Sample records for identify reaction intermediate

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

    SciTech Connect

    Foster, Andrew J.; Lobo, Raul F

    2010-01-01

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

  2. Reactions of stabilized Criegee Intermediates

    NASA Astrophysics Data System (ADS)

    Vereecken, Luc; Harder, Hartwig; Novelli, Anna

    2014-05-01

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

  3. Reactions of Stabilized Criegee intermediates

    NASA Astrophysics Data System (ADS)

    Vereecken, Luc; Harder, Hartwig; Novelli, Anna

    2013-04-01

    Carbonyl oxides (Criegee intermediates) were proposed as key intermediates in the gas phase ozonolysis of alkenes in 1975 by Rudolf Criegee. Despite the importance of ozonolysis in atmopsheric chemistry, direct observation of these intermediates remained elusive, with only indirect experimental evidence for their role in the oxidation of hydrocarbons, e.g. through scavenging experiments. Only recently did Taatjes et al (2008) directly observe thermally stabilized Criegee intermediates (SCI), while work by Welz et al (2012) and others have finally started to elucidate the reaction kinetics and products of SCI with a subset of coreactants. Given the dearth of direct experimental data, theoretical analysis of the chemistry of SCI remains a prime source of information; in general, the predictions are in agreement with the scarce experimental data. We present a set of modern theoretical studies on the chemistry of SCI, with emphasis on high-level quantum chemical calculations and theoretical kinetic analysis as a function of the substitutions in the SCI. A broad range of co-reactants is examined, as well as the unimolecular re-arrangement of SCI. In the atmosphere, the fate of SCI was long assumed to be solely its reaction with H2O, or unimolecular decomposition. However, recent re-analysis (Vereecken et al. 2012) of the available data shows that this view may need to be adjusted, with other fast bimolecular reactions playing a role in the atmosphere, with a strong dependence of the rates on the substituents in the SCI. Based on the new experimental and theoretical data, we re-evaluate the possible sinks of SCI in the atmosphere, putting forward a set of reactions that might have an impact in atmospheric or experimental reaction conditions. The reaction of SCI with SO2 receives particular attention, as it is proposed in the literature to be of importance in the atmospheric formation of H2SO4 as an aerosol precursor.

  4. 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.

    1989-01-01

    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. 7 figs.

  5. Reaction plane dispersion at intermediate energies

    E-print Network

    J. Lukasik; W. Trautmann

    2006-03-29

    A method to derive the corrections for the dispersion of the reaction plane at intermediate energies is proposed. The method is based on the correlated, non-isotropic Gaussian approximation. It allowed to construct the excitation function of genuine flow values for the Au+Au reactions at 40-150 MeV/nucleon measured with the INDRA detector at GSI.

  6. 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.

  7. The (neutron, Proton) Reaction at Intermediate Energies.

    NASA Astrophysics Data System (ADS)

    Wang, Kebin

    In nuclei with N >=q Z the (n,p) charge exchange reaction can only excite isovector transitions to the T^> states, i.e. states with isospin T + 1 where T is the isospin of the parent state. At intermediate energies (600 MeV > E_{rm n} > 100 MeV), the reaction is dominated by the spin -isospin reaction mode, so it is a good probe to explore spin excitations. If it is possible to measure cross sections down to 0^circ, the (n,p) reaction can be studied at small momentum transfer to enhance the search for the Gamow-Teller (GT) resonances. In this work, the (n,p) reaction ^{13} C(n,p)^{13}B at 65 MeV has been studied at the Crocker Nuclear Laboratory (CNL), U.C. Davis, and the (n,p) reaction ^6 Li(n,p)^6He at 118 MeV has been studied at the Indiana University Cyclotron Facility (IUCF). Prominent peaks corresponding to the GT transitions to the ground states of ^{13} B and ^6He are observed. Spin -dipole transitions to the excited states of ^ {13}B are also identified. Cross sections at 0^circ and various angles out to 40^circ at CNL, and out to 20^circ at IUCF, were measured. The angular distributions of the cross sections were obtained, and compared with the Distorted Wave Approximation (DWA) calculations. The cross sections at 0^circ are: dsigma/dOmega (0^circ) = 3.11 +/- 0.24 mb/sr for ^{13 }C(n,p)^{13}B(g.s.) at E_{rm n} = 65 MeV; dsigma/dOmega (0^circ) = 11.74 +/- 0.21 mb/sr for ^6Li(n,p) ^6He(g.s.) at E_{ rm n} = 118 MeV. Using the DWA calculations for dsigma/dOmega at 0^circ and the measured cross sections, we can extract the volume integrals of the N-N effective interaction. They are in good agreement with the theoretical predictions from Franey and Love:(UNFORMATTED TABLE OR EQUATION FOLLOWS)vbox{ halign{hfil#hfil&&quadhfil#; hfilcr E_{rm n} & (V_sp{sigmatau }{rm c})_{rm exp. } (MeV - fm^3)& (V _sp{sigmatau}{rm c})_{rm th.} (MeV - fm^3)crnoalign{ vskip4pt} 65 MeV& 179 +/- 19& 178.2cr 118 MeV& 161 +/- 17& 161cr}}(TABLE/EQUATION ENDS).

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

    ERIC Educational Resources Information Center

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

    2009-01-01

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

  9. Ligand Intermediates in Metal-Catalyzed Reactions

    SciTech Connect

    Gladysz, John A.

    1999-07-31

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

  10. 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.

  11. Spectroscopic predictions for alkali-atom-alkali-halide reaction intermediates

    NASA Astrophysics Data System (ADS)

    Thompson, J. W.; Child, M. S.

    1989-05-01

    The semi-empirical Roach-Child model is used to predict ionisation potentials, rotational constants, vibrational frequencies and the first three electronic absorption bands for the reaction intermediates Na 2Cl, K 2Cl and NaKCl, which are known to be isolatable by supersonic beam techniques.

  12. Recent results on intermediate-energy nucleon knockout reactions

    SciTech Connect

    Wimmer, K. [Department of Physics, Central Michigan University, Mount Pleasant, Michigan 48859, USA and National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824 (United States)

    2013-04-19

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

  13. 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

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

    PubMed

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

    2012-12-01

    The advanced oxidation of paracetamol (PAM) promoted by TiO(2)/UV system in aqueous medium was investigated. Monitoring this reaction by HPLC and TOC, it was demonstrated that while oxidation of paracetamol is quite efficient under these conditions, its mineralization is not complete. HPLC indicated the formation of hydroquinone, benzoquinone, p-aminophenol and p-nitrophenol in the reaction mixtures. Further evidence of p-nitrophenol formation was obtained following the reaction by UV-vis spectroscopy. Continuous monitoring by IR spectroscopy demonstrated the breaking of the aromatic amide present in PAM and subsequent formation of several aromatic intermediate compounds such as p-aminophenol and p-nitrophenol. These aromatic compounds were eventually converted into trans-unsaturated carboxylic acids. Based on these experimental results, an alternative deacylation mechanism for the photocatalytic oxidation of paracetamol is proposed. Our studies also demonstrated IR spectroscopy to be a useful technique to investigate oxidative mechanisms of pharmaceutical compounds. PMID:23123003

  15. 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

  16. Molecular shape analysis of a Maillard reaction intermediate.

    PubMed

    Jokic, A; Zimpel, Z; Huang, P M; Mezey, P G

    2001-01-01

    The Maillard (browning) reaction involving the polycondensation of sugars and amino acids is believed to be an important abiotic pathway for humic substance formation in nature. However, a major drawback is that the Maillard reaction is extremely slow at temperatures encountered under normal environmental conditions. In order to elucidate some details of this process molecular shape analysis was applied to investigate the initial reaction between D-glucose and glycine to form the Amadori compound fructosylglycine which is an intermediate product in the Maillard reaction. The structure of the Amadori compound was optimized at a quantum mechanical level and its ground state electron energy calculated. Molecular Iso-Density Contours (MIDCO's), electron density contour surfaces of constant electron density, were constructed for D-glucose, glycine and fructosylglycine in order to study the steric conditions for the reaction. The calculations indicate that the Amadori compound and water on one hand and the separate entities D-glucose and glycine on the other hand are very similar to each other in terms of their ground state energy. This agrees with the experimental observation that the reaction between D-glucose and glycine to form the Amadori compound is slow. PMID:11696926

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

    SciTech Connect

    Lin, M.C. [Emory Univ., Atlanta, GA (United States)

    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.

  18. The reaction of Fe and Ni at intermediate energies

    E-print Network

    Liddick, Sean Nicholas

    2013-02-22

    Experimentally and theoretically, the affect of isospin on nuclear reactions has been studied intensively. Among the affects that have been observed to affect reactions are neutron number and size of the reaction system. In this thesis work...

  19. Identifying combustion intermediates in premixed MTBE\\/gasoline\\/oxygen flame probed via synchrotron radiation

    Microsoft Academic Search

    Chunde Yao; Jing Li; Qi Li; Qing Ji; Chaoqun Huang; Lixia Wei; Jing Wang; Zhenyu Tian; LI Yuyang; Fei Qi

    2007-01-01

    Molecular-beam sampling mass spectrometry (MBMS) combined with tunable synchrotron radiation photoionization technique offers\\u000a obvious advantages for the study of flame chemistry over other techniques because of the precision measurement of the combustion\\u000a intermediates and products in flame. In this paper, the results to identify combustion intermediates in low-pressure premixed\\u000a gasoline\\/oxygen flame with the synchrotron radiation were reported. Based on the

  20. 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

  1. Dinitrosyl intermediate for N{sub 2}O formation from reaction of NO on Mo(110)

    SciTech Connect

    Queeney, K.T.; Friend, C.M. [Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138 (United States)] [Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138 (United States)

    1997-10-01

    The adsorption and subsequent reaction of nitric oxide (NO) on Mo(110) has been studied by temperature programmed reaction, electron energy loss, and infrared reflectance absorbance spectroscopies. The predominant reaction pathway for a saturated NO overlayer is dissociation to atomic nitrogen and oxygen; in fact, for low NO coverages, dissociation is the only reaction and largely takes place below 300 K. At NO coverages above 65{percent} of {theta}{sub sat}, evolution of N{sub 2}O, N{sub 2}, and NO is also observed at low temperature. Temperature programmed reaction of isotopically mixed overlayers demonstrates that N{sub 2}O formation occurs via reaction of two intact NO molecules, suggestive of a dimeric surface intermediate. Electron energy loss and infrared spectroscopies identify three {nu}(NO) features which are assigned to three distinct species; the frequencies of the {nu}(NO) peaks in the infrared spectrum of a saturated {sup 14}NO overlayer at 100 K are 1860, 1821, and 1720thinspcm{sup {minus}1}. The 1860 and 1720thinspcm{sup {minus}1} features are assigned to monomeric NO. Based on the infrared spectrum of a mixed overlayer of {sup 14}NO and {sup 15}NO, and on comparison to reference spectra of NO adsorbed on MoO{sub 3}, the 1821thinspcm{sup {minus}1} peak is identified as {nu}{sub s}(NO) of a surface dinitrosyl complex, i.e., two NO molecules bound to one Mo site. The weakly bound NO with the stretch frequency of 1860thinspcm{sup {minus}1} is associated with NO desorption, while the dinitrosyl leads to low-temperature N{sub 2} and N{sub 2}O formation and some dissociation. {copyright} {ital 1997 American Institute of Physics.}

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

    PubMed

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

    2006-05-01

    The degradation of pesticide methomyl in aqueous solution by UV-irradiation in the presence of TiO2 "Degussa P-25" has been studied. It was found that mineralisation to carbon dioxide, water, sulfate and ammonia took place during the process. The rate of photodecomposition of methomyl was measured using high performance liquid chromatography (HPLC), while its mineralization was followed using ion chromatography (IC), and total organic carbon (TOC) analysis. The identification of reaction intermediate products was carried out using coupled techniques HPLC-MS (electrospray ionization in positive mode) and a degradation pathway was proposed. Under our conditions, complete disappearance of 1.23 x 10(-4) mol l(-1) of pure pesticide occurred within 45 min of illumination and 80% TOC removal occurred in less than 4 h. Three main intermediates were identified resulting from (i) the rupture of the ester bond (or the N-O bond), (ii) the hydroxylation of methyl group borne by the nitrogen atom and (iii) the product resulting from the decarboxylation of the oxidized hydroxylated methyl group (photo-Kolbe reaction). In order to be sure that the photocatalytic results were consistent, hydrolysis and photolysis tests were performed. Photocatalysis proved to be an excellent new advanced oxidation technology (AOT) to eliminate methomyl present in water. PMID:16685325

  3. 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...

  4. X-ray Crystallography of A Metalloprotein: A Reaction Intermediate of Heme Oxygenase

    NASA Astrophysics Data System (ADS)

    Unno, Masaki; Matsui, Toshitaka; Ikeda-Saito, Masao

    X-ray crystallographic analysis of a metalloprotein requires knowing the electronic state of the metal center, if one wants to elucidate the exact function and/or reaction mechanism. As an example, we show our recent structural analysis of the heme oxygenase reaction intermediate which is involved in the third step of the heme degradation reaction. The reaction intermediate was crystallized under anaerobic condition, and the obtained crystals were frozen into liquid nitrogen. The absorption spectra of the single crystal before and after X-ray irradiation were compared with that of the frozen solution in 100 K cold nitrogen stream. The determined structure offers the first solid evidence for the presence of a water cluster in the distal pocket of this catalytically critical intermediate. This structure combined with the QM/MM calculation supports our proposal that the biliverdin is produced via Fe-OOH verdoheme intermediate.

  5. 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

  6. Single-Molecule Kinetics Reveals a Hidden Surface Reaction Intermediate in Single-Nanoparticle Catalysis

    E-print Network

    Chen, Peng

    polydispersion in reaction kinetics. Here we use single-molecule fluorescence microscopy to study twoSingle-Molecule Kinetics Reveals a Hidden Surface Reaction Intermediate in Single is further resolvable by single-turnover kinetics at the subparticle level. Detailed single-molecule kinetic

  7. 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)

  8. 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…

  9. Investigation of the intermediate-energy deuteron breakup reaction

    SciTech Connect

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

    1989-01-01

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

  10. Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome

    SciTech Connect

    Yang, Xiaojing; Ren, Zhong; Kuk, Jane; Moffat, Keith (UC)

    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.

  11. Detection of reaction intermediates during human cystathionine ?-synthase-monitored turnover and H2S production.

    PubMed

    Yadav, Pramod Kumar; Banerjee, Ruma

    2012-12-21

    Human cystathionine ?-synthase (CBS), a novel heme-containing pyridoxal 5'-phosphate enzyme, catalyzes the condensation of homocysteine and serine or cysteine to produce cystathionine and H(2)O or H(2)S, respectively. The presence of heme in CBS has limited spectrophotometric characterization of reaction intermediates by masking the absorption of the pyridoxal 5'-phosphate cofactor. In this study, we employed difference stopped-flow spectroscopy to characterize reaction intermediates formed under catalytic turnover conditions. The reactions of L-serine and L-cysteine with CBS resulted in the formation of a common aminoacrylate intermediate (k(obs) = 0.96 ± 0.02 and 0.38 ± 0.01 mM(-1) s(-1), respectively, at 24 °C) with concomitant loss of H(2)O and H(2)S and without detectable accumulation of the external aldimine or other intermediates. Homocysteine reacted with the aminoacrylate intermediate with k(obs) = 40.6 ± 3.8 s(-1) and re-formed the internal aldimine. In the reverse direction, CBS reacted with cystathionine, forming the aminoacrylate intermediate with k(obs) = 0.38 ± 0.01 mM(-1) s(-1). This study provides the first insights into the pre-steady-state kinetic mechanism of human CBS and indicates that the reaction is likely to be limited by a conformational change leading to product release. PMID:23124209

  12. Detection of Reaction Intermediates during Human Cystathionine ?-Synthase-monitored Turnover and H2S Production*

    PubMed Central

    Yadav, Pramod Kumar; Banerjee, Ruma

    2012-01-01

    Human cystathionine ?-synthase (CBS), a novel heme-containing pyridoxal 5?-phosphate enzyme, catalyzes the condensation of homocysteine and serine or cysteine to produce cystathionine and H2O or H2S, respectively. The presence of heme in CBS has limited spectrophotometric characterization of reaction intermediates by masking the absorption of the pyridoxal 5?-phosphate cofactor. In this study, we employed difference stopped-flow spectroscopy to characterize reaction intermediates formed under catalytic turnover conditions. The reactions of l-serine and l-cysteine with CBS resulted in the formation of a common aminoacrylate intermediate (kobs = 0.96 ± 0.02 and 0.38 ± 0.01 mm?1 s?1, respectively, at 24 °C) with concomitant loss of H2O and H2S and without detectable accumulation of the external aldimine or other intermediates. Homocysteine reacted with the aminoacrylate intermediate with kobs = 40.6 ± 3.8 s?1 and re-formed the internal aldimine. In the reverse direction, CBS reacted with cystathionine, forming the aminoacrylate intermediate with kobs = 0.38 ± 0.01 mm?1 s?1. This study provides the first insights into the pre-steady-state kinetic mechanism of human CBS and indicates that the reaction is likely to be limited by a conformational change leading to product release. PMID:23124209

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

    E-print Network

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

    2006-03-14

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-05-01

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

  15. 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

  16. 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

  17. Subduction factory 2. Are intermediate-depth earthquakes in subducting slabs linked to metamorphic dehydration reactions?

    Microsoft Academic Search

    Bradley R. Hacker; Simon M. Peacock; Geoffrey A. Abers; Stephen D. Holloway

    2003-01-01

    New thermal-petrologic models of subduction zones are used to test the hypothesis that intermediate-depth intraslab earthquakes are linked to metamorphic dehydration reactions in the subducting oceanic crust and mantle. We show that there is a correlation between the patterns of intermediate-depth seismicity and the locations of predicted hydrous minerals: Earthquakes occur in subducting slabs where dehydration is expected, and they

  18. N-heterocyclic carbene organocatalytic reductive ?,?-coupling reactions of nitroalkenes via radical intermediates.

    PubMed

    Du, Yu; Wang, Yuhuang; Li, Xin; Shao, Yaling; Li, Guohui; Webster, Richard D; Chi, Yonggui Robin

    2014-11-01

    An unprecedented N-heterocyclic carbene catalytic reductive ?,?-carbon coupling of ?,?-nitroalkenes, by using an organic substrate to mimic the one-electron oxidation role of the pyruvate ferredoxin oxidoreductase (PFOR) in living systems, has been developed. The reaction goes through a radical anion intermediate generated under a catalytic redox process. For the first time, the presence of radical anion intermediate in NHC organocatalysis is observed and clearly verified. PMID:25343564

  19. Reactions of nitrogen heterocycle-organolithium intermediates with lead halides

    E-print Network

    Kinney, Jerry Neal

    1970-01-01

    - pyridyllead (5) was isolated. MgBr N + (Ph)pPbjs (2) Pb(Ph)pI N (3) 1 + PhMgBr N Pb (Ph) qI N Pb(PW) 3 (3) (4) (5) Surprisingly, Gilman reported that trlphenyl-2-pyridyllead (5) did not form when 2-pyridylmagnesium bromide (I) was allowed.... Vacuum distillation of the residue gave four fractions: Vacuum, Pot Temp. , 01st. Head, Fraction mm 'C 'C 1. 3 60-70 2 1. 3 70-77 3 I . 3 78-85 42-43 44-48 49-50 4 1. 5 126-215 ' 93 Fractions 1-3 were identified as tetraethyllead, 5. 81 g (37. 1...

  20. Exome sequencing identifies CTSK mutations in patients originally diagnosed as intermediate osteopetrosis?

    PubMed Central

    Pangrazio, Alessandra; Puddu, Alessandro; Oppo, Manuela; Valentini, Maria; Zammataro, Luca; Vellodi, Ashok; Gener, Blanca; Llano-Rivas, Isabel; Raza, Jamal; Atta, Irum; Vezzoni, Paolo; Superti-Furga, Andrea; Villa, Anna; Sobacchi, Cristina

    2014-01-01

    Autosomal Recessive Osteopetrosis is a genetic disorder characterized by increased bone density due to lack of resorption by the osteoclasts. Genetic studies have widely unraveled the molecular basis of the most severe forms, while cases of intermediate severity are more difficult to characterize, probably because of a large heterogeneity. Here, we describe the use of exome sequencing in the molecular diagnosis of 2 siblings initially thought to be affected by “intermediate osteopetrosis”, which identified a homozygous mutation in the CTSK gene. Prompted by this finding, we tested by Sanger sequencing 25 additional patients addressed to us for recessive osteopetrosis and found CTSK mutations in 4 of them. In retrospect, their clinical and radiographic features were found to be compatible with, but not typical for, Pycnodysostosis. We sought to identify modifier genes that might have played a role in the clinical manifestation of the disease in these patients, but our results were not informative. In conclusion, we underline the difficulties of differential diagnosis in some patients whose clinical appearance does not fit the classical malignant or benign picture and recommend that CTSK gene be included in the molecular diagnosis of high bone density conditions. PMID:24269275

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  2. 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.

  3. 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

  4. 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)...

  5. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

  7. Controlling the ambiphilic nature of ?-arylpalladium intermediates in intramolecular cyclization reactions.

    PubMed

    Solé, Daniel; Fernández, Israel

    2014-01-21

    The reactivity of main group organometallics, such as organolithium compounds (RLi) and Grignard reagents (RMgX), is quite straightforward. In these species the R group usually exhibits nucleophilic reactivity without any possibility of inducing electrophilic character. In contrast, in organopalladium complexes, researchers can switch the reactivity from electrophilic to nucleophilic relatively simply. Although ?-aryl and ?-vinylpalladium complexes are commonly used as electrophiles in C-C bond-forming reactions, recent research has demonstrated that they can also react with carbon-heteroatom multiple bonds in a nucleophilic manner. Nevertheless, researchers have completely ignored the issue of controlling the ambiphilic nature of such species. This Account describes our efforts toward selectively promoting the same starting materials toward either electrophilic ?-arylation or nucleophilic addition reactions to different carbonyl groups. We could tune the properties of the ?-arylpalladium intermediates derived from amino-tethered aryl halides and carbonyl compounds to achieve chemoselective transformations. Therefore, chemists can control the ambiphilic nature of such intermediates and, consequently, the competition between the alternative reaction pathways by the adequate selection of the reaction conditions and additives (base, presence/absence of phenol, bidentate phosphines). The nature of the carbonyl group (aldehydes, ketones, esters, and amides) and the length of the tether connecting it to the aniline moiety also play an important role in the outcome of these processes. Our joint computational and experimental efforts to elucidate the reaction mechanism of these palladium-catalyzed transformations suggest that beyond the formation of the four-membered azapalladacycle, two major factors help to control the dual character of the palladium(II) intermediates derived from 2-haloanilines. First, their high nucleophilicity strongly modifies the interaction of the metal center with the carbonyl group. Second, the additive phenol exchanges the iodide ligand to give an arylpalladium(II) phenoxide complex, which has a beneficial effect on the arylation. The formation of this transient intermediate not only stabilizes the arylpalladium moiety, thus preventing the nucleophilic attack at the carbonyl group, but also assists the enolization reaction, which takes place in a more favorable intramolecular manner. The azapalladacycle intermediate is, in the words of J. R. R. Tolkien, "the one ring to bring them all and in the darkness to bind them." With this intermediate, we can easily achieve the synthesis of a variety of heterocyclic systems by selectively promoting electrophilic ?-arylation or nucleophilic addition reactions from the same precursors. PMID:23957464

  8. Macroscopic/microscopic simulation of nuclear reactions at intermediate energies. Denis Lacroix, Aymeric Van Lauwe and Dominique Durand

    E-print Network

    Boyer, Edmond

    Macroscopic/microscopic simulation of nuclear reactions at intermediate energies. Denis Lacroix- tion of nuclear collisions in the intermediate energy range is presented. The model simulates events for reactions close to the fusion barrier (5-10 MeV/A) up to higher energy (100 MeV/A) and it gives access

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

    PubMed

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

    2015-02-25

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

  10. 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 (NWU); (UIC)

    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.

  11. Fast and sequence-specific palladium-mediated cross-coupling reaction identified from phage display.

    PubMed

    Lim, Reyna K V; Li, Nan; Ramil, Carlo P; Lin, Qing

    2014-09-19

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

  12. 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

  13. Influence of two updated nuclear reaction rates on the evolution of low and intermediate mass stars

    E-print Network

    A. Weiss; A. Serenelli; A. Kitsikis; H. Schlattl; J. Christensen-Dalsgaard

    2005-07-22

    Two key reactions of hydrostatic nuclear burning in stars have recently been revised by new experimental data - the 14N(p,gamma)15O and triple alpha reaction rates. We investigate how much the new rates influence the evolution of low-mass, metal-poor and metal-free, stars and of an intermediate-mass star of solar-type composition. We concentrate on phases of helium ignition or thermally unstable helium burning. Our global result is that the new triple alpha rate has no significant influence on such stars, but that there is a noticable, though small, effect of the new 14N(p,gamma)15O rate, in particular on the core helium flash and the blue loop during core helium burning in the intermediate-mass star.

  14. Neutral current neutrino-98Mo reaction cross sections at low and intermediate energies

    NASA Astrophysics Data System (ADS)

    Divari, P. C.; Chasioti, V. C.; Kosmas, T. S.

    2010-12-01

    Inelastic neutrino-nucleus reaction cross sections at low and intermediate neutrino energies are studied. The required many-body nuclear wavefunctions are calculated in the context of a quasi-particle random phase approximation that uses realistic two-body forces. The results presented here refer to the differential, integrated and total cross sections of the neutral-current-induced reaction of ?e with the 98Mo nucleus. Exploiting the obtained results, we investigate the response of this isotope as a supernova neutrino detector, assuming a two-parameter Fermi-Dirac distribution for the supernova neutrino energy spectra.

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

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

    SciTech Connect

    Plante, Ianik, E-mail: ianik.plante-1@nasa.gov [Division of Space Life Sciences, Universities Space Research Association, 3600 Bay Area Boulevard, Houston, TX 77058 (United States)] [Division of Space Life Sciences, Universities Space Research Association, 3600 Bay Area Boulevard, Houston, TX 77058 (United States); Devroye, Luc, E-mail: lucdevroye@gmail.com [School of Computer Science, McGill University, 3480 University Street, Montreal, Canada H3A 0E9 (Canada)] [School of Computer Science, McGill University, 3480 University Street, Montreal, Canada H3A 0E9 (Canada); Cucinotta, Francis A., E-mail: Francis.A.Cucinotta@nasa.gov [NASA Johnson Space Center, Bldg 37, Mail Code SK, 2101 NASA Parkway, Houston, TX 77058 (United States)

    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.

  17. Novel association of APC with intermediate filaments identified using a new versatile APC antibody

    PubMed Central

    Wang, Yang; Azuma, Yoshiaki; Friedman, David B; Coffey, Robert J; Neufeld, Kristi L

    2009-01-01

    Background As a key player in suppression of colon tumorigenesis, Adenomatous Polyposis Coli (APC) has been widely studied to determine its cellular functions. However, inconsistencies of commercially available APC antibodies have limited the exploration of APC function. APC is implicated in spindle formation by direct interactions with tubulin and microtubule-binding protein EB1. APC also interacts with the actin cytoskeleton to regulate cell polarity. Until now, interaction of APC with the third cytoskeletal element, intermediate filaments, has remained unexamined. Results We generated an APC antibody (APC-M2 pAb) raised against the 15 amino acid repeat region, and verified its reliability in applications including immunoprecipitation, immunoblotting, and immunofluorescence in cultured cells and tissue. Utilizing this APC-M2 pAb, we immunoprecipitated endogenous APC and its binding proteins from colon epithelial cells expressing wild-type APC. Using Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS), we identified 42 proteins in complex with APC, including ?-catenin and intermediate filament (IF) proteins lamin B1 and keratin 81. Association of lamin B1 with APC in cultured cells and human colonic tissue was verified by co-immunoprecipitation and colocalization. APC also colocalized with keratins and remained associated with IF proteins throughout a sequential extraction procedure. Conclusion We introduce a versatile APC antibody that is useful for cell/tissue immunostaining, immunoblotting and immunoprecipitation. We also present evidence for interactions between APC and IFs, independent of actin filaments and microtubules. Our results suggest that APC associates with all three major components of the cytoskeleton, thus expanding potential roles for APC in the regulation of cytoskeletal integrity. PMID:19845967

  18. A new paramagnetic intermediate formed during the reaction of nitrite with deoxyhemoglobin.

    PubMed

    Salgado, Maria T; Ramasamy, Somasundaram; Tsuneshige, Antonio; Manoharan, Periakaruppan T; Rifkind, Joseph M

    2011-08-24

    The reduction of nitrite by deoxygenated hemoglobin chains has been implicated in red cell-induced vasodilation, although the mechanism for this process has not been established. We have previously demonstrated that the reaction of nitrite with deoxyhemoglobin produces a hybrid intermediate with properties of Hb(II)NO(+) and Hb(III)NO that builds up during the reaction retaining potential NO bioactivity. To explain the unexpected stability of this intermediate, which prevents NO release from the Hb(III)NO component, we had implicated the transfer of an electron from the ?-93 thiol to NO(+) producing ·SHb(II)NO. To determine if this species is formed and to characterize its properties, we have investigated the electron paramagnetic resonance (EPR) changes taking place during the nitrite reaction. The EPR effects of blocking the thiol group with N-ethyl-maleimide and using carboxypeptidase-A to stabilize the R-quaternary conformation have demonstrated that ·SHb(II)NO is formed and that it has the EPR spectrum expected for NO bound to the heme in the ?-chain plus that of a thiyl radical. This new NO-related paramagnetic species is in equilibrium with the hybrid intermediate "Hb(II)NO(+) ? Hb(III)NO", thereby further inhibiting the release of NO from Hb(III)NO. The formation of an NO-related paramagnetic species other than the tightly bound NO in Hb(II)NO was also confirmed by a decrease in the EPR signal by -20 °C incubation, which shifts the equilibrium back to the "Hb(II)NO(+) ? Hb(III)NO" intermediate. This previously unrecognized NO hemoglobin species explains the stability of the intermediates and the buildup of a pool of potentially bioactive NO during nitrite reduction. It also provides a pathway for the formation of ?-93 cysteine S-nitrosylated hemoglobin [SNOHb:S-nitrosohemoglobin], which has been shown to induce vasodilation, by a rapid radical-radical reaction of any free NO with the thiyl radical of this new paramagnetic intermediate. PMID:21755997

  19. pp i Kaon production in heavy ion reactions at intermediate energies [review article

    NASA Astrophysics Data System (ADS)

    Fuchs, Christian

    2006-01-01

    The article reviews the physics related to kaon and antikaon production in heavy ion reactions at intermediate energies. Chiral dynamics predicts substantial modifications of the kaon properties in a dense nuclear environment. The status of the theoretical predictions as well as experimental evidence for medium effects such as repulsive/attractive mass shifts for K+/K- are reviewed. In the vicinity of the thresholds, and even more pronounced below threshold, the production of strangeness is a highly collective process. Starting from elementary reaction channels the phenomenology of K+ and K- production, i.e. freeze-out densities, timescales etc. as derived from experiment and theoretical transport calculations is presented. Below threshold kaon production shows a high sensitivity to the nuclear compression reached in heavy ion reactions. This allows us to put constraints on the nuclear equation-of-state which are finally discussed.

  20. Identifying a new intermediate-polar using XMM-Newton and INTEGRAL

    E-print Network

    Middleton, Matthew J; Shaw, Craig; Ramsay, Gavin; Roberts, Timothy P; Wheatley, Peter J

    2011-01-01

    The bright X-ray source, 2XMMi J180438.7-145647 is fortunate to have long baseline observations in INTEGRAL that compliment observations taken by other missions. Optical spectroscopy of this object has suggested a distance of ~7 kpc and an identification with a low mass X-ray binary. We instead use the X-ray data from 0.3-40 keV to identify the source as a bright intermediate polar (IP) with an estimate for the white dwarf mass of~0.60 M_solar. This identification is supported by the presence of an iron triplet, the component lines of which are some of the strongest seen in IPs; and the signature of the spin period of the white dwarf at ~24 mins. We note that the lack of broad-band variability may suggest that this object is a stream-fed IP, similar in many respects to the well studied IP, V2400 Oph. Phase-binning has allowed us to create spectra corresponding to the peaks and troughs of the lightcurve from which we determine that the spectra appear harder in the troughs, consistent with the behaviour of othe...

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

    PubMed

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

    2013-05-01

    Here, we present the ITS ribosomal DNA (rDNA) sequence data on 330 larvae of nematodes of the genus Anisakis Dujardin, 1845 collected from 26 different bony fish species from 21 sampling locations and different climatic zones. New host records are provided for Anisakis simplex (Rudolphi, 1809) sensu stricto (s.s.) and A. pegreffli Campana-Rouget et Biocca, 1955 from Anoplopoma fimbria (Pallas) (Santa Barbara, East Pacific), A. typica (Diesing, 1860) from Caesio cuning (Bloch), Lepturacanthus savala (Cuvier) and Katsuwonus pelamis (Linnaeus) (Indonesia, West Pacific), A. simplex s.s. from Cololabis saira (Brevoort) (Hawaii, Central Pacific), A. simplex C of Nascetti et al. (1986) from Sebastolobus alascanus Bean (Santa Barbara, East Pacific) and A. physeteris Baylis, 1923 from Synaphobranchus kaupii Johnson (Namibia, East Atlantic). Comparison with host records from 60 previous molecular studies of Anisakis species reveals the teleost host range so far recorded for the genus. Perciform (57 species) and gadiform (21) fishes were the most frequently infected orders, followed by pleuronectiforms (15) and scorpaeniforms (15). Most commonly infected fish families were Scombridae (12), Gadidae (10), Carangidae (8) and Clupeidae (7), with Merluccius merluccius (Linnaeus) alone harbouring eight Anisakis species. Different intermediate host compositions implicate differing life cycles for the so far molecularly identified Anisakis sibling species. PMID:23724731

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

    PubMed Central

    Shiota, Atsushi; Malinakova, Helena C.

    2012-01-01

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

  3. 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

  4. REACTIONS OF PEROXYNITRITE WITH URIC ACID: FORMATION OF REACTIVE INTERMEDIATES, ALKYLATED PRODUCTS AND TRIURET, AND IN VIVO PRODUCTION OF TRIURET UNDER CONDITIONS OF OXIDATIVE STRESS

    PubMed Central

    Gersch, Christine; Palii, Sergiu P.; Imaram, Witcha; Kim, Kyung Mee; Karumanchi, S. Ananth; Angerhofer, Alexander; Johnson, Richard J.; Henderson, George N.

    2009-01-01

    Hyperuricemia is associated with hypertension, metabolic syndrome, preeclampsia, cardiovascular disease and renal disease, all conditions associated with oxidative stress. We hypothesized that uric acid, a known antioxidant, might become prooxidative following its reaction with oxidants; and, thereby contribute to the pathogenesis of these diseases. Uric acid and 1,3-15N2-uric acid were reacted with peroxynitrite in different buffers and in the presence of alcohols, antioxidants and in human plasma. The reaction products were identified using liquid chromatography-mass spectrometry (LC-MS) analyses. The reactions generate reactive intermediates that yielded triuret as their final product. We also found that the antioxidant, ascorbate, could partially prevent this reaction. Whereas triuret was preferentially generated by the reactions in aqueous buffers, when uric acid or 1,3-15N2-uric acid was reacted with peroxynitrite in the presence of alcohols, it yielded alkylated alcohols as the final product. By extension, this reaction can alkylate other biomolecules containing OH groups and others containing labile hydrogens. Triuret was also found to be elevated in the urine of subjects with preeclampsia, a pregnancy-specific hypertensive syndrome that is associated with oxidative stress, whereas very little triuret is produced in normal healthy volunteers. We conclude that under conditions of oxidative stress, uric acid can form reactive intermediates, including potential alkylating species, by reacting with peroxynitrite. These reactive intermediates could possibly explain how uric acid contributes to the pathogenesis of diseases such as the metabolic syndrome and hypertension. PMID:19219741

  5. Novel association of APC with intermediate filaments identified using a new versatile APC antibody

    E-print Network

    Wang, Yang; Azuma, Yoshiaki; Friedman, David B.; Coffey, Robert J.; Neufeld, Kristi L.

    2009-10-21

    cytoskeletal element, intermediate filaments, has remained unexamined. Results: We generated an APC antibody (APC-M2 pAb) raised against the 15 amino acid repeat region, and verified its reliability in applications including immunoprecipitation, immunoblotting...

  6. Disruption of Esrom and Ryk identifies the roof plate boundary as an intermediate target for commissure formation.

    PubMed

    Hendricks, Michael; Mathuru, Ajay Sriram; Wang, Hui; Silander, Olin; Kee, Michelle Zhi Ling; Jesuthasan, Suresh

    2008-02-01

    Growth cones are guided to their final destination by intermediate targets. Here, we identify intermediate targets and signaling components acting on zebrafish habenula commissural axons. Live imaging establishes that axons pause at the medial habenula before and after crossing the roof plate. esrom mutants axons fail to advance beyond the ipsilateral medial habenula. Tsc2 function is reduced in mutant axons, indicating cell autonomous defects in signaling. Consistent with signaling properties changing outside the roof plate, EphB is surface localized on axon segments within a zone demarcated by the medial habenula. wnt4a is expressed in the medial habenula and morpholino knockdown causes loss of the commissure. Electroporation of truncated Ryk causes axons to reenter the midline after reaching the contralateral habenula. These data identify Esrom as a mediator of growth cone navigation at an intermediate target and underscore the importance of midline boundaries as signaling centers for commissure formation. PMID:18060805

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

    SciTech Connect

    Mukhopadhyay, Tapan; Basu, D. N. [Variable Energy Cyclotron Centre, 1/AF Bidhan Nagar, Kolkata 700 064 (India)

    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)

  8. Acyl and amino intermediates in reactions catalysed by pig pepsin. Analysis of transpeptidation products.

    PubMed Central

    Wang, T T; Hofmann, T

    1976-01-01

    The action of pig pepsin on a variety of small peptides including Leu-Trp-Met-Arg, Leu-Trp-Met, Leu-Leu-NH2, benzyloxycarbonyl-Phe-Leu and Gly-Leu-Tyr was studied. Leu-Leu-Leu was found to be the major product from the substrates Leu-Trp-Met-Arg and Leu-Trp-Met, indicating that the predominant reaction at pH 3.4 was a transpeptidation of the acyl-transfer type. Leu-Leu-Leu was also formed in high yield by amino transfer from benzyloxycarbonyl-Phe-Leu. Like the amino-transfer reactions the acyl transfer proceeded via a covalent intermediate, since [14C]leucine was not incorporated into transpeptidation products and did not exchange with enzyme-bound leucine in the presence of acceptors. With Leu-Trp-Met both acyl and amino transpeptidation products, namely Leu-Leu, Leu-Leu-Leu, Met-Met and Met-Met-Met, were formed in addition to methionine and leucine. With Leu-Trp-Met-Arg (1 mM) the pH optimum for the rates of hydrolysis and acyl transfer is about pH 3.4. At this pH the rate of acyl transfer exceeds that of hydrolysis; at pH 2, however, hydrolysis was faster than transfer. A comparison of the effect of the length of substrates and products on the reaction rates allows the conclusion that the binding site can extend over eight to nine amino acid residues. Although the experiments provide no conclusive evidence for or against the involvement of amino and/or acyl intermediates in the hydrolysis of long peptides and proteins, the high yield of transpeptidation reactions of both types observed with some substrates suggests a major role for the intermediates in pepsin-catalysed reactions. The results also show that when pig pepsin is used for the digestion of proteins for sequence work, the likelihood of the formation of transpeptidation products is considerable. In this way peptides not present in the original sequence could easily form in a reasonably good yield. PMID:782445

  9. 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.

  10. Rate Equations for Reactions at High Temperatures Involving Radical Intermediates: Consecutive-Parallel and Rice–Herzfeld Mechanisms

    Microsoft Academic Search

    T. J. Houser

    1969-01-01

    For complex reactions which produce, in the initial step, radical intermediates that attack the reactant in a subsequent step, the form of the rate equation will change as the reaction temperature increases. This is caused by a change in the relative rates of the individual steps in the mechanism due to differences in activation energies. A method has been developed

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-08-01

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

  13. 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; (Michigan); (Rutgers); (Brandeis)

    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.

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

    PubMed

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

    2012-04-01

    Using an intensified spectroscopic detector CCD and a chemical shock tube, transient emission spectra of n-heptane during the reaction process of combustion were measured, with exposure time of 6 micros and a spectral range of 200 - 850 nm Experiments were conducted at an ignition temperature of 1 408 K and pressure of 2.0 atmos, with an initial fuel mole fraction of 1.0% and an equivalence ratio of 1.0. Measured emission bands were determined to be produced by OH, CH and C2 free radicals, which reveals that small OH, CH and C2 radicals are important intermediate products in the combustion process of n-heptane. Time-resolved spectra indicate that radical concentrations of OH, CH and C2 reached their peaks sharply; however, CH and C2 reduced and disappeared rapidly while the duration of OH was much longer in the reaction. This work provides experimental data for understanding the microscopic process and validating the mechanism of n-heptane combustion reaction. PMID:22715748

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

    SciTech Connect

    Nathan, A.M.; Sandorfi, A.M. [eds.

    1992-10-01

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

  16. Synthesis of Ultrastable Copper Sulfide Nanoclusters via Trapping the Reaction Intermediate: Potential Anticancer and Antibacterial Applications.

    PubMed

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

    2015-04-01

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

  17. Electron paramagnetic resonance and electron-nuclear double resonance studies of the reactions of cryogenerated hydroperoxoferric-hemoprotein intermediates.

    PubMed

    Davydov, Roman; Laryukhin, Mikhail; Ledbetter-Rogers, Amy; Sono, Masanori; Dawson, John H; Hoffman, Brian M

    2014-08-01

    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 ?-cation radical intermediate, compound I (Cpd I). Herein we have reinvestigated the mechanism of decays of the cryogenerated hydroperoxyferric intermediates of ?- and ?-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, ?-chains, and ?-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 ?-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 ?-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 when this state is not captured by reaction with a bound substrate, it is reduced to Cpd II by redox-active products of radiolysis. PMID:25046203

  18. An efficient graph theory based method to identify every minimal reaction set in a metabolic network

    PubMed Central

    2014-01-01

    Background Development of cells with minimal metabolic functionality is gaining importance due to their efficiency in producing chemicals and fuels. Existing computational methods to identify minimal reaction sets in metabolic networks are computationally expensive. Further, they identify only one of the several possible minimal reaction sets. Results In this paper, we propose an efficient graph theory based recursive optimization approach to identify all minimal reaction sets. Graph theoretical insights offer systematic methods to not only reduce the number of variables in math programming and increase its computational efficiency, but also provide efficient ways to find multiple optimal solutions. The efficacy of the proposed approach is demonstrated using case studies from Escherichia coli and Saccharomyces cerevisiae. In case study 1, the proposed method identified three minimal reaction sets each containing 38 reactions in Escherichia coli central metabolic network with 77 reactions. Analysis of these three minimal reaction sets revealed that one of them is more suitable for developing minimal metabolism cell compared to other two due to practically achievable internal flux distribution. In case study 2, the proposed method identified 256 minimal reaction sets from the Saccharomyces cerevisiae genome scale metabolic network with 620 reactions. The proposed method required only 4.5 hours to identify all the 256 minimal reaction sets and has shown a significant reduction (approximately 80%) in the solution time when compared to the existing methods for finding minimal reaction set. Conclusions Identification of all minimal reactions sets in metabolic networks is essential since different minimal reaction sets have different properties that effect the bioprocess development. The proposed method correctly identified all minimal reaction sets in a both the case studies. The proposed method is computationally efficient compared to other methods for finding minimal reaction sets and useful to employ with genome-scale metabolic networks. PMID:24594118

  19. 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.

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

    PubMed Central

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

    2012-01-01

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

  1. Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate

    PubMed Central

    Tian, Yang; Suk, Dae-Hwan; Cai, Feng; Crich, David; Mesecar, Andrew D.

    2009-01-01

    O-succinylbenzoyl-CoA (OSB-CoA) synthetase (EC 6.2.1.26) catalyzes the ATP-dependent condensation of o-succinylbenzoate (OSB) and CoA to form OSB-CoA, the fourth step of the menaquinone biosynthetic pathway in Bacillus anthracis. Gene knockout studies have highlighted this enzyme as a potential target for the discovery of new antibiotics. Here we report the first studies on the kinetic mechanism of B. anthracis OSB-CoA synthetase, classifying it as an ordered Bi Uni Uni Bi ping-pong mechanism. Through a series of pre-steady-state and steady-state kinetic studies in conjunction with direct-binding studies, it is demonstrated that CoA, the last substrate to bind, strongly activates the first half-reaction after the first round of turnover. The activation of the first-half reaction is most likely achieved by CoA stabilizing conformations of the enzyme in the ‘F’ form, which slowly isomerize back to the E form. Thus, the kinetic mechanism of OSB-CoA synthetase may be more accurately described as an ordered Bi Uni Uni Bi Iso ping-pong mechanism. The substrate specificity of OSB-CoA synthetase was probed using a series of OSB analogs with alterations in the carboxylate groups. OSB-CoA shows a strong preference for OSB over all of the analogs tested as none were active except 4-(2-trifluoromethylphenyl)-4-oxobutyric acid which exhibited a 100-fold decrease in kcat/Km. Based on an understanding of OSB-CoA synthetase’s kinetic mechanism and substrate specificity, a reaction intermediate analog of OSB-AMP, 5’-O-(N-(2-trifluoromethylphenyl)-4-oxobutyl) adenosine sulfonamide (TFMP-butyl-AMS), was designed and synthesized. This inhibitor was found to be an uncompetitive inhibitor to CoA and a mixed-type inhibitor to ATP and OSB with low micromolar inhibition constants. Collectively, these results should serve as an important forerunner to more detailed and extensive inhibitor design studies aimed at developing lead compounds against the OSB-CoA synthetase class of enzymes. PMID:18973344

  2. Identifying predictors of negative psychological reactions to stalking victimization.

    PubMed

    Johnson, Matthew C; Kercher, Glen A

    2009-05-01

    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 resulting from being stalked. Once identified, the next step was to examine the influence of demographic and stalking-related variables on the probability of subgroup membership. The results revealed that respondents who were female, had a prior relationship with the stalker, experienced a greater variety of stalking behaviors, were divorced/separated, and reported receiving government assistance were more likely to be classified into subgroups characterized by a high probability of experiencing multiple negative outcomes. PMID:18441262

  3. 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.

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

    SciTech Connect

    Foong, Chow Ming; Sani, Norrakiah Abdullah [School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor (Malaysia)

    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.

  5. A candidate LiBH4 for hydrogen storage: Crystal structures and reaction mechanisms of intermediate phases

    E-print Network

    Goddard III, William A.

    A candidate LiBH4 for hydrogen storage: Crystal structures and reaction mechanisms of intermediate usable as a hydrogen storage material in a moderate temperature range, which is also important storage medium capable of releasing the Department of Energy target of 6.5 wt. % for a hydrogen fuel cell

  6. Identification of a critical intermediate in galvanic exchange reactions by single-nanoparticle-resolved kinetics.

    PubMed

    Smith, Jeremy G; Yang, Qing; Jain, Prashant K

    2014-03-10

    The realization of common materials transformations in nanocrystalline systems is fostering the development of novel nanostructures and allowing a deep look into the atomistic mechanisms involved. Galvanic corrosion is one such transformation. We studied galvanic replacement within individual metal nanoparticles by using a combination of plasmonic spectroscopy and scanning transmission electron microscopy. Single-nanoparticle reaction trajectories showed that a Ag nanoparticle exposed to Au³? makes an abrupt transition into a nanocage structure. The transition is limited by a critical structural event, which we identified by electron microscopy to comprise the formation of a nanosized void. Trajectories also revealed a surprisingly strong nonlinearity of the reaction kinetics, which we explain by a model involving the critical coalescence of vacancies into a growing void. The critical void size for galvanic exchange to spontaneously proceed was found to be 20 atomic vacancies. PMID:24677345

  7. The axon reaction: identifying the genes that make a difference.

    PubMed

    Piehl, Fredrik; Swanberg, Maria; Lidman, Olle

    2007-09-10

    Numerous CNS diseases of primarily non-inflammatory origin, such as idiopathic neurodegenerative diseases, contain elements of inflammation, with T cell infiltration, MHC class II expression and neuron/axon damage. Gene mapping in human clinical materials have in most cases failed to unravel discrete genes, since most genes instrumental in non-Mendelian forms of these complex diseases are likely to modestly affect risk, be evolutionary conserved in the population and vary between individuals. We here describe the exploration of susceptibility to neurodegeneration and inflammatory glial activation in response to mechanical nerve injury using experimental genetic models. The response to ventral root avulsion, which is a simple and reproducible model of nerve injury-induced neurodegeneration and inflammation, was examined in a panel of inbred rat strains. A whole genome scan subsequently performed in a F2(DAxPVG) intercross identified quantitative trait loci (QTLs) regulating different features of the nerve injury response. Fine mapping in an advanced intercross line revealed polymorphisms in the Mhc2ta gene as being responsible for strain differences in MHC class II expression. Furthermore, a polymorphism in the syntenic human gene, MHC2TA, was associated both with lower expression of MHC class II-associated genes and increased susceptibility to inflammatory diseases. These results provide important insights into the genetic regulation of fundamental physiological responses of the nervous system to damage and demonstrate relevance also for human diseases. PMID:17561176

  8. Thermodynamical properties of reaction intermediates during apoplastocyanin folding in time domain

    NASA Astrophysics Data System (ADS)

    Baden, N.; Hirota, S.; Takabe, T.; Funasaki, N.; Terazima, M.

    2007-11-01

    Two intermediates observed for the folding process of apoplastocyanin (apoPC) were investigated by using a photoinduced triggering system combined with the transient grating and transient lens methods. The thermodynamic quantities, enthalpy, heat capacity, partial volume, and thermal expansion volume changes during the protein folding reaction were measured in time domain for the first time. An interesting observation is the positive enthalpy changes during the folding process. This positive enthalpy change must be compensated by positive entropy changes, which could be originated from the dehydration effect of hydrophobic residues and/or the translational entropy gain of bulk water molecules. Observed negative heat capacity change was explained by the dehydration effect of hydrophilic residues and/or motional confinement of amino acid side chains and water molecules in apoPC. The signs of the volume change and thermal expansion volume were different for two processes and these changes were interpreted in terms of the different relative contributions of the hydration and the dehydration of the hydrophilic residues. These results indicated two-step hydrophobic collapses in the early stage of the apoPC folding, but the nature of the dynamics was different.

  9. Radicals in the Reaction between Peroxynitrite and Uric Acid Identified by Electron Spin Resonance Spectroscopy and Liquid Chromatography Mass Spectrometry

    PubMed Central

    Imaram, Witcha; Gersch, Christine; Kim, Kyung Mee; Johnson, Richard J.; Henderson, George N.; Angerhofer, Alexander

    2010-01-01

    Peroxynitrite is a reactive oxidant produced in vivo in response to oxidative and other stress by the diffusion-limited reaction of nitric oxide and superoxide. This contribution is focused on the identification of free radical intermediates of uric acid formed during its reaction with peroxynitrite. The experimental approach included the ESR spin trapping of the radical generated from the reaction between uric acid and peroxynitrite at pH 7.4 and mass spectrometry studies of the trapped radicals. Using PBN (N-tert-butyl-?-phenylnitrone) as the spin trapping agent, a six-line ESR spectrum was obtained and its hyperfine coupling constants, a(N) = 15.6 G; and a(H) = 4.4 G, revealed the presence of carbon-based radicals. Further structural identification of the PBN-radical adducts was carried out using liquid chromatography-mass spectrometry. After comparison with the control reactions, two species were identified corresponding to the protonated molecules (M+1) at m/z 352 and 223, respectively. The ions of m/z 352 were characterized as the PBN-triuretcarbonyl radical adduct and the m/z 223 ion was identified as the PBN-aminocarbonyl radical adduct. Their mechanism of formation is discussed. PMID:20406679

  10. The Role of Odd-Electron Intermediates and In-Cage Electron Transfer in Ultrafast Photochemical Disproportionation Reactions in Lewis Bases

    E-print Network

    Harris, Charles B.

    The Role of Odd-Electron Intermediates and In-Cage Electron Transfer in Ultrafast Photochemical even-electron intermediates dominate a variety of transition metal reactions, the importance of odd of metal-metal bound carbonyl dimers was reported to involve odd-electron radical intermediates.2-4 While

  11. Unstable reaction intermediates and hysteresis during the catalytic cycle of 5-aminolevulinate synthase: implications from using pseudo and alternate substrates and a promiscuous enzyme variant.

    PubMed

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

    2014-08-15

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

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  14. 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

  15. 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…

  16. Intermediates produced in the reaction of chromium(VI) with dehydroascorbate cause single-strand breaks in plasmid DNA.

    PubMed

    Stearns, D M; Wetterhahn, K E

    1997-03-01

    Ascorbate (vitamin C) is a biological reductant of the human carcinogen chromium(VI). The product of this reaction is presumed to be dehydroascorbate. However, we have found that chromium(VI) can also react with dehydroascorbate. This reaction was monitored by UV/ visible and electron paramagnetic resonance (EPR) spectroscopies. In sodium acetate buffer at pH 3.8, the reaction of chromium(VI) and excess dehydroascorbate produced chromium(V) and chromium(IV) intermediates. At high reaction concentration, the chromium(V) intermediate formed an EPR silent dimer, which dissociated upon dilution to lower concentration. UV/ visible experiments at pH 3.8 demonstrated that manganese(II) catalyzed the disproportionation of chromium(IV) to chromium(V) and chromium(III). The ability of the reaction intermediates to induce strand breaks in pBR322 DNA was determined at pH 3.8 and pH 5.8. At pH 3.8, chromium(IV) appeared to be the major species responsible for induction of strand breaks because the time course for formation of strand breaks did not parallel that of chromium(V), and strand breaks were decreased in the presence of the chromium(IV) scavenger manganese(II). At pH 5.8, fewer strand breaks were observed; however, the time course for their formation followed that of chromium(V). There has been much effort devoted to identification of the intermediate responsible for the induction of strand breaks during reactions of chromium(VI) with biological reductants. The current results suggest that it is not a single type of species that universally produces the DNA strand breaks observed in different chromium(VI) systems and that the reactivity of intermediates will depend on the chosen experimental conditions. Understanding this variability in chromium(VI) reactions may help to resolve the conflicting results from in vitro studies that are aimed at deciphering mechanisms of chromium(VI)-induced cancers. PMID:9084906

  17. Effects of current conservation in continuum RPA-SK3 predictions of photonuclear reactions at intermediate energies

    Microsoft Academic Search

    M. Marangoni; A. M. Saruis

    1991-01-01

    The incidence of current conservation in (gamma, p) and (gamma, n) reactions at intermediate energies has been studied in the frame of the self-consistent RPA-SK3 continuum theory, fulfilling current conservation. Two-body exchange currents, originated from the momentum dependent terms of the Skyrme hamiltonian, are expressed in RPA-SK3 through an isovector convection current carrying an effective nucleon mass mSK(r) <=m. The

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

    PubMed

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

    2013-10-28

    Formation of the NO3 radical was observed following photolysis of the CH2I2 + O2 system at 248 nm under ambient atmospheric boundary layer conditions (~760 Torr and 297 K) in the presence of NO2. The Criegee intermediate (CI) CH2OO is believed to be responsible for the NO3 production. The potential of such reactions to enhance the rate of NO3 production in the atmosphere is discussed. PMID:24030640

  19. Direct detection of key reaction intermediates in photochemical CO2 reduction sensitized by a rhenium bipyridine complex.

    PubMed

    Kou, Youki; Nabetani, Yu; Masui, Dai; Shimada, Tetsuya; Takagi, Shinsuke; Tachibana, Hiroshi; Inoue, Haruo

    2014-04-23

    Photochemical CO2 reduction sensitized by rhenium-bipyridyl complexes has been studied through multiple approaches during the past several decades. However, a key reaction intermediate, the CO2-coordinated Re-bipyridyl complex, which should govern the activity of CO2 reduction in the photocatalytic cycle, has never been detected in a direct way. In this study on photoreduction of CO2 catalyzed by the 4,4'-dimethyl-2,2'-bipyridine (dmbpy) complex, [Re(dmbpy)(CO)3Cl] (1), we successfully detect the solvent-coordinated Re complex [Re(dmbpy)(CO)3DMF] (2) as the light-absorbing species to drive photoreduction of CO2. The key intermediate, the CO2-coordinated Re-bipyridyl complex, [Re(dmbpy)(CO)3(COOH)], is also successfully detected for the first time by means of cold-spray ionization spectrometry (CSI-MS). Mass spectra for a reaction mixture with isotopically labeled (13)CO2 provide clear evidence for the incorporation of CO2 into the Re-bipyridyl complex. It is revealed that the starting chloride complex 1 was rapidly transformed into the DMF-coordinated Re complex 2 through the initial cycle of photoreduction of CO2. The observed induction period in the time profile of the CSI-MS signals can well explain the subsequent formation of the CO2-coordinated intermediate from the solvent-coordinated Re-bipyridyl complex. An FTIR study of the reaction mixture in dimethyl sulfoxide clearly shows the appearance of a signal at 1682 cm(-1), which shifts to 1647 cm(-1) for the (13)CO2-labeled counterpart; this is assigned as the CO2-coordinated intermediate, Re(II)-COOH. Thus, a detailed understanding has now been obtained for the mechanism of the archetypical photochemical CO2 reduction sensitized by a Re-bipyridyl complex. PMID:24689747

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

    PubMed

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

    2015-02-10

    The results of quantum chemical modeling of organic and metal-containing intermediates that occur in electrocatalytic dehalogenation reactions of organic chlorides are presented. Modeling of processes that take place in successive steps of the electrochemical reduction of representative C1 and C2 chlorides - CHCl3 and Freon R113 (1,1,2-trifluoro-1,2,2-trichloroethane) - was carried out by density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2). It was found that taking solvation into account using an implicit solvent model (conductor-like screening model, COSMO) or considering explicit solvent molecules gave similar results. In addition to modeling of simple non-catalytic dehalogenation, processes with a number of complexes and their reduced forms, some of which were catalytically active, were investigated by DFT. Complexes M(L1)2 (M = Fe, Co, Ni, Cu, Zn, L1H = Schiff base from 2-pyridinecarbaldehyde and the hydrazide of 4-pyridinecarboxylic acid), Ni(L2) (H2L2 is the Schiff base from salicylaldehyde and 1,2-ethylenediamine, known as salen) and Co(L3)2Cl2, representing a fragment of a redox-active coordination polymer [Co(L3)Cl2]n (L3 is the dithioamide of 1,3-benzenedicarboxylic acid), were considered. Gradual changes in electronic structure in a series of compounds M(L1)2 were observed, and correlations between [M(L1)2](0) spin-up and spin-down LUMO energies and the relative energies of the corresponding high-spin and low-spin reduced forms, as well as the shape of the orbitals, were proposed. These results can be helpful for determination of the nature of redox-processes in similar systems by DFT. No specific covalent interactions between [M(L1)2](-) and the R113 molecule (M = Fe, Co, Ni, Zn) were found, which indicates that M(L1)2 electrocatalysts act rather like electron transfer mediators via outer-shell electron transfer. A relaxed surface scan of the adducts {M(L1)2·R113}(-) (M = Ni or Co) versus the distance between the chlorine atom leaving during reduction and the corresponding carbon atom showed an energy barrier to electron transfer (the first stage of R113 catalytic reduction), while DFT optimization of the {Ni(L2)·R113}(-) adduct showed barrier-free decomposition. The difference between the stabilities of the {Ni(L1)2·R113}(-) and {Ni(L2)·R113}(-) adducts correlates with the difference between the catalytic activities of Ni(L1)2 and Ni(L2) in the electrochemical reduction of R113. PMID:25623515

  1. Synthesis of complex benzenoids via the intermediate generation of o-benzynes through the hexadehydro-Diels–Alder reaction

    PubMed Central

    Baire, Beeraiah; Niu, Dawen; Willoughby, Patrick H.; Woods, Brian P.; Hoye, Thomas R.

    2014-01-01

    The hexadehydro-Diels–Alder (HDDA) cascade enables the synthesis of complex benzenoid products with various substitution patterns via aryne intermediates. The first stage of this cascade involves generation of a highly reactive ortho-benzyne intermediate by a net [4+2] cycloisomerization of a triyne substrate. The benzyne can be rapidly ‘trapped’ either intra- or intermolecularly with a myriad of nucleophilic or ?-bond-donating reactants. As a representative example of a general procedure to synthesize highly substituted benzenoids, this protocol describes the synthesis of a typical triyne substrate and its use as the reactant in an HDDA cascade to form a phthalide. The synthetic procedure detailed herein (four chemical reactions) takes 16–20 h of active effort over a several day period for preparation of the triyne precursor and ~2 h of active effort over a 3-day period for generation and trapping of the benzyne and isolation of the phthalide product. PMID:23411632

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

    E-print Network

    Frenkel, Anatoly

    by perfect turnover and unique reaction pathways.5 Vibrational spectroscopies,6 magnetic circular dichroism,7 detection, vibrational spectroscopies use a feature identification "fin- gerprinting" approach and thus

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

    E-print Network

    Belenguer, Ana M.; Lampronti, Giulio Isacco; Wales, David J.; Sanders, Jeremy Keith Morris

    2014-10-14

    (XRD) at a synchrotron facility.25 The resulting kinetic reaction curves clearly show a terminal plateau that may be indicative of a thermodynamic equilibrium: the au- thors do not comment on the possible driving force of the reactions studied... whose size is hard to predict or even to estimate. One report of in-situ and in real time monitoring by XRD of a ball mill grinding reaction describes the crystal size in a ball mill grinding reaction to approach the order of tens of nm, giving a...

  4. Subcellular fractionation of TGF-beta1-stimulated lung epithelial cells: a novel proteomic approach for identifying signaling intermediates.

    PubMed

    Milosevic, Jadranka; Bulau, Patrick; Mortz, Ejvind; Eickelberg, Oliver

    2009-03-01

    Members of the transforming growth factor (TGF)-beta superfamily are key regulators of lung development and homeostasis, in particular by controlling alveolar/bronchial epithelial cell function. TGF-beta signaling involves ligand-dependent activation of receptor serine/threonine kinases, activation and subsequent nuclear translocation of pathway-specific transcription factors (Smads), and ultimately, modulation of gene expression. While Smad-dependent responses represent the primary signaling components activated by TGF-beta receptors, their function is controlled by a variety of cofactors. In addition, alternative signaling systems mediating TGF-beta-induced effects have recently been described such as MAP kinase pathways. To uncover novel proteins that participate in TGF-beta signaling via nuclear/cytoplasmic shuttling in lung epithelial cells, we have analyzed A549 human lung epithelial cells, using subcellular fractionation combined with 2-D PAGE, tryptic digestion, and MS. We identified a rapid increase in the cytosolic localization of KH-type splicing regulatory protein (KHSRP), far upstream element-binding protein (FUBP1), hnRNP-L, and hnRNP-H1, concomitant with a decrease in their nuclear localization in response to TGF-beta1. Proteomic data were confirmed by immunofluorescence and immunoblot analyses. In summary, we represent a powerful novel technology for the identification of previously unknown signaling intermediates. PMID:19253281

  5. 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.

  6. Investigation into the mechanism and microstructure of reaction intermediates in the two-phase synthesis of alkanethiol-capped silver nanoparticles.

    PubMed

    Faghihi, Farhad; Hazendonk, Paul; Montina, Tony

    2015-03-24

    To gain better control over the characteristics of the alkanethiol-capped silver nanoparticles (SNP) prepared by the two-phase method, the intermediate stage of this reaction and the structure of the precursor compound were investigated. Samples taken from the intermediate stage of the reaction were analyzed by NMR and vibrational spectroscopy both in solution and after solvent removal. The (1)H NMR chemical shifts of the complexes formed during the phase-transfer step were used to detect any structural changes that occur upon introduction of nonanethiol. Moreover, the presence of silver thiolate was monitored by comparing the FTIR and Raman spectra of silver nonanethiolate with the dried samples. Further insights into the microstructure of the intermediate compounds were sought by characterizing samples differing in molar ratios of tetraoctylammonium bromide (TOAB) to silver nitrate (AgNO3). (13)C solid-state NMR chemical shifts, (13)C relaxation times, and the DSC transitions of these samples revealed a dependence of their phase structure on the initial concentration of the reagents. At least two phases with distinct mobility and conformational ordering of their octyl chains were identified in the samples prepared with excess TOAB, which was associated with the presence of multiple anionic species. The observations regarding the composition of the phase-transfer product were further related to the quality of the resulting nanoparticles. It was demonstrated that a large excess of TOAB, which is commonly used in two-phase methods, can be avoided without compromising the size and dispersity of the silver nanoparticles produced. This modification to the synthetic procedure simplifies the purification of the product, mitigates the propensity of the nanoparticles for aggregation, and facilitates their redispersion. PMID:25738982

  7. 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 (G?4), 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 G?4 was abundant in the axons and Schwann cells of peripheral nerves and that expression of G?4 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 G?4. This study identifies GNB4 mutations as a cause of CMT and highlights the importance of G?4-related GPCR signaling in peripheral-nerve function in humans. PMID:23434117

  8. Identifying Neutrinos and Antineutrinos in Neutral-Current Scattering Reactions N. Jachowicz,1,* ,1

    E-print Network

    Gent, Universiteit

    Identifying Neutrinos and Antineutrinos in Neutral-Current Scattering Reactions N. Jachowicz,1,* ,1 August 2004) We study neutrino-induced nucleon knockout from nuclei. Expressions for the induced-wave approximation. Large dissimilarities in the nucleon polarization asymmetries are observed between neutrino

  9. Structural identifiability of the yield coefficients in bioprocess models when the reaction rates are unknown

    Microsoft Academic Search

    G. Bastin

    1996-01-01

    The identification problem of bioprocesses in a stirred tank reactor essentially concerns the determination of the yield coefficients and the reaction rates involved in a general state-space model. This paper deals with the analysis of structural identifiability of the yield coefficients issuing from a two-step identification procedure. In fact, the identification of the yield coefficients can be completely decoupled from

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

    DOEpatents

    Maya, Leon (Oak Ridge, TN)

    1988-05-24

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

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

    DOEpatents

    Maya, Leon (Oak Ridge, TN)

    1991-01-01

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

  12. 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.

  13. 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 ?m-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

  14. 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.

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

    PubMed Central

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

    1980-01-01

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

  16. 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

    2014-11-18

    Psychophysiological measures of fear expression provide observable intermediate phenotypes of fear-related symptoms. Research Domain Criteria (RDoC) advocate using neurobiological intermediate phenotypes that provide dimensional correlates of psychopathology. Negative Valence Systems in the RDoC matrix include the construct of acute threat, which can be measured on a physiological level using potentiation of the acoustic startle reflex assessed via electromyography recordings of the orbicularis oculi muscle. Impairments in extinction of fear-potentiated startle due to high levels of fear (termed fear load) during the early phases of extinction have been observed in posttraumatic stress disorder (PTSD). The goals of the current work were to examine dimensional associations between fear-related symptoms of PTSD and fear load variables to test their validity as an intermediate phenotype. We examined extinction of fear-potentiated startle in a cohort (n=269) of individuals with a broad range of civilian trauma exposure (range 0-13 traumatic events per person, mean=3.5). Based on previously reported findings, we hypothesized that fear load would be significantly associated with intrusion and fear memories of an index traumatic event. The results indicated that early extinction was correlated with intrusive thoughts (p=0.0007) and intense physiological reactions to trauma reminders (p=0.036). Degree of adult or childhood trauma exposure, and depression severity were not associated with fear load. After controlling for age, sex, race, income, level of prior trauma, and level of fear conditioning, fear load during extinction was still significantly predictive of intrusive thoughts (p=0.004). The significance of these findings is that they support dimensional associations with symptom severity rather than diagnostic category and, as such, fear load may emerge as a transdiagnostic intermediate phenotype expressed across fear-related disorders (e.g., specific phobia, social phobia). PMID:25451788

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

    SciTech Connect

    Banu, A.; Trache, L. [Cyclotron Institute, Texas A and M University, College Station, Texas 77843-3366 (United States); National Institute of Physics and Nuclear Engineering, 'Horia Hulubei' (IFIN-HH), R-077125 Magurele-Bucharest (Romania); Carstoiu, F.; Negoita, F.; Rotaru, F. [National Institute of Physics and Nuclear Engineering, 'Horia Hulubei' (IFIN-HH), R-077125 Magurele-Bucharest (Romania); Orr, N. A.; Achouri, N. L.; Laurent, B. [Laboratoire de Physique Corpusculaire, IN2P3-CNRS, ISMRA et Universite, F-14050 Caen (France); Bonaccorso, A. [Instituto Nazionale di Fisica Nucleare, Sez. Di Pisa, I-56127 Pisa (Italy); Catford, W. N.; Patterson, N.; Thomas, J. S. [Department of Physics, University of Surrey, Guildford GU2 5XH (United Kingdom); Chartier, M.; Fernandez-Dominguez, B.; Paschalis, S.; Pietras, B. [Oliver Lodge Laboratory, University of Liverpool, Liverpool L69 7ZE (United Kingdom); Freer, M. [School of Physics and Astronomy, University of Birmingham, Birmingham B15 2TT (United Kingdom); Gaudefroy, L.; Roussel-Chomaz, P. [Grand Accelerateur d'Ions Lourds, BP 55027, 14076 Caen Cedex 5 (France); Horoi, M. [Department of Physics, Central Michigan University, Mount Pleasant, Michigan 48859 (United States)

    2010-11-24

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

  18. 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)

  19. Cobalt catalysis in the gas phase: experimental characterization of cobalt(I) complexes as intermediates in regioselective Diels-Alder reactions.

    PubMed

    Fiebig, Lukas; Kuttner, Julian; Hilt, Gerhard; Schwarzer, Martin C; Frenking, Gernot; Schmalz, Hans-Günther; Schäfer, Mathias

    2013-10-18

    In situ-formed cobalt(I) complexes are proposed to act as efficient catalysts in regioselective Diels-Alder reactions of unactivated substrates such as 1,3-dienes and alkynes. We report the first experimental evidence for the in situ reduction of CoBr2(dppe) [dppe = 1,2-bis(diphenylphosphino)ethane] by Zn/ZnI2 to [Co(I)(dppe)](+) by means of electrospray MS(n) experiments. Additionally, the reactivities of Co(II) and Co(I) dppe complexes toward the Diels-Alder substrates isoprene and phenylacetylene were probed in gas-phase ion/molecule reactions (IMRs). Isoprene and phenylacetylene were introduced into the mass spectrometer via the buffer gas flow of a linear ion trap. The IMR experiments revealed a significantly higher substrate affinity of [Co(I)(dppe)](+) compared with [Co(II)Br(dppe)](+). Furthermore, the central intermediate of the solution-phase cobalt-catalyzed Diels-Alder reaction, [Co(I)(dppe)(isoprene)(phenylacetylene)](+), could be generated via IMR and examined in the gas phase. Collision activation of this complex ion delivered evidence for the gas-phase reaction of isoprene with phenylacetylene in the coordination sphere of the cobalt ion. The experimental findings are consistent with the results of quantum-chemical calculations on all of the observed Co(I) dppe complex ions. The results constitute strong analytical evidence for the formation and importance of different cobalt(I) species in regioselective Diels-Alder reactions of unactivated substrates and identify [Co(I)(dppe)](+) as the active Diels-Alder catalyst. PMID:24044877

  20. 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

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

    PubMed Central

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

    2010-01-01

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

  2. Identification and quantitation of reaction intermediates and residuals in lipase-catalyzed transesterified oils by HPLC.

    PubMed

    Aryee, Alberta N A; Phillip, Leroy E; Cue, Roger I; Simpson, Benjamin K

    2011-09-01

    A high-performance liquid chromatography (HPLC) unit equipped with size exclusion column and a refractive index detector was used for simultaneous monitoring, identification, and quantitation of the reaction components from lipase-catalyzed transesterification of three oils. The procedure simultaneously separated and detected the unreacted triacylglycerols (TAG), diacyl-, and monoacyl-glycerol (DAG and MAG) co-products, residual alcohol as well as free fatty acid (FFA) based on retention times. The chromatograms showed well separated and resolved peaks. The elution of the components from the transesterification reaction in increasing order was: TAG?reaction components and products of transesterification reactions without the need for additional derivatization steps. PMID:21523356

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

    PubMed

    Jusys, Zenonas; Behm, R Jürgen

    2014-01-01

    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

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

    PubMed Central

    Behm, R Jürgen

    2014-01-01

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

  5. 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. [James Franck Institute and Department of Chemistry, University of Chicago, Chicago, Illinois 60637 (United States); Lee, S.-H. [National Synchrotron Radiation Research Center, Hsinchu, 30076 Taiwan (China); Lin, Jim Jr-Min [Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617 Taiwan (China)

    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 acrolein+H product channel is consistent with the relative barriers en route to each of these product channels calculated at the CCSD(T)/aug-cc-pVQZ level of theory, although a clean determination of the barrier energy to H+acrolein is precluded by the substantial partitioning into rotational energy during the photolytic production of the nascent radicals. We compare the measured branching fraction to the H+acrolein product channel with a statistical prediction based on the calculated transition states.

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

    SciTech Connect

    Nathan, A.M.; Sandorfi, A.M. (eds.)

    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

  7. Excitation and decay of giant multipole resonances in intermediate energy heavy ion reactions

    SciTech Connect

    Beene, J.R.; Bertrand, F.E.

    1989-01-01

    The role of intermediate energy heavy ions in the study of giant multipole resonances is explored, with emphasis on gamma decay coincidence experiments. Experiments on /sup 208/Pb bombarded by 84 MeV/nucleon /sup 17/O are discussed and compared with earlier work at 22 MeV/nucleon. The role of Coulomb excitation in the 84 MeV/nucleon data is emphasized and some consequences for study of isovector resonance strength are explored. A comparison of the excitation and decay of the isovector giant dipole resonance in /sup 208/Pb and /sup 209/Bi excited with 84 MeV/nucleon /sup 17/O scattering is presented. 35 refs., 16 figs., 1 tab.

  8. 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

  9. Direct evidence for the existence of gaseous intermediates in the calcium sulfide-calcium sulfate reaction

    Microsoft Academic Search

    Ralph T. Yang; Ming-Shing Shen

    1979-01-01

    Results of studies of the mechanism and kinetics of the reaction, CaS + 3CaSOâ ..-->.. 4CaO + 4SOâ, of importance to the development of advanced regenerative processes for fluidized-bed combustion of coal are presented. Rates were measured of the thermal decomposition of CaSOâ with and without physically separating the CaS. Gas evolved from heating at 900° and 1100°C was measured

  10. 4He(p,2p)3H reaction at intermediate energies

    Microsoft Academic Search

    W. T. H. van Oers; B. T. Murdoch; B. K. S. Koene; D. K. Hasell; R. Abegg; D. J. Margaziotis; M. B. Epstein; G. A. Moss; L. G. Greeniaus; J. M. Greben; J. M. Cameron; J. G. Rogers; A. W. Stetz

    1982-01-01

    The 4He(p,2p)3H reaction has been studied at 250, 350, and 500 MeV using coplanar symmetric and asymmetric geometries. The data are presented as energy-sharing spectra, coplanar symmetric angular distributions, and quasifree angular distributions. A comparison with distorted wave impulse approximation calculations indicates reasonable agreement for small recoil momenta (q<~150 MeV\\/c). For larger recoil momenta, the distorted-wave impulse approximation calculations increasingly

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

    SciTech Connect

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

    2009-03-25

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

  12. a Study of the DEUTERON(PROTON,2-PROTON)NEUTRON Reaction at Intermediate Energy

    NASA Astrophysics Data System (ADS)

    Punjabi, Vina Alkesh

    Exclusive cross sections for the ('2)H(p,2p)n reaction at beam energies of 507 and 508 MeV have been measured at various kinematics. The results are compared with the predictions of the impulse approximation and of a calculation of the 6 lowest order terms of a multiple scattering expansion of the (tau)-matrix. At small internal momenta larger than 200 MeV/c a drastic deviation from theory is confirmed. Possible causes for these results are discussed.

  13. A study of stopping power in nuclear reactions at intermediate energies

    E-print Network

    G. Lehaut; D. Durand; O. Lopez

    2010-01-25

    We show a systematic experimental study based on INDRA data of the stopping power in central symmetric nuclear reactions. Total mass of the systems goes from 80 to 400 nucleons while the incident energy range is from 12 AMeV to 100 AMeV. The role of isospin diffusion at 32 and 45 MeV/nucleon with 124,136Xe projectiles on 112,124Sn targets performed at GANIL is also discussed. Results suggest a strong memory of the entrance channel above 20 AMeV/A (nuclear transparency) and, as such, constitute valuable tests of the microscopic transport models.

  14. Chemistry of low-valent molybdenum phosphite complexes: Models of seven-coordinate reaction intermediates.

    PubMed

    Muetterties, E L; Kirner, J F; Evans, W J; Watson, P L; Abdel-Meguid, S; Tavanaiepour, I; Day, V W

    1978-03-01

    A simple synthesis of the zerovalent complex Mo[P(OCH(3))(3)](6) has been devised from a potassium reduction of MoCl(4)(tetrahydrofuran)(2) followed by reaction with trimethyl phosphite at 70 degrees . Protonation of this octahedral complex gave only low yields of the expected seven-coordinate hydride, HMo[P(OCH(3))(3)](6) (+). The major product was an octahedral nonhydridic cation, Mo[P(OCH(3))(3)](5)P(OCH(3))(2) (+), derived from proton cleavage of the P-O phosphite ester bond. This octahedral cation was stereochemically nonrigid, apparently through facile methoxy group migration. Close packing by methoxy groups in this fluxional cation was established through an x-ray crystallographic study of Mo[P(OCH(3))(3)](5)P(OCH(3))(2) (+)-PF(6) (-). Extended reaction of trifluoroactic acid with Mo[P(OCH(3))(3)](6) yielded the seven-coordinate hydride, HMo[P(OCH(3))(3)](4)(O(2)CCF(3)), which was near pentagonal bipyramidal and was stereochemically nonrigid. PMID:16592505

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

    PubMed

    Azrague, Kamal; Pradines, Vincent; Bonnefille, Eric; Claparols, Catherine; Maurette, Marie-Thérèse; Benoit-Marquié, Florence

    2012-10-30

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

  16. Choice reaction times for identifying the direction of first-order motion and different varieties of second-order motion

    E-print Network

    Nottingham, University of

    of the human visual system by measuring forced-choice reaction times for dis- criminating the drift directionChoice reaction times for identifying the direction of first-order motion and different varieties to near-threshold levels. Psychophysical (behavioural) reaction time paradigms have been employed

  17. 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.

  18. Nitrite reduction by biogenic hydroxycarbonate green rusts: evidence for hydroxy-nitrite green rust formation as an intermediate reaction product.

    PubMed

    Guerbois, Delphine; Ona-Nguema, Georges; Morin, Guillaume; Abdelmoula, Mustapha; Laverman, Anniet M; Mouchel, Jean-Marie; Barthelemy, Kevin; Maillot, Fabien; Brest, Jessica

    2014-04-15

    The present study investigates for the first time the reduction of nitrite by biogenic hydroxycarbonate green rusts, bio-GR(CO3), produced from the bioreduction of ferric oxyhydroxycarbonate (Fohc), a poorly crystalline solid phase, and of lepidocrocite, a well-crystallized Fe(III)-oxyhydroxide mineral. Results show a fast Fe(II) production from Fohc, which leads to the precipitation of bio-GR(CO3) particles that were roughly 2-fold smaller (2.3 ± 0.4 ?m) than those obtained from the bioreduction of lepidocrocite (5.0 ± 0.4 ?m). The study reveals that both bio-GR(CO3) are capable of reducing nitrite ions into gaseous nitrogen species such as NO, N2O, or N2 without ammonium production at neutral initial pH and that nitrite reduction proceeded to a larger extent with smaller particles than with larger ones. On the basis of the identification of intermediates and end-reaction products using X-ray diffraction and X-ray absorption fine structure (XAFS) spectroscopy at the Fe K-edge, our study shows the formation of hydroxy-nitrite green rust, GR(NO2), a new type of green rust 1, and suggests that the reduction of nitrite by biogenic GR(CO3) involves both external and internal reaction sites and that such a mechanism could explain the higher reactivity of green rust with respect to nitrite, compared to other mineral substrates possessing only external reactive sites. PMID:24708473

  19. Mechanistic studies of the ethylene trimerization reaction with chromium-diphosphine catalysts: experimental evidence for a mechanism involving metallacyclic intermediates.

    PubMed

    Agapie, Theodor; Schofer, Susan J; Labinger, Jay A; Bercaw, John E

    2004-02-11

    A system for catalytic trimerization of ethylene utilizing CrCl3(THF)3 and a diphosphine ligand PNPOMe [= (o-MeO-C6H4)2PN(Me)P(o-MeO-C6H4)2] has been investigated. The coordination chemistry of chromium with PNPOMe has been explored, and (PNPOMe)CrCl3 and (PNPOMe)CrPh3 (3) have been synthesized by ether displacement from chromium(III) precursors. Salt metathesis of (PNPOMe)CrCl3 with o,o'-biphenyldiyl Grignard affords (PNPOMe)Cr(o,o'-biphenyldiyl)Br (4). Activation of 3 with H(Et2O)2B[C6H3(CF3)2]4 or 4 with NaB[C6H3(CF3)2]4 generates a catalytic system and trimerizes a 1:1 mixture of C2D4 and C2H4 to give isotopomers of 1-hexene without H/D scrambling (C6D12, C6D8H4, C6D4H8, and C6H12 in a 1:3:3:1 ratio). The lack of crossover supports a mechanism involving metallacyclic intermediates. The mechanism of the ethylene trimerization reaction has also been studied by the reaction of trans-, cis-, and gem-ethylene-d2 with 4 upon activation with NaB[C6H3(CF3)2]4. PMID:14759164

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

    PubMed

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

    2006-11-01

    The aim of this study was to histopathologically examine the biocompatibility of the high-copper amalgam, intermediate restorative material (IRM), mineral trioxide aggregate (MTA), and MTA mixed with chlorhexidine (CHX). This study was conducted to observe the rat subcutaneous connective tissue reaction to the implanted tubes filled with amalgam, IRM, MTA, and MTA mixed with CHX. The animals were sacrificed 15, 30, and 60 days after the implantation procedure. The implant sites were excised and prepared for histological evaluation. Sections of 5 to 6 microm thickness were cut by a microtome and stained with hemotoxylin eosin and examined under a light microscope. The inflammatory reactions were categorized as weak (none or few inflammatory cells < or =25 cells), moderate (>25 cells), and severe (a lot of inflammatory cells not to be counted, giant cells, and granulation tissue). Thickness of fibrous capsules measured five different areas by the digital imaging and the mean values were scored. Amalgam, IRM, and MTA mixed with CHX caused a weak inflammatory response on days 15, 30, and 60. MTA provoked an initial severe inflammatory response that subsided at the 30 and 60 day study period. A clear fibrous capsule was observed beginning from the 15 days in all of the groups. Within the limits of this study, amalgam, IRM, MTA, and MTA mixed with CHX materials were surrounded by fibrous connective tissue indicated that they were well tolerated by the tissues, therefore, MTA/CHX seemed to be biocompatible. PMID:17055915

  1. 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

  2. Analysis of hard two-photon correlations measured in heavy-ion reactions at intermediate energies

    SciTech Connect

    Barz, H.W.; Kaempfer, B.; Wolf, G.; Bauer, W. [Institut fuer Kern-und Hadronenphysik, FZ Rossendorf, PF 510119, 01314 Dresden (Germany)] [Institut fuer Kern-und Hadronenphysik, FZ Rossendorf, PF 510119, 01314 Dresden (Germany); [Institut fuer Theoretische Physik, TU Dresden, Mommsenstr. 13, 01062 Dresden (Germany); [GSI Darmstadt, PF 110552, 64220 Darmstadt (Germany); [KFKI RMKI Budapest, POB 49, H-1525 Budapest (Hungary); [MSU Michigan, East Lansing, Michigan 48824 (United States)

    1996-02-01

    Recently reported measurements of hard photon correlations in the reactions {sup 36}Ar on {sup 27}Al at 95{ital A} MeV, {sup 86}Kr on {sup nat}Ni at 60{ital A} MeV, and {sup 181}Ta on {sup 197}Au at 39.5{ital A} MeV are analyzed. A Boltzmann-{umlt U}hling-Uhlenbeck transport model is used to describe the photon production by individual nucleon-nucleon collisions. In the lighter systems we find the best agreement with data when taking into account only photons from first-chance collisions of nucleons or photons produced during the passage of the nuclei, while the model predicts also a considerable late-time emission of photons, which leads to a depletion of the calculated correlation function. The accuracy of the present data does not allow firm conclusions on the reliability of this late-time evolution. Our investigations do not support a recently reported interference pattern in the heavy Ta + Au system. {copyright} {ital 1996 The American Physical Society.}

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

    SciTech Connect

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

    2005-03-30

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

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

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

    Calculations were performed for proton induced spallation reactions over a wide range of atomic masses on the targets: 12C, 27Al, natNi, 108Ag and 197Au using an Intra-nuclear Cascade Model (INCL4.6) with coalescence which includes the emission of protons, light clusters (d-4He), and intermediate mass fragments (up to A=8) formed by the nucleons during the first stage of the reaction. The emission of particles from excited cascade residua are described using three different theoretical models SMM, ABLA07, and GEMINI++. A comparison of calculations with experimental double differential cross-sections d2?/d?dE for light charged particles and selected intermediate mass fragments was studied at proton beam energies from 1.2-2.5 GeV. Systematic deviations of the simulated cross sections from the experimental data were found for both light charged particles and intermediate mass fragments.

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

    PubMed Central

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

    2015-01-01

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

  7. Master Equation Analysis of Thermal Activation Reactions: Energy-Transfer Constraints on Falloff Behavior in the Decomposition of Reactive Intermediates with Low Thresholds

    E-print Network

    Zachariah, Michael R.

    with the high-temperature decomposition of reactive intermediates with low reaction thresholds) molecular size (heat capacity), high-pressure rate parameters, temperature, and pressure. At 101 kPa (1 atm temperatures or low pressures, unimo- lecular decompositions begin to be affected by energy-transfer effects

  8. Direct femtosecond observation of the transient intermediate in the -cleavage reaction of (CH3)2CO to 2CH3 CO: Resolving

    E-print Network

    Kim, Sang Kyu

    Direct femtosecond observation of the transient intermediate in the -cleavage reaction of (CH3)2CO resolution of the individual C­C cleavage events was not possible. Here, for the elementary -cleavage example for addressing the issue of concertedness and belongs to the general class of -cleavage processes

  9. Photofragment imaging study of the CH{sub 2}CCH{sub 2}OH radical intermediate of the OH+allene reaction

    SciTech Connect

    Raman, Arjun S.; Justine Bell, M.; Lau, K.-C.; Butler, Laurie J. [James Franck Institute and Department of Chemistry, University of Chicago, Chicago, Illinois 60637 (United States)

    2007-10-21

    These velocity map imaging experiments characterize the photolytic generation of one of the two radical intermediates formed when OH reacts via an addition mechanism with allene. The CH{sub 2}CCH{sub 2}OH radical intermediate is generated photolytically from the photodissociation of 2-chloro-2-propen-1-ol at 193 nm. Detecting the Cl atoms using [2+1] resonance-enhanced multiphoton ionization evidences an isotropic angular distribution for the Cl+CH{sub 2}CCH{sub 2}OH photofragments, a spin-orbit branching ratio for Cl({sup 2}P{sub 1/2}):Cl({sup 2}P{sub 3/2}) of 0.28, and a bimodal recoil kinetic energy distribution. Conservation of momentum and energy allows us to determine from this data the internal energy distribution of the nascent CH{sub 2}CCH{sub 2}OH radical cofragment. To assess the possible subsequent decomposition pathways of this highly vibrationally excited radical intermediate, we include electronic structure calculations at the G3//B3LYP level of theory. They predict the isomerization and dissociation transition states en route from the initial CH{sub 2}CCH{sub 2}OH radical intermediate to the three most important product channels for the OH+allene reaction expected from this radical intermediate: formaldehyde+C{sub 2}H{sub 3}, H+acrolein, and ethene+CHO. We also calculate the intermediates and transition states en route from the other radical adduct, formed by addition of the OH to the center carbon of allene, to the ketene+CH{sub 3} product channel. We compare our results to a previous theoretical study of the O+allyl reaction conducted at the CBS-QB3 level of theory, as the two reactions include several common intermediates.

  10. A Confirmation of the Quench-Cryoannealing Relaxation Protocol for Identifying Reduction States of Freeze-Trapped Nitrogenase Intermediates

    PubMed Central

    2015-01-01

    We have advanced a mechanism for nitrogenase catalysis that rests on the identification of a low-spin EPR signal (S = 1/2) trapped during turnover of a MoFe protein as the E4 state, which has accumulated four reducing equivalents as two [Fe–H–Fe] bridging hydrides. Because electrons are delivered to the MoFe protein one at a time, with the rate-limiting step being the off-rate of oxidized Fe protein, it is difficult to directly control, or know, the degree of reduction, n, of a trapped intermediate, denoted En, n = 1–8. To overcome this previously intractable problem, we introduced a quench-cryoannealing relaxation protocol for determining n of an EPR-active trapped En turnover state. The trapped “hydride” state was allowed to relax to the resting E0 state in frozen medium, which prevents additional accumulation of reducing equivalents; binding of reduced Fe protein and release of oxidized protein from the MoFe protein both are abolished in a frozen solid. Relaxation of En was monitored by periodic EPR analysis at cryogenic temperature. The protocol rests on the hypothesis that an intermediate trapped in the frozen solid can relax toward the resting state only by the release of a stable reduction product from FeMo-co. In turnover under Ar, the only product that can be released is H2, which carries two reducing equivalents. This hypothesis implicitly predicts that states that have accumulated an odd number of electrons/protons (n = 1, 3) during turnover under Ar cannot relax to E0: E3 can relax to E1, but E1 cannot relax to E0 in the frozen state. The present experiments confirm this prediction and, thus, the quench-cryoannealing protocol and our assignment of E4, the foundation of the proposed mechanism for nitrogenase catalysis. This study further gives insights into the identity of the En intermediates with high-spin EPR signals, 1b and 1c, trapped under high electron flux. PMID:24635454

  11. 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.

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

    PubMed

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

    2014-01-01

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

  13. SABER: A computational method for identifying active sites for new reactions

    PubMed Central

    Nosrati, Geoffrey R; Houk, K N

    2012-01-01

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

  14. Mechanism of generation of volatile hydrides of trace elements by aqueous tetrahydroborate(III). Mass spectrometric studies on reaction products and intermediates.

    PubMed

    D'Ulivo, Alessandro; Mester, Zoltan; Meija, Juris; Sturgeon, Ralph E

    2007-04-01

    The mechanism of generation of volatile metal/metalloid hydrides by derivatization with borane complexes is presented. This reaction has been employed for ultratrace element analysis since 1972 and has been the source of much controversy in regard to the reaction mechanism. Here we investigated this derivatization by using As(III), Sb(III), Bi(III), MeAsO(OH)2, and Me2AsO(OH) as model analytes and NaBH4, NaBD4, tert-BuNH2BH3, and Me2NHBH3 as borane reagents. The identification of reaction products and intermediates observed under various reaction conditions was performed by gas chromatography/mass spectrometry and electrospray ionization mass spectrometry. An alternative reaction model, based on the formation of analyte-borane complex (ABC) intermediates, is able to reconcile all the experimental evidence reported in the literature. In this study, we provide definitive evidence of the ABC hydride generation mechanism, which shows that the generation of volatile hydrides occurs via formation of ABC intermediates between hydroboron species and the analyte substrate followed by the direct transfer of hydrogen from boron to the analyte atom, and fast hydrolysis leading to the final product. PMID:17338501

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

    PubMed Central

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

    2010-01-01

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

  16. 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.

  17. Structure-sensitivity and ensemble effects in reactions of strongly adsorbed intermediates. Catalytic dehydrogenation and dehydration of formic acid on nickel

    SciTech Connect

    Iglesia, E. (Exxon Research and Engineering Co., Annandale, NJ (United States)); Boudart, M. (Stanford Univ., CA (United States))

    1991-09-05

    Formic acid (HCOOH) dehydrogenates and dehydrates catalytically on Ni surfaces by unimolecular decomposition of strongly adsorbed formate intermediates. The rate of these reactions and the identity and decomposition selectivity of surface formate are not affected by Ni dispersion or by changes in Ni ensemble size resulting from Cu alloying or from coadsorption of Co and oxygen. Dehydrogenation and dehydration occur via identical intermediates that require small Ni ensembles (1-2 surface atoms) and that decompose with similar activation energy, a surprising result because the required molecular rearrangements differ markedly in the two decomposition modes. The authors suggest that reaction trajectories bifurcate after the formation of the activated complex in the rate-determining formate-decomposition step, leading to two kinetically indistinguishable decomposition paths. The decomposition selectivity on metal catalysts is controlled by entropy differences between the two reaction paths and by the binding energy of adsorbed oxygen atoms on these metal surfaces.

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

    PubMed Central

    Ribeiro, Ana Sofia; Paredes, Joana

    2014-01-01

    Epithelial–mesenchymal transition (also known as EMT) is a fundamental mechanism occurring during embryonic development and tissue differentiation, being also crucial for cancer progression. Actually, the EMT program contributes to the dissemination of cancer cells from solid tumors and to the formation of micro-metastasis that subsequently develop into clinically detectable metastases. Besides being a process that is defined by the progressive loss of epithelial cell characteristics and the acquisition of mesenchymal features, EMT has also been implicated in therapy resistance, immune escape, and maintenance of cancer stem cell properties, such as self-renewal capacity. However, the majority of the studies usually neglect the progressive alterations occurring during intermediate EMT states, which imply a range of phenotypic cellular heterogeneity that can potentially generate more metastable and plastic tumor cells. In fact, few studies have tried to identify these transitory states, partly due to the current lack of a detailed understanding of EMT, as well as of reliable readouts for its progression. Herein, a brief review of evidences is presented, showing that P-cadherin expression, which has been already identified as a breast cancer stem cell marker and invasive promoter, is probably able to identify an intermediate EMT state associated with a metastable phenotype. This hypothesis is based on our own work, as well as on the results described by others, which suggest the use of P-cadherin as a promising EMT marker, clearly functioning as an important clinical prognostic factor and putative therapeutic target in breast carcinogenesis. PMID:25601904

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

    NASA Astrophysics Data System (ADS)

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

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

  20. Multiple reaction monitoring as a method for identifying protein posttranslational modifications.

    PubMed

    Cox, David M; Zhong, F; Du, M; Duchoslav, E; Sakuma, T; McDermott, J C

    2005-06-01

    The activity of many transcriptional regulators is significantly altered by posttranslational modifications of specific sites. For example, the activity of the muscle-restricted transcription factor family myocyte enhancer factor 2 (MEF2) is tightly controlled by phosphorylation. This modification is responsible for either an increase or a decrease in transcriptional activity, depending on the specific amino acid residues that are phosphorylated by signal-dependent kinases. Although mass spectrometry-based methods, such as precursor ion and neutral loss scans, are extremely useful for identifying unknown phosphopeptides from a complex mixture, they do not take advantage of any prior knowledge about the protein being investigated. Quite often a significant amount of information is available. This may include the primary sequence, type of phosphorylation (serine/threonine vs. tyrosine), or predicted phosphoacceptor sites (consensus peptide that is targeted by a kinase). This information can be used to predict precursor and fragment ion m/z values for a multiple reaction monitoring (MRM) experiment. By using these highly sensitive MRM experiments to trigger dependent product ion scans on a hybrid quadrupole linear ion-trap instrument, we were able to identify low levels of phosphorylation of MEF2A (a member of the MEF2 family), and alpha-casein. This method of monitoring protein phosphorylation at specific phosphoacceptor sites may prove useful in understanding the physiological regulation of protein function. PMID:16030315

  1. Fuel-specific influences on the composition of reaction intermediates in premixed flames of three C5H10O2 ester isomers.

    PubMed

    Yang, Bin; Westbrook, Charles K; Cool, Terrill A; Hansen, Nils; Kohse-Höinghaus, Katharina

    2011-04-21

    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(5)H(10)O(2), enable further refinement and validation of a detailed chemical reaction mechanism originally developed in modeling studies of similar flames of methyl formate, methyl acetate, ethyl formate, and ethyl acetate. Photoionization mass spectrometry (PIMS), using monochromated synchrotron radiation, reveals significant differences in the compositions of key reaction intermediates between flames of the MB, MIB, and EP isomers studied under identical flame conditions. Detailed kinetic modeling describes how these differences are related to molecular structures of each of these isomers, leading to unique fuel destruction pathways. Despite the simple structures of these small esters, they contain structural functional groups expected to account for fuel-specific effects observed in the combustion of practical biodiesel fuels. The good agreement between experimental measurements and detailed reaction mechanisms applicable to these simple esters demonstrates that major features of each flame can be predicted with reasonable accuracy by building a hierarchical reaction mechanism based on three factors: (1) unimolecular decomposition of the fuel, especially by complex bond fission; (2) H-atom abstraction reactions followed by ?-scission of the resulting radicals, leading to nearly all of the intermediate species observed in each flame; (3) the rates of H-atom abstraction reactions for each alkoxy or alkyl group (i.e., methoxy, ethoxy, methyl, ethyl, propyl) are effectively the same as in other ester fuels with the same structural groups. PMID:21409253

  2. A quantum-chemical study of intermediates of the 1O2 photogeneration sensitized by buckminsterfullerene and accompanying photochemical reactions

    NASA Astrophysics Data System (ADS)

    Semenov, S. G.; Bedrina, M. E.

    2014-02-01

    The intermediates of hypothetical photochemical reactions that accompany the quenching of the 3C{60/*} triplet state by triplet oxygen are studied by the (U)PBE0 quantum-chemical method. The diradical C60-O-O formed from 3O2 and photoexcited buckminsterfullerene 3C{60/*} is characterized by a negative binding energy -1.11 eV (with respect to C60 and 3O2), the singlet-triplet splitting ? E ST of 0.07 eV, and the dipole moment of 3.2 D at the equilibrium internuclear separations 1.522 Å (CO) and 1.294 Å (OO). Its decay produces 1O2. The formation of a dioxetane circle lowers the energy by 0.8 eV. The ground-state energy of diketone C58(C=O)2 is 2.0 eV lower than the energy of C60-O-O. The metastable centrosymmetric diradical C60-C60, formed upon ineffective light absorption by clusters (C60)N, has a single interpolyhedral C-C bond (1.657 Å). Its triplet state T 1 lies 0.16 eV higher than the S 1 singlet. The S 1 ? S 0 relaxation leads to the formation of a stable C60-C60 dimer with a shorter (1.584 Å) bis-single exothermic (+0.24 eV) bond of polyhedra. The photoexcited C60-C60 dimer is able to form isomeric metastable diradicals C60-C60-O-O.

  3. Turning regioselectivity into stereoselectivity: efficient dual resolution of P-stereogenic phosphine oxides through bifurcation of the reaction pathway of a common intermediate.

    PubMed

    Nikitin, Kirill; Rajendran, Kamalraj V; Müller-Bunz, Helge; Gilheany, Declan G

    2014-02-10

    Synthetic routes that provide facile access to either enantiomeric form of a target compound are particularly valuable. The crystallization-free dual resolution of phosphine oxides that gives highly enantioenriched materials (up to 94?% ee) in excellent yields is reported. Both enantiomeric oxides have been prepared from a single intermediate, (RP )-alkoxyphosphonium chloride, which is formed in the course of a selective dynamic kinetic resolution using a single enantiomer of menthol as the chiral auxiliary. The origin of the dual stereoselectivity lies in bifurcation of the reaction pathway of this intermediate, which works as a stereochemical railroad switch. Under controlled conditions, Arbuzov-type collapse of this intermediate proceeds through C?O bond fission with retention of the configuration at the phosphorus center. Conversely, alkaline hydrolysis of the P?O bond leads to the opposite SP ?enantiomer. PMID:24474623

  4. 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

  5. Reversibility of the mitochondrial isocitrate dehydrogenase reaction in the perfused rat liver. Evidence from isotopomer analysis of citric acid cycle intermediates.

    PubMed

    Des Rosiers, C; Fernandez, C A; David, F; Brunengraber, H

    1994-11-01

    The reversal of the mitochondrial isocitrate dehydrogenase reaction was investigated in rat livers perfused with [U-13C5]glutamate or [U-13C5]glutamine. The mass isotopomer distribution of citric acid cycle intermediates extracted from the livers was determined by gas chromatography-mass spectrometry. Citrate was enriched in an isotopomer containing five 13C. The formation of this isotopomer can only be explained by the reversal of the isocitrate dehydrogenase reaction. Calculation of kinetic parameters from the mass isotopomer data reveals a rapid interconversion of isocitrate and alpha-ketoglutarate. This interconversion results in an isotopic exchange between carbon 6 of citrate and mitochondrial CO2 that can affect the calculation of citric acid cycle kinetic parameters. Thus, the reversal of the isocitrate dehydrogenase reaction should be included in isotope labeling models of the citric acid cycle. PMID:7961626

  6. Spectral Identification of Intermediates Generated during the Reaction of Dioxygen with the Wild-Type and EQ(I-286) Mutant of Rhodobacter sphaeroides Cytochrome c Oxidase

    PubMed Central

    Szundi, Istvan; Funatogawa, Chie; Cassano, Jennifer; McDonald, William; Ray, Jayashree; Hiser, Carrie; Ferguson-Miller, Shelagh; Gennis, Robert B.; Einarsdóttir, Ólöf

    2012-01-01

    Cytochrome c oxidase from Rhodobacter sphaeroides (Rs) is frequently used to model the more complex mitochondrial enzyme. The O2 reduction in both enzymes is generally described by a unidirectional mechanism involving the sequential formation of the ferrous-oxy complex (compound A), the PR state, the oxyferryl F form, and the oxidized state. In this study we investigated the reaction of dioxygen with the wild-type reduced Rs cytochrome oxidase and the EQ(I-286) mutant using the CO flow-flash technique. Singular value decomposition and multi-exponential fitting of the time-resolved optical absorption difference spectra showed that three apparent lifetimes, 18 ?s, 53 ?s, and 1.3 ms, are sufficient to fit the kinetics of the O2 reaction of the wild-type enzyme. A comparison of the experimental intermediate spectra with the corresponding intermediate spectra of the bovine enzyme revealed that PR is not present in the reaction mechanism of the wild-type Rs aa3. Transient absorbance changes at 440 and 610 nm support this conclusion. For the EQ(I-286) mutant, in which a key glutamic residue in the D proton pathway is replaced by glutamine, two lifetimes, 16 and 108 ?s, were observed. A spectral analysis of the intermediates shows that the O2 reaction in the EQ(I-286) mutant terminates at the PR state, with 70% of heme a becoming oxidized. These results indicate significant differences in the kinetics of O2 reduction between the bovine and wild-type Rs aa3 oxidases, which may arise from differences in the relative rates of internal electron and proton movements in the two enzymes. PMID:23057757

  7. Spectral identification of intermediates generated during the reaction of dioxygen with the wild-type and EQ(I-286) mutant of Rhodobacter sphaeroides cytochrome c oxidase.

    PubMed

    Szundi, Istvan; Funatogawa, Chie; Cassano, Jennifer; McDonald, William; Ray, Jayashree; Hiser, Carrie; Ferguson-Miller, Shelagh; Gennis, Robert B; Einarsdóttir, Ólöf

    2012-11-20

    Cytochrome c oxidase from Rhodobacter sphaeroides is frequently used to model the more complex mitochondrial enzyme. The O(2) reduction in both enzymes is generally described by a unidirectional mechanism involving the sequential formation of the ferrous-oxy complex (compound A), the P(R) state, the oxyferryl F form, and the oxidized state. In this study we investigated the reaction of dioxygen with the wild-type reduced R. sphaeroides cytochrome oxidase and the EQ(I-286) mutant using the CO flow-flash technique. Singular value decomposition and multiexponential fitting of the time-resolved optical absorption difference spectra showed that three apparent lifetimes, 18 ?s, 53 ?s, and 1.3 ms, are sufficient to fit the kinetics of the O(2) reaction of the wild-type enzyme. A comparison of the experimental intermediate spectra with the corresponding intermediate spectra of the bovine enzyme revealed that P(R) is not present in the reaction mechanism of the wild-type R. sphaeroides aa(3). Transient absorbance changes at 440 and 610 nm support this conclusion. For the EQ(I-286) mutant, in which a key glutamic residue in the D proton pathway is replaced by glutamine, two lifetimes, 16 and 108 ?s, were observed. A spectral analysis of the intermediates shows that the O(2) reaction in the EQ(I-286) mutant terminates at the P(R) state, with 70% of heme a becoming oxidized. These results indicate significant differences in the kinetics of O(2) reduction between the bovine and wild-type R. sphaeroides aa(3) oxidases, which may arise from differences in the relative rates of internal electron and proton movements in the two enzymes. PMID:23057757

  8. Food Allergy Disclaimer UMD Dining makes every attempt to identify ingredients that may cause reactions in people with food

    E-print Network

    Hill, Wendell T.

    Food Allergy Disclaimer UMD Dining makes every attempt to identify ingredients that may cause reactions in people with food allergies. We make every effort to instruct our food production staff on the severity of food allergies. In addition we label items with possible allergencontaining ingredients

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

    PubMed Central

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

    1991-01-01

    The types of reactive intermediates generated upon reduction of chromium(VI) by glutathione or hydrogen peroxide and the resulting DNA damage have been determined. In vitro, reaction of chromium(VI) with glutathione led to formation of two chromium(V) complexes and the glutathione thiyl radical. When chromium(VI) was reacted with DNA in the presence of glutathione, chromium-DNA adducts were obtained, with no DNA strand breakage. The level of chromium-DNA adduct formation correlated with chromium(V) formation. Reaction of chromium(VI) with hydrogen peroxide led to formation of hydroxyl radical. No chromium(V) was detectable at 24 degrees C (297 K); however, low levels of the tetraperoxochromium(V) complex were detected at 77 K. Reaction of chromium(VI) with DNA in the presence of hydrogen peroxide produced significant DNA strand breakage and the 8-hydroxydeoxyguanosine adduct, whose formation correlated with hydroxyl radical production. No significant chromium-DNA adduct formation was detected. Thus, the nature of chromium(VI)-induced DNA damage appears to be dependent on the reactive intermediates, i.e. chromium(V) or hydroxyl radical, produced during the reduction of chromium(VI). PMID:1657590

  10. Unimolecular decomposition of chemically activated pentatetraene (H2CCCCCH2) intermediates: A crossed beams study of dicarbon molecule reactions with allene.

    PubMed

    Guo, Ying; Gu, Xibin; Zhang, Fangtong; Mebel, Alexander M; Kaiser, Ralf I

    2006-09-21

    The reactions dynamics of the dicarbon molecule C2 in the 1Sigma (g)+ singlet ground state and 3Pi(u) first excited triplet state with allene, H2CCCH2(X1A1), was investigated under single collision conditions using the crossed molecular beam approach at four collision energies between 13.6 and 49.4 kJ mol(-1). The experiments were combined with ab initio electronic structure calculations of the relevant stationary points on the singlet and triplet potential energy surfaces. Our investigations imply that the reactions are barrier-less and indirect on both the singlet and the triplet surfaces and proceed through bound C5H4 intermediates via addition of the dicarbon molecule to the carbon-carbon double bond (singlet surface) and to the terminal as well as central carbon atoms of the allene molecule (triplet surface). The initial collision complexes isomerize to form triplet and singlet pentatetraene intermediates (H2CCCCCH2) that decompose via atomic hydrogen loss to yield the 2,4-pentadiynyl-1 radical, HCCCCCH2(X2B1). These channels result in symmetric center-of-mass angular distributions. On the triplet surface, a second channel involves the existence of a nonsymmetric reaction intermediate (HCCCH2CCH) that fragments through atomic hydrogen emission to the 1,4-pentadiynyl-3 radical [C5H3(X2B1)HCCCHCCH]; this pathway was found to account for the backward scattered center-of-mass angular distributions at higher collision energies. The identification of two resonance-stabilized free C5H3 radicals (i.e., 2,4-pentadiynyl-1 and 1,4-pentadiynyl-3) suggests that these molecules can be important transient species in combustion flames and in the chemical evolution of the interstellar medium. PMID:16970359

  11. 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 ?-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.

  12. Organic Chemistry Jasperse Acid-Base Practice Problems A. Identify each chemical as either an "acid" or a "base" in the following reactions, and

    E-print Network

    Jasperse, Craig P.

    " or a "base" in the following reactions, and identify "conjugate" relationships. -You should have one acid?) 27. 28. G. For the following acid-base reaction, a. put a box around the weakest base in the reactionOrganic Chemistry Jasperse Acid-Base Practice Problems A. Identify each chemical as either an "acid

  13. Complete and incomplete fusion competition in 11B-induced fission reaction on medium mass targets at intermediate energies

    E-print Network

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

    2014-12-22

    The cross sections for the binary fission of 197Au, 181Ta and 209Bi targets induced by 11B ions were measured at intermediate energies. The fission products cross sections were studied by means of activation analysis in off-line regime observed gamma-ray spectra. The fission cross section is reconstructed on the basis of charge and mass distribution of the fission products.

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

    PubMed Central

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

    2011-01-01

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

  15. Conserved YjgF Protein Family Deaminates Reactive Enamine/Imine Intermediates of Pyridoxal 5?-Phosphate (PLP)-dependent Enzyme Reactions*

    PubMed Central

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

    2012-01-01

    The YjgF/YER057c/UK114 family of proteins is conserved in all domains of life, suggesting that the role of these proteins arose early and was maintained throughout evolution. Metabolic consequences of lacking this protein in Salmonella enterica and other organisms have been described, but the biochemical function of YjgF remained unknown. This work provides the first description of a conserved biochemical activity for the YjgF protein family. Our data support the conclusion that YjgF proteins have enamine/imine deaminase activity and accelerate the release of ammonia from reactive enamine/imine intermediates of the pyridoxal 5?-phosphate-dependent threonine dehydratase (IlvA). Results from structure-guided mutagenesis experiments suggest that YjgF lacks a catalytic residue and that it facilitates ammonia release by positioning a critical water molecule in the active site. YjgF is renamed RidA (reactive intermediate/imine deaminase A) to reflect the conserved activity of the protein family described here. This study, combined with previous physiological studies on yjgF mutants, suggests that intermediates of pyridoxal 5?-phosphate-mediated reactions may have metabolic consequences in vivo that were previously unappreciated. The conservation of the RidA/YjgF family suggests that reactive enamine/imine metabolites are of concern to all organisms. PMID:22094463

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

    PubMed

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

    2014-12-01

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

  17. Polymerase chain reaction primers to identify Trichinella spiralis or T. pseudospiralis

    Microsoft Academic Search

    Zhiliang Wu; Isao Nagano; Souji Fukumoto; Susumu Saito; Tomio Yamaguchi; Edoardo Pozio; Yuzo Takahashi

    1997-01-01

    Three sets of polymerase chain reaction (PCR) primers for Trichinella isolates were constructed by the following method. Random amplified polymorphic DNA (RAPD) of the corresponding isolates was produced and several fragments were sequenced. Primer sets SB4-2 and SB4-4 were designed from the resulting sequence that could amplify exclusively DNA from T. spiralis. These primers produced extra fragments in addition to

  18. Selective monoterpene-like cyclization reactions achieved by water exclusion from reactive intermediates in a supramolecular catalyst.

    PubMed

    Hart-Cooper, William M; Clary, Kristen N; Toste, F Dean; Bergman, Robert G; Raymond, Kenneth N

    2012-10-31

    A polyanionic supramolecular assembly (1) is shown to catalytically cyclize the monoterpene citronellal and two homologues. In contrast to cyclization in acidic aqueous solution, the hydrophobic interior of 1 prevents the capture of reactive intermediates by water. This effect was also observed in the gold-catalyzed cycloisomerization of an enyne. Due to the steric confinement of the catalyst's interior, Prins cyclizations in 1 proceed cleanly both for substrates containing and lacking gem-dimethyl substitution. Encapsulation in 1 consequently imposes a degree of mechanistic control that, similar to enzyme catalysis, is not observed in bulk aqueous solution. PMID:23066637

  19. Delayed hemolytic transfusion reaction with multiple alloantibody (Anti S, N, K) and a monospecific autoanti-JKb in intermediate ?-thalassemia patient in Tabriz

    PubMed Central

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

    2013-01-01

    It appears that delayed hemolytic transfusion reactions may occur several days after the administration of donor red cells is true even though they have been shown to be compatible in cross match tests by the antiglobulin technique. A specific case was observed in our center, which confirms the fact. The patient was a 37-year-old male suffering from intermediate ?-thalassemia. He had a history of two previous transfusions, with unknown transfusion reaction. In the last transfusion, laboratory data showed: Hb 7.8 g/dL and Hematocrit (Hct) 24.2%. The patient received two units of cross matched, compatible concentrated red blood cells (RBCs). After eight days a severe reaction was observed with clinical evidence of tachycardia, fatigue, fever, back pain, chest discomfort, jaundice, nausea and anorexia. Accordingly delayed hemolytic transfusion reaction was suspected, and anti-RBC antibodies were tested. Laboratory tests revealed the presence of three alloantibodies: Anti-N, anti-S, anti-K, and a monospecific autoanti-JKb. PMID:24014947

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

    PubMed

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

    2013-07-01

    It appears that delayed hemolytic transfusion reactions may occur several days after the administration of donor red cells is true even though they have been shown to be compatible in cross match tests by the antiglobulin technique. A specific case was observed in our center, which confirms the fact. The patient was a 37-year-old male suffering from intermediate ?-thalassemia. He had a history of two previous transfusions, with unknown transfusion reaction. In the last transfusion, laboratory data showed: Hb 7.8 g/dL and Hematocrit (Hct) 24.2%. The patient received two units of cross matched, compatible concentrated red blood cells (RBCs). After eight days a severe reaction was observed with clinical evidence of tachycardia, fatigue, fever, back pain, chest discomfort, jaundice, nausea and anorexia. Accordingly delayed hemolytic transfusion reaction was suspected, and anti-RBC antibodies were tested. Laboratory tests revealed the presence of three alloantibodies: Anti-N, anti-S, anti-K, and a monospecific autoanti-JK(b). PMID:24014947

  1. Human immunodeficiency virus-1 protease. 1. Initial velocity studies and kinetic characterization of reaction intermediates by sup 18 O isotope exchange

    SciTech Connect

    Hyland, L.J.; Tomaszek, T.A. Jr.; Roberts, G.D.; Carr, S.A.; Magaard, V.W.; Bryan, H.L.; Fakhoury, S.A.; Moore, M.L.; Minnich, M.D.; Culp, J.S.; DesJarlais, R.L.; Meek, T.D. (Smline Beecham Pharmaceuticals, King of Prussia, PA (United States))

    1991-08-27

    The peptidolytic reaction HIV-1 protease has been investigated by using four oligopeptide substrates, Ac-Ser-Gln-Asn-Pro-Val-Val-NH{sub 2}, Ac-Arg-Ala-Ser-Gln-Asn-Tyr-Pro-Val-Val-NH{sub 2}, Ac-Ser-Gln-Ser-Tyr-Pro-Val-Val-NH{sub 2}, and Ac-Arg-Lys-Ile-Leu-Phe-Leu-Asp-Gly-NH{sub 2} that resemble two cleavage sites found within the naturally occurring polyprotein substrates Pr55{sup gag} and Pr160{sup gag-pol}. By use of a variety of inorganic salts, it was concluded that the peptidolytic reaction is nonspecifically activated by increasing ionic strength. V/K increased in an apparently parabolic fashion with increasing ionic strength, while V was either increased or decreased slightly. From product inhibition studies, the kinetic mechanism of the protease is either random or ordered uni-bi, depending on the substrate studied. The protease-catalyzed exchange of an atom of {sup 18}O from H{sub 2}{sup 18}O into the re-formed substrates occurred at a rate which was 0.01-0.12 times that the forward peptidolytic reaction. The results of these studies are in accord with the formation of a kinetically competent enzyme-bound amide hydrate intermediate, the collapse of which is the rate-limiting chemical step in the reaction pathway.

  2. Mechanistic Studies on the Reaction of Nitrocobalamin with Glutathione: Kinetic evidence for formation of an aquacobalamin intermediate.

    PubMed

    Walker, David T; Dassanayake, Rohan S; Garcia, Kamille A; Mukherjee, Riya; Brasch, Nicola E

    2013-06-01

    The essential but also toxic gaseous signaling molecule nitric oxide is scavenged by the reduced vitamin B12 complex cob(II)alamin. The resulting complex, nitroxylcobalamin (NO(-)-Cbl(III)), is rapidly oxidized to nitrocobalamin (NO2Cbl) in the presence of oxygen; however it is unlikely that nitrocobalamin is itself stable in biological systems. Kinetic studies on the reaction between NO2Cbl and the important intracellular antioxidant, glutathione (GSH), are reported. In this study, a reaction pathway is proposed in which the ?-axial ligand of NO2Cbl is first substituted by water to give aquacobalamin (H2OCbl(+)), which then reacts further with GSH to form glutathionylcobalamin (GSCbl). Independent measurements of the four associated rate constants k1, k-1, k2, and k-2 support the proposed mechanism. These findings provide insight into the fundamental mechanism of ligand substitution reactions of cob(III)alamins with inorganic ligands at the ?-axial site. PMID:24415907

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  4. 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 ? 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

  5. Identifying adverse drug reactions and drug-induced diseases using network-based drug mapping.

    PubMed

    Shoshi, Alban; Ogultarhan, Venus; Hoppe, Tobias; Kormeier, Benjamin; Müller, Ulrich; Hofestädt, Ralf

    2015-02-01

    Drugs are essential for the prevention and treatment of diseases. However, co-administration of multiple drugs may cause serious adverse drug reactions, which are usually known but sometimes unknown. Package inserts of prescription drugs are supposed to contain risks and side effects, but such information is not necessarily complete. At the core of efforts to improve prescription quality, there is reliance on the extent and quality of information used for decision of a medical doctor. To address this on-going need, GraphSAW provides users a comprehensive view on drug-related pharmacological and molecular information. The features of GraphSAW allow users to analyze drug cocktails for adverse drug reactions and drug-induced diseases. Network visualization by drug mapping enables exploring associative networks of drugs, pathways, and diseases to fully understand effects of drugs in an intuitive way. GraphSAW is meant to be a platform and starting point for health professionals and researchers for educational and scientific research in order to achieve substantial improvements in patient safety. PMID:25666653

  6. arXiv:nuclth/0406078 Identifying neutrinos and antineutrinos in neutral-current scattering reactions

    E-print Network

    Gent, Universiteit

    arXiv:nucl­th/0406078 v1 26 Jun 2004 Identifying neutrinos and antineutrinos in neutral study neutrino-induced nucleon knockout from nuclei. Expressions for the induced polarization approximation. Large dissimilarities in the nucleon polarization asymmetries are observed between neutrino

  7. Polymerase chain reaction method to identify Down syndrome model segmentally trisomic mice

    Microsoft Academic Search

    Narayan Ramakrishna; Clifford Meeker; Shuyun Li; Edmund C. Jenkins; Julia R. Currie; Michael Flory; Beena Lee; Ming S. Liu; David L. Miller

    2005-01-01

    The Ts65Dn segmentally trisomic mouse possesses an extra copy of a segment of chromosome 16 translocated to chromosome 17. This segment includes the mouse homolog of the Down syndrome critical region of human chromosome 21. The Ts65Dn mouse serves as a useful model to study the developmental regulation of the Down syndrome phenotype. To identify mice bearing the extra chromosome

  8. 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

    2014-07-01

    The degradation of 230 mL of a 0.6-mM sulfanilamide solution in 0.05 M Na?SO? 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 H?O?. 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. NH?(+), NO?(-), and SO?(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

  9. Isobaric yield ratios in heavy-ion reactions, and symmetry energy of neutron-rich nuclei at intermediate energies

    NASA Astrophysics Data System (ADS)

    Ma, Chun-Wang; Wang, Fang; Ma, Yu-Gang; Jin, Chan

    2011-06-01

    The isobaric yield ratios of the fragments produced in the neutron-rich Ca48 and Ni64 projectile fragmentation are analyzed in the framework of a modified Fisher model. The correlations between the isobaric yield ratios (R) and the energy coefficients in the Weiszäcker-Beth semiclassical mass formula (the symmetry-energy term asym, the Coulomb-energy term ac, and the pairing-energy term ap) and the difference between the chemical potentials of the neutron and proton (?n-?p) are investigated. Simple correlations between (?n-?p)/T, ac/T, asym/T, and ap/T (where T is the temperature), and lnR are obtained. It is suggested that (?n-?p)/T, ac/T, asym/T, and ap/T of neutron-rich nuclei can be extracted using isobaric yield ratios for heavy-ion collisions at intermediate energies.

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

    NASA Astrophysics Data System (ADS)

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

    2007-05-01

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

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

    E-print Network

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

    2007-03-05

    We test the effect of proton-capture reaction rate uncertainties on the abundances of the Ne, Na, Mg and Al isotopes processed by the NeNa and MgAl chains during hot bottom burning (HBB) in asymptotic giant branch (AGB) stars of intermediate mass between 4 and 6 solar masses and metallicities between Z=0.0001 and 0.02. We provide uncertainty ranges for the AGB stellar yields, for inclusion in galactic chemical evolution models, and indicate which reaction rates are most important and should be better determined. We use a fast synthetic algorithm based on detailed AGB models. We run a large number of stellar models, varying one reaction per time for a very fine grid of values, as well as all reactions simultaneously. We show that there are uncertainties in the yields of all the Ne, Na, Mg and Al isotopes due to uncertain proton-capture reaction rates. The most uncertain yields are those of 26Al and 23Na (variations of two orders of magnitude), 24Mg and 27Al (variations of more than one order of magnitude), 20Ne and 22Ne (variations between factors 2 and 7). In order to obtain more reliable Ne, Na, Mg and Al yields from IM-AGB stars the rates that require more accurate determination are: 22Ne(p,g)23Na, 23Na(p,g)24Mg, 25Mg(p,g)26Al, 26Mg(p,g)27Al and 26Al(p,g)27Si. Detailed galactic chemical evolution models should be constructed to address the impact of our uncertainty ranges on the observational constraints related to HBB nucleosynthesis, such as globular cluster chemical anomalies.

  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. Multiple intermediates, diverse conformations, and cooperative conformational changes underlie the catalytic hydride transfer reaction of dihydrofolate reductase

    PubMed Central

    Arora, Karunesh; Brooks, Charles L.

    2015-01-01

    It has become increasingly clear that protein motions play an essential role in enzyme catalysis. However, how exactly these motions are related to an enzyme’s chemical step is still intensely debated. This chapter examines the possible role of protein motions that display a hierarchy of timescales in enzyme catalysis. The linkage between protein motions and catalysis is investigated in the context of a model enzyme, E. coli dihydrofolate reductase (DHFR) that catalyzes the hydride transfer reaction in the conversion of dihydrofolate to tetrahydrofolate. The results of extensive computer simulations probing the protein motions that are manifest during different steps along the turnover cycle of DHFR are summarized. Evidence is presented that the protein motions modulate the catalytic efficacy of DHFR by generating a conformational ensemble conducive to the hydride transfer. The alteration of the equilibrium conformational ensemble rather than any protein dynamical effects is found to be sufficient to explain the rate-diminishing effects of mutation on the kinetics of the enzyme. These data support the view that the protein motions facilitate catalysis by establishing reaction competent conformations of the enzyme, but they do not directly couple to the chemical reaction itself. These findings have broad implications for our understanding of enzyme mechanisms and the design of novel protein catalysts. PMID:23420416

  14. Organic Chemistry Jasperse Acid-Base Practice Problems A. Identify each chemical as either an "acid" or a "base" in the following reactions, and

    E-print Network

    Jasperse, Craig P.

    " or a "base" in the following reactions, and identify "conjugate" relationships. -You should have one acid whether equilibrium favors products or reactants. (Why?) 27. 28. G. For the following acid-base reaction, a. put a box around the weakest base in the reaction b. put a circle around the weakest acid c. draw

  15. The mechanism of the reaction CH(X 2?) + N 2 (X 1? +g) ? HCN (X 1? +) + N ( 4S). . II. The intermediate complex region

    NASA Astrophysics Data System (ADS)

    Riad Manaa, M.; Yarkony, David R.

    1992-01-01

    The spin-forbidden reaction CH(X 2?) + N 2(X 1? +g) ? HCN (X 1? +) + N( 4S) involves a doublet ? quartet intersystem crossing. It has been postulated that although the probability for a single pass intersystem crossing is small the existence of a bound intermediate on the lowest doublet potential energy surface increases the overall transition probability by enabling multiple crossings of the doublet—quartet surface intersection. This work considers this proposition, using large scale ((3.2 - 3.8) × 10 6 term), multireference configuration interaction wavefunctions. Two local minima on the lowest doublet potential energy surface are reported, a datively bonded structure N 2 ? CH, and a C 2v structure, with HC along the perpendicular bisector of the N 2 bond, which resembles the recently reported geometrical arrangement at the transition state for this reaction, the minimum energy point on doublet—quartet intersection surface. These results enable a clear conceptual picture for the mechanism of this reaction to be presented.

  16. 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

  17. A new class of modular P,N-ligand library for asymmetric Pd-catalyzed allylic substitution reactions: a study of the key Pd-pi-allyl intermediates.

    PubMed

    Mazuela, Javier; Paptchikhine, Alexander; Tolstoy, Päivi; Pàmies, Oscar; Diéguez, Montserrat; Andersson, Pher G

    2010-01-11

    A new class of modular P,N-ligand library has been synthesized and screened in the Pd-catalyzed allylic substitution reactions of several substrate types. These series of ligands can be prepared efficiently from easily accessible hydroxyl-oxazole/thiazole derivatives. Their modular nature enables the bridge length, the substituents at the heterocyclic ring and in the alkyl backbone chain, the configuration of the ligand backbone, and the substituents/configurations in the biaryl phosphite moiety to be easily and systematically varied. By carefully selecting the ligand components, therefore, high regio- and enantioselectivities (ee values up to 96 %) and good activities are achieved in a broad range of mono-, di-, and trisubstituted linear hindered and unhindered substrates and cyclic substrates. The NMR spectroscopic and DFT studies on the Pd-pi-allyl intermediates provide a deeper understanding of the effect of ligand parameters on the origin of enantioselectivity. PMID:19937621

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

    NASA Astrophysics Data System (ADS)

    Scire, James J., Jr.

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

  19. 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.

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

    DOEpatents

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

    1997-01-01

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

  1. Stabilization and Characterization of a Heme-Oxy Reaction Intermediate in Inducible Nitric-oxide Synthase*S?

    PubMed Central

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

    2008-01-01

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

  2. Identifiers Identifiers

    E-print Network

    Brass, Stefan

    , July 1998. . Tim Berners­Lee: Cool URIs don't change. [http://www.w3.org/Provider/Style/URI] Stefan://archive.ncsa.uiuc.edu/demoweb/url­primer.html] . T. Berners­Lee, R. Fielding, L. Masinter: Uniform Resource Identifiers (URI): Generic Syntax. RFC Names. RFC 1737, December 1994, 7 pages. . T. Berners­Lee, L. Masinter, M. McCahill: Uniform Resource

  3. Identifiers Identifiers

    E-print Network

    Brass, Stefan

    , July 1998. . Tim Berners­Lee: Cool URIs don't change. [http://www.w3.org/Provider/Style/URI] . Uniform://archive.ncsa.uiuc.edu/demoweb/url­primer.html] . T. Berners­Lee, R. Fielding, L. Masinter: Uniform Resource Identifiers (URI): Generic Syntax. RFC Names. RFC 1737, December 1994, 7 pages. . T. Berners­Lee, L. Masinter, M. McCahill: Uniform Resource

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

    PubMed Central

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

    2013-01-01

    Transition-metal peroxos have been implicated as key intermediates in a variety of critical biological processes involving O2. Due to their highly reactive nature, very few metal-peroxos have been characterized. The dioxygen chemistry of manganese remains largely unexplored despite the proposed involvement of a binuclear Mn-peroxo, either as a precursor to O2, or derived from O2, in both photosynthetic H2O oxidation and DNA biosynthesis, arguably two of the most fundamental processes of life. Neither of these biological intermediates has been observed. Herein we describe the dioxygen chemistry of coordinatively unsaturated [MnII(SMe2N4(6-MeDPEN))] +(1), and the characterization of intermediates formed en route to a binuclear mono-oxo bridged Mn(III) product {[MnIII(SMe2N4(6-MeDPEN)]2-(?-O)}2+ (2), the oxo atom of which is derived from 18O2. At low-temperatures, a dioxygen intermediate, [Mn(SMe2N4(6-MeDPEN))(O2)]+ (4), is observed (by stopped-flow) to rapidly and irreversibly form in this reaction (k1(?10 °C)= 3780±180M?1s?1, ?H1‡ = 26.4±1.7 kJ mol?1, ?S1‡ = ? 75.6±6.8 J mol?1K?1), and then convert more slowly (k2(?10 °C)= 417±3.2 M?1s?1, ?H2‡ = 47.1±1.4 kJ mol?1, ?S2‡ = ? 15.0±5.7 J mol?1K?1) to a species 3 with isotopically sensitive stretches at ?o-o (?18O) = 819(47) cm?1, kO–O= 3.02 mdyn/Å, and ?Mn-O(?18O) = 611(25) cm?1 consistent with a peroxo. Intermediate 3 releases approximately 0.5 equiv of H2O2 per Mn ion upon protonation, and the rate of conversion of 4 to 3 is dependent on [Mn(II)] concentration, consistent with the formation of a binuclear Mn-peroxo. This was verified by X-ray crystallography, where the peroxo of {[MnIII(SMe2N4(6-Me-DPEN)]2(trans–?–1,2–O2)}2+ (3) is shown to be bridging between two Mn(III) ions in an end-on trans-?-1,2-fashion. This represents the first characterized example of a binuclear Mn(III)-peroxo, and a rare case in which more than one intermediate is observed en route to a binuclear ?–oxo bridged product derived from O2. Vibrational and metrical parameters for binuclear Mn-peroxo 3 are compared with those of related binuclear Fe- and Cu-peroxo compounds. PMID:23470101

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

  6. N-Phenylprotoporphyrin IX formation in the hemoglobin-phenylhydrazine reaction. Evidence for a protein-stabilized iron-phenyl intermediate.

    PubMed

    Augusto, O; Kunze, K L; Ortiz de Montellano, P R

    1982-06-10

    Hemoglobin-catalyzed phenylhydrazine oxidation, a model for Heinz-body hemolytic anemias, is known to result in hemoglobin degradation and erythrocyte lysis. The catalytic reaction is shown here to be terminated by inactivation of the prosthetic heme groups after each heme moiety catalyzes the consumption of 6 oxygen molecules and 6 phenylhydrazines, and the formation of 5 benzenes. The phenyl residue not converted to benzene is primarily found, after acidic methanol workup, covalently bound to a nitrogen of protoporphyrin IX. Analogous reactions are observed with substituted phenylhydrazines and, to a lesser degree due to their slower oxidation, with alkylhydrazines. Ortho-substituted phenylhydrazines, however, do not give the N-aryl heme derivatives even though they inactivate the hemoproteins. ESR spin-trapping experiments establish that all of the hydrazines are oxidized to carbon radicals. Direct evidence is provided for the formation of a globin-stabilized heme complex which terminates catalytic activity and which, depending on the conditions of protein denaturation, reverts to heme or is converted to the corresponding N-aryl heme derivative. The globin-stabilized intermediate appears to involve direct coordination of the aryl group through one of its carbon atoms with the prosthetic heme iron moiety. PMID:7076671

  7. Unimolecular dissociation of the propargyl radical intermediate of the CH +C2H2 and C +C2H3 reactions

    NASA Astrophysics Data System (ADS)

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

    2006-10-01

    This paper examines the unimolecular dissociation of propargyl (HCCCH2) radicals over a range of internal energies to probe the CH +HCCH and C +C2H3 bimolecular reactions from the radical intermediate to products. The propargyl radical was produced by 157nm photolysis of propargyl chloride in crossed laser-molecular beam scattering experiments. The H-loss and H2 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 H2+HCCC and H +C3H2 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.

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

    NASA Astrophysics Data System (ADS)

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

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

  9. MCNP{trademark} simulations for identifying environmental contaminants using prompt gamma-rays from thermal neutron capture reactions

    SciTech Connect

    Frankle, S.C.; Conaway, J.G.

    1996-12-31

    The primary purposes of the Multispectral Neutron Logging Project, (MSN Project, funded by the U.S. Department of Energy), were to assess the effectiveness of existing neutron- induced spectral gamma-ray logging techniques for identifying environmental contaminants along boreholes, to further improve the technology, and to transfer that technology to industry. Using a pulsed neutron source with a high-resolution gamma-ray detector, spectra from thermal neutron capture reactions may be used to identify contaminants in the borehole environment. Direct borehole measurements such as this complement physical sampling and are useful in environmental restoration projects where characterization of contaminated sites is required and long-term monitoring may be needed for many years following cleanup or stabilization. In the MSN Project, a prototype logging instrument was designed which incorporated a pulsed 14-MeV neutron source and HPGe detector. Experimental measurements to determine minimum detection thresholds with the prototype instrument were conducted in the variable-contaminant test model for Cl, Cd, Sm, Gd, and Hg. We benchmarked an enhanced version of the Monte Carlo N-Particle computer code MCNP{trademark} using experimental data for Cl provide by our collaborators and experimental data from the variable-contaminant test model. MCNP was then used to estimate detection thresholds for the other contaminants used in the variable-contaminant model with the goal of validating the use of MCNP to estimate detection thresholds for many other contaminants that were not measured.

  10. The Uncertainties in the 22Ne + alpha-capture Reaction Rates and the Production of the Heavy Magnesium Isotopes in Asymptotic Giant Branch Stars of Intermediate Mass

    E-print Network

    A. Karakas; M. Lugaro; M. Wiescher; J. Goerres; C. Ugalde

    2006-01-27

    We present new rates for the 22Ne(alpha, n)25Mg and 22Ne(alpha,gamma)26Mg reactions, with uncertainties that have been considerably reduced compared to previous estimates, and we study how these new rates affect the production of the heavy magnesium isotopes in models of intermediate mass Asymptotic Giant Branch (AGB) stars of different initial compositions. All the models have deep third dredge-up, hot bottom burning and mass loss. Calculations have been performed using the two most commonly used estimates of the 22Ne + alpha rates as well as the new recommended rates, and with combinations of their upper and lower limits. The main result of the present study is that with the new rates, uncertainties on the production of isotopes from Mg to P coming from the 22Ne + alpha-capture rates have been considerably reduced. We have therefore removed one of the important sources of uncertainty to effect models of AGB stars. We have studied the effects of varying the mass-loss rate on nucleosynthesis and discuss other uncertainties related to the physics employed in the computation of stellar structure, such as the modeling of convection, the inclusion of a partial mixing zone and the definition of convective borders. These uncertainties are found to be much larger than those coming from 22Ne + alpha-capture rates, when using our new estimates. Much effort is needed to improve the situation for AGB models.

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

    SciTech Connect

    Moure, Carmen M.; Gimble, Frederick S.; Quiocho, Florante A. (Baylor); (Purdue)

    2008-07-28

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

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

    PubMed

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

    2006-10-01

    Compound 1a (6-chloro-5-{3-[4-(1H-indazol-3-yl)-piperazin-1-yl]-propyl}-3,3-dimethyl-1,3-dihydro-indol-2-one) was mutagenic to Salmonella typhimurium TA98 in the presence of rat liver S9 subcellular fraction. The metabolism of 1a in rat liver S9 or microsomes demonstrated that it underwent a P450-mediated N-deindazolation (loss of indazole ring) as a predominant metabolic pathway. To investigate a possible link between metabolism and mutagenicity, a structural analogue 1b (6-chloro-5-{3-[4-(1H-indazol-3-yl)-piperidin-1-yl]-propyl}-3,3-dimethyl-1,3-dihydro-indol-2-one), the cleaved product 2a (6-chloro-3,3-dimethyl-5-(3-piperazin-1-yl-propyl)-1,3-dihydro-indol-2-one), and the core motif 3a (3-piperazinyl indazole) were evaluated in the Ames assay. It was found that 1b was not mutagenic to Salmonella typhimurium TA98 in the absence or presence of a metabolic activating system. In contrast to 1a, 1b did not undergo the metabolic cleavage (loss of indazole ring). Marginal mutagenicity of 2a to TA98 was observed with rat liver S9, whereas 3a was shown to be a promutagen. It was further demonstrated that 1a inactivated P450 3A, the principle enzyme catalyzing the N-deindazolation reaction, in an NADPH-, time-, and concentration-dependent manner. The kinetics of inactivation was characterized by a K(I) of 8.1 microM and k(inact) of 0.114 min(-1). The differences in mutagenicity between 1a and 1b suggest that a chemical bond extending from the 3-position of the indazole to a heteroatom (as part of another cyclic ring) is a prerequisite for the toxicity. The metabolic process leading to the elimination of the indazole from the rest of the molecule apparently plays a key role in causing mutagenicity. It is postulated that the N-deindazolation of 1a proceeds via an oxaziridine intermediate, the formation of which is indirectly inferred from the presence of benzoic acid in microsomal incubations. Benzoic acid is thought to be derived from the hydrolysis of 3-indazolone, an unstable product generated from the oxaziridine. Evidence suggests that the electrophilic oxaziridine intermediate may be responsible for the mutagenicity and inactivation of P450 3A. PMID:17040103

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

    PubMed

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

    2014-10-01

    Bacterial contamination of blood and its cellular components remains the most common microbiological cause of transfusion associated morbidity and mortality, even in developed countries. This yet unresolved complication is seen more often in platelet transfusions, as platelet concentrates are stored at room temperature, in gas permeable containers with constant agitation, which support bacterial proliferation from relatively low undetectable levels, at the beginning of storage time, to relatively high virulent bacteria titers and endotoxin generation, at the end of shelf life. Accordingly, several combined strategies are introduced and implemented to at least reduce the potential risk of bacterial contaminated products for transfusion. These embody: improved donors arms cleaning; bacterial avoidance by diversion of the first portion of collection; reducing bacterial growth through development of newer storage media for longer platelet shelf life; bacterial load reduction by leucoreduction/viral inactivation, in some countries and eliminating the use potentially contaminated units through screening, through current available testing procedures, though none are not yet fully secure. We have not seen the same reduction in bacterial associated transfusion infections as we have observed for the sharp drop in transfusion associated transmission rates of HIV and hepatitis B and C. This great viral reduction is not only caused by the introduction of newer and more sensitive and specific detection methods for different viruses, but also the identification of donor risk groups through questionnaires and personal interviews. While search for more efficient methods for identifying potential blood donors with asymptomatic bacteremia, as well as a better way for detecting bacteria in stored blood components will be continuing, it is necessary to establish more standardized guidelines for the recognition the adverse reactions in recipients of potentially contaminated units. Efforts also should be also directed to identify blood donors with significant risk of bacteremia, at the time of donation in the first place as a high priority. The goal of this review is to highlights strategies for identifying both the sources of bacterial contamination of blood components in Norway and identifying donors with a higher risk of bacteremia at the time of donation. The key to achieving this goal is initiating continual revising and upgrading the Norwegian transfusion guidelines, based on the transfusion legislation and by introducing a relevant specialized donor bacterial questionnaire. PMID:25242310

  14. Isoporphyrin Intermediate in Heme Oxygenase Catalysis

    PubMed Central

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

    2008-01-01

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

  15. reactions

    Microsoft Academic Search

    S. Reinker; R. M. Altman; J. Timmer

    Gene regulatory, signal transduction and metabolic networks are major areas of interest in the newly emerging field of systems biology. In living cells, stochastic dynamics play an important role; however, the kinetic parameters of biochemical reactions necessary for modelling these processes are often not accessible directly through experiments. The problem of estimating stochastic reaction constants from molecule count data measured,

  16. 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

    2015-01-28

    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 ±2? 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

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

    SciTech Connect

    Reineri, F.; Aime, S. [Department of Molecular Biotechnologies and Health Sciences, University of Torino, Via Nizza 52, 10123 Torino (Italy)] [Department of Molecular Biotechnologies and Health Sciences, University of Torino, Via Nizza 52, 10123 Torino (Italy); Gobetto, R.; Nervi, C. [Department of Chemistry, University of Torino, via P. Giuria 7, 10125 Torino (Italy)] [Department of Chemistry, University of Torino, via P. Giuria 7, 10125 Torino (Italy)

    2014-03-07

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  19. Follicular fluid-induced acrosome reaction distinguishes a subgroup of men with unexplained infertility not identified by semen analysis.

    PubMed

    Calvo, L; Vantman, D; Banks, S M; Tezon, J; Koukoulis, G N; Dennison, L; Sherins, R J

    1989-12-01

    We compared the ability of sperm to undergo follicular fluid-induced acrosome reaction in vitro in fertile men and patients with unexplained infertility. After capacitation under optimum conditions, 28% of sperm from fertile men undergo acrosome reaction after follicular fluid exposure, whereas only 7% of the cells react spontaneously. In 15 men with unexplained infertility, 6 patients showed lack of acrosome reaction, whereas 9 men had sperm acrosome reactions similar to that of fertile men. However, in this cohort under study, semen characteristics of AR(+) and AR(-) patients were similar. In addition to inducing sperm acrosome reaction, follicular fluid also promoted significant changes in motion characteristics of capacitated sperm. Sperm curvilinear velocity (Vc) increased significantly after exposure to follicular fluid though linearity remained unchanged. The largest difference in cumulative Vc occurred at 90 microns/s. Assessing the ability of capacitated sperm to acrosome react may have clinical significance in predicting whether such sperm are capable of fertilizing an ovum. PMID:2591562

  20. Intermediate Bengali.

    ERIC Educational Resources Information Center

    Seely, Clinton B.

    A text for intermediate Bengali contains 19 lessons emphasizing grammatical forms and constructions, with some information about the content of personal interactions and information for daily living. Much of the text is in Bengali orthography; bilingual glossaries are appended. (MSE)

  1. ENDOR/HYSCORE Studies of the Common Intermediate Trapped During Nitrogenase Reduction of N2H2, CH3N2H, and N2H4 Support an Alternating Reaction Pathway for N2 Reduction

    PubMed Central

    Lukoyanov, Dmitriy; Dikanov, Sergei A.; Yang, Zhi-Yong; Barney, Brett M.; Samoilova, Rimma I.; Narasimhulu, Kuppala V.; Dean, Dennis R.; Seefeldt, Lance C.; Hoffman, Brian M.

    2011-01-01

    Enzymatic N2 reduction proceeds along a reaction pathway comprised of a sequence of intermediate states generated as a dinitrogen bound to the active-site iron-molybdenum cofactor (FeMo-co) of the nitrogenase MoFe protein undergoes six steps of hydrogenation (e?/H+ delivery). There are two competing proposals for the reaction pathway, and they invoke different intermediates. In the ‘Distal’ (D) pathway, a single N of N2 is hydrogenated in three steps until the first NH3 is liberated, then the remaining nitrido-N is hydrogenated three more times to yield the second NH3. In the ‘Alternating’ (A) pathway, the two N’s instead are hydrogenated alternately, with a hydrazine-bound intermediate formed after four steps of hydrogenation and the first NH3 liberated only during the fifth step. A recent combination of X/Q-band EPR and 15N, 1,2H ENDOR measurements suggested that states trapped during turnover of the ?-70Ala/?-195Gln MoFe protein with diazene or hydrazine as substrate correspond to a common intermediate (here denoted I) in which FeMo-co binds a substrate-derived [NxHy] moiety, and measurements reported here show that turnover with methyldiazene generates the same intermediate. In the present report we describe X/Q-band EPR and 14/15N, 1,2H ENDOR/-HYSCORE/ESEEM measurements that characterize the N-atom(s) and proton(s) associated with this moiety. The experiments establish that turnover with N2H2, CH3N2H, and N2H4 in fact generates a common intermediate, I, and show that the N-N bond of substrate has been cleaved in I. Analysis of this finding leads us to conclude that nitrogenase reduces N2H2, CH3N2H, and N2H4 via a common A reaction pathway, and that the same is true for N2 itself, with Fe ion(s) providing the site of reaction. PMID:21744838

  2. Use of the Ligase Detection Reaction-Polymerase Chain Reaction to Identify Point Mutations in Extended-Spectrum Beta-Lactamases

    Microsoft Academic Search

    C. Niederhauser; L. Kaempf; I. Heinzer

    2000-01-01

    The aim of this study was to detect point mutations in extended-spectrum ?-lactamase (ESBL) genes in a background of wild-type\\u000a (non-ESBL-producing) bacteria using a highly sensitive and specific method developed for this purpose. The ligase detection\\u000a reaction-polymerase chain reaction (LDR-PCR) method was used to test different ESBL-producing strains and clinical isolates\\u000a for a specific point mutation in the bla SHV-ESBL

  3. An efficient synthesis of anhydrides of 2-monosubstituted succinic acid monoesters and their application to the Dakin–West reaction: Isolation of some 5-succinyloxyoxazole intermediates

    Microsoft Academic Search

    Joseph Richard Casimir; Laurent Ettouati; Joëlle Paris

    1998-01-01

    A rapid and versatile synthesis of 2-monosubstituted monosuccinates and their bimolecular anhydrides is described. The reaction of these anhydrides with N-Fmoc-protected dipeptides under the modified Dakin–West reaction affords mainly the corresponding 5-succinyloxyoxazoles.

  4. An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis.

    PubMed

    Deery, Evelyne; Schroeder, Susanne; Lawrence, Andrew D; Taylor, Samantha L; Seyedarabi, Arefeh; Waterman, Jitka; Wilson, Keith S; Brown, David; Geeves, Michael A; Howard, Mark J; Pickersgill, Richard W; Warren, Martin J

    2012-11-01

    The biosynthesis of many vitamins and coenzymes has often proven difficult to elucidate owing to a combination of low abundance and kinetic lability of the pathway intermediates. Through a serial reconstruction of the cobalamin (vitamin B(12)) pathway in Escherichia coli and by His tagging the terminal enzyme in the reaction sequence, we have observed that many unstable intermediates can be isolated as tightly bound enzyme-product complexes. Together, these approaches have been used to extract intermediates between precorrin-4 and hydrogenobyrinic acid in their free acid form and permitted the delineation of the overall reaction catalyzed by CobL, including the formal elucidation of precorrin-7 as a metabolite. Furthermore, a substrate-carrier protein, CobE, that can also be used to stabilize some of the transient metabolic intermediates and enhance their onward transformation, has been identified. The tight association of pathway intermediates with enzymes provides evidence for a form of metabolite channeling. PMID:23042036

  5. An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis

    PubMed Central

    Deery, Evelyne; Schroeder, Susanne; Lawrence, Andrew D.; Taylor, Samantha L.; Seyedarabi, Arefeh; Waterman, Jitka; Wilson, Keith S.; Brown, David; Geeves, Michael A.; Howard, Mark J.; Pickersgill, Richard W.; Warren, Martin J.

    2012-01-01

    The biosynthesis of many vitamins and coenzymes has often proved difficult to elucidate due to a combination of low abundance and kinetic lability of the pathway intermediates. Through a serial reconstruction of the cobalamin (vitamin B12) pathway in E. coli, and by His-tagging the terminal enzyme in the reaction sequence, we have observed that many unstable intermediates can be isolated as tightly-bound enzyme-product complexes. Together, these approaches have been used to extract intermediates between precorrin-4 and hydrogenobyrinic acid in their free acid form and permitted the delineation of the overall reaction catalysed by CobL, including the formal elucidation of precorrin-7 as a metabolite. Furthermore, a substrate-carrier protein, CobE, has been identified, which can also be used to stabilize some of the transient metabolic intermediates and enhance their onward transformation. The tight association of pathway intermediates with enzymes provides evidence for a form of metabolite channeling. PMID:23042036

  6. PAH intermediates: Links between the atmosphere and biological systems.

    PubMed

    Simonich, Staci L Massey; Motorykin, Oleksii; Jariyasopit, Narumol

    2011-06-30

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

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

    SciTech Connect

    Lin, Z. K.; Han, D. L.; Li, S. F. [Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Li, Y. Y.; Yuan, T. [National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029 (China)

    2009-04-21

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

  8. Selective syntheses of leuconolam, leuconoxine, and mersicarpine alkaloids from a common intermediate through regiocontrolled cyclizations by Staudinger reactions† †Electronic supplementary information (ESI) available: Experimental details and procedures, compound characterization data, copies of 1H and 13C NMR spectra for new compounds. See DOI: 10.1039/c4qo00312h Click here for additional data file.

    PubMed Central

    Li, Zining; Geng, Qian; Lv, Zhe; Pritchett, Beau P.; Baba, Katsuaki; Numajiri, Yoshitaka

    2015-01-01

    Selective syntheses of leuconolam, leuconoxine, and mersicarpine alkaloids bearing distinctive core structures were achieved through Staudinger reactions using a common intermediate. In the key cyclization step, water functioned like a switch to control which core structure to produce. The chemistry allowed for selective syntheses of the group of alkaloids from a simple intermediate through straightforward chemical operations. PMID:25717379

  9. 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

  10. Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily.

    PubMed

    Wise, Eric L; Yew, Wen Shan; Gerlt, John A; Rayment, Ivan

    2003-10-28

    3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and orotidine 5'-phosphate decarboxylase (OMPDC) are members of an enzyme suprafamily, the OMPDC suprafamily, because they are homologous enzymes that catalyze mechanistically distinct reactions using different substrates. KGPDC catalyzes the Mg(2+) ion-dependent decarboxylation of 3-keto-L-gulonate 6-phosphate to yield L-xylulose 5-phosphate and CO(2); OMPDC catalyzes the metal ion-independent decarboxylation of OMP to UMP and CO(2). Structural studies have shown that KGPDC and OMPDC share several strictly conserved active site residues that are used differently by each enzyme to catalyze their mechanistically distinct reactions. Although the mechanism of the KGPDC-catalyzed reaction has yet to be elucidated, it is thought to proceed via a Mg(2+) ion-stabilized 1,2-enediolate intermediate. Here we report the crystal structures of KGPDC complexed with L-gulonate 6-phosphate, L-threonohydroxamate 4-phosphate, and L-xylitol 5-phosphate, analogues of the substrate, enediolate intermediate, and product, as well as with the product, L-xylulose 5-phosphate, at 1.2, 1.8, 1.7, and 1.8 A resolution, respectively. These structures support a mechanism that involves the formation of a cis-1,2-enediolate intermediate. Contrary to expectations, the geometry of the intermediate does not involve bidentate coordination of both enediolate oxygen atoms to the Mg(2+) ion but rather involves only the coordination of the oxygen on C2 to the Mg(2+) ion. The oxygen atom on C1 instead forms hydrogen bonds to both Lys64 and Asp67, two strictly conserved active site residues. Lys64 also interacts with the oxygen on C2 and may serve to stabilize a cis conformation of the 1,2-enediolate. These structures also implicate His136 to be the general acid that protonates the 1,2-enediolate intermediate. This study further demonstrates that multiple unrelated enzyme functions can evolve from a single active site architecture without regard for substrate binding affinity or mechanism. PMID:14567674

  11. A mode-selective differential scattering study of the C2H2 methanol reaction: Influence of collision intermediates, collision times,

    E-print Network

    Anderson, Scott L.

    A mode-selective differential scattering study of the C2H2 methanol reaction: Influence. Anderson Chemistry Department, University of Utah, 315 S. 1400 E. RM Dock, Salt Lake City, Utah 84112 dependence of cross sections and product branching in the reaction of C2H2 with CD3OD, CD3OH, and CH3OD. We

  12. An efficient synthesis of anhydrides of 2-monosubstituted succinic acid monoesters and their application to the Dakin-West reaction: Isolation of some 5-succinyloxyoxazole intermediates

    Microsoft Academic Search

    Joseph Richard Casimir; Laurent Ettouati; Joëlle Paris

    1998-01-01

    Summary  A rapid and versatile synthesis of 2-monosubstituted monosuccinates and their bimolecular anhydrides is described. The reaction\\u000a of these anhydrides withN-Fmoc-protected dipeptides under the modified Dakin-West reaction affords mainly the corresponding 5-succinyloxyoxazoles.

  13. 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

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

    PubMed

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

    2013-06-25

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

  15. Using Random Sequence Primers in the Polymerase Chain Reaction to identify Gender-Specific Genetic Markers in House Wrens

    Microsoft Academic Search

    Jeremy J. Kirchman

    1994-01-01

    In order to fully understand the biology of asexually reproducing organism, it is essential that one is able to distinguish the males from the females. In determining the gender of monomorphic birds, standard techniques including visual identification, surgery, and karyotyping are impossible or impractical for large-scale studies. A reliable gender identification method that uses genetic markers identified within the DNA

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

    E-print Network

    Francesca Sammarruca; Larz White

    2011-05-27

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

  17. The evaluation and calculation of intermediate energy nuclear data for 56Fe(p,n), 63Cu(p,n), and 65Cu(p,n) monitor reactions.

    PubMed

    Zhuang, Y

    1994-12-01

    Proton monitor reactions have been widely used in accelerator target flux and beam energy monitoring, medical radioisotope production, research on radiation damage, and activation analysis. The excitation functions of 56Fe, 63Cu, and 65Cu(p,n) reactions were calculated and evaluated at incident energies up to 1,200 MeV, 11,500 MeV, and 1,820 MeV, respectively. PMID:7960786

  18. Carbon-carbon cross-coupling reactions catalyzed by a two-coordinate nickel(II)-bis(amido) complex via observable Ni(I) , Ni(II) , and Ni(III) intermediates.

    PubMed

    Lipschutz, Michael I; Tilley, T Don

    2014-07-01

    Recently, the development of more sustainable catalytic systems based on abundant first-row metals, especially nickel, for cross-coupling reactions has attracted significant interest. One of the key intermediates invoked in these reactions is a Ni(III) -alkyl species, but no such species that is part of a competent catalytic cycle has yet been isolated. Herein, we report a carbon-carbon cross-coupling system based on a two-coordinate Ni(II) -bis(amido) complex in which a Ni(III) -alkyl species can be isolated and fully characterized. This study details compelling experimental evidence of the role played by this Ni(III) -alkyl species as well as those of other key Ni(I) and Ni(II) intermediates. The catalytic cycle described herein is also one of the first examples of a two-coordinate complex that competently catalyzes an organic transformation, potentially leading to a new class of catalysts based on the unique ability of first-row transition metals to accommodate two-coordinate complexes. PMID:24889777

  19. The chemoselective reduction of isoxazoline ?-lactams through iminium Aza-Diels-Alder reactions: a short-cut synthesis of aminols as valuable intermediates towards nucleoside derivatives.

    PubMed

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

    2012-01-01

    Isoxazoline ?-lactams are prepared starting from the regioisomeric cycloadducts of benzonitrile oxide to the N-alkyl 2-azanorbornenes taking advantage of the efficient catalytic oxidation by RuO(4). The reduction of the amide groups is easily conducted in the presence of LiAlH(4) under mild conditions, which allowed for the chemoselective reduction of the amide moiety followed by ring opening to afford the desired conformationally locked isoxazoline-carbocyclic aminols, as valuable intermediates for nucleoside synthesis. PMID:22629174

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

    PubMed Central

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

    2012-01-01

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

  1. Human immunodeficiency virus-1 protease. 1. Initial velocity studies and kinetic characterization of reaction intermediates by sup 18 O isotope exchange

    Microsoft Academic Search

    Lawrence J. Hyland; Thaddeus A. Tomaszek; Gerald D. Roberts; Steven A. Carr; Victoria W. Magaard; Heidi L. Bryan; Stephen A. Fakhoury; Michael L. Moore; Michael D. Minnich; J. S. Culp; R. L. DesJarlais; T. D. Meek

    1991-01-01

    The peptidolytic reaction HIV-1 protease has been investigated by using four oligopeptide substrates, Ac-Ser-Gln-Asn-Pro-Val-Val-NHâ, Ac-Arg-Ala-Ser-Gln-Asn-Tyr-Pro-Val-Val-NHâ, Ac-Ser-Gln-Ser-Tyr-Pro-Val-Val-NHâ, and Ac-Arg-Lys-Ile-Leu-Phe-Leu-Asp-Gly-NHâ that resemble two cleavage sites found within the naturally occurring polyprotein substrates Pr55{sup gag} and Pr160{sup gag-pol}. By use of a variety of inorganic salts, it was concluded that the peptidolytic reaction is nonspecifically activated by increasing ionic strength. V\\/K increased in

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

    PubMed

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

    2009-12-01

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

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

    E-print Network

    Goddard III, William A.

    Hydrogen storage in LiAlH4 : Predictions of the crystal structures and reaction mechanisms in decomposition of the potential hydrogen storage material LiAlH4 . First, we explore the decomposition mechanism in the development of small light- weight hydrogen storage methods1,2 for automotive applica- tions. Hydrogen fuel

  4. Synthesis of Intermediate-Mass Elements in Classical Novae: From Si to Ca

    Microsoft Academic Search

    Jordi José; Alain Coc; Margarita Hernanz

    2001-01-01

    Thermonuclear runaways driven by accretion into degenerate white dwarf cores are the source that power classical nova outbursts. In this paper, we identify the dominant nuclear paths involved in the synthesis of intermediate-mass elements, from Si to Ca, during such violent events. New evolutionary sequences of 1.35 Msolar ONe novae have been computed using updated nuclear reaction rates. The main

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

    SciTech Connect

    Oganessian, Yuri Ts. [FLNR-JINR, Russia; Abdullin, F. Sh. [Joint Institute for Nuclear Research, Dubna, Russia; Bailey, P. D. [Oak Ridge National Laboratory (ORNL); Benker, D. E. [Oak Ridge National Laboratory (ORNL); Bennett, M. E. [University of Nevada, Las Vegas; Dmitriev, S. [FLNR-JINR, Russia; Ezold, Julie G. [Oak Ridge National Laboratory (ORNL); Hamilton, J. H. [Vanderbilt University; Henderson, R. [Lawrence Livermore National Laboratory (LLNL); Itkis, M. G. [FLNR-JINR, Russia; Lobanov, Yu. V. [Joint Institute for Nuclear Research, Dubna, Russia; Mezentsev, A. N. [Joint Institute for Nuclear Research, Dubna, Russia; Moody, K. [Lawrence Livermore National Laboratory (LLNL); Nelson, S. L. [Lawrence Livermore National Laboratory (LLNL); Polyakov, A. N. [Joint Institute for Nuclear Research, Dubna, Russia; Porter, C. E. [Oak Ridge National Laboratory (ORNL); Ramayya, A. V. [Vanderbilt University; Riley, F. D. [Oak Ridge National Laboratory (ORNL); Roberto, James B [ORNL; Ryabinin, M. A. [Research Institute of Atomic Reactors, Dimitrovgrad, Russia; Rykaczewski, Krzysztof Piotr [ORNL; Taylor, R [Oak Ridge National Laboratory (ORNL); Tsyganov, Yu. S. [Joint Institute for Nuclear Research, Dubna, Russia; Utyonkov, V. [FLNR-JINR, Russia; Voinov, A. A. [Joint Institute for Nuclear Research, Dubna, Russia; Vostokin, G. K. [Joint Institute for Nuclear Research, Dubna, Russia; Wilk, P. A. [Lawrence Livermore National Laboratory (LLNL)

    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.

  6. Evidence that the reactions of nickel in the presence of vitamin C do not produce toxic oxygen intermediates such as hydroxyl but ascorbate and carbon radicals

    Microsoft Academic Search

    Henryk J. Salacinski; Paul O'Brien

    2000-01-01

    A variety of reactions containing different amounts of nickel ions together with vitamin C were prepared and used in spin\\u000a trapping experiments designed to show nickel is not a Fenton active metal. Carbon based radicals were observed at low ratios\\u000a of ascorbate to nickel, and ascorbate radical was observed at high ratios of ascorbate to nickel. No buffer effects were

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

    NASA Astrophysics Data System (ADS)

    Norman, B.

    2004-10-01

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

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

    PubMed Central

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

    2013-01-01

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

  9. 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.

  10. Angular Distribution of Intermediate Mass Fragments Produced in 8-12 GeV Proton and Light Heavy-Ion Induced Target Multifragmentation Reactions

    NASA Astrophysics Data System (ADS)

    Tanaka, K. H.; Miyazaki, K.; Takada, E.; Murakami, T.

    2001-10-01

    In order to investigate a possible scaling rules between the proton induced and the heavy-ion induced target multifragmentation (TMF) reactions, we started a series of experiments by using 8- or 12-GeV light heavy-ion beams provided by the HIMAC of the National Institute of Radiological Sciences. Data obtained are compared with ones taken with 8- or 12-GeV proton beams of the KEK-PS. Inclusive IMF energy spectra for 8-GeV ^16O and ^20Ne induced TMF are analyzed by a single moving source model (SMSM). Even for the ^16O and ^20Ne induced TMFs, the IMF yields always exceeded the predicted yields of the SMSM at sideward angles and showed evident peaks at around 110^circ in the laboratory system. Though this angle is quite backward compared to the 70^circ appeared at the proton induced TMFs, appearance of these sideward peaks might indicate the total beam energy is a decisive role (common scaling parameter) to govern a reaction dynamics for the IMF emission in TMFs.

  11. 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).

  12. 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. [Department of Physics, American University of Beirut, Beirut (Lebanon); Champagne, Arthur [Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC (United States)

    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.

  13. 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 (?-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 ?-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 (?-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

  14. 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.

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

    PubMed

    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. PMID:24651205

  16. 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.

  17. The reactivity of thiols and disulfides with different redox states of myoglobin. Redox and addition reactions and formation of thiyl radical intermediates.

    PubMed

    Romero, F J; Ordoñez, I; Arduini, A; Cadenas, E

    1992-01-25

    The reactivity of several thiols, including glutathione, dihydrolipoic acid, cysteine, N-acetyl cysteine, and ergothioneine, as well as several disulfides, toward different redox states of myoglobin, mainly met-myoglobin (HX-FeIII) and ferrylmyoglobin (HX-FeIV=O), was evaluated by optical spectral analysis, product formation, and thiyl free radical generation. Only dihydrolipoic acid reduced met-myoglobin to oxy-myoglobin, whereas all the other thiols tested did not interact with met-myoglobin. Although the redox transitions involved in the former reduction were expected to yield the dihydrolipoate thiyl radical, the reaction was EPR silent. Conversely, all thiols interacted to different extent with the high oxidation state of myoglobin, i.e. ferrylmyoglobin, via two processes. First, direct electron transfer to heme iron in ferrylmyoglobin (HX-FeIV=O) with formation of met-myoglobin (HX-FeIII) or oxymyoglobin (HX-FeIIO2); the former transition was effected by all thiols except dihydrolipoate, which facilitated the latter, i.e. the formation of the two-electron reduction product of ferrylmyoglobin. Second, nucleophilic addition onto a pyrrole in ferrylmyoglobin with subsequent formation of sulfmyoglobin. The contribution of either direct electron transfer to the heme iron or nucleophilic addition depended on the physicochemical properties of the thiol involved and on the availability of H2O2 to reoxidize met-myoglobin to ferrylmyoglobin. The thiyl radicals of glutathione, cysteine, and N-acetylcysteine were formed during the interaction of the corresponding thiols with ferrylmyoglobin and detected by EPR in conjunction with the spin trap 5,5'-dimethyl-1-pyroline-N-oxide. The intensity of the EPR signal was insensitive to superoxide dismutase and it was decreased, but not suppressed, by catalase. The disulfides of glutathione and cysteine did not react with ferrylmyoglobin, but the disulfide bridge in lipoic acid interacted efficiently with the ferryl species by either reducing directly the heme iron to form met-myoglobin or adding onto a pyrrole ring to form sulfmyoglobin; either process depended on the presence or absence of catalase (to eliminate the excess of H2O2) in the reaction mixture, respectively. The biological significance of the above results is discussed in terms of the occurrence and distribution of high oxidation states of myoglobin, its specific participation in cellular injury, and its potential interaction with biologically important thiols leading to either recovery of myoglobin or generation of nonfunctional forms of the hemoprotein as sulfmyoglobin. PMID:1309791

  18. X-ray crystallographic snapshots of reaction intermediates in the G117H mutant of human butyrylcholinesterase, a nerve agent target engineered into a catalytic bioscavenger.

    PubMed

    Nachon, Florian; Carletti, Eugenie; Wandhammer, Marielle; Nicolet, Yvain; Schopfer, Lawrence M; Masson, Patrick; Lockridge, Oksana

    2011-02-15

    OPs (organophosphylates) exert their acute toxicity through inhibition of acetylcholinesterase, by phosphylation of the catalytic serine residue. Engineering of human butyrylcholinesterase, by substitution of a histidine residue for the glycine residue at position 117, led to the creation of OP hydrolase activity. However, the lack of structural information and poor understanding of the hydrolytic mechanism of the G117H mutant has hampered further improvements in the catalytic activity. We have solved the crystallographic structure of the G117H mutant with a variety of ligands in its active site. A sulfate anion bound to the active site suggested the positioning for an OP prior to phosphylation. A fluoride anion was found in the active site when NaF was added to the crystallization buffer. In the fluoride complex, the imidazole ring from the His117 residue was substantially shifted, adopting a relaxed conformation probably close to that of the unliganded mutant enzyme. Additional X-ray structures were obtained from the transient covalent adducts formed upon reaction of the G117H mutant with the OPs echothiophate and VX [ethyl ({2-[bis(propan-2-yl)amino]ethyl}sulfanyl](methyl)phosphinate]. The position of the His117 residue shifted in response to the introduction of these adducts, overlaying the phosphylserine residue. These structural data suggest that the dephosphylation mechanism involves either a substantial conformational change of the His117 residue or an adjacent nucleophilic substitution by water. PMID:21091433

  19. 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 which it occurs suggest an origin in a liquid/glass or dynamical transition. A discontinuity in the activation barrier for the chemical reaction is not expected in the transition temperature range. Therefore, the transition arises from a change in the properties of the protein. We propose that a protein dynamical contribution to the reaction, which is present above the transition temperature, is lost below the transition temperature, owing to an increase in the activation energy barrier for protein motions that are coupled to the reaction. For both the fast and slow phases of the low temperature decay, the dynamical transition in protein motions that are obligatorily coupled to the reaction of the Co(II)-substrate radical pair lies below 190 K. PMID:18805934

  20. Reaction of the CoII-Substrate Radical Pair Catalytic Intermediate in Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase in Frozen Aqueous Solution from 190 to 217 K

    PubMed Central

    Zhu, Chen; Warncke, Kurt

    2008-01-01

    The decay kinetics of the aminoethanol-generated CoII-substrate radical pair catalytic intermediate in ethanolamine ammonia-lyase from Salmonella typhimurium have been measured on timescales of <105 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 ? T ? 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 ? 214 K: the decay is monoexponential. The observed first-order rate constants for the monoexponential (kobs,m) and the fast phase of the biexponential decay (kobs,f) adhere to the same linear relation on an lnk versus T?1 (Arrhenius) plot. Thus, kobs,m and kobs,f correspond to the same apparent Arrhenius prefactor and activation energy (logAapp,f (s?1) = 13.0, Ea,app,f = 15.0 kcal/mol), and therefore, a common decay mechanism. We propose that kobs,m and kobs,f represent the native, forward reaction of the substrate through the radical rearrangement step. The slow phase rate constant (kobs,s) for 190 ? T ? 207 K obeys a different linear Arrhenius relation (logAapp,s (s?1) = 13.9, Ea,app,s = 16.6 kcal/mol). In the transition temperature range, kobs,s displays a super-Arrhenius increase with increasing temperature. The change in Ea,app,s with temperature and the narrow range over which it occurs suggest an origin in a liquid/glass or dynamical transition. A discontinuity in the activation barrier for the chemical reaction is not expected in the transition temperature range. Therefore, the transition arises from a change in the properties of the protein. We propose that a protein dynamical contribution to the reaction, which is present above the transition temperature, is lost below the transition temperature, owing to an increase in the activation energy barrier for protein motions that are coupled to the reaction. For both the fast and slow phases of the low temperature decay, the dynamical transition in protein motions that are obligatorily coupled to the reaction of the CoII-substrate radical pair lies below 190 K. PMID:18805934

  1. Trimeric binding of the 70-kD uncoating ATPase to the vertices of clathrin triskelia: a candidate intermediate in the vesicle uncoating reaction.

    PubMed

    Heuser, J; Steer, C J

    1989-10-01

    Clathrin-coated vesicles were uncoated with the 70-kD "uncoating ATPase" from bovine brain, and the molecular products were visualized by freeze-etch electron microscopy. This yielded images of released clathrin triskelia with up to three 70-kD uncoating ATPase molecules bound to their vertices. Likewise, incubation of soluble clathrin triskelia with purified uncoating ATPase also led to trimeric binding of the ATPase to the vertices of clathrin triskelia. However, this occurred only when either EDTA or nonhydrolyzable analogues of ATP were present, in which case the ATPase also appeared to self-associate. When ATP was present instead, no 70-kD ATPases could be found on clathrin triskelia and all ATPases remained monomeric. These observations support the notion that ATP controls an allosteric conversion of the 70-kD uncoating ATPase between two different molecular conformations, an ATP-charged state in which the molecule has relatively low affinity for itself as well as low affinity for clathrin, and an ATP-discharged state in which both of these affinities are high. We presume that in vivo, the latter condition is brought about by ATP hydrolysis and product release, at which point the ATPase will bind tightly to clathrin and/or self-associate. We further propose that these reactions, when occurring in concert within a clathrin lattice, will tend to destabilize it by a mechanism we call "protein polymer competition". We stress the analogies between such a mechanism of uncoating and the ATP-driven events in muscle contraction. Finally, we show that under experimental conditions in which the uncoating ATPase fully removes the coats from brain coated vesicles, identical aliquots of the enzyme do not affect plasmalemmal coated pits in situ. This remarkable selectivity, the mechanism of which remains a complete mystery, is at least consistent with the idea that the 70-kD ATPase indeed plays a role in uncoating coated vesicles after they have formed in vivo. PMID:2571614

  2. 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

    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 -T?Sb, and by the negative value of ?Cp. On the other hand, the large negative enthalpy is the dominant contribution to ?Gb 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

  3. 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 –T?Sb, and by the negative value of ?Cp. On the other hand, the large negative enthalpy is the dominant contribution to ?Gb 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

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

    PubMed Central

    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 ?-phosphate site. Phosphorus-31 NMR spectroscopy (31P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue ?,?-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme–product complex structure. PMID:23982515

  5. 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

  6. Nature and dynamics of the charge-separated intermediate in reaction centers in which bacteriochlorophyll replaces the photoactive bacteriopheophytin. 2. The rates and yields of charge separation and recombination

    SciTech Connect

    Kirmaier, C.; Laporte, L.; Holten, D. [Washington Univ., St. Louis, MO (United States); Schenck, C.C. [Colorado State Univ., Fort Collins, CO (United States)

    1995-05-25

    The primary photochemistry of the (M)L214H and (M)L214H/(L)E104V mutant bacterial reaction centers (RCs) from Rhodobacter sphaeroides has been investigated at room and cryogenic temperatures. In both mutants the native bacteriopheophytin electron acceptor (BPh{sub L}) is replaced with a bacteriochlorophyll (BChl) molecule denoted by {Beta}; in the double mutant a hydrogen-bonding interaction of {Beta}-is removed. The initial stage of charge separation, formation of an intermediate P{sup +}I{sup -}, is slowed somewhat in both mutants but without a detectable loss in yield. However, the yield of the subsequent stage of charge separation, P{sup +}I{sup N} {yields} P{sup +}Q{sub A}{sup -}, is significantly reduced due to the combination of slower electron transfer from I{sup -} to Q{sub A} and enhanced charge recombination of P{sup +}I{sup -} to the ground state. Models are considered in which P{sup +}{Beta}{sup -} and P{sup +}BCh1{sub L} are quantum-mechanically mixed or in thermal equilibrium. It is concluded that P{sup +}{Beta}{sup -} and P{sup +}BCh1{sub L} are very close in energy in the mutants and that P{sup +}BCh1{sub L} is very close in energy to the primary electron donor, P{sup *}, in both the mutant and wild-type RCs. 40 refs., 8 figs., 1 tab.

  7. 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-?).

    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-?) (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 ? 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

  8. 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

  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

    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.

  10. Five-coordinate [Pt(II)(bipyridine)2(phosphine)](n+) complexes: long-lived intermediates in ligand substitution reactions of [Pt(bipyridine)2](2+) with phosphine ligands.

    PubMed

    Lo, Warrick K C; Cavigliasso, Germán; Stranger, Robert; Crowley, James D; Blackman, Allan G

    2014-04-01

    The reaction of [Pt(N-N)2](2+) [N-N = 2,2'-bipyridine (bpy) or 4,4'-dimethyl-2,2'-bipyridine (4,4'-Me2bpy)] with phosphine ligands [PPh3 or PPh(PhSO3)2(2-)] in aqueous or methanolic solutions was studied by multinuclear ((1)H, (13)C, (31)P, and (195)Pt) NMR spectroscopy, X-ray crystallography, UV-visible spectroscopy, and high-resolution mass spectrometry. NMR spectra of solutions containing equimolar amounts of [Pt(N-N)2](2+) and phosphine ligand give evidence for rapid formation of long-lived, 5-coordinate [Pt(II)(N-N)2(phosphine)](n+) complexes. In the presence of excess phosphine ligand, these intermediates undergo much slower entry of a second phosphine ligand and loss of a bpy ligand to give [Pt(II)(N-N)(phosphine)2](n+) as the final product. The coordination of a phosphine ligand to the Pt(II) ion in the intermediate [Pt(N-N)2(phosphine)](n+) complexes is supported by the observation of (31)P-(195)Pt coupling in the (31)P NMR spectra. The 5-coordinate nature of [Pt(bpy)2{PPh(PhSO3)2}] is confirmed by X-ray crystallography. X-ray crystal structural analysis shows that the Pt(II) ion in [Pt(bpy)2{PPh(PhSO3)2}]·5.5H2O displays a distorted square pyramidal geometry, with one bpy ligand bound asymmetrically. These results provide strong support for the widely accepted associative ligand substitution mechanism for square planar Pt(II) complexes. X-ray structural characterization of the distorted square planar complex [Pt(bpy)(PPh3)2](ClO4)2 confirms this as the final product of the reaction of [Pt(bpy)2](2+) with PPh3 in CD3OD. The results of density functional calculations on [Pt(bpy)2](2+), [Pt(bpy)2(phosphine)](n+), and [Pt(bpy)(phosphine)2](n+) indicate that the bonding energy follows the trend of [Pt(bpy)(phosphine)2](n+) > [Pt(bpy)2(phosphine)](n+) > [Pt(bpy)2](2+) for stability and that the formation reactions of [Pt(bpy)2(phosphine)](n+) from [Pt(bpy)2](2+) and [Pt(bpy)(phosphine)2](n+) from [Pt(bpy)2(phosphine)](n+) are energetically favorable. These calculations suggest that the driving force for the formation of [Pt(bpy)(phosphine)2](n+) from [Pt(bpy)2](2+) is the formation of a more energetically favorable product. PMID:24654797

  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

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

  12. 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 [State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xi'an 710049 (China); Yuan, Tao; Zhang, Kuiwen [National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029 (China)

    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)

  13. Molecular response assessment by quantitative real-time polymerase chain reaction after induction therapy in NPM1-mutated patients identifies those at high risk of relapse

    PubMed Central

    Hubmann, Max; Köhnke, Thomas; Hoster, Eva; Schneider, Stephanie; Dufour, Annika; Zellmeier, Evelyn; Fiegl, Michael; Braess, Jan; Bohlander, Stefan K.; Subklewe, Marion; Sauerland, Maria-Cristina; Berdel, Wolfgang E.; Büchner, Thomas; Wörmann, Bernhard; Hiddemann, Wolfgang; Spiekermann, Karsten

    2014-01-01

    Monitoring minimal residual disease is an important way to identify patients with acute myeloid leukemia at high risk of relapse. In this study we investigated the prognostic potential of minimal residual disease monitoring by quantitative real-time polymerase chain reaction analysis of NPM1 mutations in patients treated in the AMLCG 1999, 2004 and 2008 trials. Minimal residual disease was monitored - in aplasia, after induction therapy, after consolidation therapy, and during follow-up - in 588 samples from 158 patients positive for NPM1 mutations A, B and D (with a sensitivity of 10?6). One hundred and twenty-seven patients (80.4%) achieved complete remission after induction therapy and, of these, 56 patients (44.1%) relapsed. At each checkpoint, minimal residual disease cut-offs were calculated. After induction therapy a cut-off NPM1 mutation ratio of 0.01 was associated with a high hazard ratio of 4.26 and the highest sensitivity of 76% for the prediction of relapse. This was reflected in a cumulative incidence of relapse after 2 years of 77.8% for patients with ratios above the cut-off versus 26.4% for those with ratios below the cut-off. In the favorable subgroup according to European LeukemiaNet, the cut-off after induction therapy also separated the cohort into two prognostic groups with a cumulative incidence of relapse of 76% versus 6% after 2 years. Our data demonstrate that in addition to pre-therapeutic factors, the course of minimal residual disease in an individual is an important prognostic factor and could be included in clinical trials for the guidance of post-remission therapy. The trials from which data were obtained were registered at www.clinicaltrials.gov (#NCT01382147, #NCT00266136) and at the European Leukemia Trial Registry (#LN_AMLINT2004_230). PMID:24816240

  14. Establishing the Intermediate Unit.

    ERIC Educational Resources Information Center

    Pennsylvania State Dept. of Education, Harrisburg.

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

  15. 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.

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

    SciTech Connect

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

    2013-09-16

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

  17. 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.

  18. Formation of Compound I and Compound II Ferryl Species in the Reaction of Hemoglobin I from Lucina pectinata with Hydrogen Peroxide

    Microsoft Academic Search

    Walleska De Jesús-Bonilla; José E. Cortés-Figueroa; Fernando A. Souto-Bachiller; Lolita Rodr??guez; Juan López-Garriga

    2001-01-01

    The formation of ferryl heme (Fe(IV) = O) species, i.e., compound I and compound II, has been identified as the main intermediates in heme protein peroxidative reactions. We report stopped-flow kinetic measurements which illustrate that the reaction of hemoglobin I (HbI) from Lucina pectinata with hydrogen peroxide produce ferryl intermediates compound I and compound II. Compound I appears relatively stable

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    The occurrence of high nitrite concentrations as a result of anthropogenic activities is an important water quality concern as it is highly toxic to human and fauna, and it is used as a nitrogen source for the assimilation process. The toxicity of nitrite is related to its transformation into carcinogenic N-nitroso compounds, which are suspected to be responsible for some gastric cancers, and to its ability to convert the hemoglobin to methaemoglobin what is then unable to fix oxygen and to transport it to the tissues, involving hypoxia and the blue-baby syndrome [1]. To reduce the adverse effect of nitrite on human health and on macroalgal blooms, any process enhancing the transformation of nitrite ions to nitrogen gas is of interest for the remediation of natural environments. To achieve this purpose the use of processes involving Fe(II)-containing minerals could be considered as one of the best options. Green-rusts are mixed Fe(II-III) layered double hydroxides commonly found in anoxic zones of natural environments such as sediments and hydromorphic soils. In such anoxic environments, green rust minerals play an important role in the biogeochemical redox cycling of iron and nitrogen, and can affect the speciation and mobility of many organic and inorganic contaminants. The present study investigates the reduction of nitrite by two synthetic and two biogenic green rusts. On the one hand, Fe(II-III) hydroxychloride and Fe(II-III) hydroxycarbonate green rusts were used as synthetic interlayer forms of GR, which are referred to as ';syn-GR(CO3)' and ';syn-GR(Cl)', respectively. On the other hand, the study was performed with biogenic Fe(II-III) hydroxycarbonate green rusts obtained from the bioreduction of two ferric precursors, either Fe(III)-oxyhydroxycarbonate or lepidocrocite; these biogenic green rusts are referred to as ';bio-GR(CO3)F' and ';bio-GR(CO3)L', respectively. For synthetic green rusts, results showed that the oxidation of both syn-GR(CO3) and syn-GR(Cl) led to the reduction of nitrite ions to ammonium, and that the production of ammonium depended on their Fe(II) content. XRD patterns indicated that both synthetic green rusts were fully oxidized into magnetite during the reaction with nitrite. For biogenic green rusts, the study revealed that both bio-GR(CO3)F and bio-GR(CO3)L were capable of reducing nitrite ions without ammonium production, suggesting the conversion of nitrite ions to nitrogen gas. Moreover, we provided evidence for the first time that the interactions of bio-GR(CO3)F with nitrite led to the formation of an hydroxy-nitrite green rust as a result of the incorporation of nitrite in the interlayer region of bio-GR(CO3)F; such an intercalation of nitrite ions was not observed in experiments with bio-GR(CO3)L. XRD analysis indicated that GR(NO2) was formed as an intermediate reaction product prior to the fully oxidation of GR to ferric oxyhydroxides. [1] Philips S., Laanbroek H. J. and Verstraete W. (2002). Rev. Environ. Sci. Biotechnol. 1, 115-141.

  20. A unified intermediate and mechanism for soot combustion on potassium-supported oxides.

    PubMed

    Li, Qian; Wang, Xiao; Xin, Ying; Zhang, Zhaoliang; Zhang, Yexin; Hao, Ce; Meng, Ming; Zheng, Lirong; Zheng, Lei

    2014-01-01

    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

  1. 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

  2. Intermediate Filament Diseases: Desminopathy

    PubMed Central

    Goldfarb, Lev G.; Olivé, Montse; Vicart, Patrick; Goebel, Hans H.

    2009-01-01

    Desminopathy is one of the most common intermediate filament human disorders associated with mutations in closely interacting proteins, desmin and alphaB-crystallin. The inheritance pattern in familial desminopathy is characterized as autosomal dominant or autosomal recessive, but many cases have no family history. At least some and likely most sporadic desminopathy cases are associated with de novo DES mutations. The age of disease onset and rate of progression may vary depending on the type of inheritance and location of the causative mutation. Typically, the illness presents with lower and later upper limb muscle weakness slowly spreading to involve truncal, neck-flexor, facial and bulbar muscles. Skeletal myopathy is often combined with cardiomyopathy manifested by conduction blocks, arrhythmias and chronic heart failure resulting in premature sudden death. Respiratory muscle weakness is a major complication in some patients. Sections of the affected skeletal and cardiac muscles show abnormal fibre areas containing chimeric aggregates consisting of desmin and other cytoskeletal proteins. Various DES gene mutations: point mutations, an insertion, small in-frame deletions and a larger exon-skipping deletion, have been identified in desminopathy patients. The majority of these mutations are located in conserved alpha-helical segments, but additional mutations have recently been identified in the tail domain. Filament and network assembly studies indicate that most but not all disease-causing mutations make desmin assembly-incompetent and able to disrupt a pre-existing filamentous network in dominant-negative fashion. AlphaB-crystallin serves as a chaperone for desmin preventing its aggregation under various forms of stress; mutant CRYAB causes cardiac and skeletal myopathies identical to those resulting from DES mutations. PMID:19181099

  3. Oxaziridines as possible intermediates in flavin monooxygenases.

    PubMed

    Orf, H W; Dolphin, D

    1974-07-01

    The enzymatic hydroxylation reactions of flavin monooxygenases are suggested to involve an oxaziridine as the active oxygenating agent. The chemistry of these monooxygenases and their nonenzymatic model systems are consistent with an oxaziridine intermediate. Several advantages of the oxaziridine model over the previously proposed "carbonyl oxide" and flavin peroxide models are discussed. PMID:4368986

  4. Kinetics : IntermediateInMech (15 Variations)

    NSDL National Science Digital Library

    Suppose that for the reaction of nitrogen dioxide and carbon monoxide NO 2 + CO NO + CO 2 the following mechanism has been proposed at high temperatures: (1) NO 2 + CO O-N-O-C-O (slow) (2) O-N-O-C-O NO + CO 2 (fast) Check the box for each species that is an intermediate in this mechanism.

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

    PubMed Central

    Gutiérrez Acosta, Olga B.; Hardt, Norman

    2013-01-01

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

  6. A pilot study to evaluate a community pharmacy–based monitoring system to identify adverse drug reactions associated with paediatric medicines use

    Microsoft Academic Search

    Mansour Tobaiqy; Derek Stewart; Peter J. Helms; Christine Bond; Amanda Jane Lee; Nick Bateman; Dorothy McCaig; James McLay

    2010-01-01

    Introduction  Current pharmacovigilance systems are limited by spontaneous reporting of adverse drug reactions (ADRs), lack of a denominator,\\u000a and lower than expected reporting rates. The aim of our study was to undertake a formal pilot evaluation of a community pharmacy–led\\u000a ADR monitoring system.\\u000a \\u000a \\u000a \\u000a \\u000a Methods  The setting was community pharmacies in five Health Boards areas of Scotland. Subjects were parents, guardians, or children

  7. Vibrational spectroscopy of intermediates in benzene-to-pheno conversion by FeO +

    Microsoft Academic Search

    Gokhan Altinay; Ricardo B. Metz

    2010-01-01

    Gas-phase FeO+ can convert benzene to phenol under thermal conditions. Two key intermediates of this reaction are the [HO-Fe-C6H5]+ insertion intermediate and Fe+(C6H5OH) exit channel complex. These intermediates are selectively formed by reaction of laser ablated Fe+ with specific organic precursors and are cooled in a supersonic expansion. Vibrational spectra of the sextet and quartet\\u000a states of the intermediates in

  8. 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.

  9. 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

    Microsoft Academic Search

    Peter C. Ford; S. M. massick

    2002-01-01

    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.

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

    PubMed Central

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

    2015-01-01

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

  11. Statistical properties of multistep enzyme-mediated reactions

    SciTech Connect

    Nemenman, Ilya [Los Alamos National Laboratory; Sinitsyn, Nikolai A [Los Alamos National Laboratory; De Ronde, Wiet H [AMOLF; Daniels, Bryan C [CORNELL; Mugler, Andrew [COLUMBIA

    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.

  12. On-line electrochemistry/thermospray/tandem mass spectrometry as a new approach to the study of redox reactions: the oxidation of uric acid.

    PubMed

    Volk, K J; Yost, R A; Brajter-Toth, A

    1989-08-01

    The electrochemical oxidation pathway of uric acid was determined by on-line electrochemistry/thermospray/tandem mass spectrometry. Intermediates and products formed as a result of electrooxidation were monitored as the electrode potential was varied. Several reaction intermediates have been identified and characterized by tandem mass spectrometry. The tandem mass spectrometric results provide convincing evidence that the primary intermediate produced during the electrooxidation of uric acid has a quinonoid diimine structure. The results indicate that once formed via electrooxidation, the primary intermediate can follow three distinct reaction pathways to produce the identified final products. The final electrochemical oxidation products observed in these studies were urea, CO2, alloxan, alloxan monohydrate, allantoin, 5-hydroxyhydantoin-5-carboxamide, and parabanic acid. The solution reactions that follow the initial electron transfer at the electrode are affected by the vaporizer tip temperature of the thermospray probe. In particular, it was found that at different tip temperatures either hydrolysis or ammonolysis reactions of the initial electrochemical oxidation products can occur. Most importantly, the results show that the on-line combination of electrochemistry with thermospray/tandem mass spectrometry provides otherwise difficult to obtain information about redox and associated chemical reactions of biological molecules such as the structure of reaction intermediates and products, as well as providing insight into reaction pathways. PMID:2774199

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

    PubMed

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

    2014-08-13

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

  14. Epidemiology of imported cutaneous leishmaniasis at the Hospital for Tropical Diseases, London, United Kingdom: use of polymerase chain reaction to identify the species.

    PubMed

    Wall, Emma C; Watson, Julie; Armstrong, Margaret; Chiodini, Peter L; Lockwood, Diana N

    2012-01-01

    This study reviewed all patients diagnosed with imported cutaneous leishmaniasis (CL) at the Hospital for Tropical Diseases in London, United Kingdom, over an 11-year period. Diagnostic and epidemiologic information was collected prospectively for all patients with imported CL to this hospital during 1998-2009. A total of 223 patients were given a diagnosis of CL. Ninety patients were diagnosed with Old World CL, which was caused most commonly by Leishmania donovani complex (n = 20). A total of 71% were tourists to the Mediterranean region, 36% were migrants or visiting friends and relatives, and 17% were soldiers. One hundred thirty-three patients were given a diagnosis of New World CL. The Leishmania subgenus Viannia caused 97 of these cases; 44% of these were in backpackers and 29% were in soldiers. Polymerase chain reaction was more sensitive and faster for detecting Leishmania DNA (86% for Old World CL and 96% for New World CL) than culture. This is the largest study of imported leishmaniasis, and demonstrates that tourists to the Mediterranean and backpackers in Central and South America are at risk for this disease. PMID:22232460

  15. Comparison of alcohol and alkane oxidative dehydrogenation reactions over supported vanadium oxide catalysts: in situ infrared, Raman and UV–vis spectroscopic studies of surface alkoxide intermediates and of their surface chemistry

    Microsoft Academic Search

    Carlo Resini; Tania Montanari; Guido Busca; Jih-Mirn Jehng; Israel E. Wachs

    2005-01-01

    The surface chemistry of adsorbed isopropoxy groups on supported vanadia–alumina and vanadia–silica catalysts was investigated with multiple in situ spectroscopic techniques. The in situ FT-IR, Raman and UV–vis spectroscopic measurements provided molecular level information about the surface intermediates and the surface vanadium oxide species as a function of different conditions. The spectroscopic insights were compared to the steady state fixed

  16. IsoTagger: Identification of isomeric nuclear states produced in fragmentation reactions with radioactive beams

    NASA Astrophysics Data System (ADS)

    Wimmer, K.; Barofsky, D.; Bazin, D.; Fraile, L. M.; Lloyd, J.; Tompkins, J. R.; Williams, S. J.

    2015-01-01

    A new method has been developed to detect and identify isomeric states produced in intermediate beam-energy reactions with secondary radioactive beams. Event-by-event identification of the reaction products allows for an unambiguous assignment of isomeric states to certain nuclei produced in fragmentation reactions. This versatile device allows for the identification of isomeric states with lifetimes between 100 ns and several ms. Combined prompt and delayed ?-ray spectroscopy give detailed information on the level schemes of exotic nuclei. This is particularly important in measurements of exclusive reaction cross-sections to several final states in the residue nucleus.

  17. Giant resonances and intermediate energy heavy ions: Electromagnetic decay experiments

    SciTech Connect

    Beene, J.R.; Bertrand, F.E.

    1991-01-01

    We briefly explore how large cross sections for excitation of both isoscalar and isovector giant multipole resonances which can be obtained using intermediate energy heavy-ion reactions can be utilized in photon-decay coincidence experiments to provide new information on subjects ranging from basic nuclear structure properties to resonance damping and pre-compound decay. We also discuss experiments in which photon-decay techniques are used as a tag to isolate and identify very weakly excited modes, enabling us to explore such diverse subjects as hadronic excitation of the giant dipole resonance, the distribution of isovector quadrupole strength in {sup 208}Pb, and the excitation of two-phonon giant resonance strength. 25 refs., 12 figs.

  18. 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.

  19. Energy spectra and angular distribution of intermediate mass fragments emitted in {Au}/{Ag(p,X)} reactions with Ep = 12 GeV (The first result of the KEK-12GeV-PS experiment; E288)

    NASA Astrophysics Data System (ADS)

    Tanaka, K. H.; Yamanoi, Y.; Ochiishi, H.; Akiyoshi, H.; Kouda, S.; Nakamura, H.; Morinobu, S.; Tanaka, Y.; Kimura, K.; Shibata, T.; Sugaya, Y.; Yasuda, K.; Ito, H.; Murakami, T.

    1995-02-01

    The latest results of the first nuclear multifragmentation experiment, E288 [1], at the KEK 12 GeV Proton Synchrotron (KEK-PS) are presented. The energy spectra of intermediate mass fragments (IMFs) were measured inclusively from 30° to 150° with 20° step in the lab. system. Coincidence measurements with one extra IMF emitted toward 90° direction in the opposite hemisphere were performed at the same time. Characteristic sideward flow of IMFs toward 70° direction was found with the usual isotropic component. This isotropic component was trongly suppressed in the coincidence measurement. These facts may indicate the formation of unusually shaped nuclear matter such as an expanding toroid.

  20. 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

  1. 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...

  2. SPACE: Intermediate Level Modules.

    ERIC Educational Resources Information Center

    Indiana State Dept. of Education, Indianapolis. Center for School Improvement and Performance.

    These modules were developed to assist teachers at the intermediate level to move away from extensive skill practice and toward more meaningful interdisciplinary learning. This packet, to be used by teachers in the summer Extended Learning Program, provides detailed thematic lesson plans matched to the Indiana Curriculum Proficiency Guide. The…

  3. THE EVOLVING INTERMEDIATE UNIT.

    ERIC Educational Resources Information Center

    ISENBERG, ROBERT M.

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

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

    PubMed

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

    2009-03-21

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

  5. Reactive Maillard intermediates leading to coloured products-5-hydroxymethyl- and 5-(1,2-dihydroxyethyl)-3(2H)-furanone.

    PubMed

    Lederer, M; Glomb, M; Fischer, P; Ledl, F

    1993-11-01

    In the course of the Maillard reaction, labile sugar degradation products are formed that are susceptible to secondary reactions and therefore have a decisive influence on the product spectrum. Such reactive intermediates may be transformed into stable derivatives with trapping reagents, and thus be protected from further reactions. Secondary processes may also be forestalled if the primary products are removed from the reaction mixture by high-vacuum distillation. By this procedure, 5-hydroxymethyl- and 5-(1,2-dihydroxyethyl)-3(2H)-furanone have been identified directly from Maillard reaction mixtures for the first time. The activated methylene group of these 3(2H)-furanones can easily enter into condensation reactions. The coloured condensation products in turn react with primary amines to pyrrolinone derivatives, which may also contribute to the colouring observed in non-enzymatic browning. PMID:8273421

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

    PubMed

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

    2014-11-01

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

  7. BLUF Domain Function Does Not Require a Metastable Radical Intermediate State

    PubMed Central

    2014-01-01

    BLUF (blue light using flavin) domain proteins are an important family of blue light-sensing proteins which control a wide variety of functions in cells. The primary light-activated step in the BLUF domain is not yet established. A number of experimental and theoretical studies points to a role for photoinduced electron transfer (PET) between a highly conserved tyrosine and the flavin chromophore to form a radical intermediate state. Here we investigate the role of PET in three different BLUF proteins, using ultrafast broadband transient infrared spectroscopy. We characterize and identify infrared active marker modes for excited and ground state species and use them to record photochemical dynamics in the proteins. We also generate mutants which unambiguously show PET and, through isotope labeling of the protein and the chromophore, are able to assign modes characteristic of both flavin and protein radical states. We find that these radical intermediates are not observed in two of the three BLUF domains studied, casting doubt on the importance of the formation of a population of radical intermediates in the BLUF photocycle. Further, unnatural amino acid mutagenesis is used to replace the conserved tyrosine with fluorotyrosines, thus modifying the driving force for the proposed electron transfer reaction; the rate changes observed are also not consistent with a PET mechanism. Thus, while intermediates of PET reactions can be observed in BLUF proteins they are not correlated with photoactivity, suggesting that radical intermediates are not central to their operation. Alternative nonradical pathways including a keto–enol tautomerization induced by electronic excitation of the flavin ring are considered. PMID:24579721

  8. Toward an understanding of the selectivity in domino reactions. A DFT study of the reaction between acetylenedicarboxylic acid and 1, 3-Bis(2-furyl)propane

    PubMed

    Domingo; Picher; Andres

    2000-06-01

    The mechanism of the domino reaction between acetylenedicarboxylic acid and 1,3-bis(2-furyl)propane has been theoretically studied in the framework of density functional theory. This domino process comprises two consecutive cycloaddition reactions: the first one is initialized by the nucleophilic attack of the C5 position of the furan ring to a conjugate position of acetylenedicarboxylic acid to give a zwitterionic intermediate, which by a subsequent ring-closure process affords an oxanorbornadiene intermediate. The second reaction is an intramolecular concerted cycloaddition of this intermediate to give the final dioxapentacyclic adduct. For the second cycloaddition, which corresponds to the step controlling the selectivity, eight alternative reaction pathways are found. Chemoselectivity, facial selectivity, and stereoselectivity of this domino reaction are related with the different approach modes of the tethered furan to the oxanorbornadiene system of the intermediate. The most favorable pathway takes place along an endo/syn approach of the furan ring relative to the bridged oxygen atom of the oxanorbornadiene system, with participation of the substituted double bond. An analysis of energetic contributions to the potential energy barriers for the intramolecular cycloadditions identifies the different factors controlling the reactive channels. Selectivity outcome is reproduced by these calculations. PMID:10843633

  9. Oxide-supported PtCo alloy catalyst for intermediate temperature polymer electrolyte fuel cells

    E-print Network

    Boyer, Edmond

    1 Oxide-supported PtCo alloy catalyst for intermediate temperature polymer electrolyte fuel cells reduction reaction in a polymer electrolyte fuel cell (PEMFC) operating between 80° and 110 °C at different, Fuel cells, Oxygen reduction reaction, Doped Ti-oxide support, Intermediate temperature

  10. The formation of the vinylidene radical as an intermediate in the combination of triplet methylene

    NASA Technical Reports Server (NTRS)

    Laufer, A. H.

    1982-01-01

    The vinylidene radical (H2C = C) is proposed as an intermediate in the combination reaction of triplet methylene. The conclusion is based upon the distribution of isotopic acetylenes produced from a 1:1 mixture of CD2 and CH2. The path of the reaction and the energetics of the intermediate species are discussed.

  11. GFP's Mechanical Intermediate States

    PubMed Central

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

    2012-01-01

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

  12. The Intermediate Neutrino Program

    E-print Network

    C. Adams; J. R. Alonso; A. M. Ankowski; J. A. Asaadi; J. Ashenfelter; S. N. Axani; K. Babu; C. Backhouse; H. R. Band; P. S. Barbeau; N. Barros; A. Bernstein; M. Betancourt; M. Bishai; E. Blucher; J. Bouffard; N. Bowden; S. Brice; C. Bryan; L. Camilleri; J. Cao; J. Carlson; R. E. Carr; A. Chatterjee; M. Chen; S. Chen; M. Chiu; E. D. Church; J. I. Collar; G. Collin; J. M. Conrad; M. R. Convery; R. L. Cooper; D. Cowen; H. Davoudiasl; A. De Gouvea; D. J. Dean; G. Deichert; F. Descamps; T. DeYoung; M. V. Diwan; Z. Djurcic; M. J. Dolinski; J. Dolph; B. Donnelly; D. A. Dwyer; S. Dytman; Y. Efremenko; L. L. Everett; A. Fava; E. Figueroa-Feliciano; B. Fleming; A. Friedland; B. K. Fujikawa; T. K. Gaisser; M. Galeazzi; D. C. Galehouse; A. Galindo-Uribarri; G. T. Garvey; S. Gautam; K. E. Gilje; M. Gonzalez-Garcia; M. C. Goodman; H. Gordon; E. Gramellini; M. P. Green; A. Guglielmi; R. W. Hackenburg; A. Hackenburg; F. Halzen; K. Han; S. Hans; D. Harris; K. M. Heeger; M. Herman; R. Hill; A. Holin; P. Huber; D. E. Jaffe; R. A. Johnson; J. Joshi; G. Karagiorgi; L. J. Kaufman; B. Kayser; S. H. Kettell; B. J. Kirby; J. R. Klein; Yu. G. Kolomensky; R. M. Kriske; C. E. Lane; T. J. Langford; A. Lankford; K. Lau; J. G. Learned; J. Ling; J. M. Link; D. Lissauer; L. Littenberg; B. R. Littlejohn; S. Lockwitz; M. Lokajicek; W. C. Louis; K. Luk; J. Lykken; W. J. Marciano; J. Maricic; D. M. Markoff; D. A. Martinez Caicedo; C. Mauger; K. Mavrokoridis; E. McCluskey; D. McKeen; R. McKeown; G. Mills; I. Mocioiu; B. Monreal; M. R. Mooney; J. G. Morfin; P. Mumm; J. Napolitano; R. Neilson; J. K. Nelson; M. Nessi; D. Norcini; F. Nova; D. R. Nygren; G. D. Orebi Gann; O. Palamara; Z. Parsa; R. Patterson; P. Paul; A. Pocar; X. Qian; J. L. Raaf; R. Rameika; G. Ranucci; H. Ray; D. Reyna; G. C. Rich; P. Rodrigues; E. Romero Romero; R. Rosero; S. D. Rountree; B. Rybolt; M. C. Sanchez; G. Santucci; D. Schmitz; K. Scholberg; D. Seckel; M. Shaevitz; R. Shrock; M. B. Smy; M. Soderberg; A. Sonzogni; A. B. Sousa; J. Spitz; J. M. St. John; J. Stewart; J. B. Strait; G. Sullivan; R. Svoboda; A. M. Szelc; R. Tayloe; M. A. Thomson; M. Toups; A. Vacheret; M. Vagins; R. G. Van de Water; R. B. Vogelaar; M. Weber; W. Weng; M. Wetstein; C. White; B. R. White; L. Whitehead; D. W. Whittington; M. J. Wilking; R. J. Wilson; P. Wilson; D. Winklehner; D. R. Winn; E. Worcester; L. Yang; M. Yeh; Z. W. Yokley; J. Yoo; B. Yu; J. Yu; C. Zhang

    2015-03-23

    The US neutrino community gathered at the Workshop on the Intermediate Neutrino Program (WINP) at Brookhaven National Laboratory February 4-6, 2015 to explore opportunities in neutrino physics over the next five to ten years. Scientists from particle, astroparticle and nuclear physics participated in the workshop. The workshop examined promising opportunities for neutrino physics in the intermediate term, including possible new small to mid-scale experiments, US contributions to large experiments, upgrades to existing experiments, R&D plans and theory. The workshop was organized into two sets of parallel working group sessions, divided by physics topics and technology. Physics working groups covered topics on Sterile Neutrinos, Neutrino Mixing, Neutrino Interactions, Neutrino Properties and Astrophysical Neutrinos. Technology sessions were organized into Theory, Short-Baseline Accelerator Neutrinos, Reactor Neutrinos, Detector R&D and Source, Cyclotron and Meson Decay at Rest sessions.This report summarizes discussion and conclusions from the workshop.

  13. The Intermediate Neutrino Program

    E-print Network

    Adams, C; Ankowski, A M; Asaadi, J A; Ashenfelter, J; Axani, S N; Babu, K; Backhouse, C; Band, H R; Barbeau, P S; Barros, N; Bernstein, A; Betancourt, M; Bishai, M; Blucher, E; Bouffard, J; Bowden, N; Brice, S; Bryan, C; Camilleri, L; Cao, J; Carlson, J; Carr, R E; Chatterjee, A; Chen, M; Chen, S; Chiu, M; Church, E D; Collar, J I; Collin, G; Conrad, J M; Convery, M R; Cooper, R L; Cowen, D; Davoudiasl, H; De Gouvea, A; Dean, D J; Deichert, G; Descamps, F; DeYoung, T; Diwan, M V; Djurcic, Z; Dolinski, M J; Dolph, J; Donnelly, B; Dwyer, D A; Dytman, S; Efremenko, Y; Everett, L L; Fava, A; Figueroa-Feliciano, E; Fleming, B; Friedland, A; Fujikawa, B K; Gaisser, T K; Galeazzi, M; Galehouse, D C; Galindo-Uribarri, A; Garvey, G T; Gautam, S; Gilje, K E; Gonzalez-Garcia, M; Goodman, M C; Gordon, H; Gramellini, E; Green, M P; Guglielmi, A; Hackenburg, R W; Hackenburg, A; Halzen, F; Han, K; Hans, S; Harris, D; Heeger, K M; Herman, M; Hill, R; Holin, A; Huber, P; Jaffe, D E; Johnson, R A; Joshi, J; Karagiorgi, G; Kaufman, L J; Kayser, B; Kettell, S H; Kirby, B J; Klein, J R; Kolomensky, Yu G; Kriske, R M; Lane, C E; Langford, T J; Lankford, A; Lau, K; Learned, J G; Ling, J; Link, J M; Lissauer, D; Littenberg, L; Littlejohn, B R; Lockwitz, S; Lokajicek, M; Louis, W C; Luk, K; Lykken, J; Marciano, W J; Maricic, J; Markoff, D M; Caicedo, D A Martinez; Mauger, C; Mavrokoridis, K; McCluskey, E; McKeen, D; McKeown, R; Mills, G; Mocioiu, I; Monreal, B; Mooney, M R; Morfin, J G; Mumm, P; Napolitano, J; Neilson, R; Nelson, J K; Nessi, M; Norcini, D; Nova, F; Nygren, D R; Gann, G D Orebi; Palamara, O; Parsa, Z; Patterson, R; Paul, P; Pocar, A; Qian, X; Raaf, J L; Rameika, R; Ranucci, G; Ray, H; Reyna, D; Rich, G C; Rodrigues, P; Romero, E Romero; Rosero, R; Rountree, S D; Rybolt, B; Sanchez, M C; Santucci, G; Schmitz, D; Scholberg, K; Seckel, D; Shaevitz, M; Shrock, R; Smy, M B; Soderberg, M; Sonzogni, A; Sousa, A B; Spitz, J; John, J M St; Stewart, J; Strait, J B; Sullivan, G; Svoboda, R; Szelc, A M; Tayloe, R; Thomson, M A; Toups, M; Vacheret, A; Vagins, M; Van de Water, R G; Vogelaar, R B; Weber, M; Weng, W; Wetstein, M; White, C; White, B R; Whitehead, L; Whittington, D W; Wilking, M J; Wilson, R J; Wilson, P; Winklehner, D; Winn, D R; Worcester, E; Yang, L; Yeh, M; Yokley, Z W; Yoo, J; Yu, B; Yu, J; Zhang, C

    2015-01-01

    The US neutrino community gathered at the Workshop on the Intermediate Neutrino Program (WINP) at Brookhaven National Laboratory February 4-6, 2015 to explore opportunities in neutrino physics over the next five to ten years. Scientists from particle, astroparticle and nuclear physics participated in the workshop. The workshop examined promising opportunities for neutrino physics in the intermediate term, including possible new small to mid-scale experiments, US contributions to large experiments, upgrades to existing experiments, R&D plans and theory. The workshop was organized into two sets of parallel working group sessions, divided by physics topics and technology. Physics working groups covered topics on Sterile Neutrinos, Neutrino Mixing, Neutrino Interactions, Neutrino Properties and Astrophysical Neutrinos. Technology sessions were organized into Theory, Short-Baseline Accelerator Neutrinos, Reactor Neutrinos, Detector R&D and Source, Cyclotron and Meson Decay at Rest sessions.This report summ...

  14. The Intermediate Neutrino Program

    E-print Network

    C. Adams; J. R. Alonso; A. M. Ankowski; J. A. Asaadi; J. Ashenfelter; S. N. Axani; K. Babu; C. Backhouse; H. R. Band; P. S. Barbeau; N. Barros; A. Bernstein; M. Betancourt; M. Bishai; E. Blucher; J. Bouffard; N. Bowden; S. Brice; C. Bryan; L. Camilleri; J. Cao; J. Carlson; R. E. Carr; A. Chatterjee; M. Chen; S. Chen; M. Chiu; E. D. Church; J. I. Collar; G. Collin; J. M. Conrad; M. R. Convery; R. L. Cooper; D. Cowen; H. Davoudiasl; A. De Gouvea; D. J. Dean; G. Deichert; F. Descamps; T. DeYoung; M. V. Diwan; Z. Djurcic; M. J. Dolinski; J. Dolph; B. Donnelly; D. A. Dwyer; S. Dytman; Y. Efremenko; L. L. Everett; A. Fava; E. Figueroa-Feliciano; B. Fleming; A. Friedland; B. K. Fujikawa; T. K. Gaisser; M. Galeazzi; D. C. Galehouse; A. Galindo-Uribarri; G. T. Garvey; S. Gautam; K. E. Gilje; M. Gonzalez-Garcia; M. C. Goodman; H. Gordon; E. Gramellini; M. P. Green; A. Guglielmi; R. W. Hackenburg; A. Hackenburg; F. Halzen; K. Han; S. Hans; D. Harris; K. M. Heeger; M. Herman; R. Hill; A. Holin; P. Huber; D. E. Jaffe; R. A. Johnson; J. Joshi; G. Karagiorgi; L. J. Kaufman; B. Kayser; S. H. Kettell; B. J. Kirby; J. R. Klein; Yu. G. Kolomensky; R. M. Kriske; C. E. Lane; T. J. Langford; A. Lankford; K. Lau; J. G. Learned; J. Ling; J. M. Link; D. Lissauer; L. Littenberg; B. R. Littlejohn; S. Lockwitz; M. Lokajicek; W. C. Louis; K. Luk; J. Lykken; W. J. Marciano; J. Maricic; D. M. Markoff; D. A. Martinez Caicedo; C. Mauger; K. Mavrokoridis; E. McCluskey; D. McKeen; R. McKeown; G. Mills; I. Mocioiu; B. Monreal; M. R. Mooney; J. G. Morfin; P. Mumm; J. Napolitano; R. Neilson; J. K. Nelson; M. Nessi; D. Norcini; F. Nova; D. R. Nygren; G. D. Orebi Gann; O. Palamara; Z. Parsa; R. Patterson; P. Paul; A. Pocar; X. Qian; J. L. Raaf; R. Rameika; G. Ranucci; H. Ray; D. Reyna; G. C. Rich; P. Rodrigues; E. Romero Romero; R. Rosero; S. D. Rountree; B. Rybolt; M. C. Sanchez; G. Santucci; D. Schmitz; K. Scholberg; D. Seckel; M. Shaevitz; R. Shrock; M. B. Smy; M. Soderberg; A. Sonzogni; A. B. Sousa; J. Spitz; J. M. St. John; J. Stewart; J. B. Strait; G. Sullivan; R. Svoboda; A. M. Szelc; R. Tayloe; M. A. Thomson; M. Toups; A. Vacheret; M. Vagins; R. G. Van de Water; R. B. Vogelaar; M. Weber; W. Weng; M. Wetstein; C. White; B. R. White; L. Whitehead; D. W. Whittington; M. J. Wilking; R. J. Wilson; P. Wilson; D. Winklehner; D. R. Winn; E. Worcester; L. Yang; M. Yeh; Z. W. Yokley; J. Yoo; B. Yu; J. Yu; C. Zhang

    2015-04-01

    The US neutrino community gathered at the Workshop on the Intermediate Neutrino Program (WINP) at Brookhaven National Laboratory February 4-6, 2015 to explore opportunities in neutrino physics over the next five to ten years. Scientists from particle, astroparticle and nuclear physics participated in the workshop. The workshop examined promising opportunities for neutrino physics in the intermediate term, including possible new small to mid-scale experiments, US contributions to large experiments, upgrades to existing experiments, R&D plans and theory. The workshop was organized into two sets of parallel working group sessions, divided by physics topics and technology. Physics working groups covered topics on Sterile Neutrinos, Neutrino Mixing, Neutrino Interactions, Neutrino Properties and Astrophysical Neutrinos. Technology sessions were organized into Theory, Short-Baseline Accelerator Neutrinos, Reactor Neutrinos, Detector R&D and Source, Cyclotron and Meson Decay at Rest sessions.This report summarizes discussion and conclusions from the workshop.

  15. 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…

  16. Modeling DNA Replication Intermediates

    SciTech Connect

    Broyde, S.; Roy, D.; Shapiro, R.

    1997-06-01

    While there is now available a great deal of information on double stranded DNA from X-ray crystallography, high resolution NMR and computer modeling, very little is known about structures that are representative of the DNA core of replication intermediates. DNA replication occurs at a single strand/double strand junction and bulged out intermediates near the junction can lead to frameshift mutations. The single stranded domains are particularly challenging. Our interest is focused on strategies for modeling the DNA of these types of replication intermediates. Modeling such structures presents special problems in addressing the multiple minimum problem and in treating the electrostatic component of the force field. We are testing a number of search strategies for locating low energy structures of these types and we are also investigating two different distance dependent dielectric functions in the coulombic term of the force field. We are studying both unmodified DNA and DNA damaged by aromatic amines, carcinogens present in the environment in tobacco smoke, barbecued meats and automobile exhaust. The nature of the structure adopted by the carcinogen modified DNA at the replication fork plays a key role in determining whether the carcinogen will cause a mutation during replication that can initiate the carcinogenic process. In the present work results are presented for unmodified DNA.

  17. Quick Fluorescence-EXAFS: an Improved Method for Collection of Conventional XAFS Data, an Improved Method for Collection of Conventional XAFS Data and for Studying Reaction Intermediates in Dilute Systems.

    PubMed

    Murphy, L M; Dobson, B R; Neu, M; Ramsdale, C A; Strange, R W; Hasnain, S S

    1995-01-01

    The quick EXAFS (QuEXAFS) technique provides an alternative way of recording X-ray absorption fine-structure (XAFS) data where the scan time is reduced by moving the monochromator at a constant angular speed and recording the data ;on the fly'. Results are presented to show that the use of fluorescence detection with QuEXAFS is eminently suitable for studying reactions in dilute systems such as metalloproteins at a sub-minute time scale. In addition, we show that the fluorescence-QuEXAFS technique can reduce the overall time for normal data collection by some 50% compared with conventional step-by-step scanning EXAFS using the same optical system, thus reducing the total X-ray exposures of the samples. The use of X-rays for studying in situ redox reactions is demonstrated. PMID:16714788

  18. Covalent functionalization of graphene with reactive intermediates.

    PubMed

    Park, Jaehyeung; Yan, Mingdi

    2013-01-15

    Graphene, a material made exclusively of sp(2) carbon atoms with its ? electrons delocalized over the entire 2D network, is somewhat chemically inert. Covalent functionalization can enhance graphene's properties including opening its band gap, tuning conductivity, and improving solubility and stability. Covalent functionalization of pristine graphene typically requires reactive species that can form covalent adducts with the sp(2) carbon structures in graphene. In this Account, we describe graphene functionalization reactions using reactive intermediates of radicals, nitrenes, carbenes, and arynes. These reactive species covalently modify graphene through free radical addition, CH insertion, or cycloaddition reactions. Free radical additions are among the most common reaction, and these radicals can be generated from diazonium salts and benzoyl peroxide. Electron transfer from graphene to aryl diazonium ion or photoactivation of benzoyl peroxide yields aryl radicals that subsequently add to graphene to form covalent adducts. Nitrenes, electron-deficient species generated by thermal or photochemical activation of organic azides, can functionalize graphene very efficiently. Because perfluorophenyl nitrenes show enhanced bimolecular reactions compared with alkyl or phenyl nitrenes, perfluorophenyl azides are especially effective. Carbenes are used less frequently than nitrenes, but they undergo CH insertion and C?C cycloaddition reactions with graphene. In addition, arynes can serve as a dienophile in a Diels-Alder type reaction with graphene. Further study is needed to understand and exploit the chemistry of graphene. The generation of highly reactive intermediates in these reactions leads to side products that complicate the product composition and analysis. Fundamental questions remain about the reactivity and regioselectivity of graphene. The differences in the basal plane and the undercoordinated edges of graphene and the zigzag versus arm-chair configurations warrant comprehensive studies. The availability of well-defined pristine graphene starting materials in large quantities remains a key obstacle to the advancement of synthetic graphene chemistry. PMID:23116448

  19. Intermediate Accounting II Spring 2012

    E-print Network

    Carter, John

    in various financial reporting environments (accounting rules and principles) and their influenceKimbro Intermediate Accounting II Spring 2012 1 ACCT 532 INTERMEDIATE ACCOUNTING II Spring 2012 allocation processes. To learn the conceptual framework underlying Financial Accounting and Financial

  20. 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.

  1. Comparative effects of the H2O2 + Fe, H2O2 + Fe?UV systems on the degradation of nitrophenols and intermediates in aqueous solution

    Microsoft Academic Search

    Kouachi Nadia; Sehili Tahar

    1999-01-01

    The kinetics of degradation of nitrophenols were studied using Fenton's reagent alone and Fenton's reagent in combination with UV radiation. The effect of varying pH, temperature, H2O2\\/ Fe ratio and molecular oxygen on the process kinetics was also examined. Hydrogencarbonate ions and chloride ions have an inhibiting effect due to the scavenging of hydroxyl radical.The reaction intermediates were identified by

  2. Advances in studying bioinorganic reaction mechanisms: isotopic probes of activated oxygen

    E-print Network

    Roth, Justine P.

    Advances in studying bioinorganic reaction mechanisms: isotopic probes of activated oxygen intermediates in metalloenzymes Justine P Roth Metalloenzymes catalyze reactions of molecular oxygen and its reduced forms through the controlled formation of metal- bound, activated oxygen intermediates

  3. 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 favorable and rapid at hydrothermal conditions [1]. These results show that several relatively stable hydrothermal products from DBK are derived from the radical-coupled intermediates, and that these intermediates can be successfully captured using the tool of hydrothermal photolysis. Analysis of the product distributions and the quantum yields for the hydrothermal photolysis also provides convincing evidence for the previously proposed radical cleavage mechanism for the thermal reactions of DBK. [1] Yang et al. (2012) Geochim. Cosmochim. Acta 98, 48-65.

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

    PubMed

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

    2007-09-01

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

  5. Infrared and EPR Spectroscopic Characterization of a Ni(I) Species Formed by Photolysis of a Catalytically Competent Ni(I)-CO Intermediate in the Acetyl-CoA Synthase Reaction

    PubMed Central

    Bender, Güne?; Stich, Troy A.; Yan, Lifen; Britt, R. David; Cramer, Stephen P.; Ragsdale, Stephen W.

    2010-01-01

    Acetyl-CoA synthase (ACS) catalyzes the synthesis of acetyl-CoA from CO, coenzyme A (CoA), and a methyl-group from the CH3-Co3+ site in the corrinoid iron-sulfur protein (CFeSP). These are the key steps in the Wood-Ljungdahl pathway of anaerobic CO and CO2 fixation. The active site of ACS is the A-cluster, which is an unusual nickel-iron-sulfur cluster. There is significant evidence for the catalytic intermediacy of a CO-bound paramagnetic Ni species, with an electronic configuration of [Fe4S4]2+-(Nip1+–CO)-(Nid2+), where Nip and Nid represent the Ni centers in the A-cluster that are proximal and distal to the [Fe4S4]2+ cluster. This well-characterized Nip1+–CO intermediate is often called NiFeC species. Photolysis of the Nip1+–CO state generates a novel Nip1+ species (Ared*) with a rhombic electron paramagnetic resonance spectrum (g-values of 2.56, 2.10, 2.01) and an extremely low (1 kJ/mol) barrier for recombination with CO. We suggest that the photolytically generated Ared* species is (or is similar to) the Nip1+ species that binds CO (to form the Nip1+–CO species) and the methyl group (to form Nip-CH3) in the ACS catalytic mechanism. The results provide support for a binding site (an “alcove”) for CO near Nip, indicated by X-ray crystallographic studies of the Xe-incubated enzyme. We propose that, during catalysis, a resting Nip2+ state predominates over the active Nip1+ species (Ared*) that is trapped by the coupling of a one-electron transfer step to the binding of CO, which pulls the equilibrium toward Nip1+-CO formation. PMID:20669901

  6. Reactive intermediates revealed in secondary organic aerosol formation from isoprene

    PubMed Central

    Surratt, Jason D.; Chan, Arthur W. H.; Eddingsaas, Nathan C.; Chan, ManNin; Loza, Christine L.; Kwan, Alan J.; Hersey, Scott P.; Flagan, Richard C.; Wennberg, Paul O.; Seinfeld, John H.

    2010-01-01

    Isoprene is a significant source of atmospheric organic aerosol; however, the oxidation pathways that lead to secondary organic aerosol (SOA) have remained elusive. Here, we identify the role of two key reactive intermediates, epoxydiols of isoprene (IEPOX = ?-IEPOX + ?-IEPOX) and methacryloylperoxynitrate (MPAN), which are formed during isoprene oxidation under low- and high-NOx conditions, respectively. Isoprene low-NOx SOA is enhanced in the presence of acidified sulfate seed aerosol (mass yield 28.6%) over that in the presence of neutral aerosol (mass yield 1.3%). Increased uptake of IEPOX by acid-catalyzed particle-phase reactions is shown to explain this enhancement. Under high-NOx conditions, isoprene SOA formation occurs through oxidation of its second-generation product, MPAN. The similarity of the composition of SOA formed from the photooxidation of MPAN to that formed from isoprene and methacrolein demonstrates the role of MPAN in the formation of isoprene high-NOx SOA. Reactions of IEPOX and MPAN in the presence of anthropogenic pollutants (i.e., acidic aerosol produced from the oxidation of SO2 and NO2, respectively) could be a substantial source of “missing urban SOA” not included in current atmospheric models. PMID:20080572

  7. 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.

  8. Serotype specific polymerase chain reaction identifies a higher prevalence of streptococcus mutans serotype k and e in a random group of children with dental caries from the Southern region of India

    PubMed Central

    Rao, Arun Prasad; Austin, Ravi David

    2014-01-01

    Background: The development of dental caries has been associated with the oral prevalence of Streptococcus mutans. Four serotypes of S. mutans have been reported, namely serotype c, e, f, and k that are classified based on the composition and linkages of cell wall polysaccharides, response to physiological reactions, sero-specificity and 16s rRNA homology. Although the oral prevalence of S. mutans serotype c in Indian subjects with or without caries is known, the prevalence of the other three serotypes, e, f, and k are not known. Hence in this study, we have investigated the occurrence of the e, f, and k serotypes in children with or without caries within the age group of 6-12 years. Materials and Methods: Genomic DNA isolated from whole saliva of caries active (CA) and caries free (CF) groups were first screened for the presence of S. mutans by strain specific polymerase chain reaction (PCR). Those samples that tested positive for the presence of S. mutans were further analyzed by serotype specific PCR to identify the prevalence of the serotypes. Results: Strain specific PCR indicated a higher prevalence of S. mutans in CA group (80%) relative to CF group (43%). Further analysis of the S. mutans positive samples in both groups indicated a higher prevalence of serotype k and e, followed by serotype f in CA group. Conclusion: The present data clearly establishes a novel S. mutans serotype prevalence hierarchy in children from this region, compared with those that have been reported elsewhere. Besides, the data are also clinically significant as the occurrence of serotype k has been associated with infective endocarditis. PMID:25191062

  9. Simple, nondestructive test identifies metals

    NASA Technical Reports Server (NTRS)

    Dodds, D. J.

    1966-01-01

    Rapid, nondestructive test for identifying metals measures the characteristic potential difference produced by galvanic reaction between a reference electrode and the test metal. A drop of water is used as an electrolyte.

  10. Metal Reactions

    NSDL National Science Digital Library

    Oregon Museum of Science and Industry

    1997-01-01

    This is written as a static display, but can easily be adapted to a hands-on experiment for learners to conduct. Sodium phosphate, a clear colorless solution, is combined with six different metal ion solutions. Each metal (copper, nickel, iron, silver, cobalt, and barium) forms a different color and texture precipitate. Learners discover that a chemical reaction can be identified by a color change, and formation of a precipitate. They also learn that metals can be identified by their precipitates. For safety reasons, this activity should be conducted as a demonstration for younger audiences.

  11. 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 (Purdue); (UNC)

    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.

  12. Identifying Erosion

    NSDL National Science Digital Library

    COSI

    2009-01-01

    In this environmental science activity (page 3 of the PDF), leaners will identify and explain the causes of erosion. They will observe the effects of erosion on the surrounding area and further explore examples of erosion online. An extension activity allows learners to make a hands-on model of soil erosion. Though this was created as a pre-visit activity for a workshop about water flow and erosion, it makes a great stand-alone activity as well!

  13. 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

  14. Acyl silicates and acyl aluminates as activated intermediates in peptide formation on clays

    NASA Technical Reports Server (NTRS)

    White, D. H.; Kennedy, R. M.; Macklin, J.

    1984-01-01

    Glycine reacts with heating on dried clays and other minerals to give peptides in much better yield than in the absence of mineral. This reaction was proposed to occur by way of an activated intermediate such as an acyl silicate or acyl aluminate analogous to acyl phosphates involved in several biochemical reactions including peptide bond synthesis. The proposed mechanism has been confirmed by trapping the intermediate, as well as by direct spectroscopic observation of a related intermediate. The reaction of amino acids on periodically dried mineral surfaces represents a widespead, geologically realistic setting for prebiotic peptide formation via in situ activation.

  15. 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 and solvation state of organometallic intermediates in the reactivity, kinetics, and mechanism of organic reactions. By utilizing multinuclear DOSY methodologies at various temperatures, we also correlated solid-state X-ray structures with those in solution and discovered new reactive complexes, including a monomeric boron enolate, a product-inhibition aggregate, and a series of intermediates in the vinyl lithiation of allyl amines. As highlighted by our efforts, DOSY techniques provide practical and feasible NMR procedures and hold the promise of even more powerful insights when extended to three-dimensional experiments. PMID:19105594

  16. 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)…

  17. Bank and Nonbank Financial Intermediation

    Microsoft Academic Search

    PHILIP BOND

    2004-01-01

    Conglomerates, trade credit arrangements, and banks are all instances of financial intermediation. However, these institutions differ significantly in the extent to which the projects financed absorb aggregate intermediary risk, in whether or not intermediation is carried out by a financial specialist, in the type of projects they fund and in the type of claims they issue to investors. The paper

  18. Financial Intermediation and Endogenous Growth

    Microsoft Academic Search

    Valerie R Bencivenga; Bruce D Smith

    1991-01-01

    An endogenous growth model with multiple assets is developed. Agents who face random future liquidity needs accumulate capital and a liquid, but unproductive, asset. The effects of introducing financial intermediation into this environment are considered. Conditions are provided under which the introduction of intermediaries shifts the composition of savings toward capital, causing intermediation to be growth promoting. In addition, intermediaries

  19. The Intermedial Practises of Fandom

    Microsoft Academic Search

    KAARINA NIKUNEN

    The article 1 discusses formations of fan cultures in terms of intermediality. It examines the construction and consumption of media in three different Finnish fan groups: the fans of Xena: The Warrior Princess (XWP), fans of Ally McBeal and the fans of Finnish TV-host Marco Bjurström. The construction of intermedial relations of each fan group interestingly reveals the institutional and

  20. Intermediate Accounting I Spring 2013

    E-print Network

    Carter, John

    environments (accounting rules and principles) and their influence in the functioning of international marketsKimbro Intermediate Accounting I Spring 2013 1 ACCT 311 INTERMEDIATE ACCOUNTING I PIGT 305 - Spring framework underlying Financial Accounting and Financial Statements. To review the process of accumulating

  1. Accounting 306 Intermediate Accounting II

    E-print Network

    Barrash, Warren

    of generally accepted accounting principles (GAAP) covering: · Current liabilities · Contingencies · BondsAccounting 306 Intermediate Accounting II Spring 2013 Syllabus Meeting Time: SECTION 1: M,W 12@boisestate.edu Required Texts: Spiceland, Sepe, and Nelson, Intermediate Accounting (7th Edition), McGraw-Hill. Course

  2. Higgs bosons: Intermediate mass range at e+e- colliders

    Microsoft Academic Search

    V. Barger; K. Cheung; A. Djouadi; B. A. Kniehl; P. M. Zerwas

    1994-01-01

    We elaborate on the production of the standard model Higgs particle at high-energy e+e- colliders through the reaction e+e--->ZH. Particular emphasis is put on the intermediate mass range. In addition to the signal we discuss in detail the background processes. Angular distributions which are sensitive to the spin and parity of the Higgs particle are analyzed.

  3. Single-stranded heteroduplex intermediates in ? Red homologous recombination

    Microsoft Academic Search

    Marcello Maresca; Axel Erler; Jun Fu; Anne Friedrich; Youming Zhang; A Francis Stewart

    2010-01-01

    BACKGROUND: The Red proteins of lambda phage mediate probably the simplest and most efficient homologous recombination reactions yet described. However the mechanism of dsDNA recombination remains undefined. RESULTS: Here we show that the Red proteins can act via full length single stranded intermediates to establish single stranded heteroduplexes at the replication fork. We created asymmetrically digestible dsDNA substrates by exploiting

  4. 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.

  5. Phospholipid synthesis: Oxazaphospholanes and dioxaphospholanes as intermediates

    PubMed Central

    Eibl, Hansjörg

    1978-01-01

    The synthesis of phospholipids described herein allows an almost quantitative conversion of 1,2-diacylglycerols to phospholipids via cyclic intermediates such as oxazaphospholanes or dioxaphospholanes, which are the only products observed when ethanolamine or ethylene glycol is allowed to react with phosphatidic acid dichlorides. The acidic hydrolysis of the cyclic intermediates occurs rapidly without the formation of by-products and results in phospholipids differing in the structure of the polar part depending on which vicinal aminoalcohols or diols are used. For instance, phosphatidylethanolamines, -(N-methyl)ethanolamines, and -serine benzyl esters are directly formed from the corresponding oxazaphospholanes. Phosphatidyl(N,N-dimethyl)ethanolamines and -cholines are prepared by amination of the bromoethyl esters of phosphatidic acids, which can be obtained by treatment of dioxaphospholanes with sodium bromide. A similar sequence of reactions starting from 1-acyl-2-benzylglycerols or monoacylpropane-1,3-diols will result in the respective monoacyl analogues such as lysophospholipids or the so-called desoxylysophospholipids. The mild reaction conditions, good yields (>90% based on diacylglycerol), and high purity of the products make this route an attractive procedure for phospholipid synthesis; in addition, it avoids the need for chromatography and thus can be utilized on a large scale. PMID:16592558

  6. Protein targets of xenobiotic reactive intermediates.

    PubMed

    Pumford, N R; Halmes, N C

    1997-01-01

    Many xenobiotics are metabolically activated to electrophilic intermediates that form covalent adducts with proteins; the mechanism of toxicity is either intrinsic or idiosyncratic in nature. Many intrinsic toxins covalently modify cellular proteins and somehow initiate a sequence of events that leads to toxicity. Major protein adducts of several intrinsic toxins have been identified and demonstrate significant decreases in enzymatic activity. The reactivity of intermediates and subcellular localization of major targets may be important in the toxicity. Idiosyncratic toxicities are mediated through either a metabolic or immune-mediated mechanism. Xenobiotics that cause hypersensitivity/autoimmunity appear to have a limited number of protein targets, which are localized within the subcellular fraction where the electrophile is produced, are highly substituted, and are accessible to the immune system. Metabolic idiosyncratic toxins appear to have limited targets and are localized within a specific subcellular fraction. Identification of protein targets has given us insights into mechanisms of xenobiotic toxicity. PMID:9131248

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

    SciTech Connect

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

    1996-06-01

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

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

    Cancer.gov

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

  9. Intermediate dosimetric quantities.

    PubMed

    Kellerer, A M; Hahn, K; Rossi, H H

    1992-04-01

    The transfer of energy from ionizing radiation to matter involves a series of steps. In wide ranges of their energy spectra photons and neutrons transfer energy to an irradiated medium almost exclusively by the production of charged particles which ionize and thereby produce electrons that can ionize in turn. The examination of these processes leads to a series of intermediate quantities. One of these is kerma, which has long been employed as a measure of the energy imparted in the first of the interactions. It depends only on the fluence of uncharged particles and is therefore--unlike absorbed dose and electron fluence--insensitive to local differences of receptor geometry and composition. An analogous quantity for charged-particle fields, cema (converted energy per unit mass), is defined, which quantifies the energy imparted in terms of the interactions of charged particles, disregarding energy dissipation by secondary electrons. Cema can be expressed as an integral over the fluence of ions times their stopping power. However, complications arise when the charged particles are electrons, and when their fluence cannot be separated from that of the secondaries. The resulting difficulty can be circumvented by the definition of reduced cema. This quantity corresponds largely to the concept employed in the cavity theory of Spencer and Attix. In reduced cema not all secondary electrons but all electrons below a chosen cutoff energy, delta, are considered to be absorbed locally. When the cutoff energy is reduced, cema approaches absorbed dose and thereby becomes sensitive to highly local differences in geometry or composition. With larger values of delta, reduced cema is a useful parameter to specify the dose-generating potential of a charged-particle field 'free in air' or in vacuo. It is nearly equal to the mean absorbed dose in a sphere with radius equal to the range of electrons of energy delta. Reduced cema is a function of the fluence at the specified location at and above the chosen cutoff energy. Its definition requires a modification of restricted linear collision stopping power, L delta, and it is recommended that the definition of L delta be so changed. PMID:1561314

  10. Identification of thioether intermediates in the reductive transformation of gonyautoxins into saxitoxins by thiols

    Microsoft Academic Search

    Shigeru Sato; Ryuichi Sakai; Masaaki Kodama

    2000-01-01

    O-Sulfate group of gonyautoxin I and IV is transformed into methylene to form neosaxitoxin by thiols such as glutathione, a common cellular scavenger, in mild conditions. We isolated the intermediate of this conversion and propose that this reaction proceeds through formation of thiohemiketal, 1,2 shift to form stable thioether intermediate, and then redox exchange at sulfur atom to form the

  11. Site Seeing: Intermediate

    NSDL National Science Digital Library

    This field activity introduces students to the concept of a system. Students identify the components, inputs and outputs of the local system at a range of biometry study sites, as well as the boundaries of their investigations at these sites in terms of space and time. Collected data from the different sites are analyzed and compared. The activity includes a student worksheet and data charts. Equipment needed to do this activity includes a compass and camera. This is a learning activity associated with the GLOBE Land Cover/Biology investigations and is supported by the GLOBE Teacher's Guide, Land Cover/Biology.

  12. 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 ?, where ? is in the range 0 < ? < 1. Our results show that at small ? values the system is reaction limited, but as ? increases it crosses over to a diffusion limited behavior. At early times, for small ? values, the particle density falls slower than for larger ? values. This fall-off goes over a crossover point, around the value of ? = 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 ? 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.

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

    PubMed Central

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

    1985-01-01

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

  14. Gas Producing Micro-Reaction

    NSDL National Science Digital Library

    2014-01-28

    In this chemistry activity, learners use common chemicals and metals to examine reactions that produce gaseous substances. Learners will identify the gases produced and write a balanced equation for each reaction. Use this activity to also introduce learners to single displacement and double displacement reactions, two types of chemical reactions.

  15. HETEROGENOUS DEGRADATION OF OXYGENATED INTERMEDIATES

    EPA Science Inventory

    Issues surrounding the importance of including heterogeneous processes when determining the fate of oxygenated intermediates in the troposphere are discussed. esults of recent investigations are reviewed and preliminary data from a laboratory study are presented. n the laboratory...

  16. Tachyon field in intermediate inflation

    SciTech Connect

    Campo, Sergio del; Herrera, Ramon; Toloza, Adolfo [Instituto de Fisica, Pontificia Universidad Catolica de Valparaiso, Casilla 4059, Valparaiso (Chile)

    2009-04-15

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

  17. Plasticity of Intermediate Filament Subunits

    E-print Network

    Kirmse, Robert

    Intermediate filaments (IFs) assembled in vitro from recombinantly expressed proteins have a diameter of 8–12 nm and can reach several micrometers in length. IFs assemble from a soluble pool of subunits, tetramers in the ...

  18. Moving beyond Intermediate English Proficiency

    ERIC Educational Resources Information Center

    Jewell, Mary

    2009-01-01

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

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

    SciTech Connect

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

    1984-03-01

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

  20. Mechanism based lumping of pyrolysis reactions: Lumping by reactive intermediates

    Microsoft Academic Search

    D. M. Fake; Abhash Nigam; M. T. Klein

    1997-01-01

    A mechanism-oriented kinetic model has been developed with a small CPU requirement which allows the model to be incorporated into a reactor simulation with fluid dynamics and heat and mass transfer. The model achieves a small CPU requirement by lumping rdicals with similar reactivity together. A 42-lump subset of the 105 or more radicals is used to describe all the

  1. Monoclonal antibodies against myofibrillar components of rat skeletal muscle decorate the intermediate filaments of cultured cells.

    PubMed

    Lin, J J

    1981-04-01

    Monospecific antibodies were produced in vitro by fusing mouse myeloma cells with spleen cells from a BALB/c mouse immunized with rat skeletal myofibrils. After cloning 3 times on agarose, two stable clones were obtained and chosen for further characterization. The first clone, JLB1, produced an antibody that recognizing an antigen distributed in the M-line region and on either site of the Z line of myofibrils. The second clone, JLB7, produced an antibody reacting only with an antigen located at the M-line region of myofibrils. Both JLB1 and JLB7 antibodies decorate the typical intermediate filaments of a variety of cultured cells. Colcemid treatment of cells before reaction with both antibodies resulted in the coiling or capping (or both) of the fibers around the nucleus. Brief treatment of cells with cytochalasin B did not affect the integrity of the fibers stained by both antibodies whereas, under the same conditions, microfilament bundles visualized by another monoclonal antibody (JLA20) against actin were disassembled into many aggregates in the cytoplasm. Identical staining patterns of the intermediate filaments are obtained by double-label immunofluorescence microscopy of the same cell stained with these monoclonal antibodies and rabbit autoimmune serum (which has been shown to react with the components of the intermediate filaments). By using immunoprecipitation, protein bands at 210,000 and 95,000 daltons from chicken embryo fibroblasts were identified as the potential antigens recognized by JLB1 and JLB7 monoclonal antibodies, respectively. The widespread occurrence of these antigenic determinants in different cultured cells suggests the highly conservative property of these intermediate-filament components. PMID:7017730

  2. Grand Unification with Intermediate Scale Gauge Symmetries

    NASA Astrophysics Data System (ADS)

    Keith, Evan J.

    Using the values of the gauge coupling constants at the scale M_{Z} derived from recent data from the CERN e^+e^ - collider LEP, we consider the breaking of the non-supersymmetric grand unification group SO(10) to the standard model gauge group through several chains. Some chains are ruled out from experimental constraints. We determine the intermediate and unification scales for chains containing one intermediate breaking scale by use of two -loop renormalization group equations with appropriate matching conditions. For the allowed chains, the intermediate scale is high, in the range of 10^9-10 ^{11} GeV. We also determine the range of intermediate and unification scales for chains containing two intermediate stages. We identify chains where new chargeless gauge bosons are possible at relatively low energy ({~}1 TeV), but as expected find none where extra light charged gauge bosons can occur. However in a supersymmetric version of SO(10) with a judicious choice of Higgs content, we find that, contrary to commonly held belief, the SU(2) _{R} breaking scale can be low and hence new charged bosons may be within the reach of existing or future colliders. We also look at an example of a larger group, SU(16), that provides the possibility for a rich low energy gauge structure. In addition, we investigate the status of predictive fermion mass ansatze which make use of the grand unification scale conditions m_{e} = m_ {d}/3, m_mu = 3m_{s }, and | V_{cb }| = sqrt{m_{c}/m _{t}} in non-supersymmetric SO(10) grand unification. The gauge symmetry below an intermediate symmetry breaking scale M_ {I} is assumed to be that of the standard model with either one Higgs doublet or two Higgs doublets. We find in both cases that a maximum of four standard model parameters may be predicted within 1sigma experimental ranges in addition to predicting the top mass. We also discuss the possibility of third generation Yukawa coupling unification in the two Higgs standard model which leads to a greater predictive ability but also requires a large top quark mass (>180 GeV) and constrains alpha_{3c}(M_{Z }) to be near its lower 1sigma bound.

  3. Highly sulfurated heterocycles via dithiiranes and trithietanes as key intermediates.

    PubMed

    Mloston, Grzegorz; Majchrzak, Agnieszka; Senning, Alexander; Søtofte, Inger

    2002-08-01

    2,2,4,4-Tetramethyl-3-thioxocyclobutanone (8b) easily reacts with gaseous chlorine to yield the stable alpha-chloro sulfenyl chloride 10. The same product was obtained when 8b was treated either with phosphorus pentachloride (PCl(5)) or sulfuryl chloride (SO(2)Cl(2)) in CCl(4) solution. Sulfur dichloride (SCl(2)) reacts with 8b to give the alpha-chloro thiosulfenyl chloride 12 along with an almost equimolar amount of the trisulfide 13b. The less reactive disulfur dichloride (S(2)Cl(2)) was shown to react slowly with 8b and the symmetrical tetrasulfide 15 was found as the exclusive product. The pure thiosulfenyl chloride 12 added to adamantanethione (8c) yielded the unsymmetrical trisulfide 13c. When 12 was treated with thioacetic acid, the acetylated trisulfide 17 was formed in high yield. "Unzipping" reactions with the acetylated disulfide 16 and trisulfide 17 with morpholine in THF at -40 degrees C led to the formation of mixtures of two sulfur-rich heterocycles identified as the pentathiepane 6b and the hexathiepane 7b. A mixture of analogous products was obtained when alpha-chloro sulfenyl chloride 10 was treated with sodium sulfide in anhydrous THF at -40 degrees C. The formation of 6b and 7b is believed to occur via the intermediate dithiirane 1b and/or the isomeric thiosulfine 2b. In the case of 17 the reaction starts probably with the formation of a nonisolable tetrathiane 18b as presented in Scheme 5. PMID:12153270

  4. Reactions of aminomalononitrile with electrophiles. [simulating prebiotic conditions

    NASA Technical Reports Server (NTRS)

    Thanassi, J. W.

    1975-01-01

    Aminomalononitrile (HCN trimer) reacts with electrophiles such as aldehydes and acrylonitrile under very mild conditions of temperature and pH to produce intermediates which, after acid hydrolysis, yield amino acids. The following amino acids have been identified and quantitated: glycine, D,L-erythro- and D,L-threo-beta-hydroxyaspartic acids, D,L glutamic acid, and D,L-threonine and allo-threonine. The mechanism of their formation and the possible significance of these reactions in prebiotic syntheses are discussed.

  5. Special Relativity and Reactions with Unstable Nuclei

    E-print Network

    C. A. Bertulani

    2005-05-04

    Dynamical relativistic effects are often neglected in the description of reactions with unstable nuclear beams at intermediate energies (E ~ 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.

  6. Stability of thioester intermediates in ubiquitin-like modifications

    PubMed Central

    Song, Jing; Wang, Jianghai; Jozwiak, Agnieszka A; Hu, Weidong; Swiderski, Piotr M; Chen, Yuan

    2009-01-01

    Ubiquitin-like modifications are important mechanisms in cellular regulation, and are carried out through several steps with reaction intermediates being thioester conjugates of ubiquitin-like proteins with E1, E2, and sometimes E3. Despite their importance, a thorough characterization of the intrinsic stability of these thioester intermediates has been lacking. In this study, we investigated the intrinsic stability by using a model compound and the Ubc9?SUMO-1 thioester conjugate. The Ubc9?SUMO-1 thioester intermediate has a half life of approximately 3.6 h (hydrolysis rate k = 5.33 ± 2.8 ×10?5 s?1), and the stability decreased slightly under denaturing conditions (k = 12.5 ± 1.8 × 10?5 s?1), indicating a moderate effect of the three-dimensional structural context on the stability of these intermediates. Binding to active and inactive E3, (RanBP2) also has only a moderate effect on the hydrolysis rate (13.8 ± 0.8 × 10?5 s?1 for active E3 versus 7.38 ± 0.7 × 10?5 s?1 for inactive E3). The intrinsically high stability of these intermediates suggests that unwanted thioester intermediates may be eliminated enzymatically, such as by thioesterases, to regulate their intracellular abundance and trafficking in the control of ubiquitin-like modifications. PMID:19785004

  7. Identification of the intermediate hosts of Habronema microstoma and Habronema muscae under field conditions.

    PubMed

    Traversa, D; Otranto, D; Iorio, R; Carluccio, A; Contri, A; Paoletti, B; Bartolini, R; Giangaspero, A

    2008-09-01

    A polymerase chain reaction (PCR)-based assay was used for the specific detection of Habronema microstoma and Habronema muscae (Nematoda, Spirurida) in order to identify the intermediate hosts of both nematode species under field conditions. A total of 1087 netted and 165 laboratory-bred flies were tested. Flies were identified as Musca domestica Linnaeus 1758, Musca autumnalis De Geer 1776, Haematobia irritans (Linnaeus 1758), Haematobia titillans (De Geer 1907) and Stomoxys calcitrans (Linnaeus 1758) (Muscidae). Genomic DNA was extracted from pools of fly heads, thoraces and abdomens, and 703 samples were subjected to a duplex two-step semi-nested PCR assay to specifically detect diagnostic regions within the ribosomal ITS2 sequence of both H. microstoma and H. muscae. Stomoxys calcitrans specimens were positive for H. microstoma DNA and M. domestica specimens were positive for H. muscae DNA. In particular, PCR-positive samples derived from both farm-netted and laboratory-bred flies. The present study represents the first evidence of the vectorial competence of different fly species as intermediate hosts of Habronema stomachworms under field conditions. We discuss the roles of S. calcitrans and M. domestica in transmitting H. microstoma and H. muscae. PMID:18816277

  8. 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

    2014-09-30

    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.

  9. 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.

  10. Cryogenic Ion Vibrational Spectroscopy of - CH Activation Intermediates

    NASA Astrophysics Data System (ADS)

    Marsh, Brett; Garand, Etienne

    2013-06-01

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

  11. 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; Batini?-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

  12. ChemTeacher: Combination Reactions

    NSDL National Science Digital Library

    2011-01-01

    ChemTeacher compiles background information, videos, articles, demonstrations, worksheets and activities for high school teachers to use in their classrooms. The Combination Reactions page includes resources for teaching students about identifying and predicting combination reactions.

  13. ChemTeacher: Decomposition Reactions

    NSDL National Science Digital Library

    2012-07-23

    ChemTeacher compiles background information, videos, articles, demonstrations, worksheets and activities for high school teachers to use in their classrooms. The Decomposition Reactions page includes resources for teaching students about identifying and predicting decomposition reactions.

  14. Formation and identification of intermediates in the visible-light-assisted photodegradation of sulforhodamine-B dye in aqueous TiO2 dispersion.

    PubMed

    Chen, Chuncheng; Zhao, Wei; Li, Jingyi; Zhao, Jincai; Hidaka, Hisao; Serpone, Nick

    2002-08-15

    The photodegradation of dye pollutants under visible light irradiation in TiO2 dispersions continues to draw considerable attention because of the greater effective utilization of solar energy and its potential application in treating wastewaters from textile and photographic industries. To get a better handle on the mechanistics details of this TiO2-assisted photodegradation of dyes with visible radiation, the process was examined by UV-visible spectroscopy, high-performance liquid chromatography, silica gel thin-layer chromatography, and matrix-assisted laser desorption ionization time-of-flight mass spectrometric techniques to separate and identify the N-de-ethylated intermediate products during the photodegradation of N,N,N,N-tetraethylsulforhodamine-B (SRB) in the absence and presence of iodide ions. Five intermediates, namely, N,N-diethyl-N'-ethyl-sulforhodamine, N,N-diethylsulforhodamine, N-ethyl-N'-ethylsulforhodamine, N-ethylsulforhodamine, and sulforhodamine were thus identified. They correspond to intermediate products having a different number of N-ethyl groups, which are removed sequentially from the SRB molecule. The reaction process was accompanied by the oxidation of I- to I3- in the presence of I- ions. Formation of radicals was assessed by spin-trap electron spin resonance spectrometry. The experimental results provided the basis for a more detailed description of the reaction mechanism(s). PMID:12214655

  15. 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…

  16. Integrated one-flow synthesis of heterocyclic thioquinazolinones through serial microreactions with two organolithium intermediates.

    PubMed

    Kim, Heejin; Lee, Hyune-Jea; Kim, Dong-Pyo

    2015-02-01

    The synthesis of pharmaceutical compounds via short-lived intermediates in a microreactor is attractive, because of the fast flow and high throughput. Additionally, intermediates can be utilized sequentially to efficiently build up a library in a short time. Here we present an integrated microfluidic synthesis of biologically active thioquinazolinone libraries. Generation of o-lithiophenyl isothiocyanate and subsequent reaction with aryl isocyanate is optimized by controlling the residence time in the microreactor to 16?ms at room temperature. Various S-benzylic thioquinazolinone derivatives are synthesized within 10?s in high yields (75-98%) at room temperature. These three-step reactions involve two organolithium intermediates, an isothiocyanate-functionalized aryllithium intermediate, and a subsequent lithium thiolate intermediate. We also demonstrate the gram-scale synthesis of a multifunctionalized thioquinazolinone in the microfluidic device with a high yield (91%) and productivity (1.25?g in 5?min). PMID:25521442

  17. Mineral catalyzed hydrothermal reactions as precursors to extant anabolic pathways

    NASA Astrophysics Data System (ADS)

    Cody, G. D.

    Investigations into hydrothermal reactions under conditions of moderate hydrostatic pressure and in the presence of transition metal sulfides reveal reaction pathways the bear remarkable similarity with extant anabolic reactions. First, it is seen that most common transition metal sulfides are capable of promoting all of the key reactions at the core of Acetyl Co-A synthesis. These include CO reduction to methyl groups and carbonyl insertion to form transferable acetyl groups. The synthesis of alpha-keto acids are also promoted, presumably by double carbonylation. A pathway starting with CO2 and H2 has been identified leading to the synthesis of citric acid. Citric acid provides a crucial abiotic, anabolic, branch point to the prebiotic synthesis of various amino acids, as well. As the pyrimidines, orotic acid and uracil. In many cases the abiotic reaction pathways differ slightly from extant anabolic pathways by shunting past particularly reactive intermediates, e.g. oxaloacetic acid. These reactions have the capacity to provide the prebiotic world with many, but not all, of the molecular constituents to aid the emergence of an RNA world.

  18. Amination-reduction reaction as simple protocol for potential boronic molecular receptors. Insight in supramolecular structure directed by weak interactions

    Microsoft Academic Search

    Agnieszka Adamczyk-Wo?niak; Izabela Madura; Alicja Pawe?ko; Andrzej Sporzy?ski; Anna ?ubrowska; Jacek ?y?a

    2011-01-01

    The synthesis of the potential molecular receptors in the amination-reduction reaction has been investigated within the model\\u000a system comprising (2-formylphenyl)boronic acid and morpholine. The 3-amine substituted benzoxaborole was identified to be\\u000a the intermediate of the synthesis and the unsubstituted benzoxaborole as the by-product resulting from reduction of the starting\\u000a material. The insight into the reactivity of the starting materials as

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

    PubMed

    Amin, Rowayda Mohamed; Hamdy, Islam; Osman, Ihab Mohamed

    2015-01-01

    Intermediate uveitis is a subset of intraocular inflammation where vitritis is the most consistent sign, with or without snowball opacities or snow banks over the pars plana. Some patients will have an associated underlying systemic disease such as sarcoidosis, multiple sclerosis, ocular tuberculosis, inflammatory bowel disease, possibly Behçet's disease and intraocular lymphoma, whereas some will be classified as pars planitis in case of the lack of an identifiable systemic disease association. Our patient, a 47-year-old woman, developed intermediate uveitis after cataract surgery in her right eye, was misdiagnosed as pars planitis, and received steroid monotherapy for 8?months. Her inflammation only fully resolved after vitrectomy with removal of the intraocular lens (IOL) and capsular bag. Oral fluconazole and intravitreal amphotericin B injection had failed to resolve her inflammation when Candida albicans was identified as the cause of her persistent intermediate uveitis. PMID:25870216

  20. 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

  1. Pegasus: An Efficient Intermediate Representation

    Microsoft Academic Search

    Mihai Budiu; Seth Copen Goldstein

    2002-01-01

    We present Pegasus, a compact and expressive intermediate representation for imperative languages. The representation is suitable for target architectures supporting predicated exe- cution and aggressive speculation. In Pegasus information about the global dataflow of the program is encoded in local structures, enabling compact and efficient algorithms for pro- gram optimizations. As a proof of the versatility of Pegasus, we have

  2. Epi Bio 401 INTERMEDIATE EPIDEMIOLOGY

    E-print Network

    Contractor, Anis

    an epidemiologic methods topic first covered in Epi Bio 301, and a 30 minute guided discussion of a paper from and critically interpret literature using epidemiologic methods. · Describe the pathophysiology and basicEpi Bio 401 INTERMEDIATE EPIDEMIOLOGY 1.0 Credit Fall Quarter 2013 (September 25 ­ December 11

  3. Intermediate language extensions for parallelism

    Microsoft Academic Search

    Jisheng Zhao; Vivek Sarkar

    2011-01-01

    An Intermediate Language (IL) specifies a program at a level of abstraction that includes precise semantics for state updates and control flow, but leaves unspecified the low-level software and hardware mechanisms that will be used to implement the semantics. Past ILs have followed the Von Neumann execution model by making sequential execution the default, and by supporting parallelism with runtime

  4. Laser spectroscopy of combustion intermediates in a supersonic jet expansion

    Microsoft Academic Search

    Prabhakar Misra

    1994-01-01

    A detailed analysis of the laser-induced fluorescence spectra of jet-cooled alkoxy, alkylthio and aromatic radicals has helped to characterize these radicals spectroscopically. All three groups of radicals are involved in the chemistry of organic fuel combustion. A clearer knowledge about the spectroscopy of these chemical intermediates is necessary for improved understanding of the free-radical controlled reaction steps occurring in combustion

  5. Laser spectroscopy of combustion intermediates in a supersonic jet expansion

    NASA Astrophysics Data System (ADS)

    Misra, Prabhakar

    1994-03-01

    A detailed analysis of the laser-induced fluorescence spectra of jet-cooled alkoxy, alkylthio and aromatic radicals has helped to characterize these radicals spectroscopically. All three groups of radicals are involved in the chemistry of organic fuel combustion. A clearer knowledge about the spectroscopy of these chemical intermediates is necessary for improved understanding of the free-radical controlled reaction steps occurring in combustion processes.

  6. Dynamical aspects of intermediate-energy heavy-ion collisons

    Microsoft Academic Search

    James Francis Dempsey

    1997-01-01

    The production of neutrons, light charged particles (LCPs), and intermediate-mass fragments (IMFs), from the four reactions 55 MeV\\/A [124,136Xe] + [112,124Sn], is studied with an experimental apparatus which is highly efficient for the detection of both charged particles and neutrons. The IMFs are found more localized in the mid-velocity region (parallel velocity close to center of mass) than are the

  7. The Utility Standard and the Patentability of Intermediate Technology

    Microsoft Academic Search

    Reiko Aoki; Sadao Nagaoka

    2003-01-01

    We explore the consequences of the utility requirement on speed of innovation, welfare and public policy. A weak utility requirement means that an intermediate technology with no immediate application or commercial value is patentable. Using a model of two stage innovation with free entry and trade secrecy, we identify cases when patentability is beneficial to society. Although a firm may

  8. Molluscicidal saponins from Anagallis arvensis against schistosome intermediate hosts.

    PubMed

    Abdel-Gawad, M M; El-Amin, S M; Ohigashi, H; Watanabe, Y; Takeda, N; Sugiyama, H; Kawanaka, M

    2000-02-01

    The molluscicidal activity of saponins isolated from the plant Anagallis arvensis (Primulaceae) was studied against schistosome intermediate hosts, Biomphalaria glabrata and Oncomelania quadrasi. @Strong molluscicidal activity was found in two compounds called desglucoanagalloside B and anagalloside B. Their structures were identified on the basis of chemical and spectroscopic analyses and their activities are comparable to that of the synthetic molluscicide, niclosamide. PMID:10777853

  9. Substrate radical intermediates in soluble methane monooxygenase

    SciTech Connect

    Liu Aimin [Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455 (United States); Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455 (United States); Jin Yi [Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 (United States); Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455 (United States); Zhang Jingyan [Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455 (United States); Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455 (United States); Brazeau, Brian J. [Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455 (United States); Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455 (United States); Lipscomb, John D. [Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455 (United States) and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455 (United States)]. 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.

  10. Photocatalytic Reductive Cyclizations of Enones: Divergent Reactivity of Photogenerated Radical and Radical Anion Intermediates

    PubMed Central

    Du, Juana; Espelt, Laura Ruiz; Guzei, Ilia A.; Yoon, Tehshik P.

    2011-01-01

    Photocatalytic reactions of enones using metal polypyridyl complexes proceed by very different reaction manifolds in the presence of either Lewis or Brønsted acid additives. Previous work from our lab demonstrated that photocatalytic [2+2] cycloadditions of enones required the presence of a Lewis acidic co-catalyst, presumably to activate the enone and stabilize the key radical anion intermediate. On the other hand, Brønsted acid activators alter this reactivity and instead promote reductive cyclization reactions of a variety of aryl and aliphatic enones via a neutral radical intermediate. These two distinct reactive intermediates give rise to transformations differing in the connectivity, stereochemistry, and oxidation state of their products. In addition, this reductive coupling method introduces a novel approach to the tin-free generation of ?-ketoradicals that react with high diastereoselectivity and with the high functional group compatibility typical of radical cyclization reactions. PMID:22121471

  11. Intermediate Temperature Solid Oxide Fuel Cell Development

    SciTech Connect

    S. Elangovan; Scott Barnett; Sossina Haile

    2008-06-30

    Solid oxide fuel cells (SOFCs) are high efficiency energy conversion devices. Present materials set, using yttria stabilized zirconia (YSZ) electrolyte, limit the cell operating temperatures to 800 C or higher. It has become increasingly evident however that lowering the operating temperature would provide a more expeditious route to commercialization. The advantages of intermediate temperature (600 to 800 C) operation are related to both economic and materials issues. Lower operating temperature allows the use of low cost materials for the balance of plant and limits degradation arising from materials interactions. When the SOFC operating temperature is in the range of 600 to 700 C, it is also possible to partially reform hydrocarbon fuels within the stack providing additional system cost savings by reducing the air preheat heat-exchanger and blower size. The promise of Sr and Mg doped lanthanum gallate (LSGM) electrolyte materials, based on their high ionic conductivity and oxygen transference number at the intermediate temperature is well recognized. The focus of the present project was two-fold: (a) Identify a cell fabrication technique to achieve the benefits of lanthanum gallate material, and (b) Investigate alternative cathode materials that demonstrate low cathode polarization losses at the intermediate temperature. A porous matrix supported, thin film cell configuration was fabricated. The electrode material precursor was infiltrated into the porous matrix and the counter electrode was screen printed. Both anode and cathode infiltration produced high performance cells. Comparison of the two approaches showed that an infiltrated cathode cells may have advantages in high fuel utilization operations. Two new cathode materials were evaluated. Northwestern University investigated LSGM-ceria composite cathode while Caltech evaluated Ba-Sr-Co-Fe (BSCF) based pervoskite cathode. Both cathode materials showed lower polarization losses at temperatures as low as 600 C than conventional manganite or cobaltite cathodes.

  12. Glycolytic intermediates induce amorphous calcium carbonate formation in crustaceans.

    PubMed

    Sato, Ai; Nagasaka, Seiji; Furihata, Kazuo; Nagata, Shinji; Arai, Isao; Saruwatari, Kazuko; Kogure, Toshihiro; Sakuda, Shohei; Nagasawa, Hiromichi

    2011-04-01

    It has been thought that phosphorus in biominerals made of amorphous calcium carbonate (ACC) might be related to ACC formation, but no such phosphorus-containing compounds have ever been identified. Crustaceans use ACC biominerals in exoskeleton and gastroliths so that they will have easy access to calcium carbonate inside the body before and after molting. We have identified phosphoenolpyruvate and 3-phosphoglycerate, intermediates of the glycolytic pathway, in exoskeleton and gastroliths and found them important for stabilizing ACC. PMID:21336282

  13. Aerobic biodegradation of odorous dimethyl disulfide in aqueous medium by isolated Bacillus cereus GIGAN2 and identification of transformation intermediates.

    PubMed

    Liang, Zhishu; An, Taicheng; Li, Guiying; Zhang, Zhengyong

    2014-11-01

    A novel, flagellated, rod-shape, Gram-positive facultative aerobe, was isolated and identified as Bacillus cereus GIGAN2. It can effectively remove model odorous organics dimethyl disulfide (DMDS) in aqueous solution under aerobic conditions. Initial concentration, pH value and temperature played important role in DMDS biodegradation, and up to 100% of 10mgL(-1) of DMDS could be removed within 96h under the optimum conditions (30°C, pH 7.0 and 200rpm) with a maximum biodegradation rate constant of 0.0330h(-1) and minimum half-life of 21.0h, respectively. Three main intermediates were identified using gas chromatography-mass spectrometry during this biodegradation process. Further, a reaction scheme is also proposed to explain the possible DMDS biodegradation mechanism by GIGAN2 based on the above-identified intermediates. Overall, this is the first report to demonstrate a newly isolated strain using high concentrated DMDS as the sole carbon and energy source with high efficiency. PMID:25459868

  14. Theoretical studies on the deacylation step of acylated Candida Antarctica lipase B: Structural and reaction pathway analysis.

    PubMed

    Sadeghi Googheri, Mohammad Sadegh; Housaindokht, Mohammad Reza; Sabzyan, Hassan

    2015-04-01

    The deacylation step of acylated Candida Antarctica lipase B, which was acylated with methylcaprylate (MEC) and acetylcholine (ACh), has been studied by using density functional theory method. Free energies of the entire reaction were calculated for enzyme deacylation by water and hydrogen peroxide that represented hydrolysis and perhydrolysis reactions, respectively. The calculations displayed that a stepwise mechanism there was with the enzyme-product complex being a deep minimum on the free energy surfaces of both of two reactions. The tetrahedral intermediate formation was the rate-determining step of all reactions, which needed 8.1 to 10.5kcalmol(-1) for activation in different reactions. In the second stage of the reaction, fewer free energy barriers, between 4.7 and 5.9kcalmol(-1), were identified to enable the proton transfer from His224 to Ser105 and the breakdown of the tetrahedral intermediate. These calculated activation free energies approved theoretical possibility of both of two reactions for two substrates. Finally, an applied tool examined the interactions role in the stability and energy levels of different chemical species. PMID:25622130

  15. Jet-Medium Interactions with Identified Particles

    SciTech Connect

    Sickles, A.n.

    2009-11-01

    Identified particles have long been of great interest at RHIC in large part because of the baryon/meson differences observed at intermediate p{sub T} and the implications for hadronization via quark coalescence. With recent high statistics data identified particles are also now central to understanding the details of the jet-medium interactions and energy loss and hadron formation at intermediate and high p{sub T}. In particular, high p{sub T} identified particle spectra along with two-particle correlations triggered with direct photons, neutral pions or electrons from heavy flavor decay with hadrons can provide information about how medium modifications to jet fragmentation depend on parton type. I will review recent results with identified particles both in heavy ion systems and the reference measurements in p+p collisions.

  16. Fundamentals of flight, intermediate text

    NSDL National Science Digital Library

    Cislunar Aerospace

    1996-01-01

    This website is an intermediate on-line textbook on the fundamentals of flight. Initially, this resource examines different kinds of flight. Specifically gliding and true flight are explored. Further topics in the principles of flight will cover aeronautics, the movement of fluids, water and liquids, movement of air, measurements, properties of flight, air moving objects, and forces in flight. This resource also provides fundamentals of flight references. Copyright 2005 International Technology Education Association

  17. Intermediate filaments in nervous tissues

    Microsoft Academic Search

    RONALD K. H. LIEM; SHU-HUI YEN; GARY D. SALOMON; MICHAEL L. SHELANSKI

    1978-01-01

    Intermediate filaments have been isolated from rabbit intradural spinal nerve roots by the axonal flotation method. This method was modified to avoid exposure of axons to low ionic strength medium. The purified filaments are morphologically 75-80% pure. The gel electrophoretogr am shows four major bands migrating at 200,000, 145,000, 68,000, and 60,000 daltons, respectively. A similar preparation from rabbit brain

  18. Price Theory: An Intermediate Text

    NSDL National Science Digital Library

    Friedman, David D.

    David D. Friedman, Professor of Law at Santa Clara University, has made his textbook, "Price Theory: An Intermediate Text" available on the web. The book focuses on trying to teach students the "economic way of thinking" and the "analytical core of economics -- price theory." Topics covered include consumer choice, market structure and economic efficiency. Price Theory also contains chapters on less conventional topics such as the political marketplace, the economics of law and law breaking; and the economics of love and marriage.

  19. 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.

  20. Novel Mechanism of Antibiotic Resistance Originating in Vancomycin-Intermediate Staphylococcus aureus

    Microsoft Academic Search

    Longzhu Cui; Akira Iwamoto; Jian-Qi Lian; Hui-min Neoh; Toshiki Maruyama; Yataro Horikawa; Keiichi Hiramatsu

    2006-01-01

    As an aggressive pathogen, Staphylococcus aureus poses a significant public health threat and is becoming increasingly resistant to currently available antibiotics, including vancomycin, the drug of last resort for gram-positive bacterial infections. S. aureus with intermediate levels of resistance to vancomycin (vancomycin- intermediate S. aureus (VISA)) was first identified in 1996. The resistance mechanism of VISA, however, has not yet

  1. MCNP6 fragmentation of light nuclei at intermediate energies

    E-print Network

    Stepan G. Mashnik; Leslie M. Kerby

    2014-04-30

    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 INC. Both CEM and LAQGSM account also for coalescence of light fragments (complex particles) up to He4 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.

  2. 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.

  3. Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines)

    PubMed Central

    Klink, Vincent P.; Overall, Christopher C.; Alkharouf, Nadim W.; MacDonald, Margaret H.; Matthews, Benjamin F.

    2010-01-01

    Background. A comparative microarray investigation was done using detection call methodology (DCM) and differential expression analyses. The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods. Laser capture microdissection (LCM) was used to isolate nearly homogeneous populations of plant root cells. Results. The analyses identified the presence of 13,291 transcripts between the 4 different sample types. The transcripts filtered down into a total of 6,267 that were detected as being present in one or more sample types. A comparative analysis of DCM and differential expression methods showed a group of genes that were not differentially expressed, but were expressed at detectable amounts within specific cell types. Conclusion. The DCM has identified patterns of gene expression not shown by differential expression analyses. DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process. PMID:20508855

  4. Intermediate Level Science Core Curriculum, Grades 5-8

    NSDL National Science Digital Library

    This guide is intended to assist teachers and supervisors for grades 5-8 as they prepare curriculum, instruction, and assessment for intermediate-level content and skills of the New York State Learning Standards for Mathematics, Science, and Technology. This Core Curriculum is not a syllabus. It addresses only the content and skills to be tested by the Intermediate Level Science Assessment. The document identifies process skills and describes their alignments with standards, key ideas, and performance indicators. It includes a description of the content of the Intermediate Level Science Examination and a set of examples of activities intended to build skills to support standards on scientific inquiry, the living environment, and the physical setting.

  5. Microfabricated electrochemiluminescence cell for chemical reaction detection

    DOEpatents

    Northrup, M. Allen (Berkeley, CA); Hsueh, Yun-Tai (Davis, CA); Smith, Rosemary L. (Davis, CA)

    2003-01-01

    A detector cell for a silicon-based or non-silicon-based sleeve type chemical reaction chamber that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The detector cell is an electrochemiluminescence cell constructed of layers of silicon with a cover layer of glass, with spaced electrodes located intermediate various layers forming the cell. The cell includes a cavity formed therein and fluid inlets for directing reaction fluid therein. The reaction chamber and detector cell may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The ECL cell may also be used in synthesis instruments, particularly those for DNA amplification and synthesis.

  6. Morphological and Ultrastructural Changes in Tissues of Intermediate and Definitive Hosts Infected by Protostrongylid Lungworms (Nematoda: Metastrongyloidea)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cellular and sub-cellular mechanisms involved in tissue responses to larval and adult lungworms (Protostrongylidae) were respectively explored through experimental and natural infections in molluscan intermediate (Xeropicta candacharica) and ruminant definitive hosts (Ovis aries). Reaction to develo...

  7. Direct detection of pyridine formation by the reaction of CH (CD) with pyrrole: a ring expansion reaction

    SciTech Connect

    Soorkia, Satchin; Taatjes, Craig A.; Osborn, David L.; Selby, Talitha M.; Trevitt, Adam J.; Wilson, Kevin R.; Leone, Stephen R.

    2010-03-16

    The reaction of the ground state methylidyne radical CH (X2Pi) with pyrrole (C4H5N) has been studied in a slow flow tube reactor using Multiplexed Photoionization Mass Spectrometry coupled to quasi-continuous tunable VUV synchrotron radiation at room temperature (295 K) and 90 oC (363 K), at 4 Torr (533 Pa). Laser photolysis of bromoform (CHBr3) at 248 nm (KrF excimer laser) is used to produce CH radicals that are free to react with pyrrole molecules in the gaseous mixture. A signal at m/z = 79 (C5H5N) is identified as the product of the reaction and resolved from 79Br atoms, and the result is consistent with CH addition to pyrrole followed by Helimination. The Photoionization Efficiency curve unambiguously identifies m/z = 79 as pyridine. With deuterated methylidyne radicals (CD), the product mass peak is shifted by +1 mass unit, consistent with the formation of C5H4DN and identified as deuterated pyridine (dpyridine). Within detection limits, there is no evidence that the addition intermediate complex undergoes hydrogen scrambling. The results are consistent with a reaction mechanism that proceeds via the direct CH (CD) cycloaddition or insertion into the five-member pyrrole ring, giving rise to ring expansion, followed by H atom elimination from the nitrogen atom in the intermediate to form the resonance stabilized pyridine (d-pyridine) molecule. Implications to interstellar chemistry and planetary atmospheres, in particular Titan, as well as in gas-phase combustion processes, are discussed.

  8. Direct detection of pyridine formation by the reaction of CH (CD) with pyrrole: a ring expansion reaction.

    PubMed

    Soorkia, Satchin; Taatjes, Craig A; Osborn, David L; Selby, Talitha M; Trevitt, Adam J; Wilson, Kevin R; Leone, Stephen R

    2010-08-21

    The reaction of the ground state methylidyne radical CH (X(2)Pi) with pyrrole (C(4)H(5)N) has been studied in a slow flow tube reactor using Multiplexed Photoionization Mass Spectrometry coupled to quasi-continuous tunable VUV synchrotron radiation at room temperature (295 K) and 363 K, at 4 Torr (533 Pa). Laser photolysis of bromoform (CHBr(3)) at 248 nm (KrF excimer laser) is used to produce CH radicals that are free to react with pyrrole molecules in the gaseous mixture. A signal at m/z = 79 (C(5)H(5)N) is identified as the product of the reaction and resolved from (79)Br atoms, and the result is consistent with CH addition to pyrrole followed by H-elimination. The photoionization efficiency curve unambiguously identifies m/z = 79 as pyridine. With deuterated methylidyne radicals (CD), the product mass peak is shifted by +1 mass unit, consistent with the formation of C(5)H(4)DN and identified as deuterated pyridine (d-pyridine). Within detection limits, there is no evidence that the addition intermediate complex undergoes hydrogen scrambling. The results are consistent with a reaction mechanism that proceeds via the direct CH (CD) cycloaddition or insertion into the five-member pyrrole ring, giving rise to ring expansion, followed by H atom elimination from the nitrogen atom in the intermediate to form the resonance stabilized pyridine (d-pyridine) molecule. Implications to interstellar chemistry and planetary atmospheres, in particular Titan, as well as gas-phase combustion processes, are discussed. PMID:20463997

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

    SciTech Connect

    Bellmann, Frank, E-mail: frank.bellmann@uni-weimar.d [Institute for Building Materials Science, Bauhaus University Weimar, 99423 Weimar (Germany); Damidot, Denis [Ecole des Mines de Douai, Civil and Environmental Engineering Department, 941 rue Charles Bourseul, BP 10838, 59508 Doua cedexi (France); Moeser, Bernd [Institute for Building Materials Science, Bauhaus University Weimar, 99423 Weimar (Germany); Skibsted, Jorgen [Instrument Center for Solid-State NMR Spectroscopy and Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University DK-8000 Aarhus C (Denmark)

    2010-06-15

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

  10. The sonochemical degradation of azobenzene and related azo dyes: Rate enhancements via Fenton's reactions

    SciTech Connect

    Joseph, J.M.; Destaillats, H.; Hung, H.M.; Hoffmann, M.R.

    2000-01-20

    The sonochemical degradation of aqueous solutions of azobenzene and related azo dyes (methyl orange, o-methyl red, and p-methyl red) was performed at 500 kHz and 50 W, under air, O{sub 2}, or Ar saturation at 288 K. Reaction products and intermediates were identified by HPLC-ES-MS. Total organic carbon (TOC) was also determined as a function of reaction time. The authors propose a reaction mechanism based on the observed species and the extent and rate of TOC depletion. The effects of the dye structures and of the background gas on the sonochemical bleaching rates were also investigated. The reaction rates for o-methyl red were approximately 30--40% faster than those for the other compounds. Saturating with Ar instead of air or O{sub 2} increased the pseudo first-order rate constants for the degradation by 10%. The acceleration of the sonochemical bleaching and the mineralization process upon addition of Fe(II) was also investigated in Ar-saturated methyl orange solutions. A 3-fold increase in the reaction rate was observed at optimal Fe(II) concentrations. This kinetic effect is quantitatively accounted for by a simple kinetic model based on the reaction of Fe(II) with sonochemically produced H{sub 2}O{sub 2} (Fenton's reaction). This latter effect illustrates a simple way of achieving a substantial improvement in the efficiency of sonochemical degradation reactions.

  11. Oxidative degradation of sulfathiazole by Fenton and photo-Fenton reactions.

    PubMed

    Velásquez, Marizú; Santander, I Paola; Contreras, David R; Yáñez, Jorge; Zaror, Claudio; Salazar, Ricardo A; Pérez-Moya, Montserrat; Mansilla, Héctor D

    2014-01-01

    This article presents experimental results on 47 ?mol L(-1) sulfathiazole (STZ) degradation by Fenton and photo-Fenton reactions using multivariate analysis. The optimal experimental conditions for reactions were obtained by Response Surface Methodology (RSM). In the case of the Fenton reactions there were 192 ?mol L(-1) ferrous ions (Fe(II)) and 1856 ?mol L(-1) hydrogen peroxide (H2O2), as compared with 157 ?mol L(-1) (Fe(II)) and 1219 ?mol L(-1) (H2O2) for photo-Fenton reactions. Under these conditions, around 90% of STZ degradation were achieved after 8 minutes treatment by Fenton and photo-Fenton reactions, respectively. Moreover, a marked difference was observed in the total organic carbon (TOC) removal after 60-min treatment, achieving 30% and 75% for the Fenton and photo-Fenton reactions, respectively. Acetic, maleic, succinic and oxamic acids could be identified as main Fenton oxidation intermediates. A similar pattern was found in the case of photo-Fenton reaction, including the presence of oxalic acid and ammonia at short periods of irradiation with UV-A. The calculated values of Average Oxidation State (AOS) corroborate the formation of oxidized products from the initial steps of the reaction. PMID:24521411

  12. Combination of overall reaction rate with Gibbs energy minimization

    Microsoft Academic Search

    Pertti Koukkari; Ismo Laukkanen; Simo Liukkonen

    1997-01-01

    A method to calculate multi-component chemical reaction mixtures as a sequence of time-dependent, intermediate thermochemical states is presented. The method combines the overall reaction kinetics with thermodynamic Gibbs energy minimization. The overall reaction is assumed to proceed according to the Arrhenius rate law. During the time-course of the reaction, the temperature and composition of the reaction mixture are calculated by

  13. Allergic reactions

    MedlinePLUS

    ... more often in people who have a family history of allergies . Substances that don't bother most people ( ... reaction is getting worse. The person has a history of severe allergic reactions (check for a medical ID ...

  14. Diradical intermediate within the context of tryptophan tryptophylquinone biosynthesis

    PubMed Central

    Yukl, Erik T.; Liu, Fange; Krzystek, J.; Shin, Sooim; Jensen, Lyndal M. R.; Davidson, Victor L.; Wilmot, Carrie M.; Liu, Aimin

    2013-01-01

    Despite the importance of tryptophan (Trp) radicals in biology, very few radicals have been trapped and characterized in a physiologically meaningful context. Here we demonstrate that the diheme enzyme MauG uses Trp radical chemistry to catalyze formation of a Trp-derived tryptophan tryptophylquinone cofactor on its substrate protein, premethylamine dehydrogenase. The unusual six-electron oxidation that results in tryptophan tryptophylquinone formation occurs in three discrete two-electron catalytic steps. Here the exact order of these oxidation steps in the processive six-electron biosynthetic reaction is determined, and reaction intermediates are structurally characterized. The intermediates observed in crystal structures are also verified in solution using mass spectrometry. Furthermore, an unprecedented Trp-derived diradical species on premethylamine dehydrogenase, which is an intermediate in the first two-electron step, is characterized using high-frequency and -field electron paramagnetic resonance spectroscopy and UV-visible absorbance spectroscopy. This work defines a unique mechanism for radical-mediated catalysis of a protein substrate, and has broad implications in the areas of applied biocatalysis and understanding of oxidative protein modification during oxidative stress. PMID:23487750

  15. Enzyme Reactions

    NSDL National Science Digital Library

    Minerva Deland School

    2011-10-03

    This video shows an enzyme reaction lab. The teacher demonstrates how the enzyme, catalase, reacts with hydrogen peroxide (a substrate found in cells). The teacher first demonstrates a normal enzyme reaction. He or she then goes on to show how manipulating temperature and pH will affect the reaction of an enzyme.

  16. Special Reactions

    NSDL National Science Digital Library

    William C. Robertson, Ph.D.

    2010-03-01

    The basics of chemical reactions were covered in the first chemistry book, including how to write and balance chemical equations that represent those reactions. There is also a quick review of chemical reactions in Chapter 1 of this book. We're going to d

  17. Chemical Reactions

    NSDL National Science Digital Library

    National Science Teachers Association (NSTA)

    2009-05-01

    We don't often stop to think about it, but underlying many of our everyday activities are chemical reactions. From the cooking of an egg to the growth of a child, chemical reactions make things happen. Although many of the reactions that support our lives

  18. In vitro insulin refolding: characterization of the intermediates and the putative folding pathway.

    PubMed

    Tang, YueHua; Wang, Shuai; Chen, Yan; Xu, GenJun; Feng, YouMin

    2007-12-01

    The in vitro refolding process of the double-chain insulin was studied based on the investigation of in vitro single-chain insulin refolding. Six major folding intermediates, named P1A, P2B, P3A, P4B, P5B, and P6B, were captured during the folding process. The refolding experiments indicate that all of these intermediates are on-pathway. Based on these intermediates and the formation of hypothetic transients, we propose a two-stage folding pathway of insulin. (1) At the early stage of the folding process, the reduced A chain and B chain individually formed the intermediates: two A chain intermediates (P1A and P3A), and four B chain intermediates (P2B, P4B, P5B, and P6B). (2) In the subsequent folding process, transient I was formed from P3A through thiol/disulfide exchange reaction; then, transients II and III, each containing two native disulfides, were formed through the recognition and interaction of transient I with P4B or P6B and the thiol group's oxidation reaction mainly using GSSG as oxidative reagent; finally, transients II and III, through thiol/mixture disulfide exchange reaction, formed the third native disulfide of insulin to complete the folding. PMID:17914645

  19. Multiple intermediates in SNARE-induced membrane fusion.

    PubMed

    Yoon, Tae-Young; Okumus, Burak; Zhang, Fan; Shin, Yeon-Kyun; Ha, Taekjip

    2006-12-26

    Membrane fusion in eukaryotic cells is thought to be mediated by a highly conserved family of proteins called SNAREs (soluble N-ethyl maleimide sensitive-factor attachment protein receptors). The vesicle-associated v-SNARE engages with its partner t-SNAREs on the target membrane to form a coiled coil that bridges two membranes and facilitates fusion. As demonstrated by recent findings on the hemifusion state, identifying intermediates of membrane fusion can help unveil the underlying fusion mechanism. Observation of SNARE-driven fusion at the single-liposome level has the potential to dissect and characterize fusion intermediates most directly. Here, we report on the real-time observation of lipid-mixing dynamics in a single fusion event between a pair of SNARE-reconstituted liposomes. The assay reveals multiple intermediate states characterized by discrete values of FRET between membrane-bound fluorophores. Hemifusion, flickering of fusion pores, and kinetic transitions between intermediates, which would be very difficult to detect in ensemble assays, are now identified. The ability to monitor the time course of fusion events between two proteoliposomes should be useful for addressing many important issues in SNARE-mediated membrane fusion. PMID:17167056

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

    PubMed

    Jiang, Yong-Hai; Zhang, Jin-Bao; Xi, Bei-Dou; An, Da; Yang, Yu; Li, Ming-Xiao

    2015-06-01

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

  1. Intermediate-Mass Black Holes

    E-print Network

    M. Coleman Miller; E. J. M Colbert

    2004-02-23

    The mathematical simplicity of black holes, combined with their links to some of the most energetic events in the universe, means that black holes are key objects for fundamental physics and astrophysics. Until recently, it was generally believed that black holes in nature appear in two broad mass ranges: stellar-mass (roughly 3-20 solar masses), which are produced by the core collapse of massive stars, and supermassive (millions to billions of solar masses), which are found in the centers of galaxies and are produced by a still uncertain combination of processes. In the last few years, however, evidence has accumulated for an intermediate-mass class of black holes, with hundreds to thousands of solar masses. If such objects exist they have important implications for the dynamics of stellar clusters, the formation of supermassive black holes, and the production and detection of gravitational waves. We review the evidence for intermediate-mass black holes and discuss future observational and theoretical work that will help clarify numerous outstanding questions about these objects.

  2. Heavy residues and intermediate-mass fragment production in dissipative 197Au+86Kr collisions at E/A=35 MeV

    NASA Astrophysics Data System (ADS)

    Djerroud, B.; Agnihotri, D. K.; Baldwin, S. P.; Skulski, W.; Tõke, J.; Schröder, W. U.; Charity, R. J.; Dempsey, J. F.; Sarantites, D. G.; Sobotka, L. G.; Lott, B.; Loveland, W.; Aleklett, K.

    2001-09-01

    Neutrons and charged light and intermediate-mass products from the 197Au+86Kr reaction at Elab/A=35 MeV were measured with 4? angular coverage, in coincidence with projectilelike (PLFs) and targetlike fragments (TLFs). The characteristics of PLF and TLF yields and their correlation with neutron, light-charged particles, and intermediate-mass fragments (IMFs) are consistent with a scenario where essentially all collisions proceed through a dissipative stage. It is found that the damping of the available kinetic energy into thermal excitation is essentially incomplete, with no positive evidence for complete damping. Slow, massive reaction products are observed with significant yields. These products, termed also heavy residues, are identified as TLF evaporation residues and as TLF fission fragments. The TLF fission mode is seen to fade away in favor of TLF evaporation residue production for excitation energies above 3-4 MeV/nucleon. The suppression of the TLF fission can be traced to the dynamical IMF production process which reduces considerably the sizes of the primary reaction fragments and, hence, their fissility.

  3. Storage Stability and Improvement of Intermediate Moisture Foods, Phase 3

    NASA Technical Reports Server (NTRS)

    Labuza, T. P.

    1975-01-01

    Methods were determined for the improvement of shelf-life stability of intermediate moisture foods (IMF). Microbial challenge studies showed that protection against molds and Staphylococcus aureus could be achieved by a combination of antimicrobial agents, humectants and food acids. Potassium sorbate and propylene glycol gave the best results. It was also confirmed that the maximum in heat resistance shown by vegetative pathogens at intermediate water activities also occurred in a solid food. Glycols and sorbitol both achieve browning inhibition because of their action as a medium for reaction and effect on viscosity of the adsorbed phase. Chemical availability results showed rapid lysine loss before visual discoloration occurred. This is being confirmed with a biological test using Tetrahymena pyriformis W. Accelerated temperature tests show that effectiveness of food antioxidants against rancidity development can be predicted; however, the protection factor changes with temperature. BHA was found to be the best antioxidant for iron catalyzed oxidation.

  4. Present status of intermediate energy data evaluation for accelerator-based transmutation of radioactive waste

    SciTech Connect

    Koning, A.J. [Netherlands Energy Research Foundation, Petten (Netherlands)

    1994-12-31

    The recent developments in the field of nuclear data evaluation for energies above 20 MeV are outlined. As a particularly interesting application we consider accelerator-based transmutation of radioactive waste. The most urgent data needs for accelerator-based transmutation have been prioritized and translated in terms of intermediate-energy data libraries. Priorities are assigned to the materials relevant to an incineration system and to the most important associated nuclear reactions (notably reactions involving nucleons). In this contribution, the proposed actions as indicated in previous work are further discussed and a sample intermediate-energy {open_quotes}starter{close_quotes} data file is presented.

  5. Chemoenzymatic Synthesis of Vitamin B5-Intermediate (R)-Pantolactone via Combined Asymmetric Organo- and Biocatalysis.

    PubMed

    Heidlindemann, Marcel; Hammel, Matthias; Scheffler, Ulf; Mahrwald, Rainer; Hummel, Werner; Berkessel, Albrecht; Gröger, Harald

    2015-04-01

    The combination of an asymmetric organocatalytic aldol reaction with a subsequent biotransformation toward a "one-pot-like" process for the synthesis of (R)-pantolactone, which to date is industrially produced by a resolution process, is demonstrated. This process consists of an initial aldol reaction catalyzed by readily available l-histidine followed by biotransformation of the aldol adduct by an alcohol dehydrogenase without the need for intermediate isolation. Employing the industrially attractive starting material isobutanal, a chemoenzymatic three-step process without intermediate purification is established allowing the synthesis of (R)-pantolactone in an overall yield of 55% (three steps) and high enantiomeric excess of 95%. PMID:25710713

  6. Intramolecular Anodic Olefin Coupling Reactions: Using Competition Studies to Probe the Mechanism of Oxidative Cyclization Reactions

    PubMed Central

    Xu, Hai-Chao; Moeller, Kevin D.

    2014-01-01

    A competition experiment was designed so that the relative rates of anodic cyclization reactions under various electrolysis conditions can be determined. Reactions with ketene dithioacetal and enol ether-based substrates that use lithium methoxide as a base were shown to proceed through radical cation intermediates that were trapped by a sulfonamide anion. Results for the oxidative coupling of a vinyl sulfide with a sulfonamide anion using the same conditions were consistent with the reaction proceeding through a nitrogen-radical. PMID:20302359

  7. Intramolecular anodic olefin coupling reactions: using competition studies to probe the mechanism of oxidative cyclization reactions.

    PubMed

    Xu, Hai-Chao; Moeller, Kevin D

    2010-04-16

    A competition experiment was designed so that the relative rates of anodic cyclization reactions under various electrolysis conditions can be determined. Reactions with ketene dithioacetal and enol ether-based substrates that use lithium methoxide as a base were shown to proceed through radical cation intermediates that were trapped by a sulfonamide anion. Results for the oxidative coupling of a vinyl sulfide with a sulfonamide anion using the same conditions were consistent with the reaction proceeding through a nitrogen-radical. PMID:20302359

  8. An investigation of a Friedel-Crafts alkylation reaction in homogeneous supercritical CO 2 and under subcritical and splitphase reaction conditions

    Microsoft Academic Search

    John E. Chateauneuf; Kan Nie

    2000-01-01

    This study investigates the Friedel-Crafts alkylation reaction of triphenylmethanol with methoxybenzene (anisole) in supercritical and subcritical carbon dioxide, and under two-phase (gas\\/liquid) reaction conditions at moderate pressures and temperatures. The reaction was initiated using trifluoroacetic acid to produce triphenylmethlycarbocation as the reaction intermediate. Isolated product yields of the Friedel-Crafts product, p-methoxytetraphenylmethane, are reported.

  9. Stepwise conversion of a single source precursor into crystalline AlN by transamination reaction

    SciTech Connect

    Schulz, Stephan [Institute of Inorganic Chemistry, University of Duisburg-Essen, Universitaetsstrasse 5-7, 45141 Essen (Germany)], E-mail: stephan.schulz@uni-due.de; Bauer, Tillmann; Hoffbauer, Wilfried [Institute of Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn (Germany); Schmedt auf der Guenne, Joern [Department of Chemistry and Biochemistry, University of Munich (LMU), Butenandtstr. 5-13, D2.076, 81377 Munich (Germany); Doerr, Markus; Marian, Christel M. [Institute of Theoretical and Computational Chemistry, University of Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf (Germany); Assenmacher, Wilfried [Institute of Inorganic Chemistry, University of Bonn, Roemerstr. 164, 53117 Bonn (Germany)

    2008-03-15

    Ammonolysis of the monomeric, base-stabilized trisaminoalane Me{sub 3}N-Al[N(H)Dipp)]{sub 3} (Dipp=2,6-{sup i}Pr{sub 2}-C{sub 6}H{sub 3}) yielded Al-N oligomers, which were characterized in detail by solid state NMR spectroscopy ({sup 1}H, {sup 13}C, {sup 15}N, {sup 27}Al) and TGA/DTA. Pyrolysis of as-prepared oligomers at different temperatures in an argon steam yielded carbon-containing black solids, whereas pyrolysis under a steady flow of NH{sub 3} produced pure aluminum nitride (AlN). The role of the pyrolysis temperature and the influence of NH{sub 3} on the formation of crystalline materials were investigated. As-prepared AlN was characterized by solid state NMR spectroscopy ({sup 15}N, {sup 27}Al), X-ray diffraction (XRD), transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS). Theoretical calculations were performed in order to identify potential reaction intermediates. - Graphical abstract: Ammonolysis reactions of Me{sub 3}N-Al(NHDipp){sub 3} in liquid NH{sub 3} yielded Al-N oligomers, which can be transformed into nanocrystalline aluminum nitride particles under thermolysis conditions at 1000 deg. C. Theoretical calculations were performed in order to identify potential reaction intermediates.

  10. Nuclear fission and heavy-ion-induced reactions

    Microsoft Academic Search

    Schroder

    1986-01-01

    There were 31 papers presented at the conference covered in this book. Topics covered include: Statistical theory of nuclear fission, Transfer and breakup reactions at intermediate energies; and Heavy ion induced light particle emission.

  11. Metabolism of postsynaptic recombination intermediates.

    PubMed

    Adelman, Carrie A; Boulton, Simon J

    2010-09-10

    DNA double strand breaks and blocked or collapsed DNA replication forks are potentially genotoxic lesions that can result in deletions, aneuploidy or cell death. Homologous recombination (HR) is an essential process employed during repair of these forms of damage. HR allows for accurate restoration of the damaged DNA through use of a homologous template for repair. Although inroads have been made towards understanding the mechanisms of HR, ambiguity still surrounds aspects of the process. Until recently, relatively little was known concerning metabolism of postsynaptic RAD51 filaments or how synthesis dependent strand annealing intermediates are processed. This review discusses recent findings implicating RTEL1, HELQ and the Caenorhabditis elegans RAD51 paralog RFS-1 in post-strand exchange events during HR. PMID:20493853

  12. Displays for future intermediate UAV

    NASA Astrophysics Data System (ADS)

    Desjardins, Daniel; Metzler, James; Blakesley, David; Rister, Courtney; Nuhu, Abdul-Razak

    2008-04-01

    The Dedicated Autonomous Extended Duration Airborne Long-range Utility System (DAEDALUS) is a prototype Unmanned Aerial Vehicle (UAV) that won the 2007 AFRL Commander's Challenge. The purpose of the Commander's Challenge was to find an innovative solution to urgent warfighter needs by designing a UAV with increased persistence for tactical employment of sensors and communication systems. DAEDALUS was chosen as a winning prototype by AFRL, AFMC and SECAF. Follow-on units are intended to fill an intermediate role between currently fielded Tier I and Tier II UAV's. The UAV design discussed in this paper, including sensors and displays, will enter Phase II for Rapid Prototype Development with the intent of developing the design for eventual production. This paper will discuss the DAEDALUS UAV prototype system, with particular focus on its communications, to include the infrared sensor and electro-optical camera, but also displays, specifically man-portable.

  13. Monoclonal antibody to intermediate filaments of cytokeratin type. I. Drug studies and reactivity with cultured cells and tissue sections.

    PubMed

    Bártek, J; Kovarík, J; Lauerová, L; Munzarová, M

    1985-01-01

    Establishment of a mouse-mouse hybridoma and partial characterization of IgM monoclonal antibody (M-04) identifying cytoplasmic filamentous structures is described. Immunofluorescence performed on a panel of various cultured human cell types as well as on frozen sections of normal and tumour tissues revealed specificity of M-04 antibody for cells of epithelial origin. Using MCF-7 cell line as a model, staining patterns of microtubules, microfilaments and M-04-target filaments in untreated cells were compared with those pretreated with Colcemid and Cytochalasin B. From both differential staining of various cell types and the results of drug studies it is concluded that monoclonal antibody M-04 binds to intermediate filaments of cytokeratin type. Furthermore, restricted expression of M-04 target determinant among epithelial tissues is suggested from the lack of reaction in stratified skin epithelium. PMID:2578996

  14. Kinetic Intermediates en Route to the Final Serpin-Protease Complex

    PubMed Central

    Maddur, Ashoka A.; Swanson, Richard; Izaguirre, Gonzalo; Gettins, Peter G. W.; Olson, Steven T.

    2013-01-01

    Serpin protein protease inhibitors inactivate their target proteases through a unique mechanism in which a major serpin conformational change, resulting in a 70-? translocation of the protease from its initial reactive center loop docking site to the opposite pole of the serpin, kinetically traps the acyl-intermediate complex. Although the initial Michaelis and final trapped acyl-intermediate complexes have been well characterized structurally, the intermediate stages involved in this remarkable transformation are not well understood. To better characterize such intermediate steps, we undertook rapid kinetic studies of the FRET and fluorescence perturbation changes of site-specific fluorophore-labeled derivatives of the serpin, ?1-protease inhibitor (?1PI), which report the serpin and protease conformational changes involved in transforming the Michaelis complex to the trapped acyl-intermediate complex in reactions with trypsin. Two kinetically resolvable conformational changes were observed in the reactions, ascribable to (i) serpin reactive center loop insertion into sheet A with full protease translocation but incomplete protease distortion followed by, (ii) full conformational distortion and movement of the protease and coupled serpin conformational changes involving the F helix-sheet A interface. Kinetic studies of calcium effects on the labeled ?1PI-trypsin reactions demonstrated both inactive and low activity states of the distorted protease in the final complex that were distinct from the intermediate distorted state. These studies provide new insights into the nature of the serpin and protease conformational changes involved in trapping the acyl-intermediate complex in serpin-protease reactions and support a previously proposed role for helix F in the trapping mechanism. PMID:24047901

  15. Subbarrier fusion of spherical nuclei of intermediate atomic number

    SciTech Connect

    Shilov, V. M. [Joint Institute for Nuclear Research, Bogolyubov Laboratory of Theoretical Physics (Russian Federation)

    2012-04-15

    A two-humped model was proposed for explaining the suppression of the cross sections for the deep-subbarrier fusion of spherical nuclei that have intermediate atomic numbers. It was shown that the suppression of these cross sections was due to the interference between the incident and reflected fluxes between the two barriers. The results of fitting the cross sections calculated within the two-humped model revealed the invariability of the distance between the vertices of the two barriers. As the charges of colliding nuclei increase, the inner barrier becomes higher than the outer one, and this determines the competition with cross sections for deep-inelastic-transfer reactions.

  16. One-nucleon transfer between heavy ions at intermediate energies

    NASA Astrophysics Data System (ADS)

    Bayman, B. F.; Lenzi, S. M.; Vitturi, A.; Zardi, F.

    1994-10-01

    One-nucleon transfer processes between heavy ions at intermediate energies are studied in the framework of the eikonal distorted-wave Born approximation. Optical phase shifts describing core-core relative motion are microscopically described in the Glauber model, starting from experimental nuclear densities and nucleon-nucleon scattering amplitudes at the corresponding energies. The interaction responsible for the nucleon transfer is a complex energy-dependent potential obtained by the Abel transform of the nucleon-core phase shift. Applications to one-proton and one-neutron transfer reactions on 208Pb induced by 12C and 16O projectiles are discussed for both angular distributions and normalization factors.

  17. Role of stabilized Criegee Intermediate in secondary organic aerosol formation from the ozonolysis of ?-cedrene

    NASA Astrophysics Data System (ADS)

    Yao, Lei; Ma, Yan; Wang, Lin; Zheng, Jun; Khalizov, Alexei; Chen, Mindong; Zhou, Yaoyao; Qi, Lu; Cui, Fenping

    2014-09-01

    Atmospheric ozonolysis of sesquiterpenes is an important source of secondary organic aerosols (SOA). The mechanisms by which Criegee Intermediates (CIs) react to form SOA precursors and the influence of environmental conditions, however, remain unclear. On the basis of environmental chamber experiments coupled with detailed characterization of gas-phase and particle-phase products, we present evidence that a significant fraction of CIs from ozonolysis of ?-cedrene are stabilized and bimolecular reactions of these stabilized CIs (SCIs) play a key role in the formation of SOA precursors. Ozonolysis experiments were conducted in a 4.5 m3 collapsible fluoropolymer chamber under various conditions in the presence of the OH radical and SCI scavengers. The size and mass of SOA particles produced during ozonolysis were measured directly and used for calculation of particle effective density and mass yield. Gaseous and particulate products were analyzed by several mass spectrometry methods. A total of 14 compounds in gas phase and 17 compounds in particle phase were tentatively identified. The major gas-phase products are secondary ozonides (SOZ) from intramolecular reactions of SCIs. Multifunctional organic acids are dominant particle-phase products. The measured density of aerosol particles is 1.04 ± 0.03 to 1.38 ± 0.03 g/cm3, and the aerosol mass yield is (23.7 ± 0.4)% to (46.4 ± 6.5)%, depending on reaction conditions. The presence of acetic acid, an SCI scavenger, inhibits new particle formation, but leads to increased aerosol mass yield. In contrast, the addition of SO2 dramatically enhances new particle formation and total aerosol yield. The calculated OH formation yield decreases from (62.4 ± 4.9)% to (9.0 ± 1.6)% upon addition of SCI scavengers CH3COOH and SO2, indicating that a large fraction of excited CIs are collisionally stabilized and unimolecular decomposition of SCIs via the hydroperoxide channel can be suppressed by bimolecular reactions. The reaction of SCIs with SO2 leads to the formation of sulfuric acid, an important nucleation precursor. From the consumption of SO2 added as SCI scavenger, a lower-limit yield of SCIs from ?-cedrene ozonolysis is estimated at ?88%. Our work underscores the key role of SCIs in SOA formation and observed composition of gas- and particle-phase products from ?-cedrene ozonolysis. Bimolecular reactions of sesquiterpene CIs with atmospherically relevant species (e.g. SO2, H2O) need to be considered when assessing the atmospheric relevance of ozonolysis of sesquiterpenes.

  18. The M intermediate of Pharaonis phoborhodopsin is photoactive.

    PubMed Central

    Balashov, S P; Sumi, M; Kamo, N

    2000-01-01

    The retinal protein phoborhodopsin (pR) (also called sensory rhodopsin II) is a specialized photoreceptor pigment used for negative phototaxis in halobacteria. Upon absorption of light, the pigment is transformed into a short-wavelength intermediate, M, that most likely is the signaling state (or its precursor) that triggers the motility response of the cell. The M intermediate thermally decays into the initial pigment, completing the cycle of transformations. In this study we attempted to determine whether M can be converted into the initial state by light. The M intermediate was trapped by the illumination of a water glycerol suspension of phoborhodopsin from Natronobacterium pharaonis called pharaonis phoborhodopsin (ppR) with yellow light (>450 nm) at -50 degrees C. The M intermediate absorbing at 390 nm is stable in the dark at this temperature. We found, however, that M is converted into the initial (or spectrally similar) state with an absorption maximum at 501 nm upon illumination with 380-nm light at -60 degrees C. The reversible transformations ppR if M are accompanied by the perturbation of tryptophan(s) and probably tyrosine(s) residues, as reflected by changes in the UV absorption band. Illumination at lower temperature (-160 degrees C) reveals two intermediates in the photoconversion of M, which we termed M' (or M'(404)) and ppR' (or ppR'(496)). A third photoproduct, ppR'(504), is formed at -110 degrees C during thermal transformations of M'(404) and ppR'(496). The absorption spectrum of M'(404) (maximum at 404 nm) consists of distinct vibronic bands at 362, 382, 404, and 420 nm that are different from the vibronic bands of M at 348, 368, 390, and 415 nm. ppR'(496) has an absorption band that is shifted to shorter wavelengths by 5 nm compared to the initial ppR, whereas ppR'(504) is redshifted by at least 3 nm. As in bacteriorhodopsin, photoexcitation of the M intermediate of ppR and, presumably, photoisomerization of the chromophore during the M --> M' transition result in a dramatic increase in the proton affinity of the Schiff base, followed by its reprotonation during the M' --> ppR' transition. Because the latter reaction occurs at very low temperature, the proton is most likely taken from the counterion (Asp(75)) rather than from the bulk. The phototransformation of M reveals a certain heterogeneity of the pigment, which probably reflects different populations of M or its photoproduct M'. Photoconversion of the M intermediate provides a possible pathway for photoreception in halobacteria and a useful tool for studying the mechanisms of signal transduction by phoborhodopsin (sensory rhodopsin II). PMID:10827991

  19. Reversible potentials for steps in methanol and formic acid oxidation to CO2; adsorption energies of intermediates on the ideal electrocatalyst for methanol oxidation and CO2 reduction.

    PubMed

    Anderson, Alfred B; Asiri, Haleema Aied

    2014-06-14

    Quantum chemical theory is used to identify the reasons for platinum's limitations as an electrocatalyst for oxidizing methanol at fuel cell anodes. The linear Gibbs energy relation (LGER) method is employed to predict reversible potentials for reaction steps for intermediates on the electrode surface. In this procedure, standard reversible potentials are calculated for the reactions in bulk solution phase and then they are perturbed using calculated adsorption bond strengths to the electrode surface, yielding the equilibrium potentials for each electron transfer step for adsorbed intermediates. Adsorption properties of ideal electrocatalysts for the methanol oxidation are found by imposing the condition that the reversible potential of each electron transfer step equals that for the overall reaction. The adsorption bond strengths that provide the ideal properties also apply to formic acid oxidation and carbon dioxide reduction. It is instructive to think of the ideal electrocatalyst as a lens that focusses the reversible potentials for the n individual electron transfer steps to the reversible potential for the n-electron process. It is found that the ideal catalyst will adsorb many intermediates, including HOOC, CO, OCH, HOC, HOCH, HOCH2, and OCH3 more weakly than platinum, and OOCH and OH more strongly. For example, for one possible pathway it is necessary to weaken adsorption bond strengths for HOCH2, HOCH, OCH, HOOC by about 0.5 eV, weaken adsorption CO by about 1.1 eV and strengthen OH adsorption by about 0.6 eV. These results imply a need for developing new multi-component catalysts. PMID:24741672

  20. Reaction Time

    NSDL National Science Digital Library

    2012-06-26

    In this activity, learners explore reaction time and challenge themselves to improve their coordination. Do you want to move faster? Catch that ball that you never seem to see in time? Use a simple test to help you improve your reaction (or response) time.

  1. Named Reactions

    NSDL National Science Digital Library

    This Web site lists 95 of the most important named reactions in organic chemistry. Each is linked to a Web page that gives the primary reference and equations for one or more recent literature examples that illustrate the use of the reaction.

  2. ChemTeacher: Single Replacement Reactions

    NSDL National Science Digital Library

    2012-07-23

    ChemTeacher compiles background information, videos, articles, demonstrations, worksheets and activities for high school teachers to use in their classrooms. The Single Replacement Reactions page includes resources for teaching students about identifying and predicting single replacement reactions.

  3. Chemical Reactions

    NSDL National Science Digital Library

    Mrs. Hicken

    2009-05-04

    We are going go over a general view of reactions to prepare us for our unit on Chemical Reactions! Have fun learning! WARNING: If you are caught looking at ANY other site, without permission, you will be sent to the ALC, and you will not participate in any other computer activities for the rest of the year. Get your worksheet and begin! Overview Take this quiz and have me come over and sign off on your worksheet when you have completed the quiz! Overview Quiz Next let's take a look at what effect the rate of a chemical reaction. Rates of Reactions Another quiz, another check off by me! Rates of Reactions Quiz Now how do we measure how fast a ...

  4. Astrophysical reaction rate for ?( ?n, ?) 9Be by photodisintegration

    Microsoft Academic Search

    K. Sumiyoshi; H. Utsunomiya; S. Goko; T. Kajino

    2002-01-01

    We study the astrophysical reaction rate for the formation of 9Be through the three body reaction ?(?n,?). This reaction is one of the key reactions which could bridge the mass gap at A=8 nuclear systems to produce intermediate-to-heavy mass elements in alpha- and neutron-rich environments such as r-process nucleosynthesis in supernova explosions, s-process nucleosynthesis in asymptotic giant branch (AGB) stars,

  5. Possible Observation of the ^3A' - ^1A' Electronic Transition of the Methylene Peroxy Criegee Intermediate

    NASA Astrophysics Data System (ADS)

    Kline, Neal D.; Miller, Terry A.; Coons, Marc; Herbert, John

    2013-06-01

    It is possible that we have observed for the first time the transition from the ground ^1A' state to the low lying ^3A' state of the methylene peroxy Criegee intermediate, CH_2O_2, which is otherwise known as carbonyl or formaldehyde oxide. Criegee intermediates are reactive intermediates that are formed in the ozonolysis of olefins in both liquid and gaseous phases with the methylene peroxy intermediate being formed specifically from the ozonolysis of ethene. In the atmosphere Criegee intermediates are formed in reactions that lead to secondary organic aerosols and participate in reactions with SO_2 and NO_2. A peroxy-like spectrum was observed in the near-IR using cavity ringdown spectroscopy after photolysis of a diiodomethane precursor at 248 nm followed by a reaction with O_2. Possible assignment of the spectrum to CH_2O_2 is based on a strong analogy between the electronic structure of methylene peroxy and ozone. However experiments and electronic structure calculations are continuing to positively attribute the spectrum to either CH_2O_2 or CH_2IO_2 which could also be formed by this chemistry.

  6. The folding intermediate of reversibly denatured human prostatic acid phosphatase.

    PubMed

    Kuciel, R; Mazurkiewicz, A; Ostrowski, W S

    1996-04-01

    Human prostatic acid phosphatase (hPAP) [EC 3.1.3.2], a homodimer of ca. 50 kDa subunit molecular weight, shows reversible denaturation in 6 M urea at pH 2.5. Rapid dilution of the denatured enzyme allowed partial renaturation of hPAP, as measured by enzyme activity, to a level which depended on the composition of the dilution solution employed and time of the reaction. The renaturation reaction of hPAP was examined using spectral analysis (circular dichroism and fluorometry), fast size-exclusion chromatography and proteolysis by trypsin. The observed results are in agreement with the concentration-dependent kinetics of hPAP reactivation, assuming that the reconstitution of the active enzyme requires the association of subunits in dimeric form. Moreover, it suggests formation of an inactive intermediate during refolding of the denatured PAP. A mechanism of renaturation of the active enzyme from denatured PAP is proposed. PMID:8729028

  7. Mechanistic insights into the Pd-catalyzed direct amination of allyl alcohols: evidence for an outer-sphere mechanism involving a palladium hydride intermediate.

    PubMed

    Sawadjoon, Supaporn; Sjöberg, Per J R; Orthaber, Andreas; Matsson, Olle; Samec, Joseph S M

    2014-02-01

    The mechanism of direct amination of allyl alcohol by a palladium triphenylphosphite complex has been explored. Labelling studies show that the reaction proceeds through a ?-allylpalladium intermediate. A second-order dependence of reaction rate on allyl alcohol concentration was observed. Kinetic isotope effect studies and ESI-MS studies are in agreement with a reaction proceeding through a palladium hydride intermediate in which both O-H bond and C-O bond cleavages are involved in rate-determining steps. A stereochemical study supports an outer-sphere nucleophilic attack of the ?-allylpalladium intermediate giving complete chiral transfer from starting material to product. PMID:24403056

  8. Atomic resolution study of reversible conversion reaction in metal oxide electrodes for lithium-ion battery.

    PubMed

    Luo, Langli; Wu, Jinsong; Xu, Junming; Dravid, Vinayak P

    2014-11-25

    Electrode materials based on conversion reactions with lithium ions have shown much higher energy density than those based on intercalation reactions. Here, nanocubes of a typical metal oxide (Co3O4) were grown on few-layer graphene, and their electrochemical lithiation and delithiation were investigated at atomic resolution by in situ transmission electron microscopy to reveal the mechanism of the reversible conversion reaction. During lithiation, a lithium-inserted Co3O4 phase and a phase consisting of nanosized Co-Li-O clusters are identified as the intermediate products prior to the subsequent formation of Li2O crystals. In delithiation, the reduced metal nanoparticles form a network and breakdown into even smaller clusters that act as catalysts to prompt reduction of Li2O, and CoO nanoparticles are identified as the product of the deconversion reaction. Such direct real-space, real-time atomic-scale observations shed light on the phenomena and mechanisms in reaction-based electrochemical energy conversion and provide impetus for further development in electrochemical charge storage devices. PMID:25337887

  9. Understanding side reactions in K-O2 batteries for improved cycle life.

    PubMed

    Ren, Xiaodi; Lau, Kah Chun; Yu, Mingzhe; Bi, Xuanxuan; Kreidler, Eric; Curtiss, Larry A; Wu, Yiying

    2014-11-12

    Superoxide based metal-air (or metal-oxygen) batteries, including potassium and sodium-oxygen batteries, have emerged as promising alternative chemistries in the metal-air battery family because of much improved round-trip efficiencies (>90%). In order to improve the cycle life of these batteries, it is crucial to understand and control the side reactions between the electrodes and the electrolyte. For potassium-oxygen batteries using ether-based electrolytes, the side reactions on the potassium anode have been identified as the main cause of battery failure. The composition of the side products formed on the anode, including some reaction intermediates, have been identified and quantified. Combined experimental studies and density functional theory (DFT) calculations show the side reactions are likely driven by the interaction of potassium with ether molecules and the crossover of oxygen from the cathode. To inhibit these side reactions, the incorporation of a polymeric potassium ion selective membrane (Nafion-K(+)) as a battery separator is demonstrated that significantly improves the battery cycle life. The K-O2 battery with the Nafion-K(+) separator can be discharged and charged for more than 40 cycles without increases in charging overpotential. PMID:25295518

  10. Visualizing virus assembly intermediates inside marine cyanobacteria.

    PubMed

    Dai, Wei; Fu, Caroline; Raytcheva, Desislava; Flanagan, John; Khant, Htet A; Liu, Xiangan; Rochat, Ryan H; Haase-Pettingell, Cameron; Piret, Jacqueline; Ludtke, Steve J; Nagayama, Kuniaki; Schmid, Michael F; King, Jonathan A; Chiu, Wah

    2013-10-31

    Cyanobacteria are photosynthetic organisms responsible for ?25% of organic carbon fixation on the Earth. These bacteria began to convert solar energy and carbon dioxide into bioenergy and oxygen more than two billion years ago. Cyanophages, which infect these bacteria, have an important role in regulating the marine ecosystem by controlling cyanobacteria community organization and mediating lateral gene transfer. Here we visualize the maturation process of cyanophage Syn5 inside its host cell, Synechococcus, using Zernike phase contrast electron cryo-tomography (cryoET). This imaging modality yields dramatic enhancement of image contrast over conventional cryoET and thus facilitates the direct identification of subcellular components, including thylakoid membranes, carboxysomes and polyribosomes, as well as phages, inside the congested cytosol of the infected cell. By correlating the structural features and relative abundance of viral progeny within cells at different stages of infection, we identify distinct Syn5 assembly intermediates. Our results indicate that the procapsid releases scaffolding proteins and expands its volume at an early stage of genome packaging. Later in the assembly process, we detected full particles with a tail either with or without an additional horn. The morphogenetic pathway we describe here is highly conserved and was probably established long before that of double-stranded DNA viruses infecting more complex organisms. PMID:24107993

  11. Intermediate care: the role of medicines management.

    PubMed

    Millar, Anna N; Hughes, Carmel M; Passmore, A Peter; Ryan, Cristín

    2014-01-01

    Healthcare systems worldwide are facing an unprecedented demographic change as globally, the number of older people will triple to 2 billion by the year 2050. The resulting pressures on acute services have been instrumental in the development of intermediate care (IC) as a new healthcare model, which has its origins in the National Health Service in the UK. IC is an umbrella term for patient services that do not require the resources of a general hospital but are beyond the scope of a traditional primary care team. IC aims to promote timely discharge from hospital, prevent unnecessary hospital admissions and reduce the need for long-term residential care by optimizing functional independence. Various healthcare providers around the world have adopted similar models of care to manage changing healthcare needs. Polypharmacy, along with age-related changes, places older people at an increased risk of adverse drug events, including inappropriate prescribing, which has been shown to be prevalent in this population in other healthcare settings. Medicines management (the practice of maximizing health through optimal use of medicines) of older people has been discussed in the literature in a variety of settings; however, its place within IC is largely unknown. Despite IC being a multidisciplinary healthcare model, there is a lack of evidence to suggest that enhanced pharmaceutical involvement is core to the service provided within IC. This review article highlights the gap in the literature surrounding medicines management within IC and identifies potential solutions aimed at improving patient outcomes in this setting. PMID:24197610

  12. Intermediate endpoint biomarkers for lung cancer chemoprevention

    NASA Astrophysics Data System (ADS)

    MacAulay, Calum E.; Lam, Stephen; Klein-Parker, Helga; Gazdar, Adi; Guillaud, Martial; Payne, Peter W.; Le Riche, Jean C.; Dawe, Chris; Band, Pierre; Palcic, Branko

    1998-04-01

    Given the demographics of current and ex-smoking populations in North America, lung cancer will be a major problem in the foreseeable future. Early detection and treatment of lung cancer holds great promise for the management of this disease. Unlike cervical cancer, the physical, complete removal/destruction of all dysplastic lesions in the bronchial tree is not possible; however, treatment of the lesions using a chemopreventive agent is. Intermediate biomarkers have been used to screen promising chemopreventive agents for larger population studies. We have examined the natural history of lung cancer development by following a group of subjects at high risk of developing lung cancer using fluorescence endoscopy to identify the areas of abnormality for biopsy. Approximately 900 biopsies have been collected in this fashion and graded by at least two experienced, expert pathologists. Using an interactive version of the Cyto-Savant (Oncometrics Imaging Corp.), cytometric and tissue architectural data were collected from these biopsies. Using only the data from the normal and invasive cancer biopsies, quantitative morphometric and architectural indices were generated and calculated for all the collected biopsies. These indices were compared with Loss of Heterozygosity (LOH) of ten sites commonly associated with cancer. These results and the application of these quantitative measures to two small chemoprevention studies will be reported.

  13. Reaction of 4-Nitrochlorobenzene with 2-Methoxyphenylacetonitrile

    Microsoft Academic Search

    V. Yu. Orlov; A. D. Kotov; V. V. Ganzha

    2003-01-01

    The reaction of 4-substituted nitroarenes with arylacetonitrile in alcoholic medium in the presence of excess alkali provides a convenient method for the preparation of 2,1-benzisoxazoles which are versatile synthons and intermediate products in manufacture of monomers and bioactive substances (tranquilizers) [1 3]. We have found that the reaction of 4-nitrochlorobenzene (I) with 2-methoxyphenylacetonitrile (II) gives a mixture of methoxy and

  14. Torquoselectivity in the nazarov reactions of allenyl vinyl ketones.

    PubMed

    Morgan, Timothy D R; LeBlanc, Luc M; Ardagh, Giselle H; Boyd, Russell J; Burnell, D Jean

    2015-01-16

    Nazarov reactions mediated by BF3-etherate of a series of carbon-substituted allenyl vinyl ketones provided intermediates in which substituents on the termini of the allenes had rotated away from the vinyl moieties, and these intermediates were trapped by (4 + 3)-cyclizations. A computational examination of the torquoselectivity of these Nazarov reactions confirmed a kinetic preference for the observed isomers and pointed to steric interactions and the degree of allene deformation as significant factors in determining the torquoselectivity. The study also suggested that the high proportion of one geometrical isomer in the Nazarov products might also be due to some preferential trapping of the major Nazarov intermediate. PMID:25521250

  15. ART F301 F71 INTERMEDIATE CERAMICS

    E-print Network

    Sikes, Derek S.

    ART F301 F71 INTERMEDIATE CERAMICS Summer 2014 3credits Meeting times: M-Th 2-5pm Fine Arts Bldg@alaska.edu COURSE DESCRIPTION: Intermediate Ceramics provides an overview of the medium of ceramics and it of various ceramic forming techniques and an understanding of visual elements and principles of design. You

  16. Radio and Television Servicing. Intermediate Course.

    ERIC Educational Resources Information Center

    Campbell, Guy; And Others

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

  17. Appliance Services. Intermediate Course. Career Education.

    ERIC Educational Resources Information Center

    Killough, Joseph

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

  18. Financial Intermediation in the Early Roman Empire

    Microsoft Academic Search

    Peter Temin

    2002-01-01

    In this paper I use a theoretical hierarchy of financial sources to evaluate the effectiveness of financial markets in the early Roman Empire. I first review the theory of financial intermediation to describe the hierarchy of financial sources and survey briefly the history of financial intermediation in pre-industrial Western Europe to provide a standard against which to evaluate the Roman

  19. Financial Intermediation in the Early Roman Empire

    Microsoft Academic Search

    PETER TEMIN

    2004-01-01

    I evaluate the effectiveness of financial markets in the early Roman Empire in this article. I review the theory of financial intermediation to describe a hierarchy of financial sources and survey briefly the history of financial intermediation in eighteenth-century Western Europe to provide a standard against which to evaluate the Roman evidence. I then describe the nature of financial arrangements

  20. Intermediate load-center photovoltaic application experiments

    Microsoft Academic Search

    E. L. Burgess

    1980-01-01

    A total of nine intermediate load-center photovoltaic systems were carried into the construction phase this year. These nine systems range in size from 20 to 225 kWp electrical output and total almost 1 MWp. They are being installed in a diverse set of applications and locations and represent the bulk of the photovoltaic initial system evaluation experiments for the intermediate

  1. Chicken & egg: competition among intermediation service providers

    Microsoft Academic Search

    Bernard Caillaud; Bruno Jullien

    2001-01-01

    We analyze a model of imperfect price competition between intermediation service providers. We insist on features that are relevant for informational intermediation via the Internet: the presence of indirect network externalities, the possibility of using the nonexclusive services of several intermediaries, and the widespread practice of price discrimination based on users' identity and on usage. Efficient market structures emerge in

  2. Chicken & Egg: Competition among Intermediation Service Providers

    Microsoft Academic Search

    Bernard Caillaud; Bruno Jullien

    2003-01-01

    We analyze a model of imperfect price competition between intermediation service providers. We insist on features that are relevant for informational intermediation via the Internet: the presence of indirect network externalities, the possibility of using the nonexclusive services of several intermediaries, and the widespread practice of price discrimination based on users' identity and on usage. Efficient market structures emerge in

  3. Magnetic properties of intermediate-mass stars

    E-print Network

    G. A. Wade

    2006-01-30

    Magnetic fields play an important role in producing and modifying the photospheric chemical peculiarities of intermediate-mass main sequence stars. This article discusses the basic theory and methods of measurement used to detect and characterise stellar magnetic fields, and reviews our current knowledge of selected characteristics of magnetic fields in intermediate-mass stars.

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

    ERIC Educational Resources Information Center

    Jones, Marion

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

  5. 4-H Textile Science Intermediate Projects.

    ERIC Educational Resources Information Center

    Scholl, Jan

    This packet contains six intermediate-level 4-H sewing projects for students in the textile sciences area. The projects cover the following topics: intermediate sewing techniques including sewing with knits, making coordinates, making accessories, sewing for other projects and people, time-saving sewing techniques, and creating your own project.…

  6. Synthesis of an Advanced Intermediate of the Jatrophane Diterpene Pl-4: A Dibromide Coupling Approach

    PubMed Central

    2013-01-01

    The preparation of an advanced intermediate toward the synthesis of the jatrophane diterpene Pl-4 is described. The key step is a regioselective chelation-controlled lithiation of the (Z)-configured bromide in the corresponding vinyl dibromide precursor. The method outlined within this Article is suitable for the facile access of sterically hindered internal vinyl halides for further coupling reactions. PMID:23895274

  7. Studies of the Di-iron(VI) Intermediate in Ferrate-Dependent Oxygen Evolution from Water

    E-print Network

    Roth, Justine P.

    by mining fossil fuels.5 Alternative technologies are being designed to use photon-absorbing materials gas as an economically viable alternative to fossil fuels. The present study focuses upon a testable a di-iron(VI) intermediate, consistent with the analysis of the reaction kinetics. Alternative

  8. Intermediate System to Intermediate System (ISIS) Extensions for Traffic Engineering (TE)

    Microsoft Academic Search

    H. Smit; T. Li

    2004-01-01

    This document describes extensions to the Intermediate System to Intermediate System (IS-IS) protocol to support Traffic Engineering (TE). This document extends the IS-IS protocol by specifying new information that an Intermediate System (router) can place in Link State Protocol (LSP) Data Units. This information describes additional details regarding the state of the network that are useful for traffic engineering computations.

  9. Hedging Your Bets: Intermediate Movements as Optimal Behavior in the Context of an Incomplete Decision

    PubMed Central

    Haith, Adrian M.; Huberdeau, David M.; Krakauer, John W.

    2015-01-01

    Existing theories of movement planning suggest that it takes time to select and prepare the actions required to achieve a given goal. These theories often appeal to circumstances where planning apparently goes awry. For instance, if reaction times are forced to be very low, movement trajectories are often directed between two potential targets. These intermediate movements are generally interpreted as errors of movement planning, arising either from planning being incomplete or from parallel movement plans interfering with one another. Here we present an alternative view: that intermediate movements reflect uncertainty about movement goals. We show how intermediate movements are predicted by an optimal feedback control model that incorporates an ongoing decision about movement goals. According to this view, intermediate movements reflect an exploitation of compatibility between goals. Consequently, reducing the compatibility between goals should reduce the incidence of intermediate movements. In human subjects, we varied the compatibility between potential movement goals in two distinct ways: by varying the spatial separation between targets and by introducing a virtual barrier constraining trajectories to the target and penalizing intermediate movements. In both cases we found that decreasing goal compatibility led to a decreasing incidence of intermediate movements. Our results and theory suggest a more integrated view of decision-making and movement planning in which the primary bottleneck to generating a movement is deciding upon task goals. Determining how to move to achieve a given goal is rapid and automatic. PMID:25821964

  10. Hedging your bets: intermediate movements as optimal behavior in the context of an incomplete decision.

    PubMed

    Haith, Adrian M; Huberdeau, David M; Krakauer, John W

    2015-03-01

    Existing theories of movement planning suggest that it takes time to select and prepare the actions required to achieve a given goal. These theories often appeal to circumstances where planning apparently goes awry. For instance, if reaction times are forced to be very low, movement trajectories are often directed between two potential targets. These intermediate movements are generally interpreted as errors of movement planning, arising either from planning being incomplete or from parallel movement plans interfering with one another. Here we present an alternative view: that intermediate movements reflect uncertainty about movement goals. We show how intermediate movements are predicted by an optimal feedback control model that incorporates an ongoing decision about movement goals. According to this view, intermediate movements reflect an exploitation of compatibility between goals. Consequently, reducing the compatibility between goals should reduce the incidence of intermediate movements. In human subjects, we varied the compatibility between potential movement goals in two distinct ways: by varying the spatial separation between targets and by introducing a virtual barrier constraining trajectories to the target and penalizing intermediate movements. In both cases we found that decreasing goal compatibility led to a decreasing incidence of intermediate movements. Our results and theory suggest a more integrated view of decision-making and movement planning in which the primary bottleneck to generating a movement is deciding upon task goals. Determining how to move to achieve a given goal is rapid and automatic. PMID:25821964

  11. C3-C4 Intermediate Species in Alternanthera (Amaranthaceae) 1

    PubMed Central

    Rajendrudu, Gedupudi; Prasad, Jasty S. R.; Das, V. S. Rama

    1986-01-01

    Two naturally occurring species of the genus Alternanthera, namely A. ficoides and A. tenella, were identified as C3-C4 intermediates based on leaf anatomy, photosynthetic CO2 compensation point (?), O2 response of ?, light intensity response of ?, and the activities of key enzymes of photosynthesis. A. ficoides and A. tenella exhibited a less distinct Kranz-like leaf anatomy with substantial accumulation of starch both in mesophyll and bundle sheath cells. Photosynthetic CO2 compensation points of these two intermediate species at 29°C were much lower than in C3 plants and ranged from 18 to 22 microliters per liter. Although A. ficoides and A. tenella exhibited similar intermediacy in ?, the apparent photorespiratory component of O2 inhibition in A. ficoides is lower than in A. tenella. The ? progressively decreases from 35 microliters per liter at lowest light intensity to 18 microliters per liter at highest light intensity in A. tenella. It was, however, constant in A. ficoides at 20 to 25 microliters per liter between light intensities measured. The rates of net photosynthesis at 21% O2 and 29°C by A. ficoides and A. tenella were 25 to 28 milligrams CO2 per square decimeter per hour which are intermediate between values obtained for Tridax procumbens and A. pungens, C3 and C4 species, respectively. The activities of key enzymes of C4 photosynthesis, phosphoenolpyruvate carboxylase, pyruvate Pi dikinase, NAD malic enzyme, NADP malic enzyme and phosphoenolpyruvate carboxykinase in the two intermediates, A. ficoides and A. tenella are very low or insignificant. Results indicated that the relatively low apparent photorespiratory component in these two species is presumably the basis for the C3-C4 intermediate photosynthesis. Images Fig. 2 PMID:16664634

  12. Intermediate temperature electrolytes for SOFC

    SciTech Connect

    Bloom, I.; Krumpelt, M.; Hash, M.C.; Zebrowski, J.P.; Zurawski, D.

    1992-09-01

    The objective of this work is to identify a new set of materials that would allow the operation of the solid oxide fuel cell in the 600--800{sup degrees}C temperature range. The approach that is being used is to start with a systematic evaluation of new electrolyte materials and then to develop compatible electrode and interconnect materials.

  13. Nitrite Dismutase Reaction Mechanism: Kinetic and Spectroscopic Investigation of the Interaction between Nitrophorin and Nitrite.

    PubMed

    He, Chunmao; Howes, Barry D; Smulevich, Giulietta; Rumpel, Sigrun; Reijerse, Edward J; Lubitz, Wolfgang; Cox, Nicholas; Knipp, Markus

    2015-04-01

    Nitrite is an important metabolite in the physiological pathways of NO and other nitrogen oxides in both enzymatic and nonenzymatic reactions. The ferric heme b protein nitrophorin 4 (NP4) is capable of catalyzing nitrite disproportionation at neutral pH, producing NO. Here we attempt to resolve its disproportionation mechanism. Isothermal titration calorimetry of a gallium(III) derivative of NP4 demonstrates that the heme iron coordinates the first substrate nitrite. Contrary to previous low-temperature EPR measurements, which assigned the NP4-nitrite complex electronic configuration solely to a low-spin (S = 1/2) species, electronic absorption and resonance Raman spectroscopy presented here demonstrate that the NP4-NO2(-) cofactor exists in a high-spin/low-spin equilibrium of 7:3 which is in fast exchange in solution. Spin-state interchange is taken as evidence for dynamic NO2(-) coordination, with the high-spin configuration (S = 5/2) representing the reactive species. Subsequent kinetic measurements reveal that the dismutation reaction proceeds in two discrete steps and identify an {FeNO}(7) intermediate species. The first reaction step, generating the {FeNO}(7) intermediate, represents an oxygen atom transfer from the iron bound nitrite to a second nitrite molecule in the protein pocket. In the second step this intermediate reduces a third nitrite substrate yielding two NO molecules. A nearby aspartic acid residue side-chain transiently stores protons required for the reaction, which is crucial for NPs' function as nitrite dismutase. PMID:25751738

  14. Drug Reactions

    MedlinePLUS

    Most of the time, medicines make our lives better. They reduce aches and pains, fight infections, and control problems such as high blood pressure or diabetes. But medicines can also cause unwanted reactions. One problem is ...

  15. ESI-MS, DFT and Synthetic Studies on the H2-Mediated Coupling of Acetylene: Insertion of C=X Bonds into Rhodacyclopentadienes and Brønsted Acid Cocatalyzed Hydrogenolysis of Organorhodium Intermediates

    PubMed Central

    Williams, Vanessa M.; Kong, Jong Rock; Ko, Byoung Joon; Mantri, Yogita; Brodbelt, Jennifer S.; Baik, Mu-Hyun; Krische, Michael J.

    2009-01-01

    The catalytic mechanism of the hydrogen-mediated coupling of acetylene to carbonyl compounds and imines has been examined using three techniques: (a) ESI-MS and ESI-CAD-MS analyses, (b) computational modeling, and (c) experiments wherein putative reactive intermediates are diverted to alternative reaction products. ESI-MS analysis of reaction mixtures from the hydrogen-mediated reductive coupling of acetylene to ?-ketoesters or N-benzenesulfonyl aldimines corroborate a catalytic mechanism involving C=X (X = O, NSO2Ph) insertion into a cationic rhodacyclopentadiene obtained by way of acetylene oxidative dimerization with subsequent Brønsted acid cocatalyzed hydrogenolysis of the resulting oxa- or azarhodacycloheptadiene. Hydrogenation of 1,6-diynes in the presence of ?-ketoesters provides analogous coupling products. ESI mass spectrometric analysis again corroborates a catalytic mechanism involving carbonyl insertion into a cationic rhodacyclopentadiene. For all ESI-MS experiments, the structural assignments of ions are supported by multi-stage collisional activated dissociation (CAD) ESI-MS analyses. Further support for the proposed catalytic mechanism derives from experiments aimed at the interception of putative reactive intermediates and their diversion to alternate reaction products. For example, rhodium catalyzed coupling of acetylene to aldehyde in the absence of hydrogen or Brønsted acid cocatalyst provides the corresponding (Z)-butadienyl ketone, which arises from ?-hydride elimination of the proposed oxarhodacycloheptadiene intermediate, as corroborated by isotopic labeling. Additionally, the putative rhodacyclopentadiene intermediate obtained from the oxidative coupling of acetylene is diverted to the product of reductive [2+2+2] cycloaddition when N-p-toluenesulfonyl-dehydroalanine ethyl ester is used as the coupling partner. The mechanism of this transformation also is corroborated by isotopic labeling. Computer model studies based on density functional theory (DFT) support the proposed mechanism and identify Brønsted acid cocatalyst assisted hydrogenolysis to be the most difficult step. The collective studies provide new insight into the reactivity of cationic rhodacyclopentadienes, which should facilitate the design of related rhodium catalyzed C-C couplings. PMID:19845357

  16. Enzyme Reactions

    NSDL National Science Digital Library

    Maryland Virtual High School

    The enzyme reaction rate activity allows students to simulate the effects of variables such as temperature and pH on the reaction rate of the enzyme catalase. This computer simulation is best used after the students have done a wet lab experiment. The value of the simulation is that it requires the students to interpret and analyze the graphical representation of data and it enables the running of mutiple experiments in a short amount of time.

  17. Intermediate scalings in holographic RG flows and conductivities

    E-print Network

    Jyotirmoy Bhattacharya; Sera Cremonini; Blaise Goutéraux

    2015-02-04

    We construct numerically finite density domain-wall solutions which interpolate between two $AdS_4$ fixed points and exhibit an intermediate regime of hyperscaling violation, with or without Lifshitz scaling. Such RG flows can be realized in gravitational models containing a dilatonic scalar and a massive vector field with appropriate choices of the scalar potential and couplings. The infrared $AdS_4$ fixed point describes a new ground state for strongly coupled quantum systems realizing such scalings, thus avoiding the well-known extensive zero temperature entropy associated with $AdS_2 \\times \\mathbb{R}^2$. We also examine the zero temperature behavior of the optical conductivity in these backgrounds and identify two scaling regimes before the UV CFT scaling is reached. The scaling of the conductivity is controlled by the emergent IR conformal symmetry at very low frequencies, and by the intermediate scaling regime at higher frequencies.

  18. Intermediate scalings in holographic RG flows and conductivities

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Jyotirmoy; Cremonini, Sera; Goutéraux, Blaise

    2015-02-01

    We construct numerically finite density domain-wall solutions which interpolate between two AdS 4 fixed points and exhibit an intermediate regime of hyperscaling violation, with or without Lifshitz scaling. Such RG flows can be realized in gravitational models containing a dilatonic scalar and a massive vector field with appropriate choices of the scalar potential and couplings. The infrared AdS 4 fixed point describes a new ground state for strongly coupled quantum systems realizing such scalings, thus avoiding the well-known extensive zero temperature entropy associated with . We also examine the zero temperature behavior of the optical conductivity in these backgrounds and identify two scaling regimes before the UV CFT scaling is reached. The scaling of the conductivity is controlled by the emergent IR conformal symmetry at very low frequencies, and by the intermediate scaling regime at higher frequencies.

  19. Absorption-Fluctuation Theorem for Nuclear Reactions: Brink-Axel, Incomplete Fusion and All That

    E-print Network

    M. S. Hussein

    2008-01-13

    We discuss the connection between absorption, averages and fluctuations in nuclear reactions. The fluctuations in the entrance channel result in the compound nucleus, Hauser-Feshbach, cross section, the fluctuations in the intermediate channels, result in modifications of multistep reaction cross sections, while the fluctuations in the final channel result in hybrid cross sections that can be used to describe incomplete fusion reactions. We discuss the latter in details and comment on the validity of the assumptions used in the develpoment of the Surrogate method. We also discuss the theory of multistep reactions with regards to intermediate state fluctuations and the energy dependence and non-locality of the intermediate channels optical potentials.

  20. Flame propagation with a sequential reaction mechanism

    Microsoft Academic Search

    Stephen B. Margolis; Bernard J. Matkowsky

    1982-01-01

    The steady propagation of a flame characterized by the production and depletion of a significant intermediate species through a premixed combustible mixture is studied. The method of matched asymptotic expansions is employed to derive a solution for the large activation energies, which confine the two chemical reactions involved to a thin layer. The small separation distance between the points where

  1. First intermediate host of the digenean trematode Proctoeces lintoni (Fellodistomidae) in Chile.

    PubMed

    Aldana, Marcela; González, Karen; Loot, Geraldine; Pulgar, José; Marquet, Pablo A

    2009-12-01

    The digenetic trematode, Proctoeces lintoni, is a parasite of the rocky intertidal ecosystems of the Chilean Pacific coastline. Although this species is relatively well known, the first intermediate host has not yet been described. In the present study, we used experimental protocols and field studies to identify the host that harbors the sporocysts and cercariae stages of the parasite. The first intermediate host was shown to be the dominant mussel of the mid-littoral zone, Perumytilus purpuratus. PMID:19545188

  2. Thermochemistry and reaction paths in the oxidation reaction of benzoyl radical: C6H5C•(?O).

    PubMed

    Sebbar, Nadia; Bozzelli, Joseph W; Bockhorn, Henning

    2011-10-27

    Alkyl substituted aromatics are present in fuels and in the environment because they are major intermediates in the oxidation or combustion of gasoline, jet, and other engine fuels. The major reaction pathways for oxidation of this class of molecules is through loss of a benzyl hydrogen atom on the alkyl group via abstraction reactions. One of the major intermediates in the combustion and atmospheric oxidation of the benzyl radicals is benzaldehyde, which rapidly loses the weakly bound aldehydic hydrogen to form a resonance stabilized benzoyl radical (C6H5C(•)?O). A detailed study of the thermochemistry of intermediates and the oxidation reaction paths of the benzoyl radical with dioxygen is presented in this study. Structures and enthalpies of formation for important stable species, intermediate radicals, and transition state structures resulting from the benzoyl radical +O2 association reaction are reported along with reaction paths and barriers. Enthalpies, ?fH298(0), are calculated using ab initio (G3MP2B3) and density functional (DFT at B3LYP/6-311G(d,p)) calculations, group additivity (GA), and literature data. Bond energies on the benzoyl and benzoyl-peroxy systems are also reported and compared to hydrocarbon systems. The reaction of benzoyl with O2 has a number of low energy reaction channels that are not currently considered in either atmospheric chemistry or combustion models. The reaction paths include exothermic, chain branching reactions to a number of unsaturated oxygenated hydrocarbon intermediates along with formation of CO2. The initial reaction of the C6H5C(•)?O radical with O2 forms a chemically activated benzoyl peroxy radical with 37 kcal mol(-1) internal energy; this is significantly more energy than the 21 kcal mol(-1) involved in the benzyl or allyl + O2 systems. This deeper well results in a number of chemical activation reaction paths, leading to highly exothermic reactions to phenoxy radical + CO2 products. PMID:21942384

  3. FTIR analysis of the SII540 intermediate of sensory rhodopsin II: Asp73 is the Schiff base proton acceptor.

    PubMed

    Bergo, V; Spudich, E N; Scott, K L; Spudich, J L; Rothschild, K J

    2000-03-21

    Sensory rhodopsin II (SRII), a repellent phototaxis receptor found in Halobacterium salinarum, has several homologous residues which have been found to be important for the proper functioning of bacteriorhodopsin (BR), a light-driven proton pump. These include Asp73, which in the case of bacteriorhodopsin (Asp85) functions as the Schiff base counterion and proton acceptor. We analyzed the photocycles of both wild-type SRII and the mutant D73E, both reconstituted in Halobacterium salinarum lipids, using FTIR difference spectroscopy under conditions that favor accumulation of the O-like, photocycle intermediate, SII540. At both room temperature and -20 degrees C, the difference spectrum of SRII is similar to the BR-->O640 difference spectrum of BR, especially in the configurationally sensitive retinal fingerprint region. This indicates that SII540 has an all-trans chromophore similar to the O640 intermediate in BR. A positive band at 1761 cm-1 downshifts 40 cm-1 in the mutant D73E, confirming that Asp73 undergoes a protonation reaction and functions in analogy to Asp85 in BR as a Schiff base proton acceptor. Several other bands in the C=O stretching regions are identified which reflect protonation or hydrogen bonding changes of additional Asp and/or Glu residues. Intense bands in the amide I region indicate that a protein conformational change occurs in the late SRII photocycle which may be similar to the conformational changes that occur in the late BR photocycle. However, unlike BR, this conformational change does not reverse during formation of the O-like intermediate, and the peptide groups giving rise to these bands are partially accessible for hydrogen/deuterium exchange. Implications of these findings for the mechanism of SRII signal transduction are discussed. PMID:10715101

  4. N-Oxidation of 4-chloroaniline by prostaglandin synthase. Redox cycling of radical intermediate(s).

    PubMed Central

    Golly, I; Hlavica, P

    1985-01-01

    4-Chloroaniline undergoes N-oxidation in ram seminal-vesicle microsomal preparations supplemented with arachidonic acid to yield N-(4-chlorophenyl)-hydroxylamine and 1-chloro-4-nitrosobenzene. H2O2 also supports metabolism of the amine substrate to the same organic-solvent-extractable products, suggesting that the hydroperoxidase activity of prostaglandin synthase is responsible for the co-oxidation. Analysis of the reaction mixtures by e.s.r. spectrometry reveals the formation of a radical intermediate bearing the characteristics of a strongly immobilized nitroxide. Arylamine-stimulated O2.- release can be observed when the arachidonic acid-containing incubation media are supplemented with NADPH. Redox cycling of the nitroxide/hydroxylamine couple is presumed to represent the major source of O2.-, but additional mechanisms, such as redox changes of nitro anion radicals resulting from potential further metabolism of 1-chloro-4-nitrosobenzene, cannot be excluded. The concerted action of carrier-bound nitroxides and O2.- in initiating damage of cellular macromolecules is discussed. PMID:2985047

  5. The axon reaction: Identifying the genes that make a difference

    Microsoft Academic Search

    Fredrik Piehl; Maria Swanberg; Olle Lidman

    2007-01-01

    Numerous CNS diseases of primarily non-inflammatory origin, such as idiopathic neurodegenerative diseases, contain elements of inflammation, with T cell infiltration, MHC class II expression and neuron\\/axon damage. Gene mapping in human clinical materials have in most cases failed to unravel discrete genes, since most genes instrumental in non-Mendelian forms of these complex diseases are likely to modestly affect risk, be

  6. Kinetic intermediates of unfolding of dimeric prostatic phosphatase.

    PubMed

    Kuciel, Rados?awa; Mazurkiewicz, Aleksandra; Dudzik, Paulina

    2007-01-01

    Kinetics of guanidine hydrochloride (GdnHCl)-induced unfolding of human prostatic acid phosphatase (hPAP), a homodimer of 50 kDa subunit molecular mass was investigated with enzyme activity measurements, capacity for binding an external hydrophobic probe, 1-anilinonaphtalene-8-sulfonate (ANS), accessibility of thiols to reaction with 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) and 2-(4'-maleimidylanilino)naphthalene-6-sulfonate (MIANS) and ability to bind Congo red dye. Kinetic analysis was performed to describe a possible mechanism of hPAP unfolding and dissociation that leads to generation of an inactive monomeric intermediate that resembles, in solution of 1.25 M GdnHCl pH 7.5, at 20 degrees C, in equilibrium, a molten globule state. The reaction of hPAP inactivation in 1.25 M GdnHCl followed first order kinetics with the reaction rate constant 0.0715 +/- 0.0024 min(-1) . The rate constants of similar range were found for the pseudo-first-order reactions of ANS and Congo red binding: 0.0366 +/- 0.0018 min(-1) and 0.0409 +/- 0.0052 min(-1), respectively. Free thiol groups, inaccessible in the native protein, were gradually becoming, with the progress of unfolding, exposed for the reactions with DTNB and MIANS, with the pseudo-first-order reaction rate constants 0.327 +/- 0.014 min(-1) and 0.216 +/- 0.010 min(-1), respectively. The data indicated that in the course of hPAP denaturation exposure of thiol groups to reagents took place faster than the enzyme inactivation and exposure of the protein hydrophobic surface. This suggested the existence of a catalytically active, partially unfolded, but probably dimeric kinetic intermediate in the process of hPAP unfolding. On the other hand, the protein inactivation was accompanied by exposure of a hydrophobic, ANS-binding surface, and with an increased capacity to bind Congo red. Together with previous studies these results suggest that the stability of the catalytically active conformation of the enzyme depends mainly on the dimeric structure of the native hPAP. PMID:17520089

  7. Pharmacogenomics of adverse drug reactions

    PubMed Central

    2013-01-01

    Considerable progress has been made in identifying genetic risk factors for idiosyncratic adverse drug reactions in the past 30 years. These reactions can affect various tissues and organs, including liver, skin, muscle and heart, in a drug-dependent manner. Using both candidate gene and genome-wide association studies, various genes that make contributions of varying extents to each of these forms of reactions have been identified. Many of the associations identified for reactions affecting the liver and skin involve human leukocyte antigen (HLA) genes and for reactions relating to the drugs abacavir and carbamazepine, HLA genotyping is now in routine use prior to drug prescription. Other HLA associations are not sufficiently specific for translation but are still of interest in relation to underlying mechanisms for the reactions. Progress on non-HLA genes affecting adverse drug reactions has been less, but some important associations, such as those of SLCO1B1 and statin myopathy, KCNE1 and drug-induced QT prolongation and NAT2 and isoniazid-induced liver injury, are considered. Future prospects for identification of additional genetic risk factors for the various adverse drug reactions are discussed. PMID:23360680

  8. Risk factors associated with adverse reactions to antituberculosis drugs*

    PubMed Central

    Resende, Laíse Soares Oliveira; dos Santos-Neto, Edson Theodoro

    2015-01-01

    This review sought to identify the available scientific evidence on risk factors associated with adverse reactions to antituberculosis drugs. We performed a systematic review of studies published in the 1965-2012 period and indexed in the MEDLINE and LILACS databases. A total of 1,389 articles were initially selected. After reading their abstracts, we selected 85 studies. Of those 85 studies, 16 were included in the review. Risk factors for adverse reactions to antituberculosis drugs included age > 60 years, treatment regimens, alcoholism, anemia, and HIV co-infection, as well as sodium, iron, and albumin deficiency. Protective factors against hepatic adverse effects of antituberculosis drugs included being male (combined OR = 0.38; 95% CI: 0.20-0.72) and showing a rapid/intermediate N-acetyltransferase 2 acetylator phenotype (combined OR = 0.41; 95% CI: 0.18-0.90). There is evidence to support the need for management of adverse reactions to antituberculosis drugs at public health care facilities.

  9. Quantitative and stereospecific dihydroxylations of ?(5)-steroids: a green synthesis of plant growth hormone intermediates.

    PubMed

    Li, Tao; Li, Chunbao

    2013-12-26

    Dihydroxylated ?(5)-steroids are key intermediates in preparing steroids bearing a 5?-hydroxy-6-oxo moiety, which are plant growth hormones. Quantitative and stereospecific dihydroxylations of ?(5)-steroids have been realized, using H2O2 catalyzed by KI and H2SO4 at 80 °C in aqueous dioxane. The workup consisted only of concentrating the solvents and filtering the products; no chromatography was needed. The reaction conditions tolerate various functional groups on the ?(5)-steroids. A mechanism for this reaction is proposed and the reason that the reaction is quantitative and stereospecific is explained. PMID:24295281

  10. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein.

    PubMed

    Tenboer, Jason; Basu, Shibom; Zatsepin, Nadia; Pande, Kanupriya; Milathianaki, Despina; Frank, Matthias; Hunter, Mark; Boutet, Sébastien; Williams, Garth J; Koglin, Jason E; Oberthuer, Dominik; Heymann, Michael; Kupitz, Christopher; Conrad, Chelsie; Coe, Jesse; Roy-Chowdhury, Shatabdi; Weierstall, Uwe; James, Daniel; Wang, Dingjie; Grant, Thomas; Barty, Anton; Yefanov, Oleksandr; Scales, Jennifer; Gati, Cornelius; Seuring, Carolin; Srajer, Vukica; Henning, Robert; Schwander, Peter; Fromme, Raimund; Ourmazd, Abbas; Moffat, Keith; Van Thor, Jasper J; Spence, John C H; Fromme, Petra; Chapman, Henry N; Schmidt, Marius

    2014-12-01

    Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1.6 angstroms. Our results open the way to the study of reversible and nonreversible biological reactions on time scales as short as femtoseconds under conditions that maximize the extent of reaction initiation throughout the crystal. PMID:25477465

  11. {gamma} induced multiparticle emissions of medium mass nuclei at intermediate energies

    SciTech Connect

    Mukhopadhyay, Tapan; Basu, D. N. [Variable Energy Cyclotron Centre, 1/AF Bidhan Nagar, Kolkata 700 064 (India)

    2009-01-15

    A comprehensive analysis of multiparticle emissions following photon induced reactions at intermediate energies is provided. Photon induced reaction is described in the energy range of {approx}30-140 MeV 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. The evaporation-fission process of the compound nucleus is simulated in a Monte-Carlo framework. The study shows almost no fission events for the medium mass nuclei and reproduces the available experimental data of photonuclear reaction cross sections satisfactorily at energies {approx}30-140 MeV.

  12. Long-lived trifluoromethanide anion: a key intermediate in nucleophilic trifluoromethylations.

    PubMed

    Prakash, G K Surya; Wang, Fang; Zhang, Zhe; Haiges, Ralf; Rahm, Martin; Christe, Karl O; Mathew, Thomas; Olah, George A

    2014-10-20

    The trifluoromethanide anion is the postulated key intermediate in nucleophilic trifluoromethylation reactions. However, for more than six decades, the trifluoromethanide anion was widely believed to exist only as a short-lived transient species in the condensed phase. It has now been prepared in bulk for the first time in THF solution. The trifluoromethanide anion with the [K(18-crown-6)](+) cation was unequivocally characterized by low-temperature (19)F and (13)C?NMR spectroscopy. Its intermediacy in nucleophilic trifluoromethylation reactions was directly evident by its reaction chemistry with various electrophilic substrates. Variable-temperature NMR spectroscopy, along with quantum mechanical calculations, support the persistence of the trifluoromethanide anion. PMID:25146595

  13. Production of fragments with more neutrons than the projectile at intermediate energies

    NASA Astrophysics Data System (ADS)

    Zhang, X. H.

    2015-03-01

    The nuclear reaction mechanism leading to the production of fragments with more neutrons than the projectile at intermediate energies is studied. A large enhancement in the production of these fragments is observed in the reactions with less neutron-rich projectiles or neutron-rich targets. This enhancement would be related to the difference of the neutron density at the nuclei surface as a factor influencing the process of nucleon exchange in peripheral collisions. From a practical viewpoint, such a nuclear reaction mechanism could provide a novel synthetic avenue to access extremely neutron-rich isotopes towards the neutron drip line.

  14. Kinetics of the benzyl + O(3P) reaction: a quantum chemical/statistical reaction rate theory study.

    PubMed

    da Silva, Gabriel; Bozzelli, Joseph W

    2012-12-14

    The resonance stabilized benzyl radical is an important intermediate in the combustion of aromatic hydrocarbons and in polycyclic aromatic hydrocarbon (PAH) formation in flames. Despite being a free radical, benzyl is relatively stable in thermal, oxidizing environments, and is predominantly removed through bimolecular reactions with open-shell species other than O(2). In this study the reaction of benzyl with ground-state atomic oxygen, O((3)P), is examined using quantum chemistry and statistical reaction rate theory. C(7)H(7)O energy surfaces are generated at the G3SX level, and include several novel pathways. Transition state theory is used to describe elementary reaction kinetics, with canonical variational transition state theory applied for barrierless O atom association with benzyl. Apparent rate constants and branching ratios to different product sets are obtained as a function of temperature and pressure from solving the time-dependent master equation, with RRKM theory for microcanonical k(E). These simulations indicate that the benzyl + O reaction predominantly forms the phenyl radical (C(6)H(5)) plus formaldehyde (HCHO), with lesser quantities of the C(7)H(6)O products benzaldehyde, ortho-quinone methide, and para-quinone methide (+H), along with minor amounts of the formyl radical (HCO) + benzene. Addition of O((3)P) to the methylene site in benzyl produces a highly vibrationally excited C(7)H(7)O* adduct, the benzoxyl radical, which can ?-scission to benzaldehyde + H and phenyl + HCHO. In order to account for the experimental observation of benzene as the major reaction product, a roaming radical mechanism is proposed that converts the nascent products phenyl and HCHO to benzene + HCO. Oxygen atom addition at the ortho and para ring sites in benzyl, which has not been previously considered, is shown to lead to the quinone methides + H; these species are less-stable isomers of benzaldehyde that are proposed as important combustion intermediates, but are yet to be identified experimentally. Franck-Condon simulations of the benzaldehyde, o-quinone methide, and p-quinone methide photoelectron spectra suggest that these C(7)H(6)O isomers could be distinguished using tunable VUV photoionization mass spectrometry. PMID:23108328

  15. Mechanistic approaches to palladium-catalyzed alkene difunctionalization reactions

    PubMed Central

    Jensen, Katrina H.; Sigman, Matthew S.

    2009-01-01

    Alkene difunctionalization, the addition of two functional groups across a double bond, exemplifies a class of reactions with significant synthetic potential. This emerging area examines recent developments of palladium-catalyzed difunctionalization reactions, with a focus on mechanistic strategies that allow for functionalization of a common palladium alkyl intermediate. PMID:18972034

  16. MICROWAVE-FACILITATED MULTICOMPONENT REACTIONS UNDER SOLVENT-FREE CONDITIONS

    EPA Science Inventory

    The application of microwave-expedited solvent-free synthetic protocols in multi-component (MCC) reactions will be exemplified by several condensation and cyclization reactions including the rapid one-pot assembly of heterocyclic compounds from in situ generated intermediates. R...

  17. Control of four stereocentres in a triple cascade organocatalytic reaction

    Microsoft Academic Search

    Dieter Enders; Matthias R. M. Hüttl; Christoph Grondal; Gerhard Raabe

    2006-01-01

    Efficient and elegant syntheses of complex organic molecules with multiple stereogenic centres continue to be important in both academic and industrial laboratories. In particular, catalytic asymmetric multi-component `domino' reactions, used during total syntheses of natural products and synthetic building blocks, are highly desirable. These reactions avoid time-consuming and costly processes, including the purification of intermediates and steps involving the protection

  18. Reaction/Momentum Wheel

    NASA Technical Reports Server (NTRS)

    1997-01-01

    CTA Space Systems, Inc. has been licensed to sell commercially a reaction/momentum wheel originally developed for NASA's scientific satellites. NASA originally identified a need for the wheel in its Small Explorer program. The Submillimeter Wave Astronomy Satellite required extremely low jitter and a reaction/momentum wheel with a torque greater than any comparably sized commercially available wheel to keep the instrument pointed at celestial objects to a high degree of precision. After development, a market assessment by Research Triangle Institute was completed, showing commercial potential for the flywheel technology. A license was granted to CTA in the fall of 1996. The company currently uses the technology in its complete spacecraft fabrication services and has built over 10 reaction/momentum wheels for commercial, scientific, and military customers.

  19. Cue usage in volleyball: a time course comparison of elite, intermediate and novice female players.

    PubMed

    Vansteenkiste, P; Vaeyens, R; Zeuwts, L; Philippaerts, R; Lenoir, M

    2014-12-01

    This study compared visual search strategies in adult female volleyball players of three levels. Video clips of the attack of the opponent team were presented on a large screen and participants reacted to the final pass before the spike. Reaction time, response accuracy and eye movement patterns were measured. Elite players had the highest response accuracy (97.50 ± 3.5%) compared to the intermediate (91.50 ± 4.7%) and novice players (83.50 ± 17.6%; p<0.05). Novices had a remarkably high range of reaction time but no significant differences were found in comparison to the reaction time of elite and intermediate players. In general, the three groups showed similar gaze behaviour with the apparent use of visual pivots at moments of reception and final pass. This confirms the holistic model of image perception for volleyball and suggests that expert players extract more information from parafoveal regions. PMID:25609887

  20. CUE USAGE IN VOLLEYBALL: A TIME COURSE COMPARISON OF ELITE, INTERMEDIATE AND NOVICE FEMALE PLAYERS

    PubMed Central

    Vaeyens, R; Zeuwts, L; Philippaerts, R; Lenoir, M

    2014-01-01

    This study compared visual search strategies in adult female volleyball players of three levels. Video clips of the attack of the opponent team were presented on a large screen and participants reacted to the final pass before the spike. Reaction time, response accuracy and eye movement patterns were measured. Elite players had the highest response accuracy (97.50 ± 3.5%) compared to the intermediate (91.50 ± 4.7%) and novice players (83.50 ± 17.6%; p<0.05). Novices had a remarkably high range of reaction time but no significant differences were found in comparison to the reaction time of elite and intermediate players. In general, the three groups showed similar gaze behaviour with the apparent use of visual pivots at moments of reception and final pass. This confirms the holistic model of image perception for volleyball and suggests that expert players extract more information from parafoveal regions. PMID:25609887