methyl ester. The structures have a common theme in that bicarbonate, phosphate, and the methyl ester of the carboxyl group of N1′-methoxycarbonyl biotin methyl ester all bound in the same pocket in the active site of biotin carboxylase and as such utilize the same set of amino acids for binding. This finding suggests a catalytic mechanism for biotin carboxylase in which the binding pocket that binds tetrahedral phosphate also accommodates and stabilizes a tetrahedral dianionic transition state resulting from direct transfer of CO2 from the carboxyphosphate intermediate to biotin. PMID:26020841

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

    PubMed

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

    2015-06-23

    Acetyl-CoA carboxylase catalyzes the first and regulated step in fatty acid synthesis. In most Gram-negative and Gram-positive bacteria, the enzyme is composed of three proteins: biotin carboxylase, a biotin carboxyl carrier protein (BCCP), and carboxyltransferase. The reaction mechanism involves two half-reactions with biotin carboxylase catalyzing the ATP-dependent carboxylation of biotin-BCCP in the first reaction. In the second reaction, carboxyltransferase catalyzes the transfer of the carboxyl group from biotin-BCCP to acetyl-CoA to form malonyl-CoA. In this report, high-resolution crystal structures of biotin carboxylase from Haemophilus influenzae were determined with bicarbonate, the ATP analogue AMPPCP; the carboxyphosphate intermediate analogues, phosphonoacetamide and phosphonoformate; the products ADP and phosphate; and the carboxybiotin analogue N1'-methoxycarbonyl biotin methyl ester. The structures have a common theme in that bicarbonate, phosphate, and the methyl ester of the carboxyl group of N1'-methoxycarbonyl biotin methyl ester all bound in the same pocket in the active site of biotin carboxylase and as such utilize the same set of amino acids for binding. This finding suggests a catalytic mechanism for biotin carboxylase in which the binding pocket that binds tetrahedral phosphate also accommodates and stabilizes a tetrahedral dianionic transition state resulting from direct transfer of CO₂ from the carboxyphosphate intermediate to biotin. PMID:26020841

  18. Reactions between Criegee Intermediates and the Inorganic Acids HCl and HNO3 : Kinetics and Atmospheric Implications.

    PubMed

    Foreman, Elizabeth S; Kapnas, Kara M; Murray, Craig

    2016-08-22

    Criegee intermediates (CIs) are a class of reactive radicals that are thought to play a key role in atmospheric chemistry through reactions with trace species that can lead to aerosol particle formation. Recent work has suggested that water vapor is likely to be the dominant sink for some CIs, although reactions with trace species that are sufficiently rapid can be locally competitive. Herein, we use broadband transient absorption spectroscopy to measure rate constants for the reactions of the simplest CI, CH2 OO, with two inorganic acids, HCl and HNO3 , both of which are present in polluted urban atmospheres. Both reactions are fast; at 295 K, the reactions of CH2 OO with HCl and HNO3 have rate constants of 4.6×10(-11)  cm(3)  s(-1) and 5.4×10(-10)  cm(3)  s(-1) , respectively. Complementary quantum-chemical calculations show that these reactions form substituted hydroperoxides with no energy barrier. The results suggest that reactions of CIs with HNO3 in particular are likely to be competitive with those with water vapor in polluted urban areas under conditions of modest relative humidity. PMID:27440012

  19. 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.

  20. 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

  1. Identifying Prolonged Grief Reactions in Children: Dimensional and Diagnostic Approaches

    PubMed Central

    Melhem, Nadine M.; Porta, Giovanna; Payne, Monica Walker; Brent, David A.

    2013-01-01

    Objective Children with prolonged grief reactions (PGR) have been found to be at increased risk for depression and functional impairment. Identifying and diagnosing PGR in children is challenging, as there are no available dimensional measures with established thresholds and no diagnostic criteria in the DSM-IV. We examine thresholds for the Inventory for Complicated Grief–Revised for Children (ICG-RC) and compare this dimensional approach to the proposed DSM-5 criteria for Persistent Complex Bereavement-Related Disorder. We also identify a screening tool for PGR. Method Parentally bereaved children, 8–17 years of age, were assessed at 9, 21, and 33 months after parental death. Receiver Operator Characteristics were used to establish the “best threshold” that would identify children with PGR and evaluate the proposed DSM-5 criteria cross-sectionally and longitudinally. Results A score of 68 or higher on the ICG-RC was found to have high sensitivity (0.942) and specificity (0.965) in differentiating cases with PGR from noncases at 9 months. We also identify a 6-item screening tool that consists of longing and yearning for the deceased, inability to accept the death, shock, disbelief, loneliness, and a changed world view. The proposed DSM-5 criteria only correctly identified 20% to 41.7% of cases with PGR at different timepoints. Conclusions For the identification of youth at risk for PGR, the dimensional approach outperformed the proposed categorical diagnostic criteria. We propose a brief screening scale that, if validated, can help clinicians identify bereaved children at risk for PGR, and guide the development of prevention and intervention strategies. PMID:23702449

  2. 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

  3. Inhibition of monoterpene cyclases by sulfonium analogs of presumptive carbocationic intermediates of the cyclization reaction.

    PubMed

    Croteau, R; Wheeler, C J; Aksela, R; Oehlschlager, A C

    1986-06-01

    The enzymatic cyclization of geranyl pyrophosphate to monoterpenes is thought to proceed through a series of carbocation-pyrophosphate anion paired intermediates. Sulfonium analogs of two putative carbocationic intermediates of the cyclization sequence were shown to be inhibitors of the conversion of the acyclic precursor to the bicyclic monoterpenes (+)-alpha-pinene and (+)-bornyl pyrophosphate by partially purified cyclase preparations from sage (Salvia officinalis). The sulfonium analog of the tertiary allylic, linalyl, intermediate (i.e. methyl-(4-methylpent-3-en-1-yl)vinyl-sulfonium perchlorate) provided respective Ki values of 2.5 microM and 3.0 microM against the cyclization to alpha-pinene and bornyl pyrophosphate at a substrate concentration of 5 microM, whereas the sulfonium analog of the monocyclic, alpha-terpinyl, intermediate (i.e. dimethyl-(4-methylcyclohex-3-en-1-yl) sulfonium iodide) exhibited respective Ki values of 3.4 microM and 3.9 microM against the same two cyclizations. The potency of inhibition in all cases increased with increasing substrate concentration, indicating that the affinity of the enzymes for the sulfonium analogs was increased by the presence of the pyrophosphate ester. Inorganic pyrophosphate at a concentration of 50 microM, which alone had little influence on the cyclizations, increased the effectiveness of inhibition of the sulfonium analogs severalfold, and the apparent Ki for inorganic pyrophosphate was reduced manyfold by the presence of either analog at 5 microM. That the combination of sulfonium analog and pyrophosphate provided synergistic inhibition of the electrophilic cyclizations indicated that the cyclases bind the paired species more tightly than either partner alone. Specificity studies suggested that inhibition by the above sulfonium ion:pyrophosphate pairs was due to both electronic and structural resemblance to intermediates of the reaction. PMID:3011779

  4. Characterization of a diiron(III) peroxo intermediate in the reaction cycle of methane monooxygenase hydroxylase from Methylococcus cupsulatus (Bath)

    SciTech Connect

    Liu, K.E.; Valentine, A.M.; Lippard, S.J.; Qiu, D.; Spiro, T.G.; Edmondson, D.E.; Appelman, E.H.

    1995-05-03

    We present new optical and resonance Raman spectroscopic data that characterize the first intermediate as a diiron(III) peroxo species. The time-resolved optical and freeze-quench resonance Raman spectroscopic experiments strongly support assignment of the first intermediate, variously designated P or L, in the MMO hydroxylase reaction cycle as a symmetrical diiron(III) peroxo species. 32 refs., 2 figs.

  5. 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

  6. 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.

  7. 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

  8. Photonuclear reactions of actinide and pre-actinide nuclei at intermediate energies

    SciTech Connect

    Mukhopadhyay, Tapan; Basu, D. N.

    2007-12-15

    Photonuclear reaction is described with an approach based on the quasideuteron nuclear photoabsorption model followed by the process of competition between light particle evaporation and fission for the excited nucleus. Thus fission process is considered as a decay mode. The evaporation-fission process of the compound nucleus is simulated in a Monte Carlo framework. Photofission reaction cross sections are analysed in a systematic manner in the energy range {approx}50-70 MeV for the actinides {sup 232}Th, {sup 233}U, {sup 235}U, {sup 238}U, and {sup 237}Np and the pre-actinide nuclei {sup 208}Pb and {sup 209}Bi. The study reproduces satisfactorily well the available experimental data of photofission cross sections at energies {approx}50-70 MeV and the increasing trend of nuclear fissility with the fissility parameter Z{sup 2}/A for the actinides and pre-actinides at intermediate energies ({approx}20-140 MeV)

  9. 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

  10. Direct Observation of Intermediates Involved in the Interruption of the Bischler–Napieralski Reaction

    PubMed Central

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

    2015-01-01

    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, 1H, 13C, and 19F 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

  11. Reaction intermediates in the catalytic mechanism of Escherichia coli MutY DNA glycosylase.

    PubMed

    Manuel, Raymond C; Hitomi, Kenichi; Arvai, Andrew S; House, Paul G; Kurtz, Andrew J; Dodson, M L; McCullough, Amanda K; Tainer, John A; Lloyd, R Stephen

    2004-11-01

    The Escherichia coli adenine DNA glycosylase, MutY, plays an important role in the maintenance of genomic stability by catalyzing the removal of adenine opposite 8-oxo-7,8-dihydroguanine or guanine in duplex DNA. Although the x-ray crystal structure of the catalytic domain of MutY revealed a mechanism for catalysis of the glycosyl bond, it appeared that several opportunistically positioned lysine side chains could participate in a secondary beta-elimination reaction. In this investigation, it is established via site-directed mutagenesis and the determination of a 1.35-A structure of MutY in complex with adenine that the abasic site (apurinic/apyrimidinic) lyase activity is alternatively regulated by two lysines, Lys142 and Lys20. Analyses of the crystallographic structure also suggest a role for Glu161 in the apurinic/apyrimidinic lyase chemistry. The beta-elimination reaction is structurally and chemically uncoupled from the initial glycosyl bond scission, indicating that this reaction occurs as a consequence of active site plasticity and slow dissociation of the product complex. MutY with either the K142A or K20A mutation still catalyzes beta and beta-delta elimination reactions, and both mutants can be trapped as covalent enzyme-DNA intermediates by chemical reduction. The trapping was observed to occur both pre- and post-phosphodiester bond scission, establishing that both of these intermediates have significant half-lives. Thus, the final spectrum of DNA products generated reflects the outcome of a delicate balance of closely related equilibrium constants. PMID:15326180

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

    PubMed

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

    2016-07-01

    Chemical transformations at the interface between solid/liquid or solid/gaseous phases of matter lie at the heart of key industrial-scale manufacturing processes. A comprehensive study of the molecular energetics and conformational dynamics that underlie these transformations is often limited to ensemble-averaging analytical techniques. Here we report the detailed investigation of a surface-catalysed cross-coupling and sequential cyclization cascade of 1,2-bis(2-ethynyl phenyl)ethyne on Ag(100). Using non-contact atomic force microscopy, we imaged the single-bond-resolved chemical structure of transient metastable intermediates. Theoretical simulations indicate that the kinetic stabilization of experimentally observable intermediates is determined not only by the potential-energy landscape, but also by selective energy dissipation to the substrate and entropic changes associated with key transformations along the reaction pathway. The microscopic insights gained here pave the way for the rational design and control of complex organic reactions at the surface of heterogeneous catalysts. PMID:27325094

  13. Inhibition of biotin carboxylase by a reaction intermediate analog: implications for the kinetic mechanism.

    PubMed

    Blanchard, C Z; Amspacher, D; Strongin, R; Waldrop, G L

    1999-12-20

    The first committed step in long-chain fatty acid synthesis is catalyzed by the multienzyme complex acetyl CoA carboxylase. One component of the acetyl CoA carboxylase complex is biotin carboxylase which catalyzes the ATP-dependent carboxylation of biotin. The Escherichia coli form of biotin carboxylase can be isolated from the other components of the acetyl CoA carboxylase complex such that enzymatic activity is retained. The synthesis of a reaction intermediate analog inhibitor of biotin carboxylase has been described recently (Organic Lett. 1, 99-102, 1999). The inhibitor is formed by coupling phosphonoacetic acid to the 1'-N of biotin. In this paper the characterization of the inhibition of biotin carboxylase by this reaction-intermediate analog is described. The analog showed competitive inhibition versus ATP with a slope inhibition constant of 8 mM. Noncompetitive inhibition was found for the analog versus biotin. Phosphonoacetate exhibited competitive inhibition with respect to ATP and noncompetitive inhibition versus bicarbonate. Biotin was found to be a noncompetitive substrate inhibitor of biotin carboxylase. These data suggested that biotin carboxylase had an ordered addition of substrates with ATP binding first followed by bicarbonate and then biotin. PMID:10600526

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  16. Photochemical studies of reactive intermediates involved in gas phase ion-neutral reactions

    SciTech Connect

    Osterheld, T.H.

    1992-01-01

    Infrared multiple photon dissociation was used to study unimolecular reactions of gas phase ions in a Fourier transform mass spectrometer. Specifically, the influence of intermediates on reactivity and dynamics was investigated. Dissociation of nitrobenzene cation displays a variety of surprising and apparently non-statistical behavior. The authors demonstrated that some of its reactions involve an isomerization to phenyl nitrite cation by a dissociation/reassociation mechanism in an ion-neutral complex. This allowed the behavior to be explained by normal statistical reactions. Previous work in other laboratories suggested that methane loss from acetone cation occurs by tunneling of a hydrogen atom. Part of the evidence came from the observation of very large isotope effects. The authors demonstrated that methane loss could not occur by tunneling. They further showed that the isotope effects result from normal zero point vibrational energy differences in an ion-neutral complex mechanism. Two simple dissociations of butanone cation do not compete as expected. They also found that the rates for the low energy reactions are much slower than statistical calculations. They explained these results by a prior isomerization to an ion-neutral complex. They calculated that the ion-neutral complex has a higher density of states than butanone cation even at energies well below a reaction threshold. McLafferty and co-workers demonstrated that acetone enol cation isomerizes to a symmetric acetone cation structure which then loses methyl groups at unequal rates. The authors have confirmed this behavior and demonstrated that the non-statistical dissociation depends on the internal energy. They proposed that an excited vibrational mode of the transition state for isomerization couples more strongly with the reaction coordinate, thus yielding more non-statistical dissociation.

  17. Identifying Multimodal Intermediate Phenotypes Between Genetic Risk Factors and Disease Status in Alzheimer's Disease.

    PubMed

    Hao, Xiaoke; Yao, Xiaohui; Yan, Jingwen; Risacher, Shannon L; Saykin, Andrew J; Zhang, Daoqiang; Shen, Li

    2016-10-01

    Neuroimaging genetics has attracted growing attention and interest, which is thought to be a powerful strategy to examine the influence of genetic variants (i.e., single nucleotide polymorphisms (SNPs)) on structures or functions of human brain. In recent studies, univariate or multivariate regression analysis methods are typically used to capture the effective associations between genetic variants and quantitative traits (QTs) such as brain imaging phenotypes. The identified imaging QTs, although associated with certain genetic markers, may not be all disease specific. A useful, but underexplored, scenario could be to discover only those QTs associated with both genetic markers and disease status for revealing the chain from genotype to phenotype to symptom. In addition, multimodal brain imaging phenotypes are extracted from different perspectives and imaging markers consistently showing up in multimodalities may provide more insights for mechanistic understanding of diseases (i.e., Alzheimer's disease (AD)). In this work, we propose a general framework to exploit multi-modal brain imaging phenotypes as intermediate traits that bridge genetic risk factors and multi-class disease status. We applied our proposed method to explore the relation between the well-known AD risk SNP APOE rs429358 and three baseline brain imaging modalities (i.e., structural magnetic resonance imaging (MRI), fluorodeoxyglucose positron emission tomography (FDG-PET) and F-18 florbetapir PET scans amyloid imaging (AV45)) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. The empirical results demonstrate that our proposed method not only helps improve the performances of imaging genetic associations, but also discovers robust and consistent regions of interests (ROIs) across multi-modalities to guide the disease-induced interpretation. PMID:27277494

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

    SciTech Connect

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

    2013-08-08

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

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

    SciTech Connect

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

    2009-04-22

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

  20. 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.

  1. Enzymatic formation of prostamide F2alpha from anandamide involves a newly identified intermediate metabolite, prostamide H2.

    PubMed

    Yang, Wu; Ni, Jinsong; Woodward, David F; Tang-Liu, Diane D-S; Ling, Kah-Hiing John

    2005-12-01

    Prostaglandin F2alpha 1-ethanolamide (prostamide F2alpha) is a potent ocular hypotensive agent in animals and represents a new class of fatty acid amide compounds. Accumulated evidence indicated that anandamide, an endogenous bioactive ligand for cannabinoid receptors, may serve as a common substrate to produce all prostamides, including prostamide F2alpha. After incubation of anandamide with cyclooxygenase 2 (COX-2), the reaction mixture was profiled by HPLC and an intermediate metabolite was discovered and characterized as a cyclic endoperoxide ethanolamide using HPLC-tandem mass spectrometry. Formation of prostamide F2alpha was also demonstrated when the intermediate metabolite was isolated and incubated with prostaglandin F synthase (PGF synthase). These results suggest that the biosynthesis of prostamide F2alpha proceeds in two consecutive steps: oxidation of anandamide to form an endoperoxide intermediate by COX-2, and reduction of the endoperoxide intermediate to form prostamide F2alpha by PGF synthase. This endoperoxide ethanolamide intermediate has been proposed as prostamide H2. PMID:16150817

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

    PubMed

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

    2008-08-28

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

  3. 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.

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

    NASA Astrophysics Data System (ADS)

    Zimányi, László; 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.

  5. Reaction of ferric cytochrome P450cam with peracids: kinetic characterization of intermediates on the reaction pathway.

    PubMed

    Spolitak, Tatyana; Dawson, John H; Ballou, David P

    2005-05-27

    Reactions of substrate-free ferric cytochrome P450cam with peracids to generate Fe=O intermediates have previously been investigated with contradictory results. Using stopped-flow spectrophotometry, the reaction with m-chloroperoxybenzoic acid demonstrated an Fe(IV)=O + porphyrin pi-cation radical (Cpd I) (Egawa, T., Shimada, H., and Ishimura, Y. (1994) Biochem. Biophys. Res. Commun. 201, 1464-1469). By contrast, with peracetic acid, Fe(IV)=O plus a tyrosyl radical were observed by freeze-quench Mossbauer and EPR spectroscopy (Schunemann, V., Jung, C., Trautwein, A. X., Mandon, D., and Weiss, R. (2000) FEBS Lett. 479, 149-154). Our detailed kinetic studies have resolved these contradictory results. At pH >7, a significant fraction of Cpd I is formed transiently, whereas at low pH only a species with a Soret band at 406 nm, presumably Fe(IV)=O + tyrosyl radical, is observed. Evidence for formation of an acylperoxo complex en route to Cpd I was obtained. Because of rapid heme destruction, steps subsequent to formation of the highly oxidized forms could not be fully characterized. Heme destruction was avoided by including peroxidase substrates (e.g. guaiacol), which were oxidized to characteristic peroxidase products as the Fe(III)-P450 was regenerated. Addition of ascorbate to either of the high valent species also reforms the Fe(III) state with only a small loss of heme absorbance. These results indicate that typical peroxidase chemistry occurs with P450cam and offer an explanation for the contrasting results reported earlier. The delineation of improved conditions (pH, temperature, choice of peracid) for generating highly oxidized species with P450cam should be valuable for their further characterization. PMID:15781454

  6. 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.

  7. Fission Fragment Charge and Mass Distributions from Intermediate-Energy Reactions of 238-U Projectiles

    NASA Astrophysics Data System (ADS)

    Souliotis, G. A.; Loveland, W.; Zyromski, K. E.; Wozniak, G. J.; Morrissey, D. J.; Aleklett, Kjell

    1999-10-01

    The charge, mass and velocity distributions of fission fragments from the interaction of 20 MeV/nucleon 238-U projectiles with 27-Al and 208-Pb have been measured using the MSU A1200 fragment separator. The observed distributions from the U+Al reaction are consistent with fission following fusion-like events giving rise to products that are very n-deficient relative to the line of beta-stability. However, the distributions from the U+Pb reaction are consistent with fission following quasielastic or deep-inelastic collisions, resulting in fragments that are neutron rich. Substantial yields of very n-rich nuclei are observed. Estimates of rates of important n-rich nuclides from a typical second generation projectile-fragmentation (PF) facility are given. Finally, the importance of the present cross section data for the planning of next generation intermediate-energy PF facilities able to produce short-lived neutron-rich radioactive beams by fission of heavy projectiles is discussed.

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

    NASA Astrophysics Data System (ADS)

    Kerby, Leslie M.; Mashnik, Stepan G.

    2015-08-01

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

  9. 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

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

    PubMed

    Itoh, Shinobu

    2015-07-21

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

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

    SciTech Connect

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

    1990-12-01

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

  13. 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

  14. 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

  15. Electron Paramagnetic Resonance and Electron-Nuclear Double Resonance Studies of the Reactions of Cryogenerated Hydroperoxoferric–Hemoprotein Intermediates

    PubMed Central

    2015-01-01

    The fleeting ferric peroxo and hydroperoxo intermediates of dioxygen activation by hemoproteins can be readily trapped and characterized during cryoradiolytic reduction of ferrous hemoprotein–O2 complexes at 77 K. Previous cryoannealing studies suggested that the relaxation of cryogenerated hydroperoxoferric intermediates of myoglobin (Mb), hemoglobin, and horseradish peroxidase (HRP), either trapped directly at 77 K or generated by cryoannealing of a trapped peroxo-ferric state, proceeds through dissociation of bound H2O2 and formation of the ferric heme without formation of the ferryl porphyrin π-cation radical intermediate, compound I (Cpd I). Herein we have reinvestigated the mechanism of decays of the cryogenerated hydroperoxyferric intermediates of α- and β-chains of human hemoglobin, HRP, and chloroperoxidase (CPO). The latter two proteins are well-known to form spectroscopically detectable quasistable Cpds I. Peroxoferric intermediates are trapped during 77 K cryoreduction of oxy Mb, α-chains, and β-chains of human hemoglobin and CPO. They convert into hydroperoxoferric intermediates during annealing at temperatures above 160 K. The hydroperoxoferric intermediate of HRP is trapped directly at 77 K. All studied hydroperoxoferric intermediates decay with measurable rates at temperatures above 170 K with appreciable solvent kinetic isotope effects. The hydroperoxoferric intermediate of β-chains converts to the S = 3/2 Cpd I, which in turn decays to an electron paramagnetic resonance (EPR)-silent product at temperature above 220 K. For all the other hemoproteins studied, cryoannealing of the hydroperoxo intermediate directly yields an EPR-silent majority product. In each case, a second follow-up 77 K γ-irradiation of the annealed samples yields low-spin EPR signals characteristic of cryoreduced ferrylheme (compound II, Cpd II). This indicates that in general the hydroperoxoferric intermediates relax to Cpd I during cryoanealing at low temperatures, but

  16. 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

  17. 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.

  18. Infrared matrix isolation and theoretical study of the initial intermediates in the reaction of ozone with cycloheptene

    NASA Astrophysics Data System (ADS)

    Pinelo, Laura; Ault, Bruce S.

    2012-10-01

    Matrix isolation combined with infrared spectroscopy resulted in the observation of early intermediates in the reaction of two conformers of cycloheptene and ozone, marking the first observation of these intermediates for a cyclic alkene with conformational isomerism. Spectral evidence supports the presence of the primary ozonide of the chair and boat conformers of cis-cycloheptene, which represents the first time two primary ozonide isomers have been observed for any alkene. In addition, at least one conformer of the Criegee intermediate formed through ring-opening of the cyclic primary ozonide, as well as stable end products. Both the Criegee intermediate and primary ozonide were observed in the spectra of the initial deposition in twin jet experiments. After the matrix was annealed to 36 K, peaks of the primary ozonide increased by ˜250% while the peak of the Criegee intermediate increased by ˜150%. Supporting data was obtained from 18O-labeled ozone experiments. In addition to experimental evidence, further justification was provided by theoretical calculations at the B3LYP/6-311++G(d,2p) level. The photochemical reactions of the trapped species were also studied. After irradiation of the secondary ozonide and stable products of the ozonolysis reaction, 1-hexanal and carbon dioxide were observed. Late, stable oxidation products of cycloheptene were observed in merged jet experiments.

  19. 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

  20. 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.

  1. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  3. Identifying 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…

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

    PubMed

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

    2016-08-10

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

  5. 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.

  6. 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.

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

    PubMed

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

    2010-12-01

    The mechanism of the reaction of the sulfur dioxide (SO(2)) with four stabilized Criegee intermediates (stabCI-CH(3)-OO, stabCI-OO, stabCIx-OO, and stabCH(2)OO) produced via the ozonolysis of limonene have been investigated using ab initio and DFT (density functional theory) methods. It has been shown that the intermediate adduct formed by the initiation of these reactions may be followed by two different reaction pathways such as H migration reaction to form carboxylic acids and rearrangement of oxygen to produce the sulfur trioxide (SO(3)) from the terminal oxygen of the COO group and SO(2). We found that the reaction of stabCI-OO and stabCH(2)OO with SO(2) can occur via both the aforementioned scenarios, whereas that of stabCI-CH(3)-OO and stabCIx-OO with SO(2) is limited to the second pathway only due to the absence of migrating H atoms. It has been shown that at the CCSD(T)/6-31G(d) + CF level of theory the activation energies of six reaction pathways are in the range of 14.18-22.59 kcal mol(-1), with the reaction between stabCIx-OO and SO(2) as the most favorable pathway of 14.18 kcal mol(-1) activation energy and that the reaction of stabCI-OO and stabCH(2)OO with SO(2) occurs mainly via the second reaction path. The thermochemical analysis of the reaction between SO(2) and stabilized Criegee intermediates indicates that the reaction of SO(2) and stabilized Criegee intermediates formed from the exocyclic primary ozonide decomposition is the main pathway of the SO(3) formation. This is likely to explain the large (~100%) difference in the production rate in the favor of the exocyclic compounds observed in recent experiments on the formation of H(2)SO(4) from exocyclic and endocyclic compounds. PMID:21053959

  8. 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…

  9. 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.

  10. 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

  11. Insights into the carboxyltransferase reaction of pyruvate carboxylase from the structures of bound product and intermediate analogs.

    PubMed

    Lietzan, Adam D; St Maurice, Martin

    2013-11-15

    Pyruvate carboxylase (PC) is a biotin-dependent enzyme that catalyzes the MgATP- and bicarbonate-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. The carboxyltransferase (CT) domain of PC catalyzes the transfer of a carboxyl group from carboxybiotin to the accepting substrate, pyruvate. It has been hypothesized that the reactive enolpyruvate intermediate is stabilized through a bidentate interaction with the metal ion in the CT domain active site. Whereas bidentate ligands are commonly observed in enzymes catalyzing reactions proceeding through an enolpyruvate intermediate, no bidentate interaction has yet been observed in the CT domain of PC. Here, we report three X-ray crystal structures of the Rhizobium etli PC CT domain with the bound inhibitors oxalate, 3-hydroxypyruvate, and 3-bromopyruvate. Oxalate, a stereoelectronic mimic of the enolpyruvate intermediate, does not interact directly with the metal ion. Instead, oxalate is buried in a pocket formed by several positively charged amino acid residues and the metal ion. Furthermore, both 3-hydroxypyruvate and 3-bromopyruvate, analogs of the reaction product oxaloacetate, bind in an identical manner to oxalate suggesting that the substrate maintains its orientation in the active site throughout catalysis. Together, these structures indicate that the substrates, products and intermediates in the PC-catalyzed reaction are not oriented in the active site as previously assumed. The absence of a bidentate interaction with the active site metal appears to be a unique mechanistic feature among the small group of biotin-dependent enzymes that act on α-keto acid substrates. PMID:24157795

  12. 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

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  15. Synthesis and reactivity of intermediates formed in the T4 RNA ligase reaction.

    PubMed Central

    Hoffmann, P U; McLaughlin, L W

    1987-01-01

    The intermediate adenylated donor derivatives A(5')pp(5')dTp and A(5')pp(5')GpGpGp have been prepared from suitable phosphorylating reagents activated by 1-hydroxybenzotriazole. Phosphodiester bond formation between donor and acceptor oligonucleotides as catalyzed by T4 RNA ligase is shown to be more efficient when the adenylated form of the donor molecule is used. PMID:3299268

  16. Water oxidation: Intermediate identification

    NASA Astrophysics Data System (ADS)

    Cowan, Alexander J.

    2016-08-01

    The slow kinetics of light-driven water oxidation on haematite is an important factor limiting the material's efficiency. Now, an intermediate of the water-splitting reaction has been identified offering hope that the full mechanism will soon be resolved.

  17. 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

  18. 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

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

    PubMed

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

    2016-09-01

    Anaphylaxis has been defined as a 'severe, life-threatening generalized or systemic hypersensitivity reaction'. However, data indicate that the vast majority of food-triggered anaphylactic reactions are not life-threatening. Nonetheless, severe life-threatening reactions do occur and are unpredictable. We discuss the concepts surrounding perceptions of severe, life-threatening allergic reactions to food by different stakeholders, with particular reference to the inclusion of clinical severity as a factor in allergy and allergen risk management. We review the evidence regarding factors that might be used to identify those at most risk of severe allergic reactions to food, and the consequences of misinformation in this regard. For example, a significant proportion of food-allergic children also have asthma, yet almost none will experience a fatal food-allergic reaction; asthma is not, in itself, a strong predictor for fatal anaphylaxis. The relationship between dose of allergen exposure and symptom severity is unclear. While dose appears to be a risk factor in at least a subgroup of patients, studies report that individuals with prior anaphylaxis do not have a lower eliciting dose than those reporting previous mild reactions. It is therefore important to consider severity and sensitivity as separate factors, as a highly sensitive individual will not necessarily experience severe symptoms during an allergic reaction. We identify the knowledge gaps that need to be addressed to improve our ability to better identify those most at risk of severe food-induced allergic reactions. PMID:27138061

  20. Analysis of the reaction products from micro-vial pyrolysis of the mixture glucose/proline and of a tobacco leaf extract:Search for Amadori intermediates.

    PubMed

    Mitsui, Kazuhisa; David, Frank; Tienpont, Bart; Sandra, Koen; Ochiai, Nobuo; Tamura, Hirotoshi; Sandra, Pat

    2015-11-27

    Micro-vial pyrolysis (PyroVial) was used to study the production of compounds important for the aroma of heat-treated natural products such as tobacco. Firstly, a mixture of glucose and proline was pyrolyzed as model, as this sugar and amino acid are also abundant in tobacco leaf (Nicotiana tobacum L.). The pyrolysate was analyzed using headspace-GC–MS, liquid injection GC–MS and LC–MS. Next, micro-vial pyrolysis in combination with LC–MS was applied to tobacco leaf extract. Using MS deconvolution, molecular feature extraction and differential analysis it was possible to identify Amadori intermediates of the Maillard reaction in the tobacco leaf extract. The intermediate disappeared as was the case for 1-deoxy-1-prolino-β-d-fructose or the concentration decreased in the pyrolysate compared to the original extract such as for the 1-deoxy-1-[2-(3-pyridyl)-1-pyrrolidinyl]-β-d-fructose isomers indicating that Amadori intermediates are important precursors for aroma compound formation. PMID:26602543

  1. Mononuclear Nonheme High-Spin (S=2) versus Intermediate-Spin (S=1) Iron(IV)-Oxo Complexes in Oxidation Reactions.

    PubMed

    Bae, Seong Hee; Seo, Mi Sook; Lee, Yong-Min; Cho, Kyung-Bin; Kim, Won-Suk; Nam, Wonwoo

    2016-07-01

    Mononuclear nonheme high-spin (S=2) iron(IV)-oxo species have been identified as the key intermediates responsible for the C-H bond activation of organic substrates in nonheme iron enzymatic reactions. Herein we report that the C-H bond activation of hydrocarbons by a synthetic mononuclear nonheme high-spin (S=2) iron(IV)-oxo complex occurs through an oxygen non-rebound mechanism, as previously demonstrated in the C-H bond activation by nonheme intermediate (S=1) iron(IV)-oxo complexes. We also report that C-H bond activation is preferred over C=C epoxidation in the oxidation of cyclohexene by the nonheme high-spin (HS) and intermediate-spin (IS) iron(IV)-oxo complexes, whereas the C=C double bond epoxidation becomes a preferred pathway in the oxidation of deuterated cyclohexene by the nonheme HS and IS iron(IV)-oxo complexes. In the epoxidation of styrene derivatives, the HS and IS iron(IV) oxo complexes are found to have similar electrophilic characters. PMID:27273456

  2. 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.

  3. Probing elastic and inelastic breakup contributions to intermediate-energy two-proton removal reactions

    NASA Astrophysics Data System (ADS)

    Wimmer, K.; Bazin, D.; Gade, A.; Tostevin, J. A.; Baugher, T.; Chajecki, Z.; Coupland, D.; Famiano, M. A.; Ghosh, T. K.; Grinyer, G. F.; Hodges, R.; Howard, M. E.; Kilburn, M.; Lynch, W. G.; Manning, B.; Meierbachtol, K.; Quarterman, P.; Ratkiewicz, A.; Sanetullaev, A.; Stroberg, S. R.; Tsang, M. B.; Weisshaar, D.; Winkelbauer, J.; Winkler, R.; Youngs, M.

    2012-05-01

    The two-proton removal reaction from 28Mg projectiles has been studied at 93 MeV/u. First coincidence measurements of the heavy 26Ne projectile residues, the removed protons, and other light charged particles enabled the relative cross sections from each of the three possible elastic and inelastic proton removal mechanisms to be determined. These more final-state-exclusive measurements are key for further interrogation of these reaction mechanisms and use of the reaction channel for quantitative spectroscopy of very neutron-rich nuclei. The relative and absolute yields of the three contributing mechanisms are compared to reaction model expectations based on the use of eikonal dynamics and sd-shell-model structure amplitudes.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

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

    SciTech Connect

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

    2005-05-24

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

  10. Studies of the primary oxygen intermediate in the reaction of fully reduced cytochrome oxidase.

    PubMed

    Blackmore, R S; Greenwood, C; Gibson, Q H

    1991-10-15

    The formation and disappearance of a photosensitive species during the reaction of reduced cytochrome c oxidase (putatively a3II.O2), EC 1.9.3.1, has been followed by (a) mixing a3II.CO with O2 in a stopped flow apparatus; (b) initiating the oxygen-oxidase reaction by removing CO with a laser flash; (c) probing the reaction mixture for photosensitivity with a second laser flash. Photosensitivity appears in the reaction mixture after the first laser flash, reaches a maximum after 50-60 microseconds ([O2] greater than 100 microM), and disappears in a further 50-100 microseconds. The kinetics can be represented by the scheme [formula: see text]. In species B, O2 is associated with the protein, possibly CuB, but not with the heme. Species C is the photosensitive a3II.O2 complex, and in D, a3 iron has been oxidized. The formation of species C is responsible for the rapid phase of absorbance change in the oxidase-oxygen reaction. The rate of reaction with oxygen approaches the limit of 35,000 s-1 at high oxygen. Nitric oxide, however, reacts with FeII oxidase with a rate of 1 x 10(8) M-1 s-1, which is accurately maintained up to an observed rate of 10(5) s-1. In flash photolysis experiments, approximately half of the photodissociated nitric oxidase recombines in a biphasic geminate reaction with rates of 1 x 10(8) s-1 and 1 x 10(7) s-1. PMID:1655779

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. Hydrogen bonding to the cysteine ligand of superoxide reductase: acid-base control of the reaction intermediates.

    PubMed

    Tremey, Emilie; Bonnot, Florence; Moreau, Yohann; Berthomieu, Catherine; Desbois, Alain; Favaudon, Vincent; Blondin, Geneviève; Houée-Levin, Chantal; Nivière, Vincent

    2013-10-01

    Superoxide reductase (SOR) is a non-heme iron metalloenzyme that detoxifies superoxide radical in microorganisms. Its active site consists of an unusual non-heme Fe(2+) center in a [His4Cys1] square pyramidal pentacoordination, with the axial cysteine ligand proposed to be an essential feature in catalysis. Two NH peptide groups from isoleucine 118 and histidine 119 establish hydrogen bonds involving the sulfur ligand (Desulfoarculus baarsii SOR numbering). To investigate the catalytic role of these hydrogen bonds, the isoleucine 118 residue of the SOR from Desulfoarculus baarsii was mutated into alanine, aspartate, or serine residues. Resonance Raman spectroscopy showed that the mutations specifically induced an increase of the strength of the Fe(3+)-S(Cys) and S-Cβ(Cys) bonds as well as a change in conformation of the cysteinyl side chain, which was associated with the alteration of the NH hydrogen bonding involving the sulfur ligand. The effects of the isoleucine mutations on the reactivity of SOR with O2 (•-) were investigated by pulse radiolysis. These studies showed that the mutations induced a specific increase of the pK a of the first reaction intermediate, recently proposed to be an Fe(2+)-O2 (•-) species. These data were supported by density functional theory calculations conducted on three models of the Fe(2+)-O2 (•-) intermediate, with one, two, or no hydrogen bonds involving the sulfur ligand. Our results demonstrated that the hydrogen bonds between the NH (peptide) and the cysteine ligand tightly control the rate of protonation of the Fe(2+)-O2 (•-) reaction intermediate to form an Fe(3+)-OOH species. PMID:23917995

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

    PubMed Central

    Ujj, L; Jäger, F; Atkinson, G H

    1998-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2004-09-01

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

  19. Nuclear spin polarization following intermediate-energy heavy-ion reactions

    SciTech Connect

    Groh, D. E.; Pinter, J. S.; Mantica, P. F.; Mertzimekis, T. J.; Stuchbery, A. E.; Khoa, D. T.

    2007-11-15

    Intermediate-energy heavy-ion collisions can produce a spin polarization of the projectile-like species. Spin polarization has been observed for both nucleon removal and nucleon pickup processes. Qualitative agreement with measured spin polarization as a function of the momentum of the projectile-like fragment is found in a kinematic model that considers conservation of linear and angular momentum and assumes peripheral interactions between the fast projectile and target. Better quantitative agreement was reached by including more realistic angular distributions and deorientation caused by {gamma}-ray emission and by correcting for the out-of-plane acceptance. The newly introduced corrections were found to apply to both nucleon removal and nucleon pickup processes.

  20. 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

  1. 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)

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. [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)

  9. 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)

  10. 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

  11. 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

  12. 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

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

    SciTech Connect

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

    2008-08-28

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

  14. Syntheses of tricyanofluoroborates M[BF(CN)3] (M = Na, K): (CH3)3SiCl catalysis, countercation effect, and reaction intermediates.

    PubMed

    Sprenger, Jan A P; Landmann, Johannes; Drisch, Michael; Ignat'ev, Nikolai; Finze, Maik

    2015-04-01

    Potassium tricyanofluoroborate, K[BF(CN)3], which is the starting material for tricyanofluoroborate room-temperature ionic liquids [N. Ignat'ev et al. J. Fluorine Chem., submitted] was obtained on a molar scale (140 g) from Na[BF4] and (CH3)3SiCN with a purity of up to 99.9%. The initial product of the reaction that was catalyzed by (CH3)3SiCl was Na[BF(CN)3]·(CH3)3SiCN that was characterized by multinuclear NMR and vibrational spectroscopy, elemental analysis, differential scanning calorimetry, and single-crystal X-ray diffraction. Na[BF(CN)3]·(CH3)3SiCN was converted to K[BF(CN)3] via a simple extraction protocol. The catalytic effect of (CH3)3SiCl was evaluated and some intermediates of the reaction, including the isocyanoborate anion [BF(NC)(CN)2](-), were identified using multinuclear NMR and vibrational spectroscopy. K[BF2(CN)2] also reacted with (CH3)3SiCN in the presence of (CH3)3SiCl, to result in K[BF(CN)3]. The interpretation of the experimental observations was supported by data derived from density functional theory (DFT) calculations. In addition, the influence of selected countercations of the tetrafluoroborate anion on the progress of the (CH3)3SiCl-catalyzed reaction was studied. The fastest reaction was observed for Na[BF4], while the conversion of [BF4](-) to [BF(CN)3](-) was slower with the countercation K(+). Li[BF4] and [Et4N][BF4] were converted under the reaction conditions applied to Li[BF2(CN)2] and [Et4N][BF2(CN)2] only. PMID:25785852

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

    DOE PAGESBeta

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

    2015-05-02

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

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

    SciTech Connect

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

    2015-05-02

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

  17. Mechanistic studies on a Cu-catalyzed aerobic oxidative coupling reaction with N-phenyl tetrahydroisoquinoline: structure of intermediates and the role of methanol as a solvent.

    PubMed

    Boess, Esther; Sureshkumar, Devarajulu; Sud, Abhishek; Wirtz, Cornelia; Farès, Christophe; Klussmann, Martin

    2011-06-01

    The mechanism of an aerobic copper-catalyzed oxidative coupling reaction with N-phenyl tetrahydroisoquinoline was investigated. The oxidized species formed from the reaction of the amine with the copper catalyst were analyzed by NMR-spectroscopy. An iminium dichlorocuprate was found to be the reactive intermediate and could be structurally characterized by X-ray crystallography. The effect of methanol to effectively stabilize the iminium ion was investigated and shown to be beneficial in an oxidative allylation reaction. PMID:21561084

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

    PubMed

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

    2009-02-10

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

  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. 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…

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

    PubMed Central

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

    1994-01-01

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

  2. Reactions of Atmospheric Particulate Stabilized Criegee Intermediates Lead to High-Molecular-Weight Aerosol Components.

    PubMed

    Wang, MingYi; Yao, Lei; Zheng, Jun; Wang, XinKe; Chen, JianMin; Yang, Xin; Worsnop, Douglas R; Donahue, Neil M; Wang, Lin

    2016-06-01

    Aging of organic aerosol particles is one of the most poorly understood topics in atmospheric aerosol research. Here, we used an aerosol flow tube together with an iodide-adduct high-resolution time-of-flight chemical-ionization mass spectrometer equipped with a Filter Inlet for Gases and AEROsols (FIGAERO-HRToF-CIMS) to investigate heterogeneous ozonolysis of oleic acid (OL), developing a comprehensive oxidation mechanism with observed products. In addition to the well-known first-generation C9 products including nonanal, nonanoic acid, azelaic acid, and 9-oxononanoic acid, the iodide-adduct chemical ionization permitted unambiguous determination of a large number of high-molecular-weight particulate products up to 670 Da with minimum amounts of fragmentation. These high-molecular-weight products are characterized by a fairly uniform carbon oxidation state but stepwise addition of a carbon backbone moiety, and hence continuous decrease in the volatility. Our results demonstrate that heterogeneous oxidation of organic aerosols has a significant effect on the physiochemical properties of organic aerosols and that reactions of particulate SCIs from ozonolysis of an unsaturated particulate species represent a previously underappreciated mechanism that lead to formation of high-molecular-weight particulate products that are stable under typical atmospheric conditions. PMID:27186797

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed

    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, CH2OO and anti/syn-CH3C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH2OO and anti-CH3C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH3C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C-H bonds. For syn-CH3C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH3 group by the terminal O atom producing CH2C(H)O-OH. At 298 K, the intramolecular insertion process in CH2OO was found to be 600 times faster than the commonly assumed ring-closing reaction. PMID:25833584

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  6. 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.

  7. 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

  8. 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

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

    PubMed Central

    Becker, Mara L; Leeder, J Steven

    2011-01-01

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

  10. 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.

  11. 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

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

    SciTech Connect

    Isied, Stephan S.

    2003-03-11

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

  13. 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

  14. Role of the reaction of stabilized Criegee intermediates with peroxy radicals in particle formation and growth in air.

    PubMed

    Zhao, Yue; Wingen, Lisa M; Perraud, Véronique; Greaves, John; Finlayson-Pitts, Barbara J

    2015-05-21

    Ozonolysis of alkenes is an important source of secondary organic aerosol (SOA) in the atmosphere. However, the mechanisms by which stabilized Criegee intermediates (SCI) react to form and grow the particles, and in particular the contributions from oligomers, are not well understood. In this study, ozonolysis of trans-3-hexene (C6H12), as a proxy for small alkenes, was investigated with an emphasis on the mechanisms of particle formation and growth. Ozonolysis experiments were carried out both in static Teflon chambers (18-20 min reaction times) and in a glass flow reactor (24 s reaction time) in the absence and presence of OH or SCI scavengers, and under different relative humidity (RH) conditions. The chemical composition of polydisperse and size-selected SOA particles was probed using different mass spectrometric techniques and infrared spectroscopy. Oligomers having SCI as the chain unit are found to be the dominant components of such SOA particles. The formation mechanism for these oligomers suggested by our results follows the sequential addition of SCI to organic peroxy (RO2) radicals, in agreement with previous studies by Moortgat and coworkers. Smaller particles are shown to have a relatively greater contribution from longer oligomers. Higher O/C ratios are observed in smaller particles and are similar to those of oligomers resulting from RO2 + nSCI, supporting a significant role for longer oligomers in particle nucleation and early growth. Under atmospherically relevant RH of 30-80%, water vapor suppresses oligomer formation through scavenging SCI, but also enhances particle nucleation. Under humid conditions, or in the presence of formic or hydrochloric acid as SCI scavengers, peroxyhemiacetals are formed by the acid-catalyzed particle phase reaction between oligomers from RO2 + nSCI and a trans-3-hexene derived carbonyl product. In contrast to the ozonolysis of trans-3-hexene, oligomerization involving RO2 + nSCI does not appear to be prevalent in the

  15. 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

  16. EnD-Seq and AppEnD: sequencing 3' ends to identify nontemplated tails and degradation intermediates.

    PubMed

    Welch, Joshua D; Slevin, Michael K; Tatomer, Deirdre C; Duronio, Robert J; Prins, Jan F; Marzluff, William F

    2015-07-01

    Existing methods for detecting RNA intermediates resulting from exonuclease degradation are low-throughput and laborious. In addition, mapping the 3' ends of RNA molecules to the genome after high-throughput sequencing is challenging, particularly if the 3' ends contain post-transcriptional modifications. To address these problems, we developed EnD-Seq, a high-throughput sequencing protocol that preserves the 3' end of RNA molecules, and AppEnD, a computational method for analyzing high-throughput sequencing data. Together these allow determination of the 3' ends of RNA molecules, including nontemplated additions. Applying EnD-Seq and AppEnD to histone mRNAs revealed that a significant fraction of cytoplasmic histone mRNAs end in one or two uridines, which have replaced the 1-2 nt at the 3' end of mature histone mRNA maintaining the length of the histone transcripts. Histone mRNAs in fly embryos and ovaries show the same pattern, but with different tail nucleotide compositions. We increase the sensitivity of EnD-Seq by using cDNA priming to specifically enrich low-abundance tails of known sequence composition allowing identification of degradation intermediates. In addition, we show the broad applicability of our computational approach by using AppEnD to gain insight into 3' additions from diverse types of sequencing data, including data from small capped RNA sequencing and some alternative polyadenylation protocols. PMID:26015596

  17. EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates

    PubMed Central

    Welch, Joshua D.; Slevin, Michael K.; Tatomer, Deirdre C.; Duronio, Robert J.

    2015-01-01

    Existing methods for detecting RNA intermediates resulting from exonuclease degradation are low-throughput and laborious. In addition, mapping the 3′ ends of RNA molecules to the genome after high-throughput sequencing is challenging, particularly if the 3′ ends contain post-transcriptional modifications. To address these problems, we developed EnD-Seq, a high-throughput sequencing protocol that preserves the 3′ end of RNA molecules, and AppEnD, a computational method for analyzing high-throughput sequencing data. Together these allow determination of the 3′ ends of RNA molecules, including nontemplated additions. Applying EnD-Seq and AppEnD to histone mRNAs revealed that a significant fraction of cytoplasmic histone mRNAs end in one or two uridines, which have replaced the 1–2 nt at the 3′ end of mature histone mRNA maintaining the length of the histone transcripts. Histone mRNAs in fly embryos and ovaries show the same pattern, but with different tail nucleotide compositions. We increase the sensitivity of EnD-Seq by using cDNA priming to specifically enrich low-abundance tails of known sequence composition allowing identification of degradation intermediates. In addition, we show the broad applicability of our computational approach by using AppEnD to gain insight into 3′ additions from diverse types of sequencing data, including data from small capped RNA sequencing and some alternative polyadenylation protocols. PMID:26015596

  18. 4′-CyanoPLP presents better prospect for the experimental detection of elusive cyclic intermediate radical in the reaction of lysine 5,6-aminomutase

    SciTech Connect

    Maity, Amarendra Nath; Ke, Shyue-Chu

    2015-02-06

    Graphical abstract: The results of our calculations suggest that the reaction of 4′-cyanoPLP with lysine 5,6-aminomutase offers better prospect for the experimental detection of elusive cyclic azacyclopropylcarbinyl radical, which is proposed to be a key intermediate in the reaction of pyridoxal-5′-phosphate dependent radical aminomutases. - Highlights: • 4′-CyanoI{sup ·} is the lowest energy radical intermediate in the reaction of 5,6-LAM. • 4′-CyanoPLP offers good prospect for the experimental observation of elusive I{sup ·}. • The calculated HFCCs would help to characterize 4′-cyanoI{sup ·} by EPR. - Abstract: The results of our calculations suggest that the reaction of 4′-cyanoPLP with lysine 5,6-aminomutase offers better prospect for the experimental detection of elusive cyclic azacyclopropylcarbinyl radical (I{sup ·}), which is proposed to be a key intermediate in the reaction of pyridoxal-5′-phosphate dependent radical aminomutases. We have calculated the corresponding hyperfine coupling constants (HFCCs) for {sup 14}N and {sup 13}C of cyano group using several basis sets to help the characterization of 4′-cyanoI{sup ·}.

  19. 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.

  20. 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.

  1. 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.

  2. 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

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

    SciTech Connect

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

    2011-01-01

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

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

    PubMed

    Tubau, Isabel; Vàzquez-Suñé, Enric; Jurado, Anna; Carrera, Jesús

    2014-02-01

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

  5. Kinetics and mechanism of the reaction of [RuIII(edta)(H2O)]- with HOBr to form an intermediate RuV=O complex in aqueous solution.

    PubMed

    Chatterjee, Debabrata; Mitra, Anannya; van Eldik, Rudi

    2006-10-21

    The interaction of [Ru(III)(edta)(H(2)O)](-) (1) (edta = ethylenediaminetetraacetate) with the oxygen transfer agent HOBr, was studied kinetically as a function of [HOBr] and temperature (5-35 degrees C) at a fixed pH of 6.2. Spectroscopic evidence is reported for the formation of a high valent intermediate (edta)Ru(V)=O complex. Water soluble 2,2'-azobis(3-ethylbenzithiazoline-6-sulfonate) (ABTS) was employed as a trap for this intermediate in order to gain further mechanistic information. Reactions were carried out under pseudo-first conditions for [ABTS] > [HOBr] > [1], and were monitored as a function of time for the formation of the one-electron oxidation product ABTS(*+). The reported kinetic data are interpreted in terms of a suggested reaction mechanism and discussed in reference to data reported before. PMID:17028677

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

    PubMed

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

    2016-01-01

    The spectroscopic and kinetic characterization of two intermediates from the H₂O₂ oxidation of three dimethyl ester [(proto), (meso), (deuteroporphyrinato) (picdien)]Fe(III) complexes ([FePPPic], [FeMPPic] and [FeDPPic], respectively) pinch-porphyrin peroxidase enzyme models, with s = 5/2 and 3/2 Fe(III) quantum mixed spin (qms) ground states is described herein. The kinetic study by UV/Vis at λmax = 465 nm showed two different types of kinetics during the oxidation process in the guaiacol test for peroxidases (1-3 + guaiacol + H₂O₂ → oxidation guaiacol products). The first intermediate was observed during the first 24 s of the reaction. When the reaction conditions were changed to higher concentration of pinch-porphyrins and hydrogen peroxide only one type of kinetics was observed. Next, the reaction was performed only between pinch-porphyrins-Fe(III) and H₂O₂, resulting in only two types of kinetics that were developed during the first 0-4 s. After this time a self-oxidation process was observed. Our hypotheses state that the formation of the π-cation radicals, reaction intermediates of the pinch-porphyrin-Fe(III) family with the ligand picdien [N,N'-bis-pyridin-2-ylmethyl-propane-1,3-diamine], occurred with unique kinetics that are different from the overall process and was involved in the oxidation pathway. UV-Vis, ¹H-NMR and ESR spectra confirmed the formation of such intermediates. The results in this paper highlight the link between different spectroscopic techniques that positively depict the kinetic traits of artificial compounds with enzyme-like activity. PMID:27355940

  7. Facile Detection of Acyl- and Peptidyl- intermediates on Thiotemplate Carrier Domains via Phosphopantetheinyl Elimination Reactions During Tandem Mass Spectrometry

    PubMed Central

    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.

    2008-01-01

    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 ultra large 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

  8. Two Reaction Mechanisms via Iminium Ion Intermediates: The Different Reactivities of Diphenylprolinol Silyl Ether and Trifluoromethyl-Substituted Diarylprolinol Silyl Ether.

    PubMed

    Gotoh, Hiroaki; Uchimaru, Tadafumi; Hayashi, Yujiro

    2015-08-24

    The reactions of α,β-unsaturated aldehydes with cyclopentadiene in the presence of diarylprolinol silyl ethers as catalyst proceed via iminium cations as intermediates, and can be divided into two types; one involving a Michael-type reaction (type A) and one involving a cycloaddition (type B). Diphenylprolinol silyl ethers and trifluoromethyl-substituted diarylprolinol silyl ethers, which are widely used proline-type organocatalysts, have been investigated in this study. As the LUMO of the iminium ion derived from trifluoromethyl-substituted diarylprolinol silyl ether is lower in energy than that derived from diphenylprolinol silyl ether, as supported by ab initio calculations, the trifluoromethyl-substituted catalyst is more reactive in a type B reaction. The iminium ion from an α,β-unsaturated aldehyde is generated more quickly with diphenylprolinol silyl ether than with the trifluoromethyl-substituted diarylprolinol silyl ether. When the generation of the iminium ion is the rate-determining step, the diphenylprolinol silyl ether catalyst is the more reactive. Because acid accelerates the generation of iminium ions and reduces the generation of anionic nucleophiles in the Michael-type reaction (type A), it is necessary to select the appropriate acid for specific reactions. In general, diphenylprolinol silyl ether is a superior catalyst for type A reactions, whereas the trifluoromethyl-substituted diarylprolinol silyl ether catalyst is preferred for type B reactions. PMID:26096559

  9. 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.

  10. 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

  11. Tracking reactive intermediates by FTIR monitoring of reactions in low-temperature sublimed solids: nitric oxide disproportionation mediated by ruthenium(II) carbonyl porphyrin Ru(TPP)(CO).

    PubMed

    Azizyan, Arsen S; Kurtikyan, Tigran S; Martirosyan, Garik G; Ford, Peter C

    2013-05-01

    Interaction of NO ((15)NO) with amorphous layers of Ru(II) carbonyl porphyrin (Ru(TPP)(CO), TPP(2-) = meso-tetraphenylporphyrinato dianion) was monitored by FTIR spectroscopy from 80 K to room temperature. An intermediate spectrally characterized at very low temperatures (110 K) with ν(CO) at 2001 cm(-1) and ν(NO) at 1810 cm(-1) (1777 cm(-1) for (15)NO isotopomer) was readily assigned to the mixed carbonyl-nitrosyl complex Ru(TPP)(CO)(NO), which is the logical precursor to CO labilization. Remarkably, Ru(TPP)-mediated disproportionation of NO is seen even at 110 K, an indication of how facile this reaction is. By varying the quantity of supplied NO, it was also demonstrated that the key intermediate responsible for NO disproportionation is the dinitrosyl complex Ru(TPP)(NO)2, supporting the conclusion previously made from solution experiments. PMID:23573997

  12. 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

  13. Structural and Kinetic Evidence That Catalytic Reaction of Human UDP-glucose 6-Dehydrogenase Involves Covalent Thiohemiacetal and Thioester Enzyme Intermediates*

    PubMed Central

    Egger, Sigrid; Chaikuad, Apirat; Klimacek, Mario; Kavanagh, Kathryn L.; Oppermann, Udo; Nidetzky, Bernd

    2012-01-01

    Biosynthesis of UDP-glucuronic acid by UDP-glucose 6-dehydrogenase (UGDH) occurs through the four-electron oxidation of the UDP-glucose C6 primary alcohol in two NAD+-dependent steps. The catalytic reaction of UGDH is thought to involve a Cys nucleophile that promotes formation of a thiohemiacetal enzyme intermediate in the course of the first oxidation step. The thiohemiacetal undergoes further oxidation into a thioester, and hydrolysis of the thioester completes the catalytic cycle. Herein we present crystallographic and kinetic evidence for the human form of UGDH that clarifies participation of covalent catalysis in the enzymatic mechanism. Substitution of the putative catalytic base for water attack on the thioester (Glu161) by an incompetent analog (Gln161) gave a UGDH variant (E161Q) in which the hydrolysis step had become completely rate-limiting so that a thioester enzyme intermediate accumulated at steady state. By crystallizing E161Q in the presence of 5 mm UDP-glucose and 2 mm NAD+, we succeeded in trapping a thiohemiacetal enzyme intermediate and determined its structure at 2.3 Å resolution. Cys276 was covalently modified in the structure, establishing its role as catalytic nucleophile of the reaction. The thiohemiacetal reactive C6 was in a position suitable to become further oxidized by hydride transfer to NAD+. The proposed catalytic mechanism of human UGDH involves Lys220 as general base for UDP-glucose alcohol oxidation and for oxyanion stabilization during formation and breakdown of the thiohemiacetal and thioester enzyme intermediates. Water coordinated to Asp280 deprotonates Cys276 to function as an aldehyde trap and also provides oxyanion stabilization. Glu161 is the Brønsted base catalytically promoting the thioester hydrolysis. PMID:22123821

  14. From bis(silylene) and bis(germylene) pincer-type nickel(II) complexes to isolable intermediates of the nickel-catalyzed Sonogashira cross-coupling reaction.

    PubMed

    Gallego, Daniel; Brück, Andreas; Irran, Elisabeth; Meier, Florian; Kaupp, Martin; Driess, Matthias; Hartwig, John F

    2013-10-16

    The first [ECE]Ni(II) pincer complexes with E = Si(II) and E = Ge(II) metallylene donor arms were synthesized via C-X (X = H, Br) oxidative addition, starting from the corresponding [EC(X)E] ligands. These novel complexes were fully characterized (NMR, MS, and XRD) and used as catalyst for Ni-catalyzed Sonogashira reactions. These catalysts allowed detailed information on the elementary steps of this catalytic reaction (transmetalation → oxidative addition → reductive elimination), resulting in the isolation and characterization of an unexpected intermediate in the transmetalation step. This complex, {[ECE]Ni acetylide → CuBr} contains both nickel and copper, with the copper bound to the alkyne π-system. Consistent with these unusual structural features, DFT calculations of the {[ECE]Ni acetylide → CuBr} intermediates revealed an unusual E-Cu-Ni three-center-two-electron bonding scheme. The results reveal a general reaction mechanism for the Ni-based Sonogashira coupling and broaden the application of metallylenes as strong σ-donor ligands for catalytic transformations. PMID:24053603

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  16. 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.

  17. 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

  18. 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

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

    NASA Astrophysics Data System (ADS)

    Dudouet, J.; Durand, D.

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  1. Modulation of the kinetics and the steady-state level of intermediates of mitochondrial coupled reactions by inhibitors and uncouplers.

    PubMed

    Yagi, T; Matsuno-Yagi, A; Vik, S B; Hatefi, Y

    1984-02-28

    In oxidative phosphorylation and ATP-driven uphill electron transfer from succinate to NAD, double-reciprocal plots of rates vs. substrate concentrations of the energy-driven reactions are a family of parallel lines at several fixed subsaturating concentrations of the substrates or at several moderate concentrations of the inhibitors of the energy-yielding reactions. Thus, as shown elsewhere [Hatefi, Y., Yagi, T., Phelps, D. C., Wong, S.-Y., Vik, S. B., & Galante, Y. M. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 1756-1760], partial uncoupling decreases the Vappmax and increases the Kappm of the substrates of the energy-driven reactions, resulting in a decrease of Vmax/Km as a function of increased uncoupling. However, partial limitation of the flow rates of the energy-yielding reactions decreases both the Vappmax and the Kappm of the substrates of the energy-driven reactions, resulting in no change in Vmax/Km. This is true as long as the rate limitation is moderate (e.g., less than 60%), under which conditions the steady-state membrane potential (delta psi) remains essentially unchanged. At high inhibition of the energy-yielding reactions, or at moderate inhibition in the presence of low levels of an uncoupler to cause partial uncoupling, then the family of double-reciprocal plots is no longer parallel and tends to converge toward the left. Under these conditions, steady-state delta psi and Vmax/Km also decrease as inhibition is increased. The relationship between the magnitude of steady-state delta psi and the rate of the energy-driven reaction was studied in oxidative phosphorylation, ATP-driven electron transfer from succinate to NAD, and respiration-driven uniport calcium transport by intact mitochondria.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:6712922

  2. Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile.

    PubMed

    Yamanaka, Yasuaki; Kato, Yuki; Hashimoto, Koichi; Iida, Keisuke; Nagasawa, Kazuo; Nakayama, Hiroshi; Dohmae, Naoshi; Noguchi, Keiichi; Noguchi, Takumi; Yohda, Masafumi; Odaka, Masafumi

    2015-09-01

    The reaction mechanism of nitrile hydratase (NHase) was investigated using time-resolved crystallography of the mutant NHase, in which βArg56, strictly conserved and hydrogen bonded to the two post-translationally oxidized cysteine ligands, was replaced by lysine, and pivalonitrile was the substrate. The crystal structures of the reaction intermediates were determined at high resolution (1.2-1.3 Å). In combination with FTIR analyses of NHase following hydration in H2 (18) O, we propose that the metal-coordinated substrate is nucleophilically attacked by the O(SO(-) ) atom of αCys114-SO(-) , followed by nucleophilic attack of the S(SO(-) ) atom by a βArg56-activated water molecule to release the product amide and regenerate αCys114-SO(-) . PMID:26333053

  3. 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

  4. 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.

  5. 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

  6. A closer look at the spectroscopic properties of possible reaction intermediates in wild-type and mutant (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase.

    PubMed

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

    2012-06-19

    (E)-4-Hydroxy-3-methylbut-2-enyl diphosphate reductase (IspH or LytB) catalyzes the terminal step of the MEP/DOXP pathway where it converts (E)-4-hydroxy-3-methylbut-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 the direct electron source for the reaction and that a reaction intermediate is bound directly to the cluster. This active form has been trapped in a state, dubbed FeS(A), that was detected by electron paramagnetic resonance (EPR) spectroscopy when one-electron-reduced IspH was incubated with HMBPP. In addition, three mutants of IspH have been prepared and studied, His42, His124, and Glu126 (Aquifex aeolicus numbering), with particular attention paid to the effects on the cluster properties and possible reaction intermediates. None of the mutants significantly affected the properties of the [4Fe-4S](+) cluster, but different effects were observed when one-electron-reduced forms were incubated with HMBPP. Replacing His42 led to an increased K(M) value and a much lower catalytic efficiency, confirming the role of this residue in substrate binding. Replacing the His124 also resulted in a lower catalytic efficiency. In this case, however, the enzyme showed the loss of the [4Fe-4S](+) EPR signal upon addition of HMBPP without the subsequent formation of the FeS(A) 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 FeS(A). Replacing the Glu126 also resulted in a lower catalytic efficiency, with yet a third type of EPR

  7. 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

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

    NASA Astrophysics Data System (ADS)

    Datta, Kakali; Mukherjee, Asok K.

    2004-06-01

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

  9. Chiral propargylic cations as intermediates in SN1-type reactions: substitution pattern, nuclear magnetic resonance studies, and origin of the diastereoselectivity.

    PubMed

    Nitsch, Dominik; Huber, Stefan M; Pöthig, Alexander; Narayanan, Arjun; Olah, George A; Prakash, G K Surya; Bach, Thorsten

    2014-02-19

    Nine propargylic acetates, bearing a stereogenic center (-C*HXR(2)) adjacent to the electrophilic carbon atom, were prepared and subjected to SN1-type substitution reactions with various silyl nucleophiles employing bismuth trifluoromethanesulfonate [Bi(OTf)3] as the Lewis acid. The diastereoselectivity of the reactions was high when the alkyl group R(2) was tertiary (tert-butyl), irrespective of the substituent X. Products were formed consistently with a diastereomeric ratio larger than 95:5 in favor of the anti-diastereoisomer. If the alkyl substitutent R(2) was secondary, the diastereoselectivity decreased to 80:20. The reaction was shown to proceed stereoconvergently, and the relative product configuration was elucidated. The reaction outcome is explained by invoking a chiral propargylic cation as an intermediate, which is preferentially attacked by the nucleophile from one of its two diastereotopic faces. Density functional theory (DFT) calculations suggest a preferred conformation in which the group R(2) is almost perpendicular to the plane defined by the three substituents at the cationic center, with the nucleophile approaching the electrophilic center opposite to R(2). Transition states calculated for the reaction of allyltrimethylsilane with two representative cations support this hypothesis. Tertiary propargylic cations with a stereogenic center (-C*HXR(2)) in the α position were generated by ionization of the respective alcohol precursors with FSO3H in SO2ClF at -80 °C. Nuclear magnetic resonance (NMR) spectra were obtained for five cations, and the chemical shifts could be unambiguously assigned. The preferred conformation of the cations as extracted from nuclear Overhauser experiments is in line with the preferred conformation responsible for the reaction of the secondary propargylic cations. PMID:24494822

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

    PubMed

    Kappelmann, Jannick; Wiechert, Wolfgang; Noack, Stephan

    2016-03-01

    Corynebacterium glutamicum is the major workhorse for the microbial production of several amino and organic acids. As long as these derive from tricarboxylic acid cycle intermediates, the activity of anaplerotic reactions is pivotal for a high biosynthetic yield. To determine single anaplerotic activities (13) C-Metabolic Flux Analysis ((13) C-MFA) has been extensively used for C. glutamicum, however with different network topologies, inconsistent or poorly determined anaplerotic reaction rates. Therefore, in this study we set out to investigate whether a focused isotopomer model of the anaplerotic node can at all admit a unique solution for all fluxes. By analyzing different scenarios of active anaplerotic reactions, we show in full generality that for C. glutamicum only certain anaplerotic deletion mutants allow to uniquely determine the anaplerotic fluxes from (13) C-isotopomer data. We stress that the result of this analysis for different assumptions on active enzymes is directly transferable to other compartment-free organisms. Our results demonstrate that there exist biologically relevant metabolic network topologies for which the flux distribution cannot be inferred by classical (13) C-MFA. PMID:26375179

  11. Nucleon-induced reactions at intermediate energies: New data at 96 MeV and theoretical status

    SciTech Connect

    Blideanu, V.; Lecolley, F.R.; Lecolley, J.F.; Lefort, T.; Marie, N.; Ban, G.; Louvel, M.; Dangtip, S.; Tippawan, U.; Elmgren, K.; Eudes, Ph.; Guertin, A.

    2004-07-01

    Double-differential cross sections for light charged particle production (up to A=4) were measured in 96 MeV neutron-induced reactions, at the TSL Laboratory Cyclotron in Uppsala (Sweden). Measurements for three targets, Fe, Pb, and U, were performed using two independent devices, SCANDAL and MEDLEY. The data were recorded with low-energy thresholds and for a wide angular range (20 deg. -160 deg. ). The normalization procedure used to extract the cross sections is based on the np elastic scattering reaction that we measured and for which we present experimental results. A good control of the systematic uncertainties affecting the results is achieved. Calculations using the exciton model are reported. Two different theoretical approaches proposed to improve its predictive power regarding the complex particle emission are tested. The capabilities of each approach is illustrated by comparison with the 96 MeV data that we measured, and with other experimental results available in the literature.

  12. Reaction of alkynes and azides: not triazoles through copper-acetylides but oxazoles through copper-nitrene intermediates.

    PubMed

    Haldón, Estela; Besora, Maria; Cano, Israel; Cambeiro, Xacobe C; Pericàs, Miquel A; Maseras, Feliu; Nicasio, M Carmen; Pérez, Pedro J

    2014-03-17

    Well-defined copper(I) complexes of composition [Tpm*(,Br) Cu(NCMe)]BF4 (Tpm*(,Br) =tris(3,5-dimethyl-4-bromo-pyrazolyl)methane) or [Tpa(*) Cu]PF6 (Tpa(*) =tris(3,5-dimethyl-pyrazolylmethyl)amine) catalyze the formation of 2,5-disubstituted oxazoles from carbonyl azides and terminal alkynes in a direct manner. This process represents a novel procedure for the synthesis of this valuable heterocycle from readily available starting materials, leading exclusively to the 2,5-isomer, attesting to a completely regioselective transformation. Experimental evidence and computational studies have allowed the proposal of a reaction mechanism based on the initial formation of a copper-acyl nitrene species, in contrast to the well-known mechanism for the copper-catalyzed alkyne and azide cycloaddition reactions (CuAAC) that is triggered by the formation of a copper-acetylide complex. PMID:24616053

  13. Time-Resolved X-Ray Absorption Spectroscopy Data for the Study of Chemical Reaction Intermediate States

    SciTech Connect

    Diaz Moreno, Sofia; Bowron, Daniel T.; Evans, John

    2007-02-02

    Energy-dispersive X-ray absorption Spectroscopy is an increasingly powerful tool for the investigation of kinetic processes in chemical systems as an element-specific local structure and electronic-state probe. In this paper we present a study of the structural evolution of the inner-sphere electron transfer reaction between [IrCl6]2- and [Co(CN)5]3-. The experimental requirements necessary for the extraction of maximal structural and electronic information are discussed.

  14. Complete and Incomplete Fusion Competition in 11B-INDUCED Fission Reactions on 197Au at the Intermediate Energy

    NASA Astrophysics Data System (ADS)

    Demekhina, N. A.; Karapetyan, G. S.; Balabekyan, A. R.

    2015-06-01

    Above Coulomb barrier cross sections of fission fragment production were measured in reactions of 11B with 197Au target. Induced-activity method was used for measurement the fission decay channel of the composite nuclei. Systematic of the fission fragment charge and mass distributions was used for fission cross section calculation. Fission fraction of the composite nuclei decay was compared with PACE-4 mode calculations. Estimated suppression for fission fraction followed the complete fusion have been obtained 35%.

  15. Electro-Fenton degradation of the antibiotic sulfanilamide with Pt/carbon-felt and BDD/carbon-felt cells. Kinetics, reaction intermediates, and toxicity assessment.

    PubMed

    El-Ghenymy, Abdellatif; Rodríguez, Rosa María; Brillas, Enric; Oturan, Nihal; Oturan, Mehmet A

    2014-01-01

    The degradation of 230 mL of a 0.6-mM sulfanilamide solution in 0.05 M Na₂SO₄ of pH 3.0 has been studied by electro-Fenton process. The electrolytic cell contained either a Pt or boron-doped diamond (BDD) anode and a carbon-felt cathode. Under these conditions, organics are oxidized by hydroxyl radicals formed at the anode surface from water oxidation and in the bulk from Fenton's reaction between initially added (and then electrochemically regenerated) Fe(2+) and cathodically generated H₂O₂. From the decay of sulfanilamide concentration determined by reversed-phase liquid chromatography, an optimum Fe(2+) concentration of 0.20 mM in both cells was found. The drug disappeared more rapidly using BDD than Pt, and, in both cases, it was more quickly removed with raising applied current. Almost total mineralization was achieved using the BDD/carbon-felt cell, whereas the alternative use of Pt anode led to a slightly lower mineralization degree. In both cells, the degradation rate was accelerated at higher current but with the concomitant fall of mineralization current efficiency due to the greater increase in rate of the parasitic reactions of hydroxyl radicals. Reversed-phase liquid chromatography allowed the identification of catechol, resorcinol, hydroquinone, p-benzoquinone, and 1,2,4-trihydroxybenzene as aromatic intermediates, whereas ion exclusion chromatography revealed the formation of malic, maleic, fumaric, acetic, oxalic, formic, and oxamic acids. NH₄(+), NO₃(-), and SO₄(2-) ions were released during the electro-Fenton process. A plausible reaction sequence for sulfanilamide mineralization involving all detected intermediates has been proposed. The toxicity of the solution was assessed from the Vibrio fischeri bacteria luminescence inhibition. Although it acquired its maximum value at short electrolysis time, the solution was completely detoxified at the end of the electro-Fenton treatment, regardless of the anode used. PMID:24687785

  16. 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

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

    PubMed

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

    2014-12-31

    The present work demonstrates the influence of Ag-loading (0.2-1.0 wt %) onto sodium titanate nanotubes (TNT) for complete photomineralization of the neurotoxic imidacloprid (IMI) insecticide under UV light illumination. It has been observed that degradation of IMI follows pseudo-first-order kinetics, where 0.5 wt % Ag-loaded TNT exhibited highest apparent rate constant (2.2 × 10(-2) min(-1)) and corresponding least half-life (t1/2) of 31 min for IMI relative to bare P25-TiO2 (3.4 × 10(-3) min(-1), t1/2 = 230 min). The mineralization of IMI intermediates to CO2 during its photooxidation has been described by time course GC-MS and GC analysis and has been correlated with the kinetic analysis. The investigation for the role and quantitative estimation of the fate of heteroatoms (N, O, and Cl) present in IMI revealed an increase in the amount of nitrate, nitrite, and chloride ions with time during its photooxidation. On the basis of these results a mechanistic pathway for photomineralization of IMI is proposed. PMID:25458204

  18. 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

  19. Spectroscopic detection of intermediates in the reaction of dioxygen with the reduced methane monooxygenase hydroxylase from Methylococcus capsulatus (bath)

    SciTech Connect

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

    1994-08-10

    Soluble methane monoxygenase (MMO), an enzyme system isolated from methanotrophic bacteria, which catalyzes the conversion of methane to methanol, has three components, a hydroxylase (H), a coupling protein (B), and a reductase (R). In this communication we present the results of stopped-flow and freeze-quench kinetic investigations of the reaction of dioxygen with the reduced hydroxylase, H[sub red], which elaborate upon and extend the findings of parallel work on MMOH from Methylosinus trichosporium OB3b. 34 refs., 1 fig.

  20. 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.

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

    PubMed Central

    Xu, X.; Sumption, M. D.

    2016-01-01

    In this work we explore the compositions of non-stoichiometric intermediate phases formed by diffusion reactions: a mathematical framework is developed and tested against the specific case of Nb3Sn superconductors. In the first part, the governing equations for the bulk diffusion and inter-phase interface reactions during the growth of a compound are derived, numerical solutions to which give both the composition profile and growth rate of the compound layer. The analytic solutions are obtained with certain approximations made. In the second part, we explain an effect that the composition characteristics of compounds can be quite different depending on whether it is the bulk diffusion or grain boundary diffusion that dominates in the compounds, and that “frozen” bulk diffusion leads to unique composition characteristics that the bulk composition of a compound layer remains unchanged after its initial formation instead of varying with the diffusion reaction system; here the model is modified for the case of grain boundary diffusion. Finally, we apply this model to the Nb3Sn superconductors and propose approaches to control their compositions. PMID:26754774

  2. 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

  3. Construction of the Octose 8-Phosphate Intermediate in Lincomycin A Biosynthesis: Characterization of the Reactions Catalyzed by LmbR and LmbN

    PubMed Central

    Sasaki, Eita; Lin, Chia-I; Lin, Ke-Yi; Liu, Hung-wen

    2012-01-01

    Lincomycin A is a potent antimicrobial agent noted for its unusual C1 methylmercapto-substituted eight-carbon sugar. Despite its long clinical history for the treatment of Grampositive infections, the biosynthesis of the C8-sugar, methylthiolincosamide (MTL), is poorly understood. Here, we report our studies of the two initial enzymatic steps in the MTL biosynthetic pathway leading to the identification of D-erythro-D-gluco-octose 8-phosphate as a key intermediate. Our experiments demonstrate that this intermediate is formed via a transaldol reaction catalyzed by LmbR using D-fructose 6-phosphate or D-sedoheptulose 7-phosphate as the C3 donor and D-ribose 5-phosphate as the C5 acceptor. Subsequent 1,2-isomerization catalyzed by LmbN converts the resulting 2-keto C8-sugar (octulose 8-phosphate) to octose 8-phosphate. These results provide, for the first time, in vitro evidence revealing the biosynthetic origin of the C8 backbone of MTL. PMID:22989310

  4. 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.

  5. Reference genes identified in SH-SY5Y cells using custom-made gene arrays with validation by quantitative polymerase chain reaction.

    PubMed

    Hoerndli, Frédéric J; Toigo, Marco; Schild, Andreas; Götz, Jürgen; Day, Philip J

    2004-12-01

    Transcriptomic methods are widely used as an initial approach to gain a mechanistic insight into physiological and pathological processes. Because differences in gene regulation to be assessed by RNA screening methods (e.g., SAGE, Affymetrix GeneChips) can be very subtle, these techniques require stable reference genes for accurate normalization. It is widely known that housekeeping genes, which are routinely used for normalization, can vary significantly depending on the tissue, and experimental test. In this study, we aimed at identifying stable reference genes for a fibrillar Abeta(42) peptide-treated, human tau-expressing SH-SY5Y neuroblastoma cell line derived to model aspects of Alzheimer's disease in tissue culture. We selected genes exhibiting potential normalization characteristics from public databases to create a custom-made microarray allowing the identification of reference genes for low, intermediate, and abundant mRNAs. A subset of these candidates was subjected to quantitative real-time polymerase chain reaction and was analyzed with geNorm software. By doing so, we were able to identify GAPD, M-RIP, and POLR2F as stable and usable reference genes irrespective of differentiation status and Abeta(42) treatment. PMID:15519568

  6. 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

  7. Detection of Intermediates in the Oxidative Half-Reaction of the FAD-Dependent Thymidylate Synthase from Thermotoga maritima: Carbon Transfer without Covalent Pyrimidine Activation

    PubMed Central

    2015-01-01

    Thymidylate, a vital DNA precursor, is synthesized by thymidylate synthases (TSs). A second class of TSs, encoded by the thyX gene, is found in bacteria and a few other microbes and is especially widespread in anaerobes. TS encoded by thyX requires a flavin adenine dinucleotide prosthetic group for activity. In the oxidative half-reaction, the reduced flavin is oxidized by 2′-deoxyuridine 5′-monophosphate (dUMP) and (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2THF), synthesizing 2′-deoxythymidine 5′-monophosphate (dTMP). dTMP synthesis is a complex process, requiring the enzyme to promote carbon transfer, probably by increasing the nucleophilicity of dUMP and the electrophilicity of CH2THF, and reduction of the transferred carbon. The mechanism of the oxidative half-reaction was investigated by transient kinetics. Two intermediates were detected, the first by a change in the flavin absorbance spectrum in stopped-flow experiments and the second by the transient disappearance of deoxynucleotide in acid quenching experiments. The effects of substrate analogues and the behavior of mutated enzymes on these reactions lead to the conclusion that activation of dUMP does not occur through a Michael-like addition, the mechanism for the activation analogous with that of the flavin-independent TS. Rather, we propose that the nucleophilicity of dUMP is enhanced by electrostatic polarization upon binding to the active site. This conclusion rationalizes many of our observations, for instance, the markedly slower reactions when two arginine residues that hydrogen bond with the uracil moiety of dUMP were mutated to alanine. The activation of dUMP by polarization is consistent with the majority of the published data on ThyX and provides a testable mechanistic hypothesis. PMID:25068636

  8. Heterolytic cleavage of peroxide by a diferrous compound generates metal-based intermediates identical to those observed with reactions utilizing oxygen-atom-donor molecules.

    PubMed

    Rowe, Gerard T; Rybak-Akimova, Elena V; Caradonna, John P

    2008-01-01

    Under cryogenic stopped-flow conditions, addition of 2-methyl-1-phenylprop-2-yl hydroperoxide (MPPH) to the diiron(II) compound, [Fe(2)(H(2)Hbamb)(2)(NMeIm)(2)] (1; NMeIm=N-methylimidazole; H(4)HBamb: 2,3-bis(2-hydroxybenzamido)dimethylbutane) results in heterolytic peroxide O-O bond cleavage, forming a high-valent species, 2. The UV/Vis spectrum of 2 and its kinetic behavior suggest parallel reactivity to that seen in the reaction of 1 with oxygen-atom-donor (OAD) molecules, which has been reported previously. Like the interaction with OAD molecules, the reaction of 1 with MPPH proceeds through a three step process, assigned to oxygen-atom transfer to the iron center to form a high-valent intermediate (2), ligand rearrangement of the metal complex, and, finally, decay to a diferric mu-oxo compound. Careful examination of the order of the reaction with MPPH reveals saturation behavior. This, coupled with the anomalous non-Arrhenius behavior of the first step of the reaction, indicates that there is a preequilibrium peroxide binding step prior to O-O bond cleavage. At higher temperatures, the addition of the base, proton sponge, results in a marked decrease in the rate of O-O bond cleavage to form 2; this is assigned as a peroxide deprotonation effect, indicating that the presence of protons is an important factor in the heterolytic cleavage of peroxide. This phenomenon has been observed in other iron-containing enzymes, the catalytic cycles of which include peroxide O-O bond cleavage. PMID:18680115

  9. Detection of intermediates in the oxidative half-reaction of the FAD-dependent thymidylate synthase from Thermotoga maritima: carbon transfer without covalent pyrimidine activation.

    PubMed

    Conrad, John A; Ortiz-Maldonado, Mariliz; Hoppe, Samuel W; Palfey, Bruce A

    2014-08-19

    Thymidylate, a vital DNA precursor, is synthesized by thymidylate synthases (TSs). A second class of TSs, encoded by the thyX gene, is found in bacteria and a few other microbes and is especially widespread in anaerobes. TS encoded by thyX requires a flavin adenine dinucleotide prosthetic group for activity. In the oxidative half-reaction, the reduced flavin is oxidized by 2'-deoxyuridine 5'-monophosphate (dUMP) and (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2THF), synthesizing 2'-deoxythymidine 5'-monophosphate (dTMP). dTMP synthesis is a complex process, requiring the enzyme to promote carbon transfer, probably by increasing the nucleophilicity of dUMP and the electrophilicity of CH2THF, and reduction of the transferred carbon. The mechanism of the oxidative half-reaction was investigated by transient kinetics. Two intermediates were detected, the first by a change in the flavin absorbance spectrum in stopped-flow experiments and the second by the transient disappearance of deoxynucleotide in acid quenching experiments. The effects of substrate analogues and the behavior of mutated enzymes on these reactions lead to the conclusion that activation of dUMP does not occur through a Michael-like addition, the mechanism for the activation analogous with that of the flavin-independent TS. Rather, we propose that the nucleophilicity of dUMP is enhanced by electrostatic polarization upon binding to the active site. This conclusion rationalizes many of our observations, for instance, the markedly slower reactions when two arginine residues that hydrogen bond with the uracil moiety of dUMP were mutated to alanine. The activation of dUMP by polarization is consistent with the majority of the published data on ThyX and provides a testable mechanistic hypothesis. PMID:25068636

  10. 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.

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

    SciTech Connect

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

    1995-10-18

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

  12. 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…

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  15. Physicochemical Changes and Glycation Reaction in Intermediate-Moisture Protein-Sugar Foods with and without Addition of Resveratrol during Storage.

    PubMed

    Sheng, Zhanwu; Gu, Mantun; Hao, Wangjun; Shen, Yixiao; Zhang, Weimin; Zheng, Lili; Ai, Binling; Zheng, Xiaoyan; Xu, Zhimin

    2016-06-22

    An intermediate-moisture food (IMF) model consisting of whey protein isolate and glucose and an IMF model fortified with resveratrol were used to study the effect of resveratrol on physicochemical changes and glycation of protein-sugar-rich foods during storage. The water activity (aw) of the storage was controlled at 0.75 or 0.56. The browning rate or hardness of fortified IMFs was significantly lower than that of IMFs after 45-day storage. The rate of Maillard reaction in the samples stored at aw 0.56 was higher than that of samples stored at aw 0.75. The fortified IMFs had lower levels of AGEs (advanced glycation end products), CML (N(ε)-(carboxymethyl)-l-lysine), and insoluble protein during storage. The inhibition capability of resveratrol against glycation was also confirmed by using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), liquid chromatography mass spectrometry (LC-MS), and Fourier transform infrared spectroscopy (FTIR) analysis to monitor glycated proteins and protein aggregation in the samples. The results of this study suggested that resveratrol could be used as an inhibitor to reduce the formation of undesirable AGEs and other Maillard reaction products in foods during storage. PMID:27218138

  16. Infrared spectroscopic observation of the stabilized intermediate complex FO{sub 3} formed by reaction of mobile fluorine atoms with ozone molecules trapped in an argon matrix

    SciTech Connect

    Misochko, E.Y.; Akimov, A.V.; Wight, C.A.

    1999-10-07

    Chemical reaction of F atoms with O{sub 3} molecules in a solid argon matrix was studied with FTIR spectroscopy. Fluorine atoms were generated by UV photolysis of F{sub 2} molecules in dilute solutions of F{sub 2} and O{sub 3} in solid argon. The FO-O{sub 2} complex is observed for the first time as an intermediate product by reaction of mobile F atoms with isolated ozone molecules. The observed complex is characterized by two intense absorption bands at 1522 and 968 cm{sup {minus}1}. Use of isotopic mixtures {sup 16}O/{sup 18}O provides strong evidence for assignment of these bands to the O-O stretch and F-O stretch fundamentals of the complex, which are red-shifted by 34 and 61 cm{sup {minus}1}, respectively, from the corresponding values for O{sub 2} and FO. Photolysis at 532 nm leads to decay of the FO-O{sub 2} complexes and to the appearance of isolated free FO radicals.

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

    PubMed

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

    2016-01-01

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

  18. 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.

  19. A kinetic and theoretical study of the borate catalysed reactions of hydrogen peroxide: the role of dioxaborirane as the catalytic intermediate for a wide range of substrates.

    PubMed

    Deary, Michael E; Durrant, Marcus C; Davies, D Martin

    2013-01-14

    Our recent work has provided new insights into the equilibria and species that exist in aqueous solution at different pHs for the boric acid - hydrogen peroxide system, and the role of these species in oxidation reactions. Most recently, (M. C. Durrant, D. M. Davies and M. E. Deary, Org. Biomol. Chem., 2011, 9, 7249-7254), we have produced strong theoretical and experimental evidence for the existence of a previously unreported monocyclic three membered peroxide species, dioxaborirane, that is the likely catalytic species in borate mediated electrophilic reactions of hydrogen peroxide in alkaline solution. In the present paper, we extend our study of the borate-peroxide system to look at a wide range of substrates that include substituted dimethyl anilines, methyl-p-tolyl sulfoxide, halides, hydrogen sulfide anion, thiosulfate, thiocyanate, and hydrazine. The unusual selectivity-reactivity pattern of borate catalysed reactions compared with hydrogen peroxide and inorganic or organic peracids previously observed for the organic sulfides (D. M. Davies, M. E. Deary, K. Quill and R. A. Smith, Chem.-Eur. J., 2005, 11, 3552-3558) is also seen with substituted dimethyl aniline nucleophiles. This provides evidence that the pattern is not due to any latent electrophilic tendency of the organic sulfides and further supports dioxaborirane being the likely reactive intermediate, thus broadening the applicability of this catalytic system. Moreover, density functional theory calculations on our proposed mechanism involving dioxaborirane are consistent with the experimental results for these substrates. Results obtained at high concentrations of both borate and hydrogen peroxide require the inclusion the diperoxodiborate dianion in the kinetic analysis. A scheme detailing our current understanding of the borate-peroxide system is presented. PMID:23188177

  20. 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.

  1. 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.

  2. 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

  3. 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.

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

    PubMed

    Shi, Hongchang; Wang, Yilei; Hua, Ruimao

    2015-12-28

    Correction for 'Acid-catalyzed carboxylic acid esterification and ester hydrolysis mechanism: acylium ion as a sharing active intermediate via a spontaneous trimolecular reaction based on density functional theory calculation and supported by electrospray ionization-mass spectrometry' by Hongchang Shi et al., Phys. Chem. Chem. Phys., 2015, DOI: 10.1039/c5cp02914g. PMID:26583937

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

    PubMed

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

    2004-05-01

    The chromophoric spin-label substrate 6-N-[3-(2,2,5,5-tetramethyl-1-oxypyrrolin-3-yl)-propen-2-oyl]penicillanic acid (SLPPEN) was synthesized by acylation of 6-aminopenicillanic acid with the acid chloride of 3-(2,2,5,5-tetramethyl-1-oxypyrrolinyl)-2-propenoic acid and characterized by physical methods. By application of angle-selected electron nuclear double resonance (ENDOR), we have determined the molecular structure of SLPPEN in solution. SLPPEN exhibited UV absorption properties that allowed accurate monitoring of the kinetics of its enzyme-catalyzed hydrolysis. The maximum value of the (substrate-product) difference extinction coefficient was 2824 M(-1) cm(-1) at 275 nm compared to 670 M(-1) cm(-1) at 232 nm for SLPEN [J. Am. Chem. Soc. 117 (1995) 6739]. For SLPPEN, the steady-state kinetic parameters kcat and kcat/KM, determined under initial velocity conditions, were 637 +/- 36 s(-1) and 13.8 +/- 1.4 x 10(6) M(-1) s(-1), respectively, for hydrolysis catalyzed by TEM-1 beta-lactamase of E. coli, and 0.5 +/- 0.04 s(-1) and 3.9 +/- 0.4 x 10(4) M(-1) s(-1) for hydrolysis catalyzed by the beta-lactamase of Enterobacter cloacae P99. We have also observed "burst kinetics" for the hydrolysis of SLPPEN with P99 beta-lactamase, indicative of formation of an acylenzyme reaction intermediate. In DMSO:H2O (30:70, v:v) cryosolvent mixtures buffered to pH* 7.0, the half-life of the acylenzyme intermediate formed with the P99 enzyme at -5 degrees C was > or = 3 min, suitable for optical characterization. The observation of burst kinetics in the hydrolysis of SLPPEN catalyzed by P99 beta-lactamase suggests that this chromophoric spin-labeled substrate is differentially sensitive to active site interactions underlying the cephalosporinase and penicillinase reactivity of this class C enzyme. PMID:15134725

  6. Real-time Monitoring of Intermediates Reveals the Reaction Pathway in the Thiol-Disulfide Exchange between Disulfide Bond Formation Protein A (DsbA) and B (DsbB) on a Membrane-immobilized Quartz Crystal Microbalance (QCM) System*

    PubMed Central

    Yazawa, Kenjiro; Furusawa, Hiroyuki; Okahata, Yoshio

    2013-01-01

    Disulfide bond formation protein B (DsbBS-S,S-S) is an inner membrane protein in Escherichia coli that has two disulfide bonds (S-S, S-S) that play a role in oxidization of a pair of cysteine residues (SH, SH) in disulfide bond formation protein A (DsbASH,SH). The oxidized DsbAS-S, with one disulfide bond (S-S), can oxidize proteins with SH groups for maturation of a folding preprotein. Here, we have described the transient kinetics of the oxidation reaction between DsbASH,SH and DsbBS-S,S-S. We immobilized DsbBS-S,S-S embedded in lipid bilayers on the surface of a 27-MHz quartz crystal microbalance (QCM) device to detect both formation and degradation of the reaction intermediate (DsbA-DsbB), formed via intermolecular disulfide bonds, as a mass change in real time. The obtained kinetic parameters (intermediate formation, reverse, and oxidation rate constants (kf, kr, and kcat, respectively) indicated that the two pairs of cysteine residues in DsbBS-S,S-S were more important for the stability of the DsbA-DsbB intermediate than ubiquinone, an electron acceptor for DsbBS-S,S-S. Our data suggested that the reaction pathway of almost all DsbASH,SH oxidation processes would proceed through this stable intermediate, avoiding the requirement for ubiquinone. PMID:24145032

  7. Real-time monitoring of intermediates reveals the reaction pathway in the thiol-disulfide exchange between disulfide bond formation protein A (DsbA) and B (DsbB) on a membrane-immobilized quartz crystal microbalance (QCM) system.

    PubMed

    Yazawa, Kenjiro; Furusawa, Hiroyuki; Okahata, Yoshio

    2013-12-13

    Disulfide bond formation protein B (DsbBS-S,S-S) is an inner membrane protein in Escherichia coli that has two disulfide bonds (S-S, S-S) that play a role in oxidization of a pair of cysteine residues (SH, SH) in disulfide bond formation protein A (DsbASH,SH). The oxidized DsbAS-S, with one disulfide bond (S-S), can oxidize proteins with SH groups for maturation of a folding preprotein. Here, we have described the transient kinetics of the oxidation reaction between DsbASH,SH and DsbBS-S,S-S. We immobilized DsbBS-S,S-S embedded in lipid bilayers on the surface of a 27-MHz quartz crystal microbalance (QCM) device to detect both formation and degradation of the reaction intermediate (DsbA-DsbB), formed via intermolecular disulfide bonds, as a mass change in real time. The obtained kinetic parameters (intermediate formation, reverse, and oxidation rate constants (kf, kr, and kcat, respectively) indicated that the two pairs of cysteine residues in DsbBS-S,S-S were more important for the stability of the DsbA-DsbB intermediate than ubiquinone, an electron acceptor for DsbBS-S,S-S. Our data suggested that the reaction pathway of almost all DsbASH,SH oxidation processes would proceed through this stable intermediate, avoiding the requirement for ubiquinone. PMID:24145032

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

    SciTech Connect

    Lee, Yuan-Pern

    2015-07-14

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

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

    PubMed Central

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

    2015-01-01

    Programs that aim to control vector-borne zoonotic diseases require information on zoonotic hosts and on the feeding behavior of bridging vectors that are capable of transmitting pathogens from those hosts to humans. Here we describe an assay developed to identify bloodmeals in field-collected cat fleas (Ctenocephalides felis 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

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

    PubMed

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

    2015-02-14

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

  11. The secondary coordination sphere controlled reactivity of a ferric-superoxo heme: unexpected conversion to a ferric hydroperoxo intermediate by reaction with a high-spin ferrous heme.

    PubMed

    Nagaraju, Perumandla; Ohta, Takehiro; Liu, Jin-Gang; Ogura, Takashi; Naruta, Yoshinori

    2016-06-01

    A bio-inspired heme complex involving both a proton donor and an axial imidazole ligand reduces the activation energy for the formation of a ferric hydroperoxo intermediate. A high-spin ferrous heme is shown to be capable of reducing its superoxy species to generate a ferric hydroperoxo intermediate for the first time. PMID:27105471

  12. Diminished CAGE Effect in {p}-H2: IR Identification of Intermediates in Addition Reactions of CL Atom with Unsaturated Hydrocarbons

    NASA Astrophysics Data System (ADS)

    Lee, Yuan-Pern; Bahou, Mohammed; Golec, Barbara

    2011-06-01

    We report infrared absorption spectra of several free radicals produced upon reaction of Cl atoms with unsaturated hydrocarbons isolated in solid {p}-H2. Cl atoms were produced by in situ photodissociation of Cl2 isolated in solid {p}-H2 at 365 nm. In experiments with the Cl2/C6H6/{p}-H2 matrices, intense absorption features at 617.0, 719.8, 956.0, and 1430.5 Cm-1 and weaker ones at 577.1, 833.6, 876.8, 833.6, 983.0, 993.5, 1008.0, 1026.4, 1112.5, 1118.5, 1179.0, 1406.5, 1509.4, 2967.2, 3054.3, 3063.4, 3070.9, and 3083.9 Cm-1 appeared upon irradiation of the matrix at 365 nm and increased in intensity upon subsequent annealing of the matrix at 4.8 K for a few minutes. By comparison of vibrational wavenumbers and deuterium isotopic shifts predicted with the B3PW91 and MPW1PW91/aug-cc-pVTZ methods, these features are readily assigned to the σ-complex of ClC6H6 (chlorocyclohexadienyl radical), rather than the previously proposed π-complex. In experiments with the Cl2/C2H2/{p}-H2 matrices, the 1-chloroethyl radicals (CHClCH3) and chloroethene (C2H3Cl) are identified as the main products of the Cl + C2H2 reaction in solid {p}-H2. The assignments of IR absorption lines at 738.2, 1027.6, 1283.4, 1377.1, 1426.6, 1442.6, and 2861.2 Cm-1 to 1-chloroethyl radicals are based on comparison of the observed vibrational wavenumbers and 13C- and D-isotopic shifts with those predicted with the B3LYP and MP2/aug-cc-pVDZ methods. These results indicate that the primary products of the addition reaction Cl + C2H2, the 2-chlorovinyl radicals, are unstable; they react readily with {p}-H2 to form CHClCH3 and C2H3Cl. If time permits, other examples such as Cl + 1, 3-butadien and H + C6H6 or C6H5Cl will be discussed. These results serve as excellent examples to demonstrate that the diminished cage effect of solid {p}-H2 makes production of free radicals via bimolecular reactions feasible.

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

    NASA Astrophysics Data System (ADS)

    Harding, Lawrence B.; Klippenstein, Stephen J.

    2015-10-01

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

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

    PubMed

    Harding, Lawrence B; Klippenstein, Stephen J

    2015-10-28

    We discuss the recent report of a roaming type mechanism for the decomposition of the Criegee intermediate. We show that the predicted barrier height for this new pathway is too low by ∼30 kcal/mol owing to an inconsistent use of spin-restricted and spin-unrestricted calculations. As a result, this new pathway is not expected to compete significantly with the well-known dioxirane pathways for the decomposition of the Criegee intermediate. PMID:26520558

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

    SciTech Connect

    Harding, Lawrence B.; Klippenstein, Stephen J.

    2015-10-28

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

  16. The ability of intermediate-band Strömgren photometry to correctly identify dwarf, subgiant, and giant stars and provide stellar metallicities and surface gravities

    NASA Astrophysics Data System (ADS)

    Árnadóttir, A. S.; Feltzing, S.; Lundström, I.

    2010-10-01

    .40 < (b-y)0 < 0.95 and 1.10 < (v-y)0 < 2.38. Conclusions: We recommend the calibrations of Ramírez & Meléndez (2005) in deriving metallicities from Strömgren photometry and find that intermediate band photometry, such as Strömgren photometry, more accurately than broad band photometry reproduces spectroscopically determined [Fe/H]. Strömgren photometry is also better at differentiating between dwarf and giant stars. We conclude that additional investigations of the differences between metallicities derived from ugriz photometry and intermediate-band photometry, such as Strömgren photometry, are required. Appendix A is only available in electronic form at http://www.aanda.org, Appendix B is available in electronic form at http://www.aanda.org and at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/521/A40

  17. DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical-protein interactome.

    PubMed

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

    2011-07-01

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

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

    DOE PAGESBeta

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

    2016-01-01

    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)2NiO4d 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 ofmore » the ORR are identified as oxygen adsorption and incorporation based on the findings in reaction orders from electrochemical impedance spectroscopy (EIS), stoichiometryrelated chemical capacitance and intrinsic anisotropic properties. The incorporation rate is proven to drastically depend on the amount of interstitial oxygen O00 i . Since the unfilled interstitial sites V i in the R–P phase serve to accommodate the adsorbed oxygen during incorporation, like vacancies in the perovskite structure V O , moreO00 i would seem to suppress the kinetics of this process. In regards to this, for the first time, a physical model is proposed to reconcile the discrepancy between the experimental results and intuitive reasoning. Based on supporting evidence, this model illustrates a possibility of how O00 i works to regulate the exchange rate, and how the contradiction between V O and O00 i is harmonized so that the latter in the R–P structure also positively promotes the incorporation rate in the ORR« less

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

    SciTech Connect

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

    2016-01-01

    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#2;d 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), stoichiometryrelated chemical capacitance and intrinsic anisotropic properties. The incorporation rate is proven to drastically depend on the amount of interstitial oxygen O00 i #2;#3;. Since the unfilled interstitial sites V#3; i #2;#3; in the R–P phase serve to accommodate the adsorbed oxygen during incorporation, like vacancies in the perovskite structure V#4;#4; O #2;#3;, moreO00 i would seem to suppress the kinetics of this process. In regards to this, for the first time, a physical model is proposed to reconcile the discrepancy between the experimental results and intuitive reasoning. Based on supporting evidence, this model illustrates a possibility of how O00 i works to regulate the exchange rate, and how the contradiction between V#4;#4; O and O00 i is harmonized so that the latter in the R–P structure also positively promotes the incorporation rate in the ORR

  20. A thiamin-bound, pre-decarboxylation reaction intermediate analogue in the pyruvate dehydrogenase E1 subunit induces large scale disorder-to-order transformations in the enzyme and reveals novel structural features in the covalently bound adduct.

    PubMed

    Arjunan, Palaniappa; Sax, Martin; Brunskill, Andrew; Chandrasekhar, Krishnamoorthy; Nemeria, Natalia; Zhang, Sheng; Jordan, Frank; Furey, William

    2006-06-01

    The crystal structure of the E1 component from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc) has been determined with phosphonolactylthiamin diphosphate (PLThDP) in its active site. PLThDP serves as a structural and electrostatic analogue of the natural intermediate alpha-lactylthiamin diphosphate (LThDP), in which the carboxylate from the natural substrate pyruvate is replaced by a phosphonate group. This represents the first example of an experimentally determined, three-dimensional structure of a thiamin diphosphate (ThDP)-dependent enzyme containing a covalently bound, pre-decarboxylation reaction intermediate analogue and should serve as a model for the corresponding intermediates in other ThDP-dependent decarboxylases. Regarding the PDHc-specific reaction, the presence of PLThDP induces large scale conformational changes in the enzyme. In conjunction with the E1-PLThDP and E1-ThDP structures, analysis of a H407A E1-PLThDP variant structure shows that an interaction between His-407 and PLThDP is essential for stabilization of two loop regions in the active site that are otherwise disordered in the absence of intermediate analogue. This ordering completes formation of the active site and creates a new ordered surface likely involved in interactions with the lipoyl domains of E2s within the PDHc complex. The tetrahedral intermediate analogue is tightly held in the active site through direct hydrogen bonds to residues His-407, Tyr-599, and His-640 and reveals a new, enzyme-induced, strain-related feature that appears to aid in the decarboxylation process. This feature is almost certainly present in all ThDP-dependent decarboxylases; thus its inclusion in our understanding of general thiamin catalysis is important. PMID:16531404

  1. 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

  2. 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.

  3. 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

  4. 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

  5. Sterol biosynthesis: strong inhibition of maize delta 5,7-sterol delta 7-reductase by novel 6-aza-B-homosteroids and other analogs of a presumptive carbocationic intermediate of the reduction reaction.

    PubMed

    Rahier, A; Taton, M

    1996-06-01

    A series of mono- and diazasteroids have been synthesized as analogs of a predicted carbocationic intermediate of delta 5,7-sterol delta 7-reductase (delta 7-SR). 6-Aza-B-homo-5 alpha-cholest-7-en-3 beta-ol (4), a novel compound whose synthesis is described for the first time, and 6,7-diaza-5 alpha-cholest-8(14)-en-3 beta-ol (6) were shown to be very powerful inhibitors of delta 7-SR in a preparation isolated from maize (Zea mays) (K(i),app = 50-70 nM, Ki,app/Km,app = 1.0 x 10(-4) to 1.3 x 10(-4). The data are consistent with a carbonium ion mechanism for the reduction; compounds 4 and 6 probably act as reaction intermediate analogs. Compound 4, in contrast to compound 6, displayed in the same microsomal preparation more than 50-fold selectivity for inhibition of the delta 7-SR versus delta 8-delta 7-sterol isomerase, cycloeucalenol isomerase, and delta 8,14-sterol delta 14-reductase, the mechanism of these four enzymes involving presumptive cationic intermediates centered respectively at C7, C8, C9, and C14. These observations highlight the paramount importance of the location of the positively charged nitrogen atom(s) in the B-ring structure for selectivity among these enzymes involving structurally close cationic reaction intermediates. Efficient in vivo inhibition of sterol biosynthesis in bramble cell suspension cultures by a low concentration of compound 4 was demonstrated and confirmed the in vitro properties of this derivative.) PMID:8679532

  6. An early intermediate in the folding reaction of the B1 domain of protein G contains a native-like core.

    PubMed

    Park, S H; O'Neil, K T; Roder, H

    1997-11-25

    The folding kinetics of a 57-residue IgG binding domain of streptococcal protein G has been studied under varying solvent conditions, using stopped-flow fluorescence methods. Although GB1 has been cited as an example of a protein that obeys a two-state folding mechanism, the following kinetic observations suggest the presence of an early folding intermediate. Under stabilizing conditions (low denaturant concentrations, especially in the presence of sodium sulfate), the kinetics of folding shows evidence of a major unresolved fluorescence change during the 1.5 ms dead time of the stopped-flow experiment (burst phase). Together with some curvature in the rate profile for the single observable folding phase, this provides clear evidence of the rapid formation of compact states with native-like fluorescence for the single tryptophan at position 43. In refolding experiments at increasing denaturant concentrations, the amplitude of the sub-millisecond phase decreases sharply and the corresponding slope (m value) is only about 30% lower than that of the equilibrium unfolding curve indicative of a pre-equilibrium transition involving cooperative unfolding of an ensemble of compact intermediates. The dependence on guanidine hydrochloride concentration of both rates and amplitudes (including the equilibrium transition) is described quantitatively by a sequential three-state mechanism, U [symbol: see text] I [symbol: see text] N, where an intermediate (I) in rapid equilibrium with the unfolded state (U) precedes the rate-limiting formation of the native state (N). A 66-residue fragment of GB1 with an N-terminal extension containing five apolar side chains exhibits three-state kinetic behavior virtually identical to that of the 57-residue fragment. This is consistent with the presence of a well-shielded native-like core excluding the N-terminal tail in the early folding intermediate and argues against a mechanism involving random hydrophobic collapse, which would predict a

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

    PubMed Central

    2015-01-01

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

  8. 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

  9. 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

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

    NASA Astrophysics Data System (ADS)

    Huang, Yu-Hsuan; Lee, Yuan-Pern

    2014-06-01

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

  11. 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

  12. Nanoelectrochemical approach to detecting short-lived intermediates of electrocatalytic oxygen reduction.

    PubMed

    Zhou, Min; Yu, Yun; Hu, Keke; Mirkin, Michael V

    2015-05-27

    Development of better catalysts for the oxygen reduction reaction (ORR) and other electrocatalytic processes requires detailed knowledge of reaction pathways and intermediate species. Here we report a new methodology for detecting charged reactive intermediates and its application to the mechanistic analysis of ORR. A nanopipette filled with an organic phase that is immiscible with the external aqueous solution was used as a tip in the scanning electrochemical microscope to detect and identify a short-lived superoxide (O2(●-)) intermediate and to determine the rate of its generation at the catalytic Pt substrate and its lifetime in neutral aqueous solution. The voltammogram of the O2(●-) anion transfer to the organic phase provides a unique signature for unambiguous identification of superoxide. The extremely short attainable separation distance between the pipette tip and substrate surface (∼1 nm) makes this technique suitable for detecting and identifying charged intermediates of catalytic processes with a lifetime of a few nanoseconds. PMID:25978070

  13. Ni/Fe-supported over hydrotalcites precursors as catalysts for clean and selective oxidation of Basic Yellow 11: reaction intermediates determination.

    PubMed

    Ovejero, G; Rodríguez, A; Vallet, A; García, J

    2013-01-01

    In this work, Basic Yellow 11 (BY 11) was employed as model compound to study catalytic wet air oxidation as a pre-treatment step to the conventional biological oxidation. Ni and Fe catalysts supported over hydrotalcite (HT) were prepared by incipient wetness and excess impregnation to obtain catalysts with different metal loadings (from 1 to 10 wt.%). HTs were synthesized by co-precipitation and characterized with XRD, X-ray fluorescence (XRF), BET, thermogravimetric analysis and SEM. Results showed that dye conversion increased with Ni and Fe content up to 7 wt.% and that the most effective catalyst were prepared by incipient wetness impregnation. The influence of metal loading in the catalyst, and the preparation method as well as the reaction conditions was investigated. A mechanism and reaction pathways for BY 11 during catalytic liquid phase oxidation have also been proposed. PMID:22960061

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

    PubMed

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

    2015-09-01

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

  15. Vocational and Psychosocial Mentoring Functions: Identifying Mentors Who Serve Both [and] Invited Reaction: Challenging Research in Mentoring.

    ERIC Educational Resources Information Center

    Mullen, Ellen J.; Chao, Georgia T.

    1998-01-01

    Mullen's survey of 160 mentors and 140 proteges showed that mentors who initiated relationships, who felt valued by the organization, who were older, or who perceived proteges as competent were most likely to perform both career-related and psychosocial mentoring functions. Chao's response identifies problems in the research. (SK)

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

    NASA Astrophysics Data System (ADS)

    Sarkar, Debojit; Choudhury, Subikash; Chattopadhyay, Subhasis

    2016-09-01

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

  17. Intramolecular hydroarylation of aryl propargyl ethers catalyzed by indium: the mechanism of the reaction and identifying the catalytic species.

    PubMed

    Menkir, Mengistu Gemech; Lee, Shyi-Long

    2016-07-01

    The mechanism and regioselectivity of the intramolecular hydroarylation of phenyl propargyl ether catalyzed by indium in gas and solvent phases were investigated by means of the density functional theory method. The computed results revealed that the reaction proceeds through initial π-coordination of the propargyl moiety to the catalyst, which triggers the nucleophilic attack of the phenyl ring via an exo- or endo-dig pathway in a Friedel-Crafts type mechanism. Calculation results obtained employing InI2(+) as the possible catalyst show similar activation energies for the 5-exo-dig and 6-endo-dig pathways. In contrast, the neural catalyst InI3 shows a kinetic preference for 6-endo-dig versus 5-exo-dig cyclizations leading to the experimentally observed product, 2H-chromene. The calculation results suggest that InI3 could be the real catalytic species for this reaction as it shows regioselectivity in agreement with the experimental observation. Furthermore, the 6-endo-dig cyclization through deprotonation/protonation steps is kinetically more favored than the stepwise two consecutive [1,2]-H shift steps. The rate determining step of the whole catalytic cycle is the deprotonation step with an energy barrier of 18.9 kcal mol(-1) in toluene solvent. The effects of substituents on both the phenyl ring and the propargyl moiety on the selectivity and elementary steps of the hydroarylation process were investigated. A methoxy group, particularly at the meta-position, on the phenyl ring largely decreases the energy barrier of the first step for the 6-endo path, though it shows little effect on the activation energies of the second and third steps. Our calculation results are in good agreement with the experimental results. PMID:27298068

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

    PubMed

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

    2013-01-01

    We report a case of Arthroderma vanbreuseghemii (a teleomorph of Trichophyton interdigitale) infection around the nostrils in a 3-year-old girl. The culture was negative, so the pathogenic agent was identified using polymerase chain reaction-based sequencing of the crusts taken from the lesion on the nostril. Treatment with oral itraconazole and topical 1% naftifine/0.25% ketoconazole cream after a topical wash with ketoconazole shampoo was effective. PMID:23278484

  19. 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

  20. Magnetic field effects on electron transfer reactions involving sextet-spin ( S = 5/2) intermediates generated on photoexcitation of a Cr(III)-porphyrin complex

    NASA Astrophysics Data System (ADS)

    Mori, Yukie; Hoshino, Mikio; Hayashi, Hisaharu

    The excited trip-sextet ( 6 T 1 ) state of chloro-(3-methylimidazol)-( meso -tetraphenylporphyrinato) chromium(III) (Cr III P) is quenched by 1,1 '-dibenzyl-4,4 '-bipyridinium (BV 2+ ) in acetonitrile through electron transfer to give 5 (Cr III P .+ ) and 2 BV .+ . The intermediate is a geminate ion pair in the sextet (Sx) state 6 [ 5 (Cr III P .+ ) 2 BV .+ ], which decays through either the escape from a solvent cage to give the free ions or the spin conversion to the quartet (Qa) state followed by back electron transfer. The free ion yield ( ΦFI ) increased with increasing magnetic field from 0 to 4 T and then slightly decreased from 4 T to 10 T. These magnetic field effects are explained as follows. Under low fields where the Zeeman splitting of the spin sublevels is lower than or comparable with the electron spin dipole-dipole interaction within 5 (Cr III P .+ ), this interaction effectively induces the Sx ⇔Qa conversion of [ 5 (Cr III P .+ ) 2 BV + ] to result in low ΦFI values. Under high fields where the Zeeman splitting is larger than the dipole-dipole interaction, the Sx Qa conversion is decreased with increasing field to cause higher ΦFI values. The slight decrease in ΦFI above 4 T may be due to the Δg mechanism.

  1. 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.

  2. Degradation mechanisms of geosmin and 2-MIB during UV photolysis and UV/chlorine reactions.

    PubMed

    Kim, Tae-Kyoung; Moon, Bo-Ram; Kim, Taeyeon; Kim, Moon-Kyung; Zoh, Kyung-Duk

    2016-11-01

    We conducted chlorination, UV photolysis, and UV/chlorin reactions to investigate the intermediate formation and degradation mechanisms of geosmin and 2-methylisoborneol (2-MIB) in water. Chlorination hardly removed geosmin and 2-MIB, while the UV/chlorine reaction at 254 nm completely removed geosmin and 2-MIB within 40 min and 1 h, respectively, with lesser removals of both compounds during UV photolysis. The kinetics during both UV photolysis and UV/chlorine reactions followed a pseudo first-order reaction. Chloroform was found as a chlorinated intermediate during the UV/chlorine reaction of both geosmin and 2-MIB. The pH affected both the degradation and chloroform production during the UV/chlorine reaction. The open ring and dehydration intermediates identified during UV/chlorine reactions were 1,4-dimethyl-adamantane, and 1,3-dimethyl-adamantane from geosmin, 2-methylenebornane, and 2-methyl-2-bornene from 2-MIB, respectively. Additionally, 2-methyl-3-pentanol, 2,4-dimethyl-1-heptene, 4-methyl-2-heptanone, and 1,1-dichloro-2,4-dimethyl-1-heptane were newly identified intermediates from UV/chlorine reactions of both geosmin and 2-MIB. These intermediates were degraded as the reaction progressed. We proposed possible degradation pathways during the UV photolysis and UV/chlorine reactions of both compounds using the identified intermediates. PMID:27494316

  3. Reactions of C{sub 2}H{sub 5} radicals with O, O{sub 3}, and NO{sub 3}: Decomposition pathways of the intermediate C{sub 2}H{sub 5}O radical

    SciTech Connect

    Hoyermann, K.; Seeba, J.; Olzmann, M.; Viskolcz

    1999-07-22

    Alkoxy radicals are important species in the atmospheric degradation of hydrocarbons as well as in combustion processes. Additionally, they play a crucial role in the pyrolysis of oxygen-containing hydrocarbons. The reactions of C{sub 2}H{sub 5} with O, O{sub 3}, and NO{sub 3} have been investigated in a discharge flow reactor at room temperature and pressures between 1 and 3 mbar. The reaction products were detected by mass spectrometry with electron-impact ionization. The product pattern observed is explained in terms of the decomposition of an intermediately formed, chemically activated ethoxy radical. It is shown that, with this assumption, the experimentally determined branching ratios of the different product channels can be reproduced nearly quantitatively by RRKM calculations based on ab initio results for the stationary points of the potential energy surface of C{sub 2}H{sub 5}O. For C{sub 2}H{sub 5} + O and C{sub 2}H{sub 5} + O{sub 3}, the existence of an additional, parallel channel leading to OH has to be assumed.. High-pressure Arrhenius parameters for the unimolecular reactions of the ethoxy radical are given and discussed.

  4. 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).

  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. Improving the Production of L-Phenylalanine by Identifying Key Enzymes Through Multi-Enzyme Reaction System in Vitro

    PubMed Central

    Ding, Dongqin; Liu, Yongfei; Xu, Yiran; Zheng, Ping; Li, Haixing; Zhang, Dawei; Sun, Jibin

    2016-01-01

    L-Phenylalanine (L-Phe) is an important amino acid used in both food and medicinal applications. We developed an in vitro system that allowed a direct, quantitative investigation of phenylalanine biosynthesis in E. coli. Here, the absolute concentrations of six enzymes (AroK, AroL, AroA, AroC, PheA and TyrB) involved in the shikimate (SHIK) pathway were determined by a quantitative proteomics approach and in vitro enzyme titration experiments. The reconstitution of an in vitro reaction system for these six enzymes was established and their effects on the phenylalanine production were tested. The results showed that the yield of phenylalanine increased 3.0 and 2.1 times when the concentrations of shikimate kinase (AroL) and 5-enolpyruvoyl shikimate 3-phosphate (EPSP) synthase (AroA) were increased 2.5 times. Consistent results were obtained from in vivo via the overexpression of AroA in a phenylalanine-producing strain, and the titer of phenylalanine reached 62.47 g/l after 48 h cultivation in a 5-liter jar fermentor. Our quantitative findings provide a practical method to detect the potential bottleneck in a specific metabolic pathway to determine which gene products should be targeted to improve the yield of the desired product. PMID:27558633

  7. Improving the Production of L-Phenylalanine by Identifying Key Enzymes Through Multi-Enzyme Reaction System in Vitro.

    PubMed

    Ding, Dongqin; Liu, Yongfei; Xu, Yiran; Zheng, Ping; Li, Haixing; Zhang, Dawei; Sun, Jibin

    2016-01-01

    L-Phenylalanine (L-Phe) is an important amino acid used in both food and medicinal applications. We developed an in vitro system that allowed a direct, quantitative investigation of phenylalanine biosynthesis in E. coli. Here, the absolute concentrations of six enzymes (AroK, AroL, AroA, AroC, PheA and TyrB) involved in the shikimate (SHIK) pathway were determined by a quantitative proteomics approach and in vitro enzyme titration experiments. The reconstitution of an in vitro reaction system for these six enzymes was established and their effects on the phenylalanine production were tested. The results showed that the yield of phenylalanine increased 3.0 and 2.1 times when the concentrations of shikimate kinase (AroL) and 5-enolpyruvoyl shikimate 3-phosphate (EPSP) synthase (AroA) were increased 2.5 times. Consistent results were obtained from in vivo via the overexpression of AroA in a phenylalanine-producing strain, and the titer of phenylalanine reached 62.47 g/l after 48 h cultivation in a 5-liter jar fermentor. Our quantitative findings provide a practical method to detect the potential bottleneck in a specific metabolic pathway to determine which gene products should be targeted to improve the yield of the desired product. PMID:27558633

  8. Microeconomic Concepts Students Should Learn before Intermediate Macroeconomics.

    ERIC Educational Resources Information Center

    Salemi, Michael K.

    1996-01-01

    Identifies four microeconomic concepts students should learn before entering the study of intermediate macroeconomics. Included are relative prices, general versus partial equilibrium, constrained optimization, and the nature of production concepts. Recommends making intermediate microeconomics a prerequisite for intermediate macroeconomics. (MJP)

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed

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

    2016-09-01

    The structures and vibrational spectra of the reacting species upon guanosine triphosphate (GTP) hydrolysis to guanosine diphosphate and inorganic phosphate (Pi) trapped inside the protein complex Ras-GAP were analyzed following the results of QM/MM simulations. The frequencies of the phosphate vibrations referring to the reactants and to Pi were compared to those observed in the experimental FTIR studies. A good correlation between the theoretical and experimental vibrational data provides a strong support to the reaction mechanism of GTP hydrolysis by the Ras-GAP enzyme system revealed by the recent QM/MM modeling. Evolution of the vibrational bands associated with the inorganic phosphate Pi during the elementary stages of GTP hydrolysis is predicted. PMID:27214270

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

    SciTech Connect

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

    2012-12-10

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

  12. 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

  13. 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.

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

    SciTech Connect

    Hoffman, M.Z.

    1997-12-31

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

  15. 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.

  16. 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.

  17. 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.

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

    SciTech Connect

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

    2011-01-01

    The heaviest isotopes of elements Z = 117 to Z = 105, 294117, 293117, 290115, 289115, 286113, 285113, 282Rg, 281Rg, 278Mt, 274Bh, and 270Db, were identified by means of the Dubna gas-filled recoil separator among the products of the 249Bk + 48Ca reaction. The details of the observed six decay chains, indicating the production and decay of isotopes 293117 and 294117, are presented and discussed. The decay energies and resulting half-lives of these new nuclei show a strong rise of stability with increasing neutron number, validating the concept of the island of enhanced stability for superheavy nuclei.

  19. endo/exo stereoselectivity in Diels-Alder reactions of α,β-dialkylated conjugated enals to cyclic 1,3-dienes: intermediates in the synthesis of (-)-β-santalol and its analogs.

    PubMed

    Chapuis, Christian; Skuy, David; de Saint Laumer, Jean-Yves; Brauchli, Robert

    2014-10-01

    Highly exo-selective [4+2] cycloadditions of cyclopenta-1,3-diene 2a to α,β-dialkyl conjugated enals 5 are compared with the analogous endo-favored Diels-Alder reaction of cyclohexa-1,3-diene 7. The exo-stereoselectivity is lower in the homologous case of methylcyclopenta-1,3-diene 9. This diastereoselectivity is discussed either in terms of a retro-homo-Diels-Alder reaction, associated with thermodynamic control, or with respect to either a competing hetero-Diels-Alder/Claisen or Cope domino pathway, or retro-Claisen/retro-hetero-Diels-Alder of the endo-homo-cycloadducts. These hypothetical mechanisms have been examined by DFT calculations at the MPW1K(CH2 Cl2 )/6-31+G** level of theory for the AlCl3 -mediated cycloadditions of 5d to 2a and 7. Application of Corey's methodology to the γ-halogeno-α-methyl-substituted dienophiles 5a and 5b allowed an enantioselective preparation of known and useful intermediates for the synthesis of either the naturally occurring (-)-β-santalol or its potentially olfactive structural analogs. PMID:25329781

  20. 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.

  1. 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.

  2. Reaction of [TpRh(C2 H4 )2 ] with Dimethyl Acetylenedicarboxylate: Identification of Intermediates of the [2+2+2] Alkyne and Alkyne-Ethylene Cyclo(co)trimerizations.

    PubMed

    Bottari, Giovanni; Santos, Laura L; Posadas, Cristina M; Campos, Jesús; Mereiter, Kurt; Paneque, Margarita

    2016-09-12

    The reaction between the bis(ethylene) complex [TpRh(C2 H4 )2 ], 1, (Tp=hydrotris(pyrazolyl)borate), and dimethyl acetylenedicarboxylate (DMAD) has been studied under different experimental conditions. A mixture of products was formed, in which TpRh(I) species were prevalent, whereas the presence of trapping agents, like water or acetonitrile, allowed for the stabilization and isolation of octahedral TpRh(III) compounds. An excess of DMAD gave rise to a small amount of the [2+2+2] cyclotrimerization product hexamethyl mellitate (6). Although no catalytic application of 1 was achieved, mechanistic insights shed light on the formation of stable rhodium species representing the resting state of the catalytic cycle of rhodium-mediated [2+2+2] cyclo(co)trimerization reactions. Metallacyclopentene intermediate species, generated from the activation of one alkyne and one ethylene molecule from 1, and metallacyclopentadiene species, formed by oxidative coupling of two alkynes to the rhodium centre, are crucial steps in the pathways leading to the final organometallic and organic products. PMID:27535720

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

    PubMed

    Shi, Hongchang; Wang, Yilei; Hua, Ruimao

    2015-11-11

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

  4. Reaction of the Co(II)-substrate radical pair catalytic intermediate in coenzyme B12-dependent ethanolamine ammonia-lyase in frozen aqueous solution from 190 to 217 K.

    PubMed

    Zhu, Chen; Warncke, Kurt

    2008-12-15

    The decay kinetics of the aminoethanol-generated Co(II)-substrate radical pair catalytic intermediate in ethanolamine ammonia-lyase from Salmonella typhimurium have been measured on timescales of <10(5) s in frozen aqueous solution from 190 to 217 K. X-band continuous-wave electron paramagnetic resonance (EPR) spectroscopy of the disordered samples has been used to continuously monitor the full radical pair EPR spectrum during progress of the decay after temperature step reaction initiation. The decay to a diamagnetic state is complete and no paramagnetic intermediate states are detected. The decay exhibits three kinetic regimes in the measured temperature range, as follows. i), Low temperature range, 190 < or = T < or = 207 K: the decay is biexponential with constant fast (0.57 +/- 0.04) and slow (0.43 +/- 0.04) phase amplitudes. ii), Transition temperature range, 207 < T < 214 K: the amplitude of the slow phase decreases to zero with a compensatory rise in the fast phase amplitude, with increasing temperature. iii), High temperature range, T > or = 214 K: the decay is monoexponential. The observed first-order rate constants for the monoexponential (k(obs,m)) and the fast phase of the biexponential decay (k(obs,f)) adhere to the same linear relation on an lnk versus T(-1) (Arrhenius) plot. Thus, k(obs,m) and k(obs,f) correspond to the same apparent Arrhenius prefactor and activation energy (logA(app,f) (s(-1)) = 13.0, E(a,app,f) = 15.0 kcal/mol), and therefore, a common decay mechanism. We propose that k(obs,m) and k(obs,f) represent the native, forward reaction of the substrate through the radical rearrangement step. The slow phase rate constant (k(obs,s)) for 190 < or = T < or = 207 K obeys a different linear Arrhenius relation (logA(app,s) (s(-1)) = 13.9, E(a,app,s) = 16.6 kcal/mol). In the transition temperature range, k(obs,s) displays a super-Arrhenius increase with increasing temperature. The change in E(a,app,s) with temperature and the narrow range over

  5. 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.

  6. The Children's Interaction Matrix: Intermediate Form, Primary Form. Preliminary Manual. Research Edition 1975.

    ERIC Educational Resources Information Center

    Drummond, Robert J.; And Others

    The Children's Interaction Matrix, Intermediate and Primary Forms, are designed to identify the preferred work and content styles of children in group situations. These factors aid the researcher, teacher, and counselor in understanding the individual's preferred mode of behavior in groups as well as indicating the students' reaction to group…

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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

  13. Time-resolved observations of water oxidation intermediates on a cobalt oxide nanoparticle catalyst

    NASA Astrophysics Data System (ADS)

    Zhang, Miao; de Respinis, Moreno; Frei, Heinz

    2014-04-01

    In any artificial photosynthetic system, the oxidation of water to molecular oxygen provides the electrons needed for the reduction of protons or carbon dioxide to a fuel. Understanding how this four-electron reaction works in detail is important for the development of improved robust catalysts made of Earth-abundant materials, like first-row transition-metal oxides. Here, using time-resolved Fourier-transform infrared spectroscopy and under reaction conditions, we identify intermediates of water oxidation catalysed by an abundant metal-oxide catalyst, cobalt oxide (Co3O4). One intermediate is a surface superoxide (three-electron oxidation intermediate absorbing at 1,013 cm-1), whereas a second observed intermediate is attributed to an oxo Co(IV) site (one-electron oxidation intermediate absorbing at 840 cm-1). The temporal behaviour of the intermediates reveals that they belong to different catalytic sites. Knowledge of the structure and kinetics of surface intermediates will enable the design of improved metal-oxide materials for more efficient water oxidation catalysis.

  14. Ligand intermediates in metal-catalyzed reactions

    SciTech Connect

    Gladysz, J.A.

    1991-09-06

    This report consists of six sections, which cover pi/sigma equilibria in aldehyde and ketone complexes, abstraction of vinylic protons from alkene complexes, mechanism of rearrangement of alkylidene to alkene complexes, rearrangement of terminal acetylene to vinylidene complexes, synthesis and reactivity of lithiocarbide complexes, and new catalysts for the epimerization of secondary alcohols; carbon-hydrogen bond activation in alkoxide complexes. (WET)

  15. 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)].

  16. 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

  17. Surprisingly high activity for oxygen reduction reaction of selected oxides lacking long oxygen-ion diffusion paths at intermediate temperatures: a case study of cobalt-free BaFeO(3-δ).

    PubMed

    Dong, Feifei; Chen, Yubo; Chen, Dengjie; Shao, Zongping

    2014-07-23

    The widespread application of solid oxide fuel cell technology requires the development of innovative electrodes with high activity for oxygen reduction reaction (ORR) at intermediate temperatures. Here, we demonstrate that a cobalt-free parent oxide BaFeO(3-δ) (BF), which lacks long-range oxygen-ion diffusion paths, has surprisingly high electrocatalytic activity for ORR. Both in situ high-temperature X-ray diffraction analysis on room-temperature powder and transmission electron microscopy on quenched powder are applied to investigate the crystal structure of BF. Despite the lack of long oxygen-ion diffusion paths, the easy redox of iron cations as demonstrated by thermal gravimetric analysis (TGA) and oxygen temperature-programmed desorption and the high oxygen vacancy concentration as supported by iodometric titration and TGA benefit the reduction of oxygen to oxygen ions. Moreover, the electrical conductivity relaxation technique in conjunction with a transient thermogravimetric study reveals very high surface exchange kinetics of BF oxide. At 700 °C, the area specific resistance of BF cathode, as expressed by a symmetrical cell configuration, is only ∼0.021 Ω cm(2), and the derived single fuel cell achieves high power output with a peak power density of 870 mW cm(-2). It suggests that an undoped BF parent oxide can be used as a high-efficiency catalyst for ORR. PMID:24978102

  18. Dihydrogen catalysis: a degradation mechanism for N2-fixation intermediates.

    PubMed

    Asatryan, Rubik; Bozzelli, Joseph W; Ruckenstein, Eli

    2012-11-29

    Molecular hydrogen plays multiple roles in activation of nitrogen. Among others, it inhibits the overall process of N(2)-reduction catalyzed by nitrogenase enzyme. The H(2)-assisted dehydrogenation and the H-atom transfer reactions (called dihydrogen catalysis, DHC) are suggested as possible mechanisms for the degradation and removal of potential intermediates formed during the reduction of nitrogen. Several iron-organic model reactions associated with the core stereospecific reaction (cis-N(2)H(2) + H(2) → N(2) + H(2) + H(2)) are examined using a comprehensive density functional theory and ab initio analysis of the corresponding potential energy surfaces. A variety of energetically feasible decomposition pathways are identified for the DHC-oxidation of iron-bound [N(x)H(y)]-species. A liberated diazene intermediate (HN═NH) is suggested to interact in situ with two proximal hydridic H-atoms of an activated (hydrided) Fe-catalyst to produce N(2) and H(2) with a low or even no activation barrier. The majority of identified pathways are shown to be highly sensitive to the electronic environment and spin configuration of metallocomplexes. The H(2)-assisted transport of a single H-atom from a bound [N(x)H(y)] moiety to either the proximal or distal (Fe, S or N) active centers of a catalyst provides an alternative degradation (interconversion) mechanism for the relevant intermediates. The two types of molecular hydrogen-assisted reactions highlighted above, namely, the H(2)-assisted dehydrogenation and the transport of H-atoms, suggest theoretical interpretations for the observed H(2)-inhibition of N(2) activation and HD formation (in the presence of D(2)). The DHC reactions of various [N(x)H(y)] moieties are expected to play significant roles in the industrial high-pressure hydrodenitrification and other catalytic processes involving the metabolism of molecular hydrogen. PMID:23095090

  19. Development and evaluation of real-time polymerase chain reaction assays to identify mosquito (Diptera: Culicidae) bloodmeals originating from native Australian mammals.

    PubMed

    van den Hurk, Andrew F; Smith, Ina L; Smith, Greg A

    2007-01-01

    Real-time TaqMan polymerase chain reaction (PCR) assays were developed for the identification of mosquito (Diptera: Culicidae) bloodmeals originating from three groups of native Australian mammals. Primers and probes were designed to amplify a partial fragment of the cytochrome b gene of the agile wallaby, Macropus agilis (Gould); brushtail possum, Trichosurus vulpecula (Kerr); and the consensus sequence of the four species of Australian flying fox: Pteropus alecto Temminck, Pteropus conspicillatus Gould, Pteropus poliocephalus Temminck, and Pteropus scapulatus Peters. When tested on DNA extracted from whole tissue, each assay was shown to be specific for the vertebrate host that it was designed to identify. To evaluate the TaqMan assays, 137 field-collected blood-fed mosquitoes were analyzed, from which 128 (93.4%) were identified using one of the assays. Compared with other PCR-based techniques for bloodmeal identification, the TaqMan assays are sensitive, specific, and provide a rapid result without the need for post-PCR manipulation and visualization of products. PMID:17294925

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

    PubMed Central

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

    2013-01-01

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

  1. 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.

  2. Chloroacetone photodissociation at 193 nm and the subsequent dynamics of the CH3C(O)CH2 radical--an intermediate formed in the OH + allene reaction en route to CH3 + ketene.

    PubMed

    Alligood, Bridget W; FitzPatrick, Benjamin L; Szpunar, David E; Butler, Laurie J

    2011-02-01

    We use a combination of crossed laser-molecular beam experiments and velocity map imaging experiments to investigate the primary photofission channels of chloroacetone at 193 nm; we also probe the dissociation dynamics of the nascent CH(3)C(O)CH(2) radicals formed from C-Cl bond fission. In addition to the C-Cl bond fission primary photodissociation channel, the data evidence another photodissociation channel of the precursor, C-C bond fission to produce CH(3)CO and CH(2)Cl. The CH(3)C(O)CH(2) radical formed from C-Cl bond fission is one of the intermediates in the OH + allene reaction en route to CH(3) + ketene. The 193 nm photodissociation laser allows us to produce these CH(3)C(O)CH(2) radicals with enough internal energy to span the dissociation barrier leading to the CH(3) + ketene asymptote. Therefore, some of the vibrationally excited CH(3)C(O)CH(2) radicals undergo subsequent dissociation to CH(3) + ketene products; we are able to measure the velocities of these products using both the imaging and scattering apparatuses. The results rule out the presence of a significant contribution from a C-C bond photofission channel that produces CH(3) and COCH(2)Cl fragments. The CH(3)C(O)CH(2) radicals are formed with a considerable amount of energy partitioned into rotation; we use an impulsive model to explicitly characterize the internal energy distribution. The data are better fit by using the C-Cl bond fission transition state on the S(1) surface of chloroacetone as the geometry at which the impulsive force acts, not the Franck-Condon geometry. Our data suggest that, even under atmospheric conditions, the reaction of OH with allene could produce a small branching to CH(3) + ketene products, rather than solely producing inelastically stabilized adducts. This additional channel offers a different pathway for the OH-initiated oxidation of such unsaturated volatile organic compounds, those containing a C=C=C moiety, than is currently included in atmospheric models

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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,…

  8. 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.

  9. 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.

  10. Water-Shale interactions in bench-top and high pressure/high temperature autoclave experiments: Identifying geochemical reaction controlling flow back water chemistry

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

    increase in alkalinity during the experiment. Molar comparisons between Na-Cl and Ca-SO4 suggest Ca is preferentially removed from solution and Na is added to solution through interactions with clay minerals. Cation exchange and desorption during clay hydration likely has a secondary effect on the observed geochemical trend. Ca is sorbed and Na is released preferentially resulting in a Ca depletion seen on the Ca vs. SO4 plot and a Na excess seen in the Na vs. Cl plot. Although this study does not consider mixing of HF-water with formation brines, the identified water-rock reactions may provide insights into observed flow-back water chemistry.

  11. Water-Shale interactions in bench-top and high pressure/high temperature autoclave experiments: Identifying geochemical reaction controlling flow back water chemistry

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    increase in alkalinity during the experiment. Molar comparisons between Na-Cl and Ca-SO4 suggest Ca is preferentially removed from solution and Na is added to solution through interactions with clay minerals. Cation exchange and desorption during clay hydration likely has a secondary effect on the observed geochemical trend. Ca is sorbed and Na is released preferentially resulting in a Ca depletion seen on the Ca vs. SO4 plot and a Na excess seen in the Na vs. Cl plot. Although this study does not consider mixing of HF-water with formation brines, the identified water-rock reactions may provide insights into observed flow-back water chemistry.

  12. 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.

  13. 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.

  14. A comparative study of nitrite reduction by synthetic and biogenic Fe(II-III) hydroxysalts green rusts: Evidence for hydroxyl-nitrite green rust formation as an intermediate reaction product.

    NASA Astrophysics Data System (ADS)

    Ona-Nguema, G.; Guerbois, D.; Morin, G.; Zhang, Y.; Noel, V.; Brest, J.

    2013-12-01

    -GR(Cl) led to the reduction of nitrite ions to ammonium, and that the production of ammonium depended on their Fe(II) content. XRD patterns indicated that both synthetic green rusts were fully oxidized into magnetite during the reaction with nitrite. For biogenic green rusts, the study revealed that both bio-GR(CO3)F and bio-GR(CO3)L were capable of reducing nitrite ions without ammonium production, suggesting the conversion of nitrite ions to nitrogen gas. Moreover, we provided evidence for the first time that the interactions of bio-GR(CO3)F with nitrite led to the formation of an hydroxy-nitrite green rust as a result of the incorporation of nitrite in the interlayer region of bio-GR(CO3)F; such an intercalation of nitrite ions was not observed in experiments with bio-GR(CO3)L. XRD analysis indicated that GR(NO2) was formed as an intermediate reaction product prior to the fully oxidation of GR to ferric oxyhydroxides. [1] Philips S., Laanbroek H. J. and Verstraete W. (2002). Rev. Environ. Sci. Biotechnol. 1, 115-141.

  15. Degradation of Methyl Bromide and Methyl Chloride in Soil Microcosms: Use of Stable C Isotope Fractionation and Stable Isotope Probing to Identify Reactions and the Responsible Microorganisms

    NASA Astrophysics Data System (ADS)

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

    2003-12-01

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

  16. [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

  17. 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)

  18. Time Resolved Spectroscopic Studies Relevant to Reactive Intermediates in Homogeneous Catalysis. The Migratory Insertion Reaction, P. C. Ford, S. M. Massick Coord. Chem. Rev. 2002, 226, 39-49

    SciTech Connect

    Ford, Peter C.; S.M. massick

    2002-12-31

    OAK-B135 Mechanisms of the homogeneous catalytic and photocatalytic activation of small molecules such as carbon monoxide, dihydrogen and various hydrocarbons. Time-resolved spectroscopic investigations of rhodium and iridium halo carbonyl complex intermediates proposed in methanol carbonylation catalysts.

  19. Transient Ru-methyl formate intermediates generated with bifunctional transfer hydrogenation catalysts

    PubMed Central

    Perry, Richard H.; Brownell, Kristen R.; Chingin, Konstantin; Cahill, Thomas J.; Waymouth, Robert M.; Zare, Richard N.

    2012-01-01

    Desorption electrospray ionization (DESI) coupled to high-resolution Orbitrap mass spectrometry (MS) was used to study the reactivity of a (β-amino alcohol)(arene)RuCl transfer hydrogenation catalytic precursor in methanol (CH3OH). By placing [(p-cymene)RuCl2]2 on a surface and spraying a solution of β-amino alcohol in methanol, two unique transient intermediates having lifetimes in the submillisecond to millisecond range were detected. These intermediates were identified as Ru (II) and Ru (IV) complexes incorporating methyl formate (HCOOCH3). The Ru (IV) intermediate is not observed when the DESI spray solution is sparged with Ar gas, indicating that O2 dissolved in the solvent is necessary for oxidizing Ru (II) to Ru (IV). These proposed intermediates are supported by high-resolution and high mass accuracy measurements and by comparing experimental to calculated isotope profiles. Additionally, analyzing the bulk reaction mixture using gas chromatography-MS and nuclear magnetic resonance spectroscopy confirms the formation of HCOOCH3. These results represent an example that species generated from the (β-amino alcohol)(arene)RuCl (II) catalytic precursor can selectively oxidize CH3OH to HCOOCH3. This observation leads us to propose a pathway that can compete with the hydrogen transfer catalytic cycle. Although bifunctional hydrogen transfer with Ru catalysts has been well-studied, the ability of DESI to intercept intermediates formed in the first few milliseconds of a chemical reaction allowed identification of previously unrecognized intermediates and reaction pathways in this catalytic system. PMID:22315417

  20. Reaction pathways of the diketonitrile degradate of isoxaflutole with hypochlorite in water.

    PubMed

    Lerch, R N; Lin, C H; Leigh, N D

    2007-03-01

    Isoxaflutole (IXF; Balance) belongs to a new class of isoxazole herbicides. Isoxaflutole has a very short half-life in soil and rapidly degrades to a stable and phytotoxic degradate, diketonitrile (DKN). DKN was previously discovered to rapidly react with hypochlorite (OCl-) in tap water, yielding the benzoic acid (BA) degradate as a major product, but the complete reaction pathway and mechanism have not been elucidated. Thus, the objectives of this work were to (1) determine the stoichiometry of the reaction between DKN and OCl-; (2) identify products in addition to BA; and (3) propose a complete pathway and reaction mechanism for oxidation of DKN by OCl-. Stoichiometry of the reaction showed a molar ratio of OCl-/DKN of 2. In addition, two previously uncharacterized chlorinated intermediates were identified under conditions in which OCl- was the limiting reactant. The proposed chemical structure of a chlorinated benzoyl intermediate was inferred from a series of HPLC/MS and HPLC/MS/MS experiments and the use of mass spectral simulation software. A chlorinated ketone intermediate was also identified using ion trap GC/MS. Two additional end products were also identified: cyclopropanecarboxylic acid (CPCA) and dichloroacetonitrile (DCAN). On the basis of the reaction stoichiometry, the structure of the chlorinated intermediates, and the identification of the products, two reaction pathways are proposed. Both pathways involve a two-step nucleophilic attack and oxidation of the diketone structure of DKN, leading to formation of BA, DCAN, and CPCA. PMID:17284050

  1. Discovery-Oriented Approach To Organic Synthesis: Tandem Aldol Condensation-Michael Addition Reactions. Identifying Diastereotopic Hydrogens in an Achiral Molecule by NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wachter-Jurcsak, Nanette; Reddin, Kendra

    2001-09-01

    We have found a beautiful example of anisochrony of diastereotopic acyclic methylene hydrogens in a symmetric diketone, synthesized by techniques traditionally performed in an introductory organic laboratory course. Synthesis of the diketone is high-yielding and easy to carry out, and the products can be directly isolated with a good degree of purity with no need of further manipulation. The reaction can be accomplished in a single laboratory session.

  2. 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.

  3. Branching of keratin intermediate filaments.

    PubMed

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

    2016-06-01

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

  4. Laser Cavity Ringdown Studies of Peroxy Radical Intermediates in the Oxidation of Volatile Organic Compounds

    NASA Astrophysics Data System (ADS)

    Okumura, M.; Takematsu, K.; Eddingsaas, N. C.; Dodson, L. G.; Voss, M.; Nishimura, A.

    2012-12-01

    The detection of reactive intermediates in laboratory kinetics experiments provides a powerful method for determining reaction pathways in the oxidation of Volatile Organic Compounds (VOCs). Many Biogenic VOCs (BVOCs) such as isoprene are unsaturated, and their oxidation can proceed through initial addition of an OH, Cl or NO3 radicals, followed by addition of O2 to form peroxy radicals. We have used cavity ringdown spectroscopy to directly detect substituted peroxy radical intermediates formed in the initial oxidation of a number of unsaturated species, including ethene, propene, butene, butadiene, MBO-232, and MPAN. These experiments have allowed us to identify specific pathways in the oxidation of the parent unsaturated VOC species and to begin studying the rates of subsequent peroxy radical reactions. These studies shed light on the possible pathways for OVOC formation and likely impact on secondary aerosol formation.

  5. 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

  6. 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

  7. Repair of gaps in retroviral DNA integration intermediates.

    PubMed

    Yoder, K E; Bushman, F D

    2000-12-01

    Diverse mobile DNA elements are believed to pirate host cell enzymes to complete DNA transfer. Prominent examples are provided by retroviral cDNA integration and transposon insertion. These reactions initially involve the attachment of each element 3' DNA end to staggered sites in the host DNA by element-encoded integrase or transposase enzymes. Unfolding of such intermediates yields DNA gaps at each junction. It has been widely assumed that host DNA repair enzymes complete attachment of the remaining DNA ends, but the enzymes involved have not been identified for any system. We have synthesized DNA substrates containing the expected gap and 5' two-base flap structure present in retroviral integration intermediates and tested candidate enzymes for the ability to support repair in vitro. We find three required activities, two of which can be satisfied by multiple enzymes. These are a polymerase (polymerase beta, polymerase delta and its cofactor PCNA, or reverse transcriptase), a nuclease (flap endonuclease), and a ligase (ligase I, III, or IV and its cofactor XRCC4). A proposed pathway involving retroviral integrase and reverse transcriptase did not carry out repair under the conditions tested. In addition, prebinding of integrase protein to gapped DNA inhibited repair reactions, indicating that gap repair in vivo may require active disassembly of the integrase complex. PMID:11070016

  8. Intermediate Strength Gravitational Lensing

    SciTech Connect

    Irwin, John

    2005-03-17

    Weak lensing is found in the correlations of shear in {approx}10{sup 4} galaxy images, strong lensing is detected by the obvious distortion of a single galaxy image, whereas intermediate lensing requires detection of less obvious curvature in several neighboring galaxies. Small impact-parameter lensing causes a sextupole distortion whose orientation is correlated with the quadrupole distortion (shear). By looking within a field for the spatial correlation of this sextupole-quadrupole correlation, an intermediate lensing regime is observed. This technique requires correction for the sextupole as well as the quadrupole content of the PSF. We remove the HST PSF and uncover intermediate lensing in the Hubble deep fields. Correlations of the type expected are found.

  9. 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.

  10. Hispanic American Heritage, Intermediate.

    ERIC Educational Resources Information Center

    Shepherd, Mike

    This resource book features the cultural heritage of Hispanics living within the United States and includes ideas, materials, and activities to be used with students in the intermediate grades and middle school. This book explores the definition of the term "Hispanic Americans" and suggests a multilayered population with a variety of cultural…

  11. English 200: Intermediate Composition

    ERIC Educational Resources Information Center

    Ritter, Kelly

    2005-01-01

    "English 200: Intermediate Composition" is a program elective for English majors and a writing-intensive elective for nonmajors at Southern Connecticut State University (SCSU), a comprehensive institution of 11,000 undergraduate and graduate (master's level) students. English 200 is described in the departmental course catalog as a course "in…

  12. INTERMEDIATE READINGS IN TAGALOG.

    ERIC Educational Resources Information Center

    BOWEN, J. DONALD, ED.

    THE SECOND IN A SERIES OF TEXTS DESIGNED TO HELP THE STUDENT ACHIEVE AN UNDERSTANDING OF FILIPINO CULTURE AND ACQUIRE ENOUGH PROFICIENCY IN TAGALOG TO COMMUNICATE EASILY AND MEANINGFULLY, THESE INTERMEDIATE READINGS ARE COORDINATED WITH THE EDITOR'S "BEGINNING TAGALOG" (ED 014 696). INCLUDED IN PART I ARE READINGS WRITTEN ESPECIALLY FOR THIS TEXT…

  13. GLOSSARY TO INTERMEDIATE HINDI.

    ERIC Educational Resources Information Center

    Wisconsin Univ., Madison. Indian Language and Area Center.

    INCLUDED IN THIS GLOSSARY ARE THE VOCABULARY ITEMS FOR THE READINGS IN "INTERMEDIATE HINDI." THE ITEMS ARE ARRANGED BY SELECTION IN SERIAL ORDER. EACH ENTRY INCLUDES NAGARI (DEVANAGARI) SCRIPT SPELLING, A NOTATION OF THE FORM CLASS, AND A SHORT ENGLISH GLOSS. THESE TWO VOLUMES ARE ALSO AVAILABLE AS A SET FOR $7.00 FROM THE COLLEGE PRINTING…

  14. 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…

  15. Intermediate Cambodian Reader.

    ERIC Educational Resources Information Center

    Huffman, Franklin E., Ed.; Proum, Im, Ed.

    This book is a sequel to the "Cambodian System of Writing and Beginning Reader." It is intended to serve as an intermediate reader to develop the student's ability to the point of reading Cambodian texts with the aid of a dictionary. Part One of the book consists of 37 readings, graded in length and difficulty, and selected to provide a wide range…

  16. 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

  17. 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.

  18. Kinetics of oxidation of chlorobenzenes and phenyl-ureas by Fe(II)/H2O2 and Fe(III)/H2O2. Evidence of reduction and oxidation reactions of intermediates by Fe(II) or Fe(III).

    PubMed

    Gallard, H; De Laat, J

    2001-02-01

    The rates of degradation of 1,2,4-trichlorobenzene (TCB), 2,5-dichloronitrobenzene (DCNB), diuron and isoproturon by Fe(II)/H2O2 and Fe(III)/H2O2 have been investigated in dilute aqueous solution ([Organic compound]0 approximately 1 microM, at 25.0 +/- 0.2 degrees C and pH < or = 3). Using the relative rate method with atrazine as the reference compound, and the Fe(II)/H2O2 (with an excess of Fe(II)) and Fe(III)/H2O2 systems as sources of OH radicals, the rate constants for the reaction of OH* with TCB and DCNB were determined as (6.0 +/- 0.3)10(9) and (1.1 +/- 0.2)10(9) M(-1) s(-1). Relative rates of degradation of diuron and isoproturon by Fe(II)/H2O2 were about two times smaller in the absence of dissolved oxygen than in the presence of oxygen. These data indicate that radical intermediates are reduced back to the parent compound by Fe(II) in the absence of oxygen. Oxidation experiments with Fe(III)/H2O2 showed that the rate of decomposition of atrazine markedly increased in the presence of TCB and this increase has been attributed to a regeneration of Fe(II) by oxidation reactions of intermediates (radical species and dihydroxybenzenes) by Fe(III). PMID:11100792

  19. 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

  20. Unveiling the crucial intermediates in androgen production

    PubMed Central

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

    2015-01-01

    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

  1. Substrate Activation by Iron Superoxo Intermediates

    PubMed Central

    van der Donk, Wilfred A.; Krebs, Carsten; Bollinger, J. Martin

    2010-01-01

    A growing number of non-heme-iron oxygenases and oxidases catalyze reactions for which the well-established mechanistic paradigm involving a single C-H-bond cleaving intermediate of the Fe(IV)-oxo (ferryl) type [1] is insufficient to explain the chemistry. It is becoming clear that, in several of these cases, Fe(III)-superoxide complexes formed by simple addition of O2 to the reduced [Fe(II)] cofactor initiate substrate oxidation by abstracting hydrogen [2]. This substrate-oxidizing entry route into high-valent-iron intermediates makes possible an array of complex and elegant oxidation reactions without consumption of valuable reducing equivalents. Examples of this novel mechanistic strategy are discussed with the goal of bringing forth unifying principles. PMID:20951572

  2. Highly enantioselective trapping of zwitterionic intermediates by imines

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

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

  3. 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.

  4. 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.

  5. Mesoscopic statistical properties of multistep enzyme-mediated reactions.

    PubMed

    de Ronde, W H; Daniels, B C; Mugler, A; Sinitsyn, N A; Nemenman, I

    2009-09-01

    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 study, the authors address this problem by solving the chemical master equations for various enzymatic reactions. A perturbation theory analogous to that used in quantum mechanics allows the determination of the first (n) and the second (σ2) 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(n)/dt (or 'dose-response' curve) and the Fano factor F= σ2/(n) are both realistically measurable quantities, and whereas 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 the authors explore this possibility in the context of four sample multistep enzymatic reactions. 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. PMID:21028932

  6. Reactions of nitrogen oxides with heme models. Characterization of NO and NO2 dissociation from Fe(TPP)(NO2)(NO) by flash photolysis and rapid dilution techniques: Fe(TPP)(NO2) as an unstable intermediate.

    PubMed

    Lim, Mark D; Lorkovic, Ivan M; Wedeking, Katrin; Zanella, Andrew W; Works, Carmen F; Massick, Steve M; Ford, Peter C

    2002-08-21

    Described are studies directed toward elucidating the controversial chemistry relating to the solution phase reactions of nitric oxide with the iron(II) porphyrin complex Fe(TPP)(NO) (1, TPP = meso-tetraphenylporphinato2-). The only reaction observable with clean NO is the formation of the diamagnetic dinitrosyl species Fe(TPP)(NO)2 (2), and this is seen only at low temperatures (K(1) < 3 M(-1) at ambient temperature). However, 1 does readily react reversibly with N2O3 in the presence of excess NO to give the nitro nitrosyl complex Fe(TPP)(NO2)(NO) (3), suggesting that previous claims that 1 promotes NO disproportionation to give 3 may have been compromised by traces of air in the nitric oxide sources. It is also noted that 3 undergoes reversible loss of NO to give the elusive nitro species Fe(TPP)(NO2) (4), which has been implicated as a powerful oxygen atom transfer agent in reactions with various substrates. Furthermore, in the presence of excess NO2, the latter undergoes oxidation to the stable nitrato analogue Fe(TPP)(NO3) (5). Owing to such reactivity of Fe(TPP)(NO2), flash photolysis and stopped-flow kinetics rather than static techniques were necessary for the accurate measurement of dissociation equilibria characteristic of Fe(TPP)(NO2)(NO) in 298 K toluene solution. Flash photolysis of 3 resulted in competitive NO2 and NO dissociation to give Fe(TPP)(NO) and Fe(TPP)(NO2), respectively. The rate constant for the reaction of 1 with N2O3 to generate Fe(TPP)(NO2)(NO) was determined to be 1.8 x 10(6) M(-1) s(-1), and that for the NO reaction with 4 was similarly determined to be 4.2 x 10(5) M(-1) s(-1). Stopped-flow rapid dilution techniques were used to determine the rate constant for NO dissociation from 3 as 2.6 s(-1). The rapid dilution experiments also demonstrated that Fe(TPP)(NO2) readily undergoes further oxidation to give Fe(TPP)(NO3). The mechanistic implications of these observations are discussed, and it is suggested that NO2 liberated

  7. 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...

  8. 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…

  9. 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…

  10. Membrane Fission: Model for Intermediate Structures

    PubMed Central

    Kozlovsky, Yonathan; Kozlov, Michael M.

    2003-01-01

    Membrane budding-fission is a fundamental process generating intracellular carriers of proteins. Earlier works were focused only on formation of coated buds connected to the initial membrane by narrow membrane necks. We present the theoretical analysis of the whole pathway of budding-fission, including the crucial stage where the membrane neck undergoes fission and the carrier separates from the donor membrane. We consider two successive intermediates of the reaction: 1), a constricted membrane neck coming out of aperture of the assembling protein coat, and 2), hemifission intermediate resulting from self-fusion of the inner monolayer of the neck, while its outer monolayer remains continuous. Transformation of the constricted neck into the hemifission intermediate is driven by the membrane stress produced in the neck by the protein coat. Although apparently similar to hemifusion, the fission is predicted to have an opposite dependence on the monolayer spontaneous curvature. Analysis of the further stages of the process demonstrates that in all practically important cases the hemifission intermediate decays spontaneously into two separate membranes, thereby completing the fission process. We formulate the “job description” for fission proteins by calculating the energy they have to deliver and the radii of the protein coat aperture which have to be reached to drive the fission process. PMID:12829467

  11. Experiments in intermediate energy physics

    SciTech Connect

    Dehnhard, D.

    2003-02-28

    Research in experimental nuclear physics was done from 1979 to 2002 primarily at intermediate energy facilities that provide pion, proton, and kaon beams. Particularly successful has been the work at the Los Alamos Meson Physics Facility (LAMPF) on unraveling the neutron and proton contributions to nuclear ground state and transition densities. This work was done on a wide variety of nuclei and with great detail on the carbon, oxygen, and helium isotopes. Some of the investigations involved the use of polarized targets which allowed the extraction of information on the spin-dependent part of the triangle-nucleon interaction. At the Indiana University Cyclotron Facility (IUCF) we studied proton-induced charge exchange reactions with results of importance to astrophysics and the nuclear few-body problem. During the first few years, the analysis of heavy-ion nucleus scattering data that had been taken prior to 1979 was completed. During the last few years we created hypernuclei by use of a kaon beam at Brookhaven National Laboratory (BNL) and an electron beam at Jefferson Laboratory (JLab). The data taken at BNL for a study of the non-mesonic weak decay of the A particle in a nucleus are still under analysis by our collaborators. The work at JLab resulted in the best resolution hypernuclear spectra measured thus far with magnetic spectrometers.

  12. A Mechanochemical Switch to Control Radical Intermediates

    PubMed Central

    2015-01-01

    B12-dependent enzymes employ radical species with exceptional prowess to catalyze some of the most chemically challenging, thermodynamically unfavorable reactions. However, dealing with highly reactive intermediates is an extremely demanding task, requiring sophisticated control strategies to prevent unwanted side reactions. Using hybrid quantum mechanical/molecular mechanical simulations, we follow the full catalytic cycle of an AdoB12-dependent enzyme and present the details of a mechanism that utilizes a highly effective mechanochemical switch. When the switch is “off”, the 5′-deoxyadenosyl radical moiety is stabilized by releasing the internal strain of an enzyme-imposed conformation. Turning the switch “on,” the enzyme environment becomes the driving force to impose a distinct conformation of the 5′-deoxyadenosyl radical to avoid deleterious radical transfer. This mechanochemical switch illustrates the elaborate way in which enzymes attain selectivity of extremely chemically challenging reactions. PMID:24846280

  13. A mechanochemical switch to control radical intermediates.

    PubMed

    Brunk, Elizabeth; Kellett, Whitney F; Richards, Nigel G J; Rothlisberger, Ursula

    2014-06-17

    B₁₂-dependent enzymes employ radical species with exceptional prowess to catalyze some of the most chemically challenging, thermodynamically unfavorable reactions. However, dealing with highly reactive intermediates is an extremely demanding task, requiring sophisticated control strategies to prevent unwanted side reactions. Using hybrid quantum mechanical/molecular mechanical simulations, we follow the full catalytic cycle of an AdoB₁₂-dependent enzyme and present the details of a mechanism that utilizes a highly effective mechanochemical switch. When the switch is "off", the 5'-deoxyadenosyl radical moiety is stabilized by releasing the internal strain of an enzyme-imposed conformation. Turning the switch "on," the enzyme environment becomes the driving force to impose a distinct conformation of the 5'-deoxyadenosyl radical to avoid deleterious radical transfer. This mechanochemical switch illustrates the elaborate way in which enzymes attain selectivity of extremely chemically challenging reactions. PMID:24846280

  14. Formation of a stalled early intermediate of pseudouridine synthesis monitored by real-time FRET

    PubMed Central

    Hengesbach, Martin; Voigts-Hoffmann, Felix; Hofmann, Benjamin; Helm, Mark

    2010-01-01

    Pseudouridine is the most abundant of more than 100 chemically distinct natural ribonucleotide modifications. Its synthesis consists of an isomerization reaction of a uridine residue in the RNA chain and is catalyzed by pseudouridine synthases. The unusual reaction mechanism has become the object of renewed research effort, frequently involving replacement of the substrate uridines with 5-fluorouracil (f5U). f5U is known to be a potent inhibitor of pseudouridine synthase activity, but the effect varies among the target pseudouridine synthases. Derivatives of f5U have previously been detected, which are thought to be either hydrolysis products of covalent enzyme-RNA adducts, or isomerization intermediates. Here we describe the interaction of pseudouridine synthase 1 (Pus1p) with f5U-containing tRNA. The interaction described is specific to Pus1p and position 27 in the tRNA anticodon stem, but the enzyme neither forms a covalent adduct nor stalls at a previously identified reaction intermediate of f5U. The f5U27 residue, as analyzed by a DNAzyme-based assay using TLC and mass spectrometry, displayed physicochemical properties unaltered by the reversible interaction with Pus1p. Thus, Pus1p binds an f5U-containing substrate, but, in contrast to other pseudouridine synthases, leaves the chemical structure of f5U unchanged. The specific, but nonproductive, interaction demonstrated here thus constitutes an intermediate of Pus turnover, stalled by the presence of f5U in an early state of catalysis. Observation of the interaction of Pus1p with fluorescence-labeled tRNA by a real-time readout of fluorescence anisotropy and FRET revealed significant structural distortion of f5U-tRNA structure in the stalled intermediate state of pseudouridine catalysis. PMID:20106954

  15. Density Functional Theory Insights into the Role of the Methionine-Tyrosine-Tryptophan Adduct Radical in the KatG Catalase Reaction: O2 Release from the Oxyheme Intermediate.

    PubMed

    Kruft, Bonnie I; Magliozzo, Richard S; Jarzęcki, Andrzej A

    2015-07-01

    Density functional theory was employed for a comprehensive study that provided electronic and structural insights into the KatG catalase reaction that involves oxyheme. The catalytic role of a unique amino acid cofactor Met-Tyr-Trp (MYW) in its radical form found in KatG was thereby elucidated. It was established that the MYW-radical is flexible such that a "hinge-like opening" rotation of the Trp-107 ring with respect to the Tyr-229 ring along their covalent C-C bond is an inherent feature of its catalytic properties. Also, an H-bond between the Tyr-229 and the mobile side chain of Arg-418 further enables the catalytic events. The opening process breaks an H-bond between the N-H of Trp-107 and the inner oxygen of the Fe-O2 (oxyheme) complex present in the closed conformation of the MYW-radical. This motion lowers the spin-crossing energy barrier between the ground state and the catalytically active high-spin states and enables electron transfer from the oxyheme group to the MYW-radical. The release of molecular oxygen is thereby catalyzed and leaves ferric-heme poised for another catalytic cycle. The energy barrier for the oxyheme state to complete the catalytic event, when assisted by the radical opening process, is thereby reduced and estimated to be 5.6 kcal/mol. PMID:26050709

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

    PubMed

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

    2011-09-19

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

  17. Electronic energy levels of intermediates in the laboratory

    NASA Astrophysics Data System (ADS)

    Howard, I. A.; Horlick, G.

    1980-12-01

    Using the multiple scattering X-alpha method, electronic energy levels have been found self-consistently for the intermediates Ni(CO)(n), n = 1,2,3 in the formation of nickel tetracarbonyl via the Ni-CO surface reaction. Linear geometries have been assumed for NiCO and Ni(CO)2, and a trigonal planar conformation for Ni(CO)3, in accordance with previously published IR spectra. The intermediates were assumed to be in the gas phase, free of surface interaction. From the energy level structure found, all three of the intermediates were determined to be diamagnetic, as Ni(CO)4 is known to be.

  18. 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.

  19. Noncanonical Reactions of Flavoenzymes

    PubMed Central

    Sobrado, Pablo

    2012-01-01

    Enzymes containing flavin cofactors are predominantly involved in redox reactions in numerous cellular processes where the protein environment modulates the chemical reactivity of the flavin to either transfer one or two electrons. Some flavoenzymes catalyze reactions with no net redox change. In these reactions, the protein environment modulates the reactivity of the flavin to perform novel chemistries. Recent mechanistic and structural data supporting novel flavin functionalities in reactions catalyzed by chorismate synthase, type II isopentenyl diphosphate isomerase, UDP-galactopyranose mutase, and alkyl-dihydroxyacetonephosphate synthase are presented in this review. In these enzymes, the flavin plays either a direct role in acid/base reactions or as a nucleophile or electrophile. In addition, the flavin cofactor is proposed to function as a “molecular scaffold” in the formation of UDP-galactofuranose and alkyl-dihydroxyacetonephosphate by forming a covalent adduct with reaction intermediates. PMID:23203060

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

    PubMed

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

    2008-07-11

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

  1. 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.

  2. Reaction coordinates for electron transfer reactions

    SciTech Connect

    Rasaiah, Jayendran C.; Zhu Jianjun

    2008-12-07

    The polarization fluctuation and energy gap formulations of the reaction coordinate for outer sphere electron transfer are linearly related to the constant energy constraint Lagrangian multiplier m in Marcus' theory of electron transfer. The quadratic dependence of the free energies of the reactant and product intermediates on m and m+1, respectively, leads to similar dependence of the free energies on the reaction coordinates and to the same dependence of the activation energy on the reorganization energy and the standard reaction free energy. Within the approximations of a continuum model of the solvent and linear response of the longitudinal polarization to the electric field in Marcus' theory, both formulations of the reaction coordinate are expected to lead to the same results.

  3. Intermediate BL Lac objects

    NASA Astrophysics Data System (ADS)

    Bondi, M.; Marchã, M. J. M.; Dallacasa, D.; Stanghellini, C.

    2001-08-01

    The 200-mJy sample, defined by Marchã et al., contains about 60 nearby, northern, flat-spectrum radio sources. In particular, the sample has proved effective at finding nearby radio-selected BL Lac objects with radio luminosities comparable to those of X-ray-selected objects, and low-luminosity flat-spectrum weak emission-line radio galaxies (WLRGs). The 200-mJy sample contains 23 BL Lac objects (including 6 BL Lac candidates) and 19 WLRGs. We will refer to these subsamples as the 200-mJy BL Lac sample and the 200-mJy WLRG sample, respectively. We have started a systematic analysis of the morphological pc-scale properties of the 200-mJy radio sources using VLBI observations. This paper presents VLBI observations at 5 and 1.6GHz of 14 BL Lac objects and WLRGs selected from the 200-mJy sample. The pc-scale morphology of these objects is briefly discussed. We derive the radio beaming parameters of the 200-mJy BL Lac objects and WLRGs and compare them with those of other BL Lac samples and with a sample of FR I radio galaxies. The overall broad-band radio, optical and X-ray properties of the 200-mJy BL Lac sample are discussed and compared with those of other BL Lac samples, radio- and X-ray-selected. We find that the 200-mJy BL Lac objects fill the gap between HBL and LBL objects in the colour-colour plot, and have intermediate αXOX as expected in the spectral energy distribution unification scenario. Finally, we briefly discuss the role of the WLRGs.

  4. Full Kinetics from First Principles of the Chlorine Evolution Reaction over a RuO2 (110) Model Electrode.

    PubMed

    Exner, Kai S; Anton, Josef; Jacob, Timo; Over, Herbert

    2016-06-20

    Current progress in modern electrocatalysis research is spurred by theory, frequently based on ab initio thermodynamics, where the stable reaction intermediates at the electrode surface are identified, while the actual energy barriers are ignored. This approach is popular in that a simple tool is available for searching for promising electrode materials. However, thermodynamics alone may be misleading to assess the catalytic activity of an electrochemical reaction as we exemplify with the chlorine evolution reaction (CER) over a RuO2 (110) model electrode. The full procedure is introduced, starting from the stable reaction intermediates, computing the energy barriers, and finally performing microkinetic simulations, all performed under the influence of the solvent and the electrode potential. Full kinetics from first-principles allows the rate-determining step in the CER to be identified and the experimentally observed change in the Tafel slope to be explained. PMID:27168427

  5. 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…

  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. 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)…

  8. Probing Hydrothermal Organic Reaction Mechanisms with Hydrothermal Photochemistry

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  9. Novel Reagents for Multi-Component Reactions

    NASA Astrophysics Data System (ADS)

    Wang, Yanguang; Basso, Andrea; Nenajdenko, Valentine G.; Gulevich, Anton V.; Krasavin, Mikhail; Bushkova, Ekaterina; Parchinsky, Vladislav; Banfi, Luca; Basso, Andrea; Cerulli, Valentina; Guanti, Giuseppe; Riva, Renata; Rozentsveig, Igor B.; Rozentsveig, Gulnur N.; Popov, Aleksandr V.; Serykh, Valeriy J.; Levkovskaya, Galina G.; Cao, Song; Shen, Li; Liu, Nianjin; Wu, Jingjing; Li, Lina; Qian, Xuhong; Chen, Xiaopeng; Wang, Hongbo; Feng, Jinwu; Wang, Yanguang; Lu, Ping; Heravi, Majid M.; Sadjadi, Samaheh; Kazemizadeh, Ali Reza; Ramazani, Ali; Kudyakova, Yulia S.; Goryaeva, Marina V.; Burgart, Yanina V.; Saloutin, Victor I.; Mossetti, Riccardo; Pirali, Tracey; Tron, Gian Cesare; Rozhkova, Yulia S.; Mayorova, Olga A.; Shklyaev, Yuriy V.; Zhdanko, Alexander G.; Nenajdenko, Valentine G.; Stryapunina, Olga G.; Plekhanova, Irina V.; Glushkov, Vladimir A.; Shklyaev, Yurii V.

    Ketenimines are a class of versatile and highly reactive intermediates that can participate in a variety of organic reactions, such as nucleophilic additions, radical additions, [2 + 2] and [2 + 4] cycloadditions, and sigmatropic rearrangements. In this presentation, we report on a series of multi-component reactions that involve a ketenimine intermediate. These reactions could furnish diverse heterocyclic compounds, including functionalized iminocoumarin, iminodihydroqunolines, iminothiochromens, pyrrolines, isoquinolines, pyridines, β-lactams, imino-1,2-dihydrocoumarins, and benzimidazoles.

  10. 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.

  11. A new method for analysis of reactive adsorbed intermediates: Bismuth postdosing in thermal desorption mass spectroscopy

    NASA Astrophysics Data System (ADS)

    Campbell, Charles T.; Rodriguez, J. A.; Henn, F. C.; Campbell, J. M.; Dalton, P. J.; Seimanides, S. G.

    1988-05-01

    A new method which should have relatively general applicability for the identification and quantitative analysis of reactive adsorbed molecular intermediates in surface reactions will be described, and the first examples of its application will be presented. When a reactive intermediate is generated on a surface, it often has a tendency to dissociate before desorbing. Since dissociation generally requires additional free sites on the surface, dissociation can be suppressed and desorption correspondingly enhanced if the free sites on the surface can be properly poisoned. We have found that bismuth adatoms are very good inert site blockers, which can be postdosed to the surface of a transition metal containing a reactive adsorbed hydrocarbon without destroying the hydrocarbon. Whereas in the absence of bismuth, the hydrocarbon would completely dehydrogenate during thermal desorption spectroscopy (TDS) and liberate only H2 into the gas phase, after bismuth postdosing the reactive hydrocarbon desorbs intact for mass spectral identification and quantitative analysis. This method has been used to prove that adsorbed benzene is the initial product of the dehydrogenation of cyclohexane on Pt(111) at ˜235 K. In the absence of bismuth, this benzene all dissociates during TDS to liberate only H2, leaving graphitic carbon residue on the surface. When one-third monolayer of Bi is postdosed at 110 K, the dehydrogenation pathway is sterically poisoned and the adsorbed benzene quantitatively desorbs during TDS, where it is unambiguously identified by mass spectroscopy. By briefly heating the reactive adsorbed intermediate to increasing temperatures prior to Bi deposition, the thermal stability limits of the intermediate and the kinetic parameters for its dissociation can be established. This is demonstrated for the dehydrogenation reaction of adsorbed cyclopentene on Pt(111). Bismuth postdosing in thermal desorption mass spectroscopy (BPTDS) should be a very useful but

  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. 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

  14. 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

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

    PubMed

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

    2014-07-01

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

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

    SciTech Connect

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

    2013-04-08

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

  17. Intermediate depth seismicity - a reflection seismic approach

    NASA Astrophysics Data System (ADS)

    Haberland, C.; Rietbrock, A.

    2004-12-01

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

  18. Noncovalent Intermediate of Thymidylate Synthase: Fact or Fiction?

    PubMed

    Kholodar, Svetlana A; Kohen, Amnon

    2016-07-01

    Thymidylate synthase is an attractive target for antibiotic and anticancer drugs due to its essential role in the de novo biosynthesis of the DNA nucleotide thymine. The enzymatic reaction is initiated by a nucleophilic activation of the substrate via formation of a covalent bond to an active site cysteine. The traditionally accepted mechanism is then followed by a series of covalently bound intermediates, where that bond is only cleaved upon product release. Recent computational and experimental studies suggest that the covalent bond between the protein and substrate is actually quite labile. Importantly, these findings predict the existence of a noncovalently bound bisubstrate intermediate, not previously anticipated, which could be the target of a novel class of drugs inhibiting DNA biosynthesis. Here we report the synthesis of the proposed intermediate and findings supporting its chemical and kinetic competence. These findings substantiate the predicted nontraditional mechanism and the potential of this intermediate as a new drug lead. PMID:27327197

  19. How much can an intermediate state influence competing reactive pathways?

    NASA Astrophysics Data System (ADS)

    Despa, Florin; Berry, R. Stephen

    2004-03-01

    A molecule undergoing reaction may form a short-lived intermediate. Under certain conditions, the rate at which the reaction proceeds toward the product state via the intermediate may exceed that of a simple, direct path. The competition of two alternative reactive pathways is analyzed here in terms of a stochastic model. The approach allows one to diagnose this competition as a function of the energy of the intermediate relative to the barrier heights of the potential surface and values of the reactive vibrational modes. The result has applications to a variety of problems in chemical physics, ranging from the "lock-and-key" mechanism for the enzymatic activity to control of temporal evolution of complex systems by optimal laser fields.

  20. 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.

  1. Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H.

    PubMed

    Rosta, Edina; Woodcock, H Lee; Brooks, Bernard R; Hummer, Gerhard

    2009-08-01

    We describe a method for the systematic improvement of reaction coordinates in quantum mechanical/molecular mechanical (QM/MM) calculations of reaction free-energy profiles. In umbrella-sampling free-energy calculations, a biasing potential acting on a chosen reaction coordinate is used to sample the system in reactant, product, and transition states. Sharp, nearly discontinuous changes along the resulting reaction path are used to identify coordinates that are relevant for the reaction but not properly sampled. These degrees of freedom are then included in an extended reaction coordinate. The general formalism is illustrated for the catalytic cleavage of the RNA backbone of an RNA/DNA hybrid duplex by the RNase H enzyme of Bacillus halodurans. We find that in the initial attack of the phosphate diester by water, the oxygen-phosphorus distances alone are not sufficient as reaction coordinates, resulting in substantial hysteresis in the proton degrees of freedom and a barrier that is too low (approximately 10 kcal/mol). If the proton degrees of freedom are included in an extended reaction coordinate, we obtain a barrier of 21.6 kcal/mol consistent with the experimental rates. As the barrier is approached, the attacking water molecule transfers one of its protons to the O1P oxygen of the phosphate group. At the barrier top, the resulting hydroxide ion forms a penta-coordinated phosphate intermediate. The method used to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free-energy calculations. PMID:19462398

  2. Artificial reaction coordinate “tunneling” in free energy calculations: the catalytic reaction of RNase H

    PubMed Central

    Rosta, Edina; Woodcock, H. Lee; Brooks, Bernard R.; Hummer, Gerhard

    2011-01-01

    We describe a method for the systematic improvement of reaction coordinates in quantum mechanical / molecular mechanical (QM/MM) calculations of reaction free energy profiles. In umbrella-sampling free energy calculations, a biasing potential acting on a chosen reaction coordinate is used to sample the system in reactant, product, and transition states. Sharp, nearly discontinuous changes along the resulting reaction path are used to identify coordinates that are relevant for the reaction but not properly sampled. These degrees of freedom are then included in an extended reaction coordinate. The general formalism is illustrated for the catalytic cleavage of the RNA backbone of an RNA/DNA hybrid duplex by the RNase H enzyme of bacillus halodurans. We find that in the initial attack of the phosphate diester by water, the oxygen-phosphorus distances alone are not sufficient as reaction coordinates, resulting in substantial hysteresis in the proton degrees of freedom and a barrier that is too low (~10 kcal/mol). If the proton degrees of freedom are included in an extended reaction coordinate, we obtain a barrier of 21.6 kcal/mol consistent with the experimental rates. As the barrier is approached, the attacking water molecule transfers one of its protons to the O1P oxygen of the phosphate group. At the barrier top, the resulting hydroxide ion forms a penta-coordinated phosphate intermediate. The method used to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free energy calculations. PMID:19462398

  3. Correlations in Intermediate Energy Two-Proton Removal Reactions

    NASA Astrophysics Data System (ADS)

    Wimmer, K.; Bazin, D.; Gade, A.; Tostevin, J. A.; Baugher, T.; Chajecki, Z.; Coupland, D.; Famiano, M. A.; Ghosh, T. K.; Grinyer, G. F.; Hodges, R.; Howard, M. E.; Kilburn, M.; Lynch, W. G.; Manning, B.; Meierbachtol, K.; Quarterman, P.; Ratkiewicz, A.; Sanetullaev, A.; Simpson, E. C.; Stroberg, S. R.; Tsang, M. B.; Weisshaar, D.; Winkelbauer, J.; Winkler, R.; Youngs, M.

    2012-11-01

    We report final-state-exclusive measurements of the light charged fragments in coincidence with Ne26 residual nuclei following the direct two-proton removal from a neutron-rich Mg28 secondary beam. A Dalitz-plot analysis and comparisons with simulations show that a majority of the triple-coincidence events with two protons display phase-space correlations consistent with the (two-body) kinematics of a spatially correlated pair-removal mechanism. The fraction of such correlated events, 56(12)%, is consistent with the fraction of the calculated cross section, 64%, arising from spin S=0 two-proton configurations in the entrance-channel (shell-model) Mg28 ground state wave function. This result promises access to an additional and more specific probe of the spin and spatial correlations of valence nucleon pairs in exotic nuclei produced as fast secondary beams.

  4. Intermediate Reactions of Oxidative Phosphorylation in Mitochondria From Cabbage 12

    PubMed Central

    Lotlikar, Prabhakar D.; Remmert, Lemar F.

    1968-01-01

    Respiratory control ratios between 2.0 and 9.0 were obtained by comparison of the respiratory rates of cabbage mitochondria in the presence and in the absence of individual components of the system used to provide ADP and by comparing the rates before and after exhaustion of added ADP. These results indicate that respiration in cabbage mitochondria is controlled by the availability of ADP, which serves as the phosphate acceptor. Pentachlorophenol (PCP), 2,4-dinitrophenol (DNP), gramicidin and oleic acid inhibited phosphorylation to a greater extent than respiration in the cabbage mitochondria, but these reagents did not stimulate respiration in the absence of a phosphate acceptor. Respiration was stimulated by DNP only in the presence of added ATP. 2,4-Dinitrophenol, pentachlorophenol, dicumarol and gramicidin did not stimulate ATPase activity either in the presence or absence of added Mg2+. Oleic acid stimulated ATPase activity in the presence of added Mg2+, but did not stimulate respiration even in the presence of added ATP. The ATP-32Pi exchange rate was increased many fold in the presence of added Mg2+. Oleic acid and 2,4-dinitrophenol inhibited the exchange almost completely. PMID:5641190

  5. Photoreactions of cyclic sulfite esters: Evidence for diradical intermediates

    PubMed Central

    Arney, Benny E; Ihmels, Heiko

    2012-01-01

    Summary The photochemistry of a phenyl and 1,2-diphenyl substituted sulfite ester is reported. The performance of photoreactions under relatively mild reaction conditions enables the detection of products that have not been observed in previous studies. It is concluded that, complementary to the initially proposed carbene intermediates, diradicals may also be considered. PMID:23019449

  6. Neutrino interactions with nucleons and nuclei at intermediate energies

    SciTech Connect

    Alvarez-Ruso, L.; Leitner, T.; Mosel, U.

    2006-07-11

    We investigate neutrino-nucleus collisions at intermediate energies incorporating quasielastic scattering and {delta}(1232) excitation as elementary processes, together with Fermi motion, Pauli blocking and mean-field potentials in the nuclear medium. A full coupled-channel treatment of final state interactions is achieved with a semiclassical BUU transport model. Results for inclusive reactions and nucleon knockout are presented.

  7. 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.

  8. 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

  9. Characterization of reactive intermediates by multinuclear diffusion-ordered NMR spectroscopy (DOSY).

    PubMed

    Li, Deyu; Keresztes, Ivan; Hopson, Russell; Williard, Paul G

    2009-02-17

    Nuclear magnetic resonance (NMR) is the most powerful and widely utilized technique for determining molecular structure. Although traditional NMR data analysis involves the correlation of chemical shift, coupling constant, and NOE interactions to specific structural features, a largely overlooked method introduced more than 40 years ago, pulsed gradient spin-echo (PGSE), measures diffusion coefficients of molecules in solution, thus providing their relative particle sizes. In the early 1990s, the PGSE sequence was incorporated into a two-dimensional experiment, dubbed diffusion-ordered NMR spectroscopy (DOSY), in which one dimension represents chemical shift data while the second dimension resolves species by their diffusion properties. This combination provides a powerful tool for identifying individual species in a multicomponent solution, earning the nickname "chromatography by NMR". In this Account, we describe our efforts to utilize DOSY techniques to characterize organometallic reactive intermediates in solution in order to correlate structural data to solid-state crystal structures determined by X-ray diffraction and to discover the role of aggregate formation and solvation states in reaction mechanisms. In 2000, we reported our initial efforts to employ DOSY techniques in the characterization of reactive intermediates such as organolithium aggregates. Since then, we have explored DOSY experiments with various nuclei beyond (1)H, including (6)Li, (7)Li, (11)B, (13)C, and (29)Si. Additionally, we proposed a diffusion coefficient-formula weight relationship to determine formula weight, aggregation number, and solvation state of reactive intermediates. We also introduced an internal reference system to correlate the diffusion properties of unknown reactive intermediates with known inert molecular standards, such as aromatic compounds, terminal olefins, cycloolefins, and tetraalkylsilanes. Furthermore, we utilized DOSY to interpret the role of aggregation number

  10. Learning to predict chemical reactions.

    PubMed

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

    2011-09-26

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

  11. 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

  12. Benzoxazinone-Mediated Triazine Degradation: A Proposed Reaction Mechanism.

    PubMed

    Willett, C D; Lerch, R N; Lin, C-H; Goyne, K W; Leigh, N D; Roberts, C A

    2016-06-22

    The role of benzoxazinones (Bx, 2-hydroxy-2H-1,4-benzoxazin-3(4H)-one) in triazine resistance in plants has been studied for over half a century. In this research, fundamental parameters of the reaction between DIBOA-Glc (2-β-d-glucopyranosyloxy-4-hydroxy-1,4-benzoxazin-3-one) and atrazine (ATR, 6-chloro-N-ethyl-N'-(1-methylethyl)-1,3,5-triazine-2,4-diamine) were examined. Through a series of experiments employing a variety of chromatographic and spectroscopic techniques, the DIBOA-Glc/ATR reaction was characterized in terms of reactant and product kinetics, stoichiometry, identification of a reaction intermediate, and reaction products formed. Results of these experiments demonstrated that the reaction mechanism proceeds via nucleophilic attack of the hydroxamic acid moiety of DIBOA-Glc at the C-2 position of the triazine ring to form hydroxyatrazine (HA, 2-hydroxy-4-ethylamino-6-isopropylamino-s-triazine), with associated degradation of DIBOA-Glc. Degradation of reactants followed first-order kinetics with a noncatalytic role of DIBOA-Glc. A reaction intermediate was identified as a DIBOA-Glc-HA conjugate, indicating a 1:1 DIBOA-Glc:ATR stoichiometry. Reaction products included HA and Cl(-), but definitive identification of DIBOA-Glc reaction product(s) was not attained. With these reaction parameters elucidated, DIBOA-Glc can be evaluated in terms of its potential for a myriad of applications, including its use to address the problem of widespread ATR contamination of soil and water resources. PMID:27215133

  13. 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.

  14. Reaction efficiency effects on binary chemical reactions

    NASA Astrophysics Data System (ADS)

    Lazaridis, Filippos; Savara, Aditya; Argyrakis, Panos

    2014-09-01

    We study the effect of the variation of reaction efficiency in binary reactions. We use the well-known A + B → 0 model, which has been extensively studied in the past. We perform simulations on this model where we vary the efficiency of reaction, i.e., when two particles meet they do not instantly react, as has been assumed in previous studies, but they react with a probability γ, where γ is in the range 0 < γ < 1. Our results show that at small γ values the system is reaction limited, but as γ increases it crosses over to a diffusion limited behavior. At early times, for small γ values, the particle density falls slower than for larger γ values. This fall-off goes over a crossover point, around the value of γ = 0.50 for high initial densities. Under a variety of conditions simulated, we find that the crossover point was dependent on the initial concentration but not on the lattice size. For intermediate and long times simulations, all γ values (in the depleted reciprocal density versus time plot) converge to the same behavior. These theoretical results are useful in models of epidemic reactions and epidemic spreading, where a contagion from one neighbor to the next is not always successful but proceeds with a certain probability, an analogous effect with the reaction probability examined in the current work.

  15. Time-resolved heme protein intermediates

    NASA Astrophysics Data System (ADS)

    Rousseau, Denis

    2005-03-01

    To determine the enzymatic mechanisms of heme proteins, it is necessary to identify the intermediates along the catalytic pathway and measure the times of their formation and decay. Resonance Raman scattering spectra are especially powerful for obtaining such information as the electronic structure of the heme group and the nature of the ligand coordinated to the heme iron atom may be monitored. The oxygen intermediates of two physiologically important enzymes will be presented. Nitric oxide synthase (NOS) uses oxygen to convert arginine to NO and citrulline; and cytochrome c oxidase (CcO) reduces oxygen to water to support oxidative phosphorylation. The fate or the oxygen in each of these enzymes has been followed by resonance Raman scattering. In NOS the oxygen is slowly converted to an activated species that then reacts fast, whereas in CcO the oxygen is rapidly converted to a reactive species that subsequently reacts slowly. The properties of the intermediates and the origin of the differences between these enzymes will be discussed.

  16. A regioselective double Stille coupling reaction of bicyclic stannolanes.

    PubMed

    Kamimura, Akio; Tanaka, Toshiyuki; So, Masahiro; Itaya, Tomoyuki; Matsuda, Kantaro; Kawamoto, Takuji

    2016-09-14

    A regioselective double Stille coupling reaction was explored using bicyclic stannolanes that were easily prepared from the radical cascade reaction of β-amino-α-methylene esters. Various 1-bromo-2-iodoarenes underwent the double coupling reaction to afford benzoisoindole derivatives in a regioselective manner, where the carbon attached to the iodine selectively coupled with the vinylic carbon, and then the carbon attached to bromine coupled with the alkyl carbon. The combination of intra- and intermolecular coupling reactions provided hexahydroindeno[1,2-b]pyrrole derivatives in good yields. The yields were further improved in the presence of excess amounts of CsF. An attempt to identify the reaction intermediate was made wherein the decomposition of the stannolanes with aqueous HCl and HBr afforded trigonal bipyramidal (TBP) pentacoordinated tin complexes, as confirmed by microanalyses and (119)Sn NMR. Using DCl for the decomposition selectively introduced a deuterium to the E-position of the exomethylene unit. The complexes smoothly underwent the intramolecular Stille coupling reaction in the presence of both a palladium catalyst and DABCO, affording hexahydroindeno[1,2-b]pyrroles in good yields. These results suggest that the double coupling reaction progresses through a TBP tin complex, promoting the second intramolecular coupling reaction between the aryl halide and Csp(3)-tin bond. PMID:27506959

  17. 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.

  18. Barrierless tautomerization of Criegee intermediates via acid catalysis.

    PubMed

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

    2014-11-14

    The tautomerization of Criegee intermediates via a 1,4 β-hydrogen atom transfer to yield a vinyl hydroperoxide has been examined in the absence and presence of carboxylic acids. Electronic structure calculations indicate that the organic acids catalyze the tautomerization reaction to such an extent that it becomes a barrierless process. In contrast, water produces only a nominal catalytic effect. Since organic acids are present in parts-per-billion concentrations in the troposphere, the present results suggest that the acid-catalyzed tautomerization, which can also result in formation of hydroxyl radicals, may be a significant pathway for Criegee intermediates. PMID:25259380

  19. 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

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. Structure based prediction of protein folding intermediates.

    PubMed

    Xie, D; Freire, E

    1994-09-01

    The complete unfolding of a protein involves the disruption of non-covalent intramolecular interactions within the protein and the subsequent hydration of the backbone and amino acid side-chains. The magnitude of the thermodynamic parameters associated with this process is known accurately for a growing number of globular proteins for which high-resolution structures are also available. The existence of this database of structural and thermodynamic information has facilitated the development of statistical procedures aimed at quantifying the relationships existing between protein structure and the thermodynamic parameters of folding/unfolding. Under some conditions proteins do not unfold completely, giving rise to states (commonly known as molten globules) in which the molecule retains some secondary structure and remains in a compact configuration after denaturation. This phenomenon is reflected in the thermodynamics of the process. Depending on the nature of the residual structure that exists after denaturation, the observed enthalpy, entropy and heat capacity changes will deviate in a particular and predictable way from the values expected for complete unfolding. For several proteins, these deviations have been shown to exhibit similar characteristics, suggesting that their equilibrium folding intermediates exhibit some common structural features. Employing empirically derived structure-energetic relationships, it is possible to identify in the native structure of the protein those regions with the higher probability of being structured in equilibrium partly folded states. In this work, a thermodynamic search algorithm aimed at identifying the structural determinants of the molten globule state has been applied to six globular proteins; alpha-lactalbumin, barnase, IIIGlc, interleukin-1 beta, phage T4 lysozyme and phage 434 repressor. Remarkably, the structural features of the predicted equilibrium intermediates coincide to a large extent with the known

  7. Special Relativity and Reactions with Unstable Nuclei

    SciTech Connect

    Bertulani, C.A.

    2005-10-14

    Dynamical relativistic effects are often neglected in the description of reactions with unstable nuclear beams at intermediate energies (ELab {approx_equal} 100 MeV/nucleon). Evidently, this introduces sizable errors in experimental analysis and theoretical descriptions of these reactions. This is particularly important for the experiments held in GANIL/France, MSU/USA, RIKEN/Japan and GSI/Germany. I review a few examples where relativistic effects have been studied in nucleus-nucleus scattering at intermediate energies.

  8. Baeyer-Villiger C-C bond cleavage reaction in gilvocarcin and jadomycin biosynthesis

    PubMed Central

    Tibrewal, Nidhi; Pahari, Pallab; Wang, Guojun; Kharel, Madan K.; Morris, Caleb; Downey, Theresa; Hou, Yanpeng; Bugni, Tim S.; Rohr, Jürgen

    2012-01-01

    GilOII has been unambiguously identified as the key enzyme performing the crucial C-C bond cleavage reaction responsible for the unique rearrangement of a benz[a]anthracene skeleton to the benzo[d]naphthopyranone backbone typical for the gilvocarcin type natural anticancer antibiotics. Further investigations of this enzyme led to the isolation of a hydroxy-oxepinone intermediate which allowed important conclusions regarding the cleavage mechanism. PMID:23102024

  9. 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)…

  10. Intermediality and the Child Performer

    ERIC Educational Resources Information Center

    Budd, Natasha

    2016-01-01

    This report details examples of praxis in the creation and presentation of "Joy Fear and Poetry": an intermedial theatre performance in which children aged 7-12 years generated aesthetic gestures using a range of new media forms. The impetus for the work's development was a desire to make an intervention into habituated patterns of…

  11. Material Voices: Intermediality and Autism

    ERIC Educational Resources Information Center

    Trimingham, Melissa; Shaughnessy, Nicola

    2016-01-01

    Autism continues to be regarded enigmatically; a community that is difficult to access due to perceived disruptions of interpersonal connectedness. Through detailed observations of two children participating in the Arts and Humanities Research Council funded project "Imagining Autism: Drama, Performance and Intermediality as Interventions for…

  12. Susu Intermediate Course. Final Report.

    ERIC Educational Resources Information Center

    Sangster, Linda W.; Faber, Emmanuel

    This intermediate text in Susu is intended to provide the student of Susu with further practice on the grammatical constructions learned in the Basic Course. (See related document AL 001 956.) It is also intended to provide the student with some practice in reading Susu, and to help him gain some appreciation of the cultural life of the Susu in…

  13. Intermediate Filaments: A Historical Perspective

    PubMed Central

    Oshima, Robert G.

    2007-01-01

    Intracellular protein filaments intermediate in size between actin microfilaments and microtubules are composed of a surprising variety of tissue specific proteins commonly interconnected with other filamentous systems for mechanical stability and decorated by a variety of proteins that provide specialized functions. The sequence conservation of the coiled-coil, alpha-helical structure responsible for polymerization into individual 10 nm filaments defines the classification of intermediate filament proteins into a large gene family. Individual filaments further assemble into bundles and branched cytoskeletons visible in the light microscope. However, it is the diversity of the variable terminal domains that likely contributes most to different functions. The search for the functions of intermediate filament proteins has led to discoveries of roles in diseases of the skin, heart, muscle, liver, brain, adipose tissues and even premature aging. The diversity of uses of intermediate filaments as structural elements and scaffolds for organizing the distribution of decorating molecules contrasts with other cytoskeletal elements. This review is an attempt to provide some recollection of how such a diverse field emerged and changed over about 30 years. PMID:17493611

  14. Intermediate Nepali Structure. Volume 1.

    ERIC Educational Resources Information Center

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

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

  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. Oxidation of Refractory Benzothiazoles with PMS/CuFe2O4: Kinetics and Transformation Intermediates.

    PubMed

    Zhang, Tao; Chen, Yin; Leiknes, TorOve

    2016-06-01

    Benzothiazole (BTH) and its derivatives 2-(methylthio)bezothiazole (MTBT), 2-benzothiazolsulfonate (BTSA), and 2-hydroxybenzothiazole (OHBT) are refractory pollutants ubiquitously existing in urban runoff at relatively high concentrations. Here, we report their oxidation by CuFe2O4-activated peroxomonosulfate (PMS/CuFe2O4), focusing on kinetics and transformation intermediates. These benzothiazoles can be efficiently degraded by this oxidation process, which is confirmed to generate mainly sulfate radicals (with negligible hydroxyl-radical formation) under slightly acidic to neutral pH conditions. The molar exposure ratio of sulfate radical to residual PMS (i.e., Rct) for this process is a constant that is related to the reaction condition and can be easily determined. The reaction rate constants of these benzothiazoles toward sulfate radical are (3.3 ± 0.3) × 10(9), (1.4 ± 0.3) × 10(9), (1.5 ± 0.1) × 10(9), and (4.7 ± 0.5) × 10(9) M(-1) s(-1), respectively (pH 7 and 20 °C). On the basis of Rct and these rate constants, their degradation in the presence of organic matter can be well-predicted. A number of transformation products were detected and tentatively identified using triple-quadruple/linear ion trap MS/MS and high-resolution MS. It appears that sulfate radicals attack BTH, MTBT, and BTSA on their benzo ring via electron transfer, generating multiple hydroxylated intermediates that are reactive toward common oxidants. For OHBT oxidation, the thiazole ring is preferentially broken down. Due to competitions of the transformation intermediates, a minimum PMS/pollutant molar ratio of 10-20 is required for effective degradation. The flexible PMS/CuFe2O4 could be a useful process to remove the benzothiazoles from low dissolved organic carbon waters like urban runoff or polluted groundwater. PMID:27144396

  17. Kinetically Competent Intermediate(s) in the Translocation Step of Protein Synthesis

    PubMed Central

    Pan, Dongli; Kirillov, Stanislav V.; Cooperman, Barry S.

    2007-01-01

    SUMMARY Translocation requires large-scale movements of ribosome-bound tRNAs. Using tRNAs that are proflavin-labeled and single turnover rapid kinetics assays, we identify one or possibly two kinetically competent intermediates in translocation. EF-G.GTP binding to the pretranslocation (PRE) complex and GTP hydrolysis is rapidly followed by formation of the securely identified intermediate complex (INT), which is more slowly converted to the posttranslocation (POST) complex. Peptidyl tRNA within the INT complex occupies a hybrid site, having puromycin reactivity intermediate between those of the PRE and POST complexes. Thiostrepton and viomycin inhibit INT formation, whereas spectinomycin selectively inhibits INT disappearance. The effects of other translocation modulators suggest that EF-G-dependent GTP hydrolysis is more important for INT complex formation than for INT complex conversion to POST complex, and that subtle changes in tRNA structure influence coupling of tRNA movement to EF-G.GTP-induced conformational changes. PMID:17317625

  18. 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

  19. 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

  20. 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.

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

    PubMed

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

    2015-12-21

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

  2. 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

  3. 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.

  4. 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

  5. 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…

  6. Monte Carlo Simulation of Heavy Nuclei Photofission at Intermediate Energies

    SciTech Connect

    Andrade-II, E.; Freitas, E.; Garcia, F.; Tavares, O. A. P.; Duarte, S. B.

    2009-06-03

    A detailed description of photofission process at intermediate energies (200 to 1000 MeV) is presented. The study of the reaction is performed by a Monte Carlo method which allows the investigation of properties of residual nuclei and fissioning nuclei. The information obtained indicate that multifragmentation is negligible at the photon energies studied here, and that the symmetrical fission is dominant. Energy and mass distributions of residual and fissioning nuclei were calculated.

  7. Electrochemical incineration of 4-chlorophenol and the identification of products and intermediates by mass spectrometry

    SciTech Connect

    Johnson, S.K.; Houk, L.L.; Feng, J.; Houk, R.S.; Johnson, D.C. )

    1999-08-01

    This report summarizes results obtained as part of a larger effort to demonstrate the applicability of electrolytic procedures for the direct anodic (oxidative) degradation of toxic organic wastes. The authors refer to this process as electrochemical incineration (ECI) because the ultimate degradation products are equivalent to those achieved by thermal incineration processes. In this work, the ECI of 4-chlorophenol is achieved in an aqueous medium using a platinum anode coated with a quaternary metal oxide film containing Ti, Ru, Sn, and Sb oxides. The electrode is stable and active when used with a solid Nafion membrane without the addition of soluble supporting electrolyte. Liquid chromatography (LC), including reverse phase and ion exchange chromatography, is coupled with electrospray mass spectrometry (ES-MS) and used, along with gas chromatography-mass spectrometry (GC-MS) and measurements of pH, chemical oxygen demand (COD), and total organic carbon (TOC), to study the reaction and identify the intermediate products from the ECI of 4-chlorophenol. Twenty-six intermediate products are identified and reported. The most abundant of these products are benzoquinone, 4-chlorocatechol, maleic acid, succinic acid, malonic acid, and the inorganic anions chloride, chlorate, and perchlorate. After 24 h of ECI, a solution that initially contained 108 ppm 4-chlorophenol yields only 1 ppm TOC with 98% of the original chlorine remaining in the specified inorganic forms. LC-ES-MS and direct infusion ES-MS detection limits are between 80 ppb and 4 ppm for these intermediate products. Elemental analysis of the electrolyzed solutions by inductively coupled plasma mass spectrometry ICP-MS showed that only trace amounts of the metallic elements comprising the metal oxide film were present in the solution.

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

    PubMed Central

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

    2012-01-01

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

  9. Detailed mechanism of the autoxidation of N-hydroxyurea catalyzed by a superoxide dismutase mimic Mn(III) porphyrin: formation of the nitrosylated Mn(II) porphyrin as an intermediate.

    PubMed

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

    2012-10-14

    The in vitro autoxidation of N-hydroxyurea (HU) is catalyzed by Mn(III)TTEG-2-PyP(5+), a synthetic water soluble Mn(III) porphyrin which is also a potent mimic of the enzyme superoxide dismutase. The detailed mechanism of the reaction is deduced from kinetic studies under basic conditions mostly based on data measured at pH = 11.7 but also including some pH-dependent observations in the pH range 9-13. The major intermediates were identified by UV-vis spectroscopy and electrospray ionization mass spectrometry. The reaction starts with a fast axial coordination of HU to the metal center of Mn(III)TTEG-2-PyP(5+), which is followed by a ligand-to-metal electron transfer to get Mn(II)TTEG-2-PyP(4+) and the free radical derived from HU (HU˙). Nitric oxide (NO) and nitroxyl (HNO) are minor intermediates. The major pathway for the formation of the most significant intermediate, the {MnNO} complex of Mn(II)TTEG-2-PyP(4+), is the reaction of Mn(II)TTEG-2-PyP(4+) with NO. We have confirmed that the autoxidation of the intermediates opens alternative reaction channels, and the process finally yields NO(2)(-) and the initial Mn(III)TTEG-2-PyP(5+). The photochemical release of NO from the {MnNO} intermediate was also studied. Kinetic simulations were performed to validate the deduced rate constants. The investigated reaction has medical implications: the accelerated production of NO and HNO from HU may be utilized for therapeutic purposes. PMID:22911446

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

    NASA Astrophysics Data System (ADS)

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

    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.

  11. 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.

  12. 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

  13. Communications: Elementary oxygen electrode reactions in the aprotic Li-air battery.

    PubMed

    Hummelshøj, J S; Blomqvist, J; Datta, S; Vegge, T; Rossmeisl, J; Thygesen, K S; Luntz, A C; Jacobsen, K W; Nørskov, J K

    2010-02-21

    We discuss the electrochemical reactions at the oxygen electrode of an aprotic Li-air battery. Using density functional theory to estimate the free energy of intermediates during the discharge and charge of the battery, we introduce a reaction free energy diagram and identify possible origins of the overpotential for both processes. We also address the question of electron conductivity through the Li(2)O(2) electrode and show that in the presence of Li vacancies Li(2)O(2) becomes a conductor. PMID:20170208

  14. 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.

  15. 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

  16. 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…

  17. 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)…

  18. Crystal Structure and Promiscuous Partitioning of a Covalent Intermediate Common in the Pentein Superfamily

    PubMed Central

    Linsky, Thomas W.; Monzingo, Arthur F.; Stone, Everett M.; Robertus, Jon D.; Fast, Walter

    2008-01-01

    Summary Many enzymes in the pentein superfamily use a transient covalent intermediate in their catalytic mechanisms. Here, we use a mutant (H162G) dimethylarginine dimethylaminohydrolase from Pseudomonas aeruginosa and an alternative substrate, S-methyl-L-thiocitrulline, to trap, crystallize and determine the 2.8 Å resolution structure of a stable covalent adduct which mimics this reaction intermediate. Observed interactions between the trapped adduct and active site residues along with comparison to a previously known product-bound structure provide insight into the normal catalytic mechanism. The plane of the trapped thiouronium intermediate is angled away from that seen in the product and substrate complexes, allowing for an altered angle of attack between the nucleophiles of the first and second half reactions. The stable covalent adduct is also capable of further reaction. Addition of exogenous imidazole can rescue the original hydrolytic activity. Notably, addition of other exogenous amines can instead yield substituted arginine products. These alternative products arise from partitioning of the trapped intermediate into the evolutionarily related amidinotransferase reaction pathway. The enzyme scaffold provides both selectivity and catalysis for the amidinotransferase reaction, underscoring commonalities between different reaction pathways found in this mechanistically diverse enzyme superfamily. The promiscuous partitioning of this covalent intermediate may also help to illuminate the evolutionary history of these enzymes. PMID:18482699

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

    NASA Astrophysics Data System (ADS)

    Wink, David A.; Desrosiers, Marc F.

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

  20. 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.'

  1. Role of Intermediate Filaments in Vesicular Traffic

    PubMed Central

    Margiotta, Azzurra; Bucci, Cecilia

    2016-01-01

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

  2. 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

  3. 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

  4. Elucidation of Intermediates and Mechanisms in Heterogeneous Catalysis Using Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Savara, Aditya; Weitz, Eric

    2014-04-01

    Infrared spectroscopy has a long history as a tool for the identification of chemical compounds. More recently, various implementations of infrared spectroscopy have been successfully applied to studies of heterogeneous catalytic reactions with the objective of identifying intermediates and determining catalytic reaction mechanisms. We discuss selective applications of these techniques with a focus on several heterogeneous catalytic reactions, including hydrogenation, deNOx, water-gas shift, and reverse-water-gas shift. The utility of using isotopic substitutions and other techniques in tandem with infrared spectroscopy is discussed. We comment on the modes of implementation and the advantages and disadvantages of the various infrared techniques. We also note future trends and the role of computational calculations in such studies. The infrared techniques considered are transmission Fourier transform infrared spectroscopy, infrared reflection-absorption spectroscopy, polarization-modulation infrared reflection-absorption spectroscopy, sum-frequency generation, diffuse reflectance infrared Fourier transform spectroscopy, attenuated total reflectance, infrared emission spectroscopy, photoacoustic infrared spectroscopy, and surface-enhanced infrared absorption spectroscopy.

  5. Elucidation of intermediates and mechanisms in heterogeneous catalysis using infrared spectroscopy.

    PubMed

    Savara, Aditya; Weitz, Eric

    2014-01-01

    Infrared spectroscopy has a long history as a tool for the identification of chemical compounds. More recently, various implementations of infrared spectroscopy have been successfully applied to studies of heterogeneous catalytic reactions with the objective of identifying intermediates and determining catalytic reaction mechanisms. We discuss selective applications of these techniques with a focus on several heterogeneous catalytic reactions, including hydrogenation, deNOx, water-gas shift, and reverse-water-gas shift. The utility of using isotopic substitutions and other techniques in tandem with infrared spectroscopy is discussed. We comment on the modes of implementation and the advantages and disadvantages of the various infrared techniques. We also note future trends and the role of computational calculations in such studies. The infrared techniques considered are transmission Fourier transform infrared spectroscopy, infrared reflection-absorption spectroscopy, polarization-modulation infrared reflection-absorption spectroscopy, sum-frequency generation, diffuse reflectance infrared Fourier transform spectroscopy, attenuated total reflectance, infrared emission spectroscopy, photoacoustic infrared spectroscopy, and surface-enhanced infrared absorption spectroscopy. PMID:24689797

  6. 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

  7. 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.

  8. The LMC Intermediate and Populations

    NASA Astrophysics Data System (ADS)

    Olszewski, E. W.

    I will discuss our current understanding of the intermediate and old populations of the LMC. Dominant themes will be what those populations tell us about the relative ages of the oldest components of the Milky Way and LMC, what they tell us about the star formation history of the LMC, and what they tell us about the presence or absence of a halo (as we understand that term in the Milky Way) in the LMC. Topics not discussed at previous Magellanic Cloud meetings include the ages of the oldest LMC clusters from HST data, and the seeming lack of agreement between deep luminosity function analyses and distributions of abundances of red giants.

  9. Reactions of methanethiol on cobalt-covered Mo(110)

    SciTech Connect

    Chen, D.A.; Friend, C.M.; Xu, H.

    1996-03-20

    The reactions of methanethiol on cobalt overlayers grown on Mo(110) were studied using a temperature-programmed reaction and X-ray photoelectron and high-resolution electron energy loss spectroscopies. Methyl thiolate was identified as the reaction intermediate on the basis of X-ray photoelectron and high resolution electron energy loss data. Methane, methyl radical, and H{sub 2} were the only gaseous products. The peak temperature for methane production from methyl thiolate hydrogenolysis was relatively insensitive to the Co coverage and geometric structure of the Co layer. However, less methyl radical formation was observed as the Co coverage increased from 1 to 2.5 monolayers. The selectivity for hydrocarbon formation was essentially the same, nearly 48{+-}5%, for all Co coverages. The total amount of methyl thiolate deposited in the initial S-H bond breaking was independent of Co coverage. At 400 K, sulfur-induced structural rearrangement of the Co overlayer was insignificant and therefore did not affect the reaction of methanethiol. The mixed Co-S overlayer had a substantially lower activity for the methanethiol reaction than any of the clean surfaces; the total amount of reaction on both the sulfur and Co-S overlayers was 30% that of the clean Mo(110) and pure Co overlayers. 53 refs., 5 figs., 1 tab.

  10. Identification of free radical intermediates in oxidized wine using electron paramagnetic resonance spin trapping.

    PubMed

    Elias, Ryan J; Andersen, Mogens L; Skibsted, Leif H; Waterhouse, Andrew L

    2009-05-27

    Free radicals are thought to be key intermediates in the oxidation of wine, but their nature has not been established. Electron paramagnetic resonance spectroscopy was used to detect and identify several free radical species in wine under oxidative conditions with the aid of spin traps. The 1-hydroxylethyl radical was the sole radical species observed when α-(4-pyridyl-1-oxide)-N-tert-butylnitrone was used as a spin trap in a heated (55 °C), low-sulfite (15 mg L(-1)) red wine. This radical appears to arise from ethanol oxidation via the hydroxyl radical, and this latter species was confirmed by using a high concentration (1.5 M) of the 5,5-dimethylpyrroline-N-oxide spin trap, thus providing the first direct evidence of the Fenton reaction in wine. Hydroxyl radical formation in wine was corroborated by converting hydroxyl radicals to methyl radicals by its reaction with dimethyl sulfoxide. The novel spin trap 5-tert-butoxycarbonyl 5-methyl-1-pyrroline N-oxide was also used in this study to identify sulfite radicals in wine for the first time. This spin trap has also been shown to trap hydroperoxyl radicals, the generation of which is predicted in wine; however, no evidence of this species was observed. PMID:19358607

  11. 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.

  12. 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.

  13. MCNP6 fragmentation of light nuclei at intermediate energies

    NASA Astrophysics Data System (ADS)

    Mashnik, Stepan G.; Kerby, Leslie M.

    2014-11-01

    Fragmentation reactions induced on light target nuclei by protons and light nuclei of energies around 1 GeV/nucleon and below are studied with the latest Los Alamos Monte Carlo transport code MCNP6 and with its cascade-exciton model (CEM) and Los Alamos version of the quark-gluon string model (LAQGSM) event generators, version 03.03, used as stand-alone codes. Such reactions are involved in different applications, like cosmic-ray-induced single event upsets (SEU's), radiation protection, and cancer therapy with proton and ion beams, among others; therefore, it is important that MCNP6 simulates them as well as possible. CEM and LAQGSM assume that intermediate-energy fragmentation reactions on light nuclei occur generally in two stages. The first stage is the intranuclear cascade (INC), followed by the second, Fermi breakup disintegration of light excited residual nuclei produced after the INC. Both CEM and LAQGSM account also for coalescence of light fragments (complex particles) up to 4He from energetic nucleons emitted during INC. We investigate the validity and performance of MCNP6, CEM, and LAQGSM in simulating fragmentation reactions at intermediate energies and discuss possible ways of further improving these codes.

  14. Intermediate reboiler and condenser arrangement for binary distillation columns

    SciTech Connect

    Agrawal, R.; Herron, D.M.

    1998-06-01

    The most thermodynamically efficient configuration for adding or removing heat from an intermediate location of an ideal binary distillation column distilling pure products is derived. The optimal policy requires that preconditioning of the feed be part of the overall decision-making process. The optimal configuration can be determined through the use of two parameters, {alpha}{sub IR} and {alpha}{sub IC}, that are solely functions of feed composition. Simple and readily usable heuristics using these parameters are developed that help instantly identify the most efficient selection among (1) totally vaporizing and returning a side-draw liquid stream from an intermediate location of the distillation column, (2) partially or totally vaporizing a portion of the given saturated liquid feed, (3) partially or totally condensing a portion of the given saturated vapor feed, and (4) totally condensing and returning a side-draw vapor stream from an intermediate location of the distillation column.

  15. 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.

  16. 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

  17. Ab initio calculations of the reaction pathways for methane decomposition over the Cu (111) surface

    NASA Astrophysics Data System (ADS)

    Gajewski, Grzegorz; Pao, Chun-Wei

    2011-08-01

    Growth of large-area, few-layer graphene has been reported recently through the catalytic decomposition of methane (CH4) over a Cu surface at high temperature. In this study, we used ab initio calculations to investigate the minimum energy pathways of successive dehydrogenation reactions of CH4 over the Cu (111) surface. The geometries and energies of all the reaction intermediates and transition states were identified using the climbing image nudged elastic band method. The activation barriers for CH4 decomposition over this Cu surface are much lower than those in the gas phase; furthermore, analysis of electron density differences revealed significant degrees of charge transfer between the adsorbates and the Cu atoms along the reaction path; these features reveal the role of Cu as the catalytic material for graphene growth. All the dehydrogenation reactions are endothermic, except for carbon dimer (C2) formation, which is, therefore, the most critical step for subsequent graphene growth, in particular, on Cu (111) surface.

  18. Dearomatization through Halofunctionalization Reactions.

    PubMed

    Liang, Xiao-Wei; Zheng, Chao; You, Shu-Li

    2016-08-16

    Recent advances in dearomatization through halofunctionalization reactions are summarized in this Minireview. Two general categories of strategies are currently employed in this field. On one hand, the reaction can be initiated with electrophilic halogenation at an alkyne or alkene moiety. The resulting halonium ion intermediate is then captured by a pendant aromatic ring at the ipso position, affording the dearomatization product. On the other hand, electrophilic halogenation can directly take place at a substituted arene, and the final dearomatization product is furnished by deprotonation or intramolecular nucleophilic trap. Highly enantioselective variants have been realized in the latter case by organocatalysis or transition metal catalysis. By applying these methods, various valuable halogenated polycyclic molecular architectures have been obtained from readily available starting materials. PMID:27377184

  19. Characterization of dihydro-A2PE: an Intermediate in the A2E Biosynthetic Pathway†

    PubMed Central

    Kim, So R.; He, Jiangtao; Yanase, Emiko; Jang, Young P.; Berova, Nina; Nakanishi, Koji; Sparrow, Janet R.

    2008-01-01

    Bisretinoid lipofuscin pigments that accumulate in retinal pigment epithelial cells are implicated in the etiology of several forms of macular degeneration including juvenile onset Stargardt disease, Best vitelliform macular degeneration and age-related macular degeneration. One of these compounds, A2E, is generated by phosphate hydrolysis of a phosphatidylpyridinium bisretinoid (A2PE) that forms within photoreceptor outer segments. Here we demonstrate that the formation of the aromatic pyridinium ring of A2PE follows from the oxidation of a dihydropyridinium intermediate. Time-dependent density functional theory calculation, based on the structure of dihydro-A2E, produced a simulated UV-visible absorbance spectrum characterized by maxima of 494 and 344 nm. Subsequently, a compound exhibiting similar UV-visible absorbance maxima (λmax 490 and 330 nm) was identified in the A2E biomimetic reaction mixture. By liquid chromatography-mass spectrometry (LC-MS) this bischromophore had the expected mass of the dihydro-pyridinium bisretinoid. The compound also exhibited the behavior of a biosynthetic intermediate, since it formed in advance of the final product A2E and was consumed as A2E accumulated. Moreover, under deoxygenated conditions, conversion to the aromatic pyridinium bisretinoid was inhibited. Taken together, these findings indicate that A2E biosynthesis involves the oxidation of a dihydropyridinium intermediate dihydro-A2PE. An understanding of the biosynthetic pathways of retinal pigment epithelial lipofuscin pigments is critical to the development of therapies for macular degeneration that are based on limiting the formation of these damaging compounds. PMID:17685561

  20. 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