Sample records for identify reaction intermediate

  1. Fission in intermediate energy heavy ion reactions

    SciTech Connect

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

    1989-04-01

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

  2. Phosphorylation and reaction intermediates of the prokaryotic Ca(2+)-ATPase.

    PubMed

    Gambel, A M; Menick, D R

    1993-09-25

    A P-type Ca(2+)-ATPase activity has been identified previously in membranes of the Gram-negative bacteria Flavobacterium odoratum. The reaction mechanism of the prokaryotic Ca(2+)-ATPase was examined by isolation of reaction cycle intermediates formed during reversal of the normal cycle using inorganic P(i). The eukaryotic ATPase can be directly phosphorylated by P(i) only in the absence of calcium, and half-maximal inhibition is observed at 1-2 microM calcium. The F. odoratum Ca(2+)-ATPase is also phosphorylated by P(i) in the absence of calcium, but in contrast to the eukaryotic pump, a 30-35-fold increase in phosphoenzyme (E-P) formation is observed when the enzyme is preincubated in millimolar calcium. Furthermore, the half-maximal activation of E-P formation is observed at approximately 100 microM calcium, similar to the value for low-affinity calcium binding in the sarcoplasmic reticulum Ca(2+)-ATPase. The data suggest that the prokaryotic Ca(2+)-ATPase forward reaction is ordered and that the prokaryotic enzyme does not appear to bind calcium at the high-affinity site until ATP binds. Thus, calcium does not inhibit phosphoenzyme formation by P(i) because the high-affinity Ca2+ binding site is not exposed on the free enzyme (E1). PMID:8376412

  3. International chemical identifier for chemical reactions

    E-print Network

    Grethe, Guenter; Goodman, Jonathan; Allen, Chad

    2013-03-22

    ORAL PRESENTATION Open Access International chemical identifier for chemical reactions Guenter Grethe1*, Jonathan Goodman2, Chad Allen2 From 8th German Conference on Chemoinformatics: 26 CIC-Workshop Goslar, Germany. 11-13 November 2012 An open... -access software for creating a unique, text-based identifier for reactions (RInChI) was developed by the Goodman group at the University of Cambridge, based on the IUPAC International Chemical Identifier (InChI) stan- dard. RInChIs describe the substances...

  4. Ligand Intermediates in Metal-Catalyzed Reactions

    SciTech Connect

    Gladysz, John A.

    1999-07-31

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

  5. Reaction products and intermediates of tryptophan tryptophylquinone enzymes

    Microsoft Academic Search

    Victor L. Davidson; Zhenyu Zhu

    2000-01-01

    Methylamine dehydrogenase and aromatic amine dehydrogenase each possess the tryptophan tryptophylquinone (TTQ) cofactor which catalyzes the oxidative deamination of primary amines and transfer of substrate-derived electrons to type I copper proteins. The reaction steps and intermediates in the overall oxidation–reduction reactions catalyzed by these enzymes are described. An important feature of the reaction mechanism of TTQ-dependent amine dehydrogenases is that

  6. dd ? 3 Hen Reaction at Intermediate Energies

    NASA Astrophysics Data System (ADS)

    Ladygina, N. B.

    2012-10-01

    The dd ? 3 Hen reaction is considered at the energies between 200 and 520 MeV. The Alt-Grassberger-Sandhas equations are iterated up to the lowest order terms over the nucleon-nucleon t-matrix. The parameterized 3 He wave function including five components is used. The angular dependence of the differential cross section and energy dependence of tensor analyzing power T 20 at the zero scattering angle are presented in comparison with the experimental data.

  7. Ferryl and hydroxy intermediates in the reaction of oxygen with reduced cytochrome c oxidase.

    PubMed

    Han, S; Ching, Y C; Rousseau, D L

    1990-11-01

    Cytochrome c oxidase catalyses the 4-electron reduction of dioxygen to water and translocates protons vectorially across the inner mitochondrial membrane. Proposed reaction pathways for the catalytic cycle of the O2 reduction are difficult to verify without knowing the structures of the intermediates, but we now have such information for the catalytic intermediates in the first steps of the reaction of O2 with cytochrome c oxidase from resonance Raman spectroscopy, a technique that enables iron-ligand stretching modes to be identified. Here we report on two more key intermediates: a ferryl-oxo (Fe4 = O2-) and a ferric-hydroxy (Fe3+--OH-) intermediate at the level of 3- and 4-electron reduction, respectively. We identified these intermediates by their characteristic iron-oxygen stretching frequencies (786 cm-1 for Fe4+ = O2-, and 450 cm-1 for Fe3+ -- OH-) and oxygen and deuterium isotope shifts. The oxo atom in the ferryl intermediate is hydrogen-bonded and the iron-oxygen bond in the hydroxy intermediate is anomalously weak. With the identification of the primary, ferryl and hydroxy intermediates, the predominant structures at almost all stages of O2 reduction are now known and the catalytic pathway can be described with more certainty. PMID:2172834

  8. 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.

  9. Kaon production in heavy ion reactions at intermediate energies

    E-print Network

    Christian Fuchs

    2005-09-01

    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 evidences 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, time scales etc. as derived from experiment and theoretical transport calculations is presented. Below threshold kaon production shows a high sensitivity on the nuclear compression reached in heavy ion reactions. This allows to put constraints on the nuclear equation-of-state which are finally discussed.

  10. Reaction intermediates of methanol synthesis and the water-gas-shift reaction on the ZnO(0001) surface

    NASA Astrophysics Data System (ADS)

    Chuasiripattana, Katawut; Warschkow, Oliver; Delley, Bernard; Stampfl, Cathy

    2010-09-01

    The polar Zn-ZnO(0001) surface is involved in the catalysis of methanol synthesis and the water-gas-shift reaction. We use density functional theory calculations to explore the favorable binding geometries and energies of adsorption of several molecular species relevant to these reactions, namely carbon monoxide (CO), carbon dioxide (CO 2), water (H 2O) and methanol (CH 3OH). We also consider several proposed reaction intermediates, including hydroxymethyl (CH 2OH), methoxyl (CH 3), formaldehyde (CH 2O), methyl (CH 3), methylene (CH 2), formic acid (HCOOH), formate (HCOO), formyl (HCO), hydroxyl (OH), oxygen (O) and hydrogen (H). For each, we identify the preferred binding geometry at a coverage of 1/4 monolayers (ML), and report calculated vibrational frequencies that could aid in the identification of these species in experiment. We further explore the effects on the binding energy when the adsorbate coverage is lowered to 1/9 and 1/16 ML.

  11. 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.

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

    SciTech Connect

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

    2004-04-12

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

  13. Metamorphic dehydration reactions control the location of intermediate-depth seismicity

    NASA Astrophysics Data System (ADS)

    van Keken, Peter E.; Kita, Saeko; Nakajima, Junichi; Abers, Geoff; Hacker, Brad

    2013-04-01

    The cause of intermediate-depth seismicity in subduction zones is not well understood. The viability of proposed mechanisms, that include dehydration embrittlement, shear instablities, and the presence of fluids in general, depends significantly on local conditions, including pressure, temperature, and composition. A number of high resolution seismic studies have improved the location of earthquakes within the slab in Japan, Alaska and Cascadia. Intriguingly, the warm subduction zones of Nankai and Cascadia show that intermediate depth seismicity is located below the oceanic crust. In contrast, the colder subduction zones Alaska, Tohoku and Hokkaido have the upper plane of seismicity confined to the subducting crust, with a systematic deepening of the seismic belt with respect to the top of the slab with depth. We use high resolution thermal-petrological models to determine the metamorphic facies in the downgoing slab and to identify the main phase changes that cause dehydration. In Alaska and Northern Japan, the seismicity occurs at, or at shallower depths than, the blueschist-out boundary. In Nankai and Cascadia the seismicity disappears above the antigorite-out boundary. Seismicity in the lower plane of the double seismic zone in Northern Japan also occurs at pressures and temperatures below the antigorite-out boundary. These observations strongly suggest that intermediate-depth seismicity is limited by the first major dehydration reaction in the crust and mantle and that fluids liberated by this phase change are primarily responsible for causing the earthquakes.

  14. Kinetics and intermediates of the reaction of fully reduced Escherichia coli bo? ubiquinol oxidase with O?.

    PubMed

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

    2014-08-26

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

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

    PubMed Central

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

    2013-01-01

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

  16. 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...

  17. 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

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

    E-print Network

    Chen, Peng

    Single-Molecule Kinetics Reveals a Hidden Surface Reaction Intermediate in Single polydispersion in reaction kinetics. Here we use single-molecule fluorescence microscopy to study two.3 nm pseudospherical Au nanoparticlesat the single-particle, single- turnover resolution in catalyzing

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

    PubMed

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

    2015-06-15

    Unprecedented insight into the carbonylation of dimethyl ether over Mordenite is provided through the identification of ketene (CH2 CO) as a reaction intermediate. The formation of ketene is predicted by detailed DFT calculations and verified experimentally by the observation of doubly deuterated acetic acid (CH2 DCOOD), when D2 O is introduced in the feed during the carbonylation reaction. PMID:25967363

  20. Theoretical investigation on hydroformylation reactions. III. Hydrocarbonyliron-propylene ?-intermediates

    NASA Astrophysics Data System (ADS)

    Bellagamba, V.; Ercoli, R.; Gamba, A.

    The formation of possible intermediates from a hydrocarbonyliron and propylene, the simplest model system of an olefin withan asymmetric double bond, was investigated. Extended Hückel calculations predict four stable isomers of the ?-complex H 2Fe(CO) 3-propylene generated by reciprocal rotation of the component moieties. Their optimized geometries were calculated, and their stabilization curves turned out to have no barriers. The minimum energies of the conformers are strictly comparable, and their interconversion path was determined. Two of these isomers seem apter to turn into a linear alkyl and the other ones are more favourable to a branched alkyl.

  1. International chemical identifier for reactions (RInChI)

    PubMed Central

    2013-01-01

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

  2. 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.

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

    SciTech Connect

    Obertelli, A.; Gade, A.; Bazin, D.; Hansen, P.G.; Hoagland, T.; Lecouey, J.-L.; Mueller, W.F.; Yoneda, K. [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824 (United States); Campbell, C.M.; Cook, J.M.; Davies, A.D.; Dinca, D.-C.; Glasmacher, T.; Terry, J.R.; Zwahlen, H. [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824 (United States); Cottle, P.D.; Kemper, K.W.; Reynolds, R.R.; Roeder, B.T. [Department of Physics, Florida State University, Tallahassee, Florida 32306 (United States); Tostevin, J.A. [Department of Physics, School of Electronics and Physical Sciences, University of Surrey, Guildford, Surrey GU2 7XH (United Kingdom)

    2006-04-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-04-01

    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.

  5. 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…

  6. 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.

  7. 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.

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

    E-print Network

    Kinney, Jerry Neal

    1970-01-01

    formed (based on GLC examina- tion of organic layer at 210 C). A similar reac+ion carried out between lead dichloride and 3-pyridyllithium gave 94. 2$ unreacted lead dichloride. Examination of the organic layer (GLC, TLC, and infrared) gave... dichloride with 4-picolyllithium was carried out in an attempt to prepare tetra- 4-picolyllead. Lead dichloride (95$) was recovered unreacted, again with no indication of any organolead compounds being formed. Failure of the preceeding reactions to give...

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

    E-print Network

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

    2005-01-26

    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 12-C to 208-Pb, at several incident energies from 95 to 600 MeV/A 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.

  10. Methane activation by metal-free radical cations: experimental insight into the reaction intermediate.

    PubMed

    de Petris, Giulia; Troiani, Anna; Rosi, Marzio; Angelini, Giancarlo; Ursini, Ornella

    2009-01-01

    A precise jab to methane: The SO(2)(*+) radical cation (see figure) effectively activates CH(4) at room temperature through a [H(3)C(*)...HOSO(+)] methyl intermediate isolated in the gas phase by mass spectrometry. Methanol and ionized methyl hydrogen sulfoxylate, CH(3)OSOH(*+), are formed by selective, direct attack of the incipient methyl radical at the O atom of the intermediate. The reaction shows radical and charge effects in the activation of methane by metal-free radical cations. PMID:19291717

  11. 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

  12. Investigation of the reaction intermediates and catalyst composition that are relevant for CO hydrogenation

    Microsoft Academic Search

    Kaminsky

    1985-01-01

    Methyne, methylene, and methyl intermediates have been directly observed by SIMS to be adsorbed on a Ni(111) surface after reaction of CO + Hâ at 50-100 Torr. Deuterium and ¹³CO labeling studies confirm that these intermediates are formed from the reactant gases. The variation in ion intensity with temperature indicates all three species exists as a separate entities on the

  13. Detection of a C4a-Hydroperoxyflavin Intermediate in the Reaction of a Flavoprotein Oxidase †

    Microsoft Academic Search

    Jeerus Sucharitakul; Methinee Prongjit; Dietmar Haltrich; Pimchai Chaiyen

    2008-01-01

    This work describes for the first time the identification of a reaction intermediate, C4a- hydroperoxyflavin, during the oxidative half-reaction of a flavoprotein oxidase, pyranose 2-oxidase (P2O) from Trametes multicolor, by using rapid kinetics. The reduced P2O reacted with oxygen with a forward rate constant of 5.8 × 104 M-1 s-1 and a reverse rate constant of 2 s-1, resulting in

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

    PubMed Central

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

    2006-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  16. Cycloheptyne intermediate in the reaction of chiral cyclohexylidenemethyliodonium salt with sulfonates.

    PubMed

    Fujita, Morifumi; Sakanishi, Yuichi; Nishii, Masayoshi; Okuyama, Tadashi

    2002-11-15

    Reactions of (R)-4-methylcyclohexylidenemethyl(phenyl)iodonium salt and its 3-trifluoromethylphenyl and 4-methoxyphenyl derivatives (1) with tetrabutylammonium mesylate and triflate were carried out in chloroform at 60 degrees C. The products include (S)-4-methylcyclohexylidenemethyl sulfonate (2) and (R)-5-methylcyclohept-1-enyl sulfonate (3) as well as iodoarene. Reactions of (S)-1 were confirmed to provide the counterpart results. The rearranged triflate (R)-3Tf formed in the reaction with triflate maintains mostly the ee (enantiomeric excess) of (R)-1, while the ee of the mesylate product 3Ms is largely lost. The (13)C-labeling at the exocyclic position of 1 results in the isotopic scrambling of C-1 and C-2 of 3Ms in the mesylate reaction. The degree of the scrambling agrees well with that of the loss of ee of (R)-3Ms obtained from (R)-1, implying that the racemization is not due to the intermediate formation of achiral, primary 4-methylcyclohexylidenemethyl cation. Reaction of 1 with mesylate in the presence of CH(3)OD provided the 3Ms deuterated at the 2-position. When tetraphenylcyclopentadienone was added to the mesylate reaction system, the adduct of the 4-methylcycloheptyne intermediate was obtained in 24% yield, but the normal products 2Ms and 3Ms were still formed. The 3Ms obtained here in a low yield maintains the high ee of 1. These results indicate that the cycloheptyne is an intermediate responsible for the formation of racemic product 3Ms in the mesylate reaction. It is also concluded that the unrearranged products 2 are formed via the competitive pathways of in-plane and out-of-plane S(N)2 reactions. PMID:12423143

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

    PubMed

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

    2015-02-01

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

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

    PubMed Central

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

    2011-01-01

    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. PMID:21087925

  19. High-Resolution Spectroscopic Studies of Reaction Intermediates Relevant to Atmospheric Chemistry

    NASA Astrophysics Data System (ADS)

    Endo, Yasuki

    2014-06-01

    We have been studying short lived reaction intermediates and complexes containing short lived species by high-resolution spectroscopic means. Laser induced fluorescence spectrosocpy with resolutions up to 0.02 wn is used for observations of electronic transitions, and Fourier-transform microwave (FTMW) spectroscopy and FTMW-mm-wave double resonance spectroscopy are used for observations of pure rotational spectra. Both of the methods are combined with supersonic jet sytems equipped with pulse discharge nozzles to produce short lived species. Last several years, we are concentrating on observations of short lived oxygen bearing species and their complexes especially with water. Such species are considred to be important in atmospheric chemistry, since chemistry in the earth's atmosphere mainly proceeds as oxidation reactions of trace species existing in the atmosphere, where various oxygen bearing reaction intermediates are playing important roles. Detections by high-resolution spectroscopy are expected to provide valuable information on these species. Furthermore, importance of molecular complexes containing reaction intermediates with water in atmospheric chemistry has been discussed recently, where detections of such species are highly required since quite limited experimental information has been obtained so far. In the talk, results of a number of such species, either monomers or complexes, studied recently in our laboratory will be reviewed.

  20. Topaquinone-dependent amine oxidases: identification of reaction intermediates by Raman spectroscopy.

    PubMed

    Nakamura, N; Moënne-Loccoz, P; Tanizawa, K; Mure, M; Suzuki, S; Klinman, J P; Sanders-Loehr, J

    1997-09-23

    Resonance Raman (RR) spectroscopy has proven to be an excellent technique for providing structural information about the 2,4, 5-trihydroxyphenylalaninequinone (TPQ) cofactor and for identifying the source of oxygen atoms during the posttranslational synthesis of the cofactor. Through specific labeling of the C2, C4, and C5 oxygens of TPQ in phenylethylamine oxidase (PEAO) from Arthrobacter globiformis, we have identified the C=O stretch of the C5 carbonyl at 1683 cm-1 (-27 in 18O) and the C=O stretch of the C2 carbonyl at 1575 cm-1 (-21 in 18O). These vibrational frequencies show that the C-O moiety at C5 has far greater double-bond character than at C2 or C4, thereby explaining the exclusive nucleophilic attack at the C5 position by substrates and substrate analogs. Bovine serum amine oxidase (BSAO) exhibits a similar nu(C=O) mode at 1678 cm-1 (-22 cm-1 in 18O). Aniline reacts with the TPQ cofactor of PEAO to form a new derivative (lambdamax at 450 nm) with properties similar to the proposed substrate-imine intermediate in the catalytic cycle. It retains the C2=O spectral features of the native enzyme and exhibits a new C5=N stretch at 1603 cm-1 (-29 in 15N). In contrast, methylamine reacts with both PEAO and BSAO under anaerobic conditions to form a different stable adduct (lambdamax at 385 nm) with properties closer to the proposed product-imine intermediate in the catalytic cycle. This species has a distinctive RR spectrum with a C=N stretch at 1617 cm-1 that corresponds to the atoms of the added methylamine (-58 cm-1 with CD3NH2, -19 cm-1 with CH315NH2). The lack of D2O dependence of nu(C=N) shows that this is a deprotonated imine, which would be more stable toward hydrolysis than the postulated protonated imine in the enzymatic reaction. However, the BSAO product imine (from methylamine) does undergo hydrolysis and conversion to semiquinone upon addition of cyanide. It is possible that the inactive form of the product imine is stabilized by deprotonation and flipping of the TPQ ring [Cai, D., Dove, J., Nakamura, N., Sanders-Loehr, J., and Klinman, J. P. (1997) Biochemistry 36, 11472-11478]. PMID:9298968

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

    SciTech Connect

    Hung, C.H.; Marinas, B.J. [Purdue Univ., West Lafayette, IN (United States)

    1996-11-01

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

  2. 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.

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

    SciTech Connect

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

    1986-05-01

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

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

    PubMed

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

    2015-06-23

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

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

    SciTech Connect

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

    1986-05-01

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

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

    PubMed Central

    Vora, Harit U.; Wheeler, Philip

    2013-01-01

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

  7. Catching catalysis in the act: using single crystal kinetics to trap methylamine dehydrogenase reaction intermediates.

    PubMed

    Pearson, Arwen R; Wilmot, Carrie M

    2003-04-11

    Methylamine dehydrogenase (MADH) is produced by a range of gram-negative methylotrophic and autotrophic bacteria, and allows the organisms to utilise methylamine as the sole source of carbon. The enzyme catalyses the oxidation of methylamine to formaldehyde and ammonia, leaving it in a two-electron reduced state. To complete the catalytic cycle, MADH is reoxidised via an electron transfer (ET) chain. The redox center in the enzyme is the organic cofactor tryptophan tryptophylquinone (TTQ) derived from the posttranslational modification of two Trp residues in the protein. This cofactor has spectral features in the visible region, which change during catalytic turnover, defining spectrally distinct reaction intermediates that reflect the electronic state of the TTQ. In the case of the Paracoccus denitrificans enzyme the physiologic ET chain involves the protein redox partner amicyanin (a blue copper protein). A stable binary (MADH/amicyanin) complex can be formed, and its crystal structure has been solved to 2.5 A resolution by Chen et al. [Biochemistry 21 (1992) 4959]. These crystals were shown to be competent for catalysis and ET by Merli et al. [J. Biol. Chem. 271 (1996) 9177] using single crystal polarised absorption spectroscopy. Through a novel combination of single crystal visible microspectrophotometry, X-ray crystallography and freeze-trapping, we have trapped reaction intermediates of the enzyme in complex with its physiological redox partner amicyanin in the crystalline state. We will present data confirming that catalysis and ET in the binary complex crystals can be tracked by single crystal visible microspectrophotometry. We will also show that the reaction pathway is unperturbed by the presence of cryoprotectant solution, enabling direct freeze-trapping of reaction intermediates within the crystal. We will present new data demonstrating that the binary complex crystals are also capable of exhibiting UV light-dependent oxidase activity, as observed in solution [Biochim. Biophys. Acta 1364 (1998) 297]. PMID:12686162

  8. A model-independent approach to assigning bacteriorhodopsin's intramolecular reactions to photocycle intermediates.

    PubMed Central

    Hessling, B; Souvignier, G; Gerwert, K

    1993-01-01

    By using factor analysis and decomposition, bacteriorhodopsin's intramolecular reactions have been assigned to photocycle intermediates. Independent of specific kinetic models, the pure BR-L, BR-M, BR-N, and BR-O difference spectra were calculated by analyzing simultaneously two different measurements in the visible and infrared spectral region performed at pH 6.5, 298 K, 1 M KCl, and pH 7.5, 288 K, 1 M KCl. Even though after M formation L, M, N, and O intermediates kinetically overlap under physiological conditions, their pure spectra have been separated by this analysis in contrast to other approaches at which unphysiological conditions or mutants have been used or specific photocycle models have been assumed. The results now provide a set reference spectra for further studies. The following conclusions for physiologically relevant reactions are drawn: (a) the catalytic proton release binding site, asp 85, is protonated in the L to M transition and remains protonated in the intermediates N and O; (b) the catalytic proton uptake binding site asp 96 is deprotonated in the M to N transition and already reprotonated in the N to O transition; (c) proton transfer between asp 96 and the Schiff base is facilitated by backbone movements of a few peptide carbonyl groups in the M to N transition. Images FIGURE 4 PMID:8298022

  9. Probing the intermediates in the MO + CH4 M + CH3OH reactions by matrix isolation infrared spectroscopy

    Microsoft Academic Search

    Guanjun Wang; Mingfei Zhou

    2008-01-01

    In this review, we present our recent studies on the MO + CH4 and M + CH3OH model reactions (M = transition metals) in order to provide quantitative information regarding the mechanisms for the catalytic methane-to-methanol conversion process. The reaction intermediates were trapped and probed by matrix isolation infrared absorption spectroscopy. Various important intermediates including OM(CH4), M(CH3OH), CH3MOH, CH3M(O)H and

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

    NASA Astrophysics Data System (ADS)

    Zimányi, László; Khoroshyy, Petro; Mair, Thomas

    2010-06-01

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

  11. A multi-element detector array for heavy fragments emitted in intermediate energy nuclear reactions

    NASA Astrophysics Data System (ADS)

    Iori, I.; Manduci, L.; Moroni, A.; Scardaoni, R.; Chongwen, Sun; Yuzhao, Zhang; Guangming, Zhang; Giglio, F.; Mora, E.; di Pietro, G.; Dellera, L.; Cortesi, A.; Bassini, R.; Boiano, C.; Brambilla, S.; Malatesta, M.; Bruno, M.; D'Agostino, M.; Fiandri, M. L.; Fuschini, E.; Milazzo, P. M.; Busacchi, G.; Cunsolo, A.; Foti, A.; Gianino, C.; Sava, G.; Gramegna, F.; Buttazzo, P.; Margagliotti, G. V.; Vannini, G.; Auger, G.; Plagnol, E.

    1993-02-01

    To investigate complex fragment emission in intermediate energy nucleus-nucleus collisions, an array of three-element telescopes has been constructed. The array is designed to measure energy, charge and emission angles of fragments with Z values from 2 up to the projectile atomic number when studying reactions in reverse kinematics. In this case it has a good efficiency even for events with complex fragment high multiplicity. Each telescope is made of an ionization chamber (filled with CF4 at a pressure up to 300 mbar), a Si detector (500 ?m thick, position sensitive in two dimensions) and a CsI(Tl) scintillator with photodiode readout.

  12. How to identify carbonate rock reactions in concrete

    SciTech Connect

    Katayama, Tetsuya [Department of Concrete Maintenance, Kawasaki Geological Engineering Co. Ltd., 2-11-15 Mita, Minato-ku, Tokyo 108-8337 (Japan)]. E-mail: katayamat@kge.co.jp

    2004-11-15

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

  13. Charged current neutrino-nucleus reaction cross sections at intermediate energies

    SciTech Connect

    Kosmas, T.S. [Division of Theoretical Physics, University of Ioannina, GR-451 10 Ioannina (Greece)] [Division of Theoretical Physics, University of Ioannina, GR-451 10 Ioannina (Greece); Oset, E. [Departamento de Fisica Teorica and Instituto de Fisica Corpuscular, Centro Mixto Universidad de Valencia, Consejo Superior de Investigaciones Cientificas, 46100, Burjassot (Valencia) (Spain)] [Departamento de Fisica Teorica and Instituto de Fisica Corpuscular, Centro Mixto Universidad de Valencia, Consejo Superior de Investigaciones Cientificas, 46100, Burjassot (Valencia) (Spain)

    1996-03-01

    Inclusive and semi-inclusive neutrino-nucleus reaction cross sections at intermediate energies (20 MeV{le}{ital E}{sub {nu}}{le}500 MeV) are calculated throughout the Periodic Table for the most interesting nuclei from an experimental point of view. The method used had previously proved to be very accurate in calculating the inclusive reaction cross section for light nuclei ({sup 12}C and {sup 16}O) and in the study of other similar processes and has been further improved to deal with low energy neutrinos. The electron neutrino ({nu}{sub {ital e}}) and muon neutrino ({nu}{sub {mu}}) cross sections weighted by their energy distributions are also calculated and discussed in conjunction with the existing experimental results at LAMPF and the KARMEN Collaboration. {copyright} {ital 1996 The American Physical Society.}

  14. 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)

  15. 3He(d, p)4He Reaction at Intermediate Energies

    NASA Astrophysics Data System (ADS)

    Uesaka, T.; Satou, Y.; Sakamoto, N.; Itoh, K.; Sakai, H.; Tamii, A.; Ohnishi, T.; Sekiguchi, K.; Yako, K.; Sakoda, S.; Okamura, H.; Suda, K.; Wakasa, T.

    2000-10-01

    We have measured the cross sections and the polarization observables for the 3He(d,p)4He reaction at Ed =140, 200, and 270 MeV. This work aims to investigate the high momentum component of deuteron D-state wave function and the mechanism for the one-nucleon transfer reaction at intermediate energies. The measurement was carried out by using the spectrograph SMART at RIKEN Accelerator Research Facility. A cryogenic 3He gas target with a density of 6.6 ×1020 cm-3 was bombarded by a polarized deuteron beam. The data are compared with the calculation based on the one-nucleon exchange approximation and data from the d + p backward scattering.

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

    PubMed

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

    2014-10-01

    Selective functionalization of unactivated C-H bonds, water oxidation, and dioxygen reduction are extremely important reactions in the context of finding energy carriers and conversion processes that are alternatives to the current fossil-based oil for energy. A range of metalloenzymes achieve these challenging tasks in biology by using cheap and abundant transition metals, such as iron, copper, and manganese. High-valent metal-oxo and metal-dioxygen (superoxo, peroxo, and hydroperoxo) cores act as active intermediates in many of these processes. The generation of well-described model compounds can provide vital insights into the mechanisms of such enzymatic reactions. This perspective provides a focused rather than comprehensive review of the recent advances in the chemistry of biomimetic high-valent metal-oxo and metal-dioxygen complexes, which can be related to our understanding of the biological systems. PMID:25215462

  17. Catalytic Mechanism of Kdo8P Synthase:  Transient Kinetic Studies and Evaluation of a Putative Reaction Intermediate

    Microsoft Academic Search

    Po-Huang Liang; Julian Lewis; Karen S. Anderson; Amnon Kohen; Francis Wallace D'Souza; Yaakov Benenson; Timor Baasov

    1998-01-01

    The mechanistic pathway for the reaction catalyzed by Kdo8P synthase has been investigated, and the cyclic bisphosphate 2 has been examined as a putative reaction intermediate. Two parallel approaches were used: (1) chemical synthesis of 2 and evaluation as an alternate substrate for the enzyme and (2) transient kinetic studies using rapid chemical quench methodology to provide direct observation and

  18. 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.

  19. O(-) + acetaldehyde reaction products: search for singlet formylmethylene, a Wolff rearrangement intermediate.

    PubMed

    Goebbert, Daniel J; Khuseynov, Dmitry; Sanov, Andrei

    2011-04-21

    The mass-resolved anionic products of the reaction of O(•-) with acetaldehyde, H(3)CCHO, are studied using photoelectron imaging. The primary anionic products are vinoxide, H(2)CCHO(-), formylmethylene anion, HCCHO(•-), and ketenylidene anion, CCO(•-). From photoelectron spectra of HCCHO(•-), the electron affinity of triplet (ground state) formylmethylene (1.87 ± 0.02 eV) and the vertical detachment energy corresponding to the first excited triplet state (3.05 eV) are determined, but no unambiguous assignment for singlet HCCHO could be made. The elusive singlet is a key intermediate in the Wolff rearrangement, resulting in formation of ketene. The fast rearrangement associated with a large geometry change upon photodetachment to the singlet surface may be responsible for the low intensity of the singlet compared to the triplet bands in the photoelectron spectrum. The title reaction also yields CCO(•-), whose formation from acetaldehyde is novel and intriguing, since it requires a multistep net-H(4)(+) abstraction. A possible mechanism is proposed, involving an [H(2)CCO(•-)]* intermediate. From the measured electron affinities of HCCHO (above), H(2)CCHO (1.82 ± 0.01 eV), and CCO (2.31 ± 0.01 eV), several new thermochemical properties are determined, including the C-H bond dissociation energies and heats of formation of several organic molecules and/or their anions. Overall, the reactivity of O(•-) with organic molecules demonstrates the utility of this anion in the formation of a variety of reactive intermediates via a single process. PMID:21438615

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  1. 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.

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

    PubMed

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

    2013-10-21

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

  3. Criteria for identifying homogeneous transition metal cluster-catalyzed reactions

    SciTech Connect

    Laine, R.M.

    1980-01-01

    Four criteria were developed for distinguishing homogeneous cluster from mononuclear catalysis. A criterion based on reaction kinetics, which distinguishes catalysis by clusters from catalysis by mononuclear complexes in equilibrium with the clusters, is illustrated with the hydroformylation of 1-pentene by Ru/sub 3/(CO)/sub 12/ clusters in equilibrium with 3Ru(CO)/sub 5/ complexes in the presence of CO. A criterion based on selectivity is illustrated by the water gas shift and deuterium-exchange reactions catalyzed by ruthenium and rhodium carbonyl clusters in methanol and triethylamine; the scope of this criterion is limited to deuterium exchange reactions. A criterion based on mixed-metal catalysis, in which a mixed-metal system has higher catalytic activity than each transition metal cluster alone, is illustrated with hydroformylation of 1-pentene and the water gas shift reaction catalyzed by Ru/sub 3/(CO)/sub 12//Fe/sub 3/(CO)/sub 2/ and Rh/sub 6/(CO)/sub 16//Fe/sub 3/(CO)/sub 12/. A criterion based on changes in asymmetric induction is a special case of the selectivity criterion, in which specific starting metal complexes may produce either of two enantiomers. Catalysis by metal clusters is an analytical tool for modeling heterogeneous catalytic mechanisms.

  4. Structure of the Biliverdin Radical Intermediate in Phycocyanobilin:Ferredoxin Oxidoreductase Identified by

    E-print Network

    Fisher, Andrew J.

    Structure of the Biliverdin Radical Intermediate in Phycocyanobilin:Ferredoxin Oxidoreductase@ucdavis.edu (S.S.); rdbritt@ucdavis.edu (R.D.B.) Abstract: The cyanobacterial enzyme phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the two- step four-electron reduction of biliverdin IXR to phycocyanobilin

  5. Biomphalaria havanensis Identified as a Potential Intermediate Host for the Digenetic Trematode Bolbophorus damnificus

    Microsoft Academic Search

    Marlena C. Yost; Linda M. Pote; David J. Wise; Brian S. Dorr; Terry D. Richardson

    2009-01-01

    The digenetic trematode Bolbophorus damnificus has been associated with mortalities in commercial channel catfish Ictalurus punctatus in the Mississippi Delta. In the life cycle of B. damnificus, the only confirmed first intermediate host is the ram's horn snail Planorbella trivolvis. Recently, the exotic snail Biomphalaria havanensis has been isolated in several channel catfish ponds in the Mississippi Delta. The aim

  6. 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.

  7. Acyl intermediates in penicillopepsin-catalysed reactions and a discussion of the mechanism of action of pepsins.

    PubMed Central

    Takahashi, M; Hofmann, T

    1975-01-01

    Penicillopepsin catalyses transpeptidation reactions involving the transfer of the N-terminal amino acids of suitable substrates via covalent acyl intermediates to acceptor peptides, usually the substrate. The major products obtained when Phe-Tyr-Thr-Pro-Lys-Ala and Met-Leu-Gly were used as substrates were Phe-Phe and Met-Met respectively. With Met-Leu-Gly the tetrapeptide Met-Met-Leu-Gly was observed as probable intermediate. Co-incubation of Leu-Tyr-Leu and Phe-Tyr-Thr-Pro-Lys-Ala led to the formation of Leu-Phe and Phe-Leu as well as Leu-Leu and Phe-Phe. No reaction was observed with tripeptides in which the first or second amino acid is glycine. It appears that two amino aicds with large hydrophobic residues are needed for the transpeptidation reaction. Nucleophilic compounds other than peptides, such as hydroxylamine, aliphatic alcohols and dinitrophenylhydrazine, were not acceptors for the acyl group. Leucine, phenylalanine and leucine methyl ester also had no effect on the reaction. The transpeptidation reaction proceeded readily at pH 3.6 and 4.7. At pH 6.0 the reaction was slow and at pH 1.9 little or no transpeptidation was observed. Porcine pepsin catalyses similar transpeptidation reactions. Sequence studies show that porcine pepsin and penicillopepsin are homologous. The present study also suggests that they have a very similar mechanism. Evidence available at this time indicates that the mechanism of these enzymes is complex and may be modulated by secondary substrate-enzyme interactions. A hypothesis is presented which proposes that pepsin-catalysed reactions proceed via different covalent intermediates (amino-intermediates or acylintermediates) depending on the nature of the substrate. The possibility that some reactions do not involve covalent intermediates is also discussed. PMID:1172664

  8. [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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  10. Investigation of the reaction intermediates and catalyst composition that are relevant for CO hydrogenation

    SciTech Connect

    Kaminsky, M.P.

    1985-01-01

    Methyne, methylene, and methyl intermediates have been directly observed by SIMS to be adsorbed on a Ni(111) surface after reaction of CO + H/sub 2/ at 50-100 Torr. Deuterium and /sup 13/CO labeling studies confirm that these intermediates are formed from the reactant gases. The variation in ion intensity with temperature indicates all three species exists as a separate entities on the surface. The activation energy and turnover numbers for the Ni single crystal are similar to those of more conventional catalysts, indicating that their kinetic behavior is similar. These data are most consistent with a mechanism involving sequential hydrogenation of surface carbon. ESCA analysis indicates a linear increase of surface carbon with increasing reaction temperature. A series of FeMn and KFeMn carbonyl clusters were supported on a high surface area carbon so that a variety of stoichiometric metal compositions could be obtained. There is a maximum in activity and selectivity towards C/sub 2/-C/sub 4/, olefins with the K(Fe/sub 2/Mn(CO)/sub 12/) and Et/sub 4/NFe/sub 2/Mn(CO)/sub 12/ clusters where Et/sub 4/N is a tetraethylammonium cation. The metal ratio is optimized for the formation of a manganospinel (MnFe/sub 2/)O/sub 4/. Potassium incorporation into these FeMn catalysts helps retain their selectivity toward olefins after high temperature pretreatments. Potassium also increases the olefin/paraffin ratio such that, except for methane, only C/sub 2/-C/sub 4/ olefins are produced. FeCO and KFeCo carbonyl clusters were deposited on carbon supports. The effects of increasing Co and K concentrations are reported. Results are also presented for a series of FeRu catalysts.

  11. 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

  12. A New Reaction Manifold for the Barton Radical Intermediates: Synthesis of N-Heterocyclic Furanosides and Pyranosides via the Formation of the C1-C2

    E-print Network

    RajanBabu, T. V. "Babu"

    A New Reaction Manifold for the Barton Radical Intermediates: Synthesis of N of the corresponding xanthate and thiourethane derivatives (The Barton- McCombie reaction) is one of the most useful). The substrates with Scheme 1. Intermediates in the Barton Deoxygenation Reaction Scheme 2. Synthesis of Imidazole

  13. Identifying Predictors of Negative Psychological Reactions to Stalking Victimization

    ERIC Educational Resources Information Center

    Johnson, Matthew C.; Kercher, Glen A.

    2009-01-01

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

  14. Intermediate mass fragment emission and iso-scaling in dissipative Ca+Sn reactions at 45 AMeV

    NASA Astrophysics Data System (ADS)

    Singh, H.; Quinlan, M. J.; Tõke, J.; Pawelczak, I.; Henry, E.; Schröder, W. U.; Amorini, F.; Anzalone, A.; Maiolino, C.; Auditore, L.; Loria, D.; Trifiro, A.; Trimarchi, M.; Cardella, G.; De Filippo, E.; Pagano, A.; Chatterjee, M. B.; Cavallaro, S.; Geraci, E.; Papa, M.; Pirrone, S.; Verde, G.; Grzeszczuk, A.; Guazzoni, P.; Zetta, L.; La Guidara, E.; Lanzalone, G.; Lo Nigro, S.; Politi, G.; Loria, D.; Porto, F.; Rizzo, F.; Russotto, P.; Vigilante, M.

    2013-04-01

    The production mechanism of intermediate-mass fragments (IMFs) with atomic numbers Z = 3 - 7 is explored in the intermediate energy regime, studying dissipative 48Ca+112Sn and 48Ca+124Sn reactions at E/A = 45MeV. Various aspects of IMF emission patterns point to an inelastic break-up type production mechanism involving excited projectile-like fragment from dissipative interactions. Isotopic yield ratios of identical IMFs from the above two dissipative reactions have been analysed using the "isoscaling" method. Observed trends are correlated with ground-state binding energy systematics and their relevance for an evaluation of the symmetry energy is discussed.

  15. A Combined DFT and NMR Investigation of the Zinc Organometallic Intermediate Proposed in the Syn-Selective Tandem Chain Extension-Aldol Reaction of ?-Keto Esters

    PubMed Central

    Aiken, Karelle S.; Eger, Wilhelm A.; Williams, Craig M.; Spencer, Carley M.

    2012-01-01

    The tandem chain extension-aldol (TCA) reaction of ?-keto esters provides a ?-substituted ?-keto ester with an average syn:anti selectivity of 10:1. It is proposed that the reaction proceeds via a carbon-zinc bound organometallic intermediate potentially bearing mechanistic similarity to the Reformatsky reaction. Evidence, derived from control Reformatsky reactions and a study of the structure of the TCA intermediate utilizing DFT methods and NMR-spectroscopy, suggests the ?-keto group of the TCA intermediate plays a significant role in diastereoselectivity observed in this reaction. Such coordination effects have design implications for future zinc mediated reactions. PMID:22703563

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

    NASA Astrophysics Data System (ADS)

    Wujcik, Kevin; Balsara, Nitash

    2013-03-01

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

  17. RCL hydrolyzes 2'-deoxyribonucleoside 5'-monophosphate via formation of a reaction intermediate.

    PubMed

    Doddapaneni, Kiran; Zahurancik, Walter; Haushalter, Adam; Yuan, Chunhua; Jackman, Jane; Wu, Zhengrong

    2011-05-31

    RCL is an enzyme that catalyzes the N-glycosidic bond cleavage of purine 2'-deoxyribonucleoside 5'-monophosphates. Recently, the structures of both free wild type and GMP-bound mutant complex have been determined by multidimensional NMR, revealing a doubly wound ?/? protein existing in a symmetric homodimer. In this work, we investigated the catalytic mechanism by rational site-directed mutagenesis, steady-state and pre-steady-state kinetics, ITC binding analysis, methanolysis, and NMR study. First, we provide kinetic evidence in support of the structural studies that RCL functions in a dimeric form, with an apparent dissociation constant around 0.5 ?M in the presence of substrate dGMP. Second, among the eight residues under investigation, the highly conserved Glu93 is absolutely critical and Tyr13 is also important likely contributing to the chemical step, whereas Ser117 from the neighboring subunit and Ser87 could be the key residues for the phosphate group recognition. Lastly, we demonstrate by methanolysis study that the catalytic reaction proceeds via the formation of a reaction intermediate, which is subsequently hydrolyzed by solvent nucleophile resulting in the formation of normal product deoxyribose monophosphate (dR5P) or methoylated-dR5P. In conclusion, the current study provides mechanistic insights into a new class of nucleotide hydrolase, which resembles nucleoside 2'-deoxyribosyltransferases structurally and functionally but also possesses clear distinction. PMID:21510673

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Frekers, Dieter

    2005-04-01

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

  20. Analysis of intermediate energy proton-induced spallation reactions by an improved quantum molecular dynamics plus statistical decay model

    Microsoft Academic Search

    Li Ou; Yingxun Zhang; Junlong Tian; Zhuxia Li

    2007-01-01

    Intermediate energy proton-induced spallation reactions with various targets are studied by the improved quantum molecular dynamics (ImQMD05) model incorporated with the statistical decay model. The influences of the different Skyrme interactions on the mechanism of spallation reaction and the double differential cross sections of emitted neutrons are studied. It is found that the different Skyrme interactions influence the low energy

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

    PubMed

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

    2015-02-21

    The C1 Criegee intermediate, CH2OO, reaction with water vapour has been studied. The removal rate constant shows a quadratic dependence on [H2O], implying reaction with the water dimer, (H2O)2. The rate constant, kCH2OO+(H2O)2 = (4.0 ± 1.2) × 10(-12) cm(3) molecule(-1) s(-1), is such that this is the major atmospheric sink for CH2OO. PMID:25600757

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

    NASA Astrophysics Data System (ADS)

    Smith, Jeremy George; Jain, Prashant

    2014-06-01

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

  3. Identifying unfolding intermediates of FN-III(10) by steered molecular dynamics.

    PubMed

    Gao, Mu; Craig, David; Vogel, Viola; Schulten, Klaus

    2002-11-01

    Experimental studies have indicated that FN-III modules undergo reversible unfolding as a mechanism of elasticity. The unfolding of FN-III modules, including the cell-binding FN-III(10) module, has further been suggested to be functionally relevant by exposing buried cryptic sites or modulating cell binding. While steered molecular dynamics (SMD) simulations have provided one tool to investigate this process, computational requirements so far have limited detailed analysis to the early stages of unfolding. Here, we use an extended periodic box to probe the unfolding of FN-III(10) for extensions longer than 60A. Up to three plateaus, corresponding to three metastable intermediates, were observed in the extension-time profile from SMD stretching of FN-III(10). The first and second plateaus correspond to a twisted and an aligned state prior to unraveling FN-III(10) beta-strands. The third plateau, at an extension of approximately 100A, follows unraveling of FN-III(10) A and B-strands and precedes breaking of inter-strand hydrogen bonds between F and G-strands. The simulations revealed three forced unfolding pathways of FN-III(10), one of which is preferentially selected under physiological conditions. Implications for fibronectin fibrillogenesis are discussed. PMID:12417205

  4. 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

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

    PubMed

    Fukutome, Asuka; Kawamoto, Haruo; Saka, Shiro

    2015-07-01

    The gas-phase pyrolysis of levoglucosan (LG), the major intermediate species during cellulose gasification, was studied experimentally over the temperature range of 400-900?°C. Gaseous LG did not produce any dehydration products, which include coke, furans, and aromatic substances, although these are characteristic products of the pyrolysis of molten LG. Alternatively, at >500?°C, gaseous LG produced only fragmentation products, such as noncondensable gases and condensable C1 -C3 fragments, as intermediates during noncondensable gas formation. Therefore, it was determined that secondary reactions of gaseous LG can result in the clean (tar- and coke-free) gasification of cellulose. Cooling of the remaining LG in the gas phase caused coke formation by the transition of the LG to the molten state. The molecular mechanisms that govern the gas- and molten-phase reactions of LG are discussed in terms of the acid catalyst effect of intermolecular hydrogen bonding to promote the molten-phase dehydration reactions. PMID:26099988

  6. The (p, ? +) reaction on 9Be and 10B at intermediate energies and a coherent ?-exchange analysis

    NASA Astrophysics Data System (ADS)

    Dillig, M.; Couvert, P.; Bauer, Th. S.; Beurtey, R.; Boudard, A.; Bruge, G.; Catz, H.; Chaumeaux, A.; Duhm, H. H.; Escudie, J. L.; Garcon, M.; Garreta, D.; Igo, G. J.; Lugol, J. C.; Matoba, M.; Schecter, L.; Tabet, J. P.; Terrien, Y.; Aslanides, E.; Bertini, R.; Bing, O.; Brochard, F.; Hibou, F.; Gorodetzky, P.; Bimbot, L.; Brissaud, I.; Le Bornec, Y.; Tatischeff, B.

    1980-01-01

    Proton-induced pion production at intermediate energies, leaving the final nucleus in discrete, resolved states, has been measured at the Saclay Synchrotron Saturne I, using the high resolution spectrometer facility SPES I. The (p, ?+) reaction has been investigated on 9Be at proton energies of 410 and 605 MeV, and on 10B at incident energies of 320,410, 483 and 605 MeV. These data are presented and analysed in a coherent way, together with previous results at intermediate energies, by means of a pion exchange model. It is found that all the characteristic features of the data are reproduced satisfactorily.

  7. Key reaction intermediates of the photochemical oxygenation of alkene sensitized by Ru(II)-porphyrin with water by visible light.

    PubMed

    Funyu, Shigeaki; Kinai, Miki; Masui, Dai; Takagi, Shinsuke; Shimada, Tetsuya; Tachibana, Hiroshi; Inoue, Haruo

    2010-07-30

    Two key reaction intermediates in the photochemical oxygenation of alkene sensitized by carbonyl-coordinated ruthenium(ii)-porphyrin complex, with water acting both as an electron and oxygen atom donor, are postulated. Under the low concentration of hydroxide ion (<2 x 10(-3) M) added to the reaction mixture of tetra(2,4,6-trimethyl)phenylporphyrinatoruthenium(ii) (Ru(II)TMP(CO)), K(4)PtCl(6) as a sacrificial electron acceptor, and cyclohexene as a substrate in aqueous acetonitrile, the major reaction product was cyclohexaneoxide ("Epoxide"), while it drastically decreased along with an increase of 2-cyclohexenol ("Alcohol") by increasing the amount of hydroxide ion (>2 x 10(-3) M). The tendency was more obvious in the case of tetrasodium tetra(4-sulfonate)phenylporphyrinatoruthenium(ii) (Ru(II)TSPP(CO)) in aqueous solution. The "Alcohol" was exclusively formed in the higher concentration region of OH(-), strongly suggesting the presence of acid-base equilibrium among two reaction intermediates. Theoretical DFT calculation indicates that the hydroxyl-coordinated one-electron oxidized Ru-porphyrin (Intermediate (I)), which is formed by the axial ligation of hydroxide ion to the cation radical of Ru-porphyrin generated through electron transfer from the excited triplet state of the sensitizer porphyrins, suffers deprotonation of its axial hydroxide group to lead to an oxo-type complex (Intermediate (II)) formation. The DFT calculation also indicates that the electron spin on the Intermediate (I) is shared by the axial oxygen atom and the central Ru metal, while it is mostly localized on the axial oxygen atom to behave as an oxygen radical in the case of the Intermediate (II). These are very strong indications towards understanding how OH(-) (water molecule) is oxidatively activated on the Ru center: the water molecule is serving as an electron donor ion in the redox cycles. Theoretical calculation predicts that Intermediate (I) allows the epoxidation of alkene and Intermediate (II) can proceed through hydrogen abstraction from the substrate and is rebound to form hydroxylated compound, "Alcohol." PMID:20464022

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

    SciTech Connect

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

    1986-11-04

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

  9. On the mechanism of action of cytochrome P-450. Spectral intermediates in the reaction with iodosobenzene and its derivatives.

    PubMed

    Blake, R C; Coon, M J

    1989-03-01

    Cytochrome P-450 is known to catalyze the following oxygen transfer reaction: RH + PhIO----ROH + PhI where RH represents a variety of hydroxylatable substrates and PhIO a variety of iodosobenzene derivatives that serve as oxygen donors, and neither molecular oxygen nor an external electron donor is required. To determine whether the cytochrome functions in such reactions by a peroxidase-type mechanism, the kinetics of its interaction with a variety of substituted iodosobenzenes and iodobenzene diacetates have been determined by stopped flow spectrophotometry. The reaction of phenobarbital-induced rabbit liver microsomal cytochrome P-450 form 2 with iodosobenzenes or iodobenzene diacetates leads to the reversible formation of three spectral intermediates, termed E, F, and G. Complex E is characterized by a type I difference spectrum, representing the iodosobenzene-dependent partial shift of the low spin hexacoordinate form of the ferric enzyme to the high spin pentacoordinate form, F represents a transient intermediate whose spectrum cannot be determined for kinetic reasons, and G represents a blue-shifted intermediate with an absorption maximum at about 393 nm in the absolute spectrum. The striking and principal feature of these observations is that the spectrum of Complex G does not vary with structural differences in the iodosobenzene derivatives, in contrast to the transient species observed in previous studies in this laboratory in the reaction between cytochrome P-450 form 2 and aromatic peroxy compounds. Complex G exhibits the spectral properties one might anticipate for an iron-oxo intermediate containing only one oxygen atom derived from the starting iodosobenzene. PMID:2917971

  10. Reactions of Diphenyl(phenylethynyl)selenonium Salts with Active Methylene Compounds and Amides: First Isolation of Oxyselenuranes [10-Se-4(C3O)] as a Reaction Intermediate.

    PubMed

    Kataoka, Tadashi; Watanabe Si, Shin-ichi; Yamamoto, Keiichirou; Yoshimatsu, Mitsuhiro; Tanabe, Genzoh; Muraoka, Osamu

    1998-09-01

    The reaction of the diphenyl(phenylethynyl)selenonium triflate 1a with active methylene compounds 5 and t-BuOK in THF gave furan derivatives 6. The [10-Se-4(C3O)] selenuranes 8a and 8b could be isolated from the reactions with benzoylacetonitrile 5f and with 1,3-indandione 5g, respectively, as reaction intermediates. The structures of the selenuranes 8 were elucidated by X-ray crystallography and (77)Se high-resolution solid-state NMR spectroscopy. The selenuranes 8 underwent ligand coupling on standing at room temperature or refluxing in chloroform and gave the furan derivatives 6 and the ring-opened product 9. Similarly, the reaction of 1a with benzamide 13a and pivalamide 13d in the presence of NaH in THF afforded oxazole derivatives 14. PMID:11672273

  11. Mechanism of the EPSP synthase catalyzed reaction: evidence for the lack of a covalent carboxyvinyl intermediate in catalysis

    SciTech Connect

    Wibbenmeyer, J.; Brundage, L.; Padgette, S.R.; Likos, J.J.; Kishore, G.M.

    1988-06-16

    In order to detect covalent reaction intermediates in the 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase reaction, we have investigated the interaction of EPSP synthase with the reaction product EPSP. An exchange of EPSP-methylene protons could be demonstrated by incubating EPSPS with EPSP in D/sub 2/O. Since trace amounts of contaminating Pi would lead to reversal of EPSPS reaction and hence methylene proton exchange, we added pyruvate kinase, ADP, Mg++ and K+. Under these conditions, any contaminating Pi that is converted to PEP is trapped as ATP. No exchange of EPSP protons with those of the solvent could be detected in the presence of this trap system, suggesting that enzyme-bound EPSP is unable to form a covalent tetrahedral complex. Incorporation of (/sup 14/C) from (/sup 14/C)-S3P and (/sup 14/C)-PEP into EPSP could be detected, but only in the absence of a PEP (or Pi) trap system. This indicates that for the exchange reaction, Pi is required, and also indicates the absence of a covalent intermediate, unless the carboxyvinyl-enzyme-bound S3P is completely restricted from exchange.

  12. Electrophilic addition reaction of ethene with hydrogen chloride on cold molecular films: evidence of ethyl cationic intermediate.

    PubMed

    Lee, Poong-Ryul; Lee, Chang-Woo; Kim, Joon-Ki; Moon, Eui-Seong; Kang, Heon

    2011-03-01

    We studied the initial-stage mechanism of the electrophilic addition reaction of ethene with HCl by examining the interactions between ethene and HCl on water-ice and frozen molecular films at temperatures of 80-140?K. Cs(+) reactive ion scattering (RIS) and low-energy sputtering (LES) techniques were used to probe the reaction intermediates that were kinetically trapped on the surface, in conjunction with temperature-programmed desorption (TPD) mass spectrometry to monitor the desorbing species. The reaction initially produced the ??complex of HCl and ethene at temperatures below about 93?K and an "ethyl cationic species" at temperatures below about 100?K. The ethyl cationic species was formed via direct proton transfer from the HCl molecule to ethene with the assistance of water solvation, rather than via the interaction of hydronium ions and ethene. At high temperatures, this species dissociated into ethene and hydronium and chloride ions. The reaction did not, however, complete the final transition state on the ice surface to produce ethyl chloride. The observation gives evidence that the electrophilic addition reaction of ethene occurs through an ethyl-like intermediate with an ionic character. PMID:21108286

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

    NASA Astrophysics Data System (ADS)

    Heilbronn, Lawrence Harvey

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

  14. 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

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

    PubMed

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

    2015-02-28

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

  16. Nature and thermal stability of adsorbed intermediates formed during the reaction of diesel soot with nitrogen dioxide

    NASA Astrophysics Data System (ADS)

    Azambre, B.; Collura, S.; Trichard, J. M.; Weber, J. V.

    2006-12-01

    The reactivity of a diesel exhaust soot sample towards 1000 ppm NO 2/balance Ar was investigated at moderate temperature using thermogravimetric analysis (TGA), temperature-programmed desorption (TPD-MS) and diffuse reflectance infrared spectroscopy (DRIFTS) with the aim to evidence the nature and thermal stability of adsorbed intermediates formed during the reaction. In the range 25-200 °C, the reaction pathways are influenced by the temperature dependency of the reaction regimes. While weak adsorption of NO 2 prevails at temperatures under ca. 60 °C, it is found that associative and dissociative chemisorption occurs on the whole range of temperatures investigated, creating, respectively, nitrogenated (RNO x) and oxygenated (RO x) adsorbed intermediates on soot surface. DRIFTS and TPD experiments reveal that major surface species include on the one hand alkyl-nitrite and -nitrate esters adopting presumably a chelated or bidentate configuration on soot surface and on the other hand more stable acidic oxygenated surface complexes formed by reduction of NO 2.

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  18. Probing the Reaction Intermediates for the Water–gas Shift over Inverse CeOx / Au(1 1 1) Catalysts

    SciTech Connect

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

    2010-01-01

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

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

    SciTech Connect

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

    2010-05-04

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

  20. 3-Hydroxy-3-methylglutaryl-CoA synthase: participation of invariant acidic residues in formation of the acetyl-S-enzyme reaction intermediate.

    PubMed

    Chun, K Y; Vinarov, D A; Miziorko, H M

    2000-11-28

    Inactivation of HMG-CoA synthase by a carboxyl-directed reagent, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), in a concentration-dependent and substrate-protectable manner suggested that the active site contains reactive acidic amino acids. This observation prompted functional evaluation of 11 invariant acidic amino acids by site-directed mutagenesis. Characterization of the isolated synthase variants' ability to catalyze overall and partial reactions identified three mutant synthases (D99A, D159A, and D203A) that exhibit significant diminution of k(cat) for the overall reaction (10(2)-, 10(3)-, and 10(4)-fold decreases, respectively). D99A, D159A, and D203A form the acetyl-S-enzyme intermediate very slowly (0.0025, 0.0026, 0.0015 U/mg, respectively, measured at pH 7. 0 and 22 degrees C) as compared to the wild-type synthase (1.59 U/mg), where intermediate formation approaches rate-limiting status. Differences in substrate saturation do not account for impaired activities or rates of intermediate formation. The structural integrity of the purified mutants' active sites is demonstrated by their abilities to bind a spin-labeled acyl-CoA analogue (R.CoA) with affinities and stoichiometries comparable to values measured for wild-type synthase. The impact of three distinct amino acids on reaction intermediate formation supports a mechanism of acetyl-S-enzyme formation that probably requires formation and directed collapse of a tetrahedral adduct. (18)O-induced shift of the (13)C NMR signal of (13)C acetyl-S-enzyme demonstrates that an analogous tetrahedral species is produced upon solvent exchange with the acetyl-S-enzyme. Partial discrimination between the functions of D99, D159, and D203 becomes possible based on the observation that D159A and D203A synthases exhibit retarded kinetics of solvent (18)O exchange while D99A fails to support (18)O exchange. PMID:11087424

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

    PubMed

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

    2013-01-18

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

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

    SciTech Connect

    Banerjee, R.

    1987-01-01

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

  3. Local structure of reaction intermediates probed by time-resolved x-ray absorption near edge structure spectroscopy

    SciTech Connect

    Smolentsev, G.; Soldatov, A. V. [Center for Nanoscale Structure of Matter and Faculty of Physics, Southern Federal University, Rostov-on-Don 344090 (Russian Federation); Guilera, G. [ALBA Synchrotron, Barcelona 08193 (Spain); Tromp, M. [University of Southampton, Southampton SO17 1BJ (United Kingdom); Pascarelli, S. [European Synchrotron Radiation Facility, Grenoble 38000 (France)

    2009-05-07

    A method for the analysis of time-resolved x-ray absorption near edge structure (XANES) spectra is proposed. It combines principal component analysis of the series of experimental spectra, multidimensional interpolation of theoretical XANES as a function of structural parameters, and ab initio XANES calculations. It allows to determine the values of structural parameters for intermediates of chemical reactions and the concentrations of different states as a function of time. This approach is tested using numerically generated data and its possibilities and limitations are discussed. The application of this method to a reaction with methylrhenium trioxide catalyst in solution, for which experimental data were measured using stopped-flow energy-dispersive x-ray absorption spectroscopy technique, is demonstrated. Possibilities and limitations of this experimental technique are also discussed.

  4. Experimental determination of the effective nucleon-nucleon interaction for p-nucleus reactions at intermediate energies

    SciTech Connect

    McClelland, J.B.; Aas, B.; Azizi, A.

    1982-01-01

    A complete measurement of the polarization transfer observables has been made for the first time in the (p,p') reaction at intermediate energies. Measurements are reported for the /sup 12/C(p,p') /sup 12/C reaction to the 1/sup +/, T = 0(12.71 MeV) and 1/sup +/, T = 1(15.11 MeV) states at 500 MeV at laboratory scattering angles of 3.5/sup 0/, 5.5/sup 0/, 7.5/sup 0/, and 12.0/sup 0/. Linear combinations of these observables are shown to exhibit a very selective dependence on the isoscalar and isovector spin-dependent components of the nucleon-nucleon interaction. To the extent of the validity of the single collision approximation, these amplitudes are compared directly to the free nucleon-nucleon amplitudes at small momentum transfers ( < 1 fm/sup -1/).

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

    PubMed

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

    2012-11-12

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

  6. A crystallographic description of experimentally identified formation reactions of Cu(In,Ga)Se{sub 2}

    SciTech Connect

    Hergert, F. [Chair for Crystallography and Structural Physics, University of Erlangen-Nuernberg, Staudtstrasse 3, D-91058 Erlangen (Germany)]. E-mail: frank.hergert@krist.uni-erlangen.de; Jost, S. [Chair for Crystallography and Structural Physics, University of Erlangen-Nuernberg, Staudtstrasse 3, D-91058 Erlangen (Germany); Hock, R. [Chair for Crystallography and Structural Physics, University of Erlangen-Nuernberg, Staudtstrasse 3, D-91058 Erlangen (Germany); Purwins, M. [Crystal Growth Laboratory, Department of Materials Science VI, University of Erlangen-Nuernberg, Martensstr. 7, D-91058 Erlangen (Germany)

    2006-08-15

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

  7. Mechanistic Studies of Reactions of Peroxodiiron(III) Intermediates in T201 Variants of Toluene/o-Xylene Monooxygenase Hydroxylase†

    PubMed Central

    Song, Woon Ju; Lippard, Stephen J.

    2011-01-01

    Site-directed mutagenesis studies of a strictly conserved T201 residue in the active site of toluene/o-xylene monooxygenase hydroxylase (ToMOH) revealed that a single mutation can facilitate kinetic isolation of two distinctive peroxodiiron(III) species, designated T201peroxo and ToMOHperoxo, during dioxygen activation. Previously we characterized both oxygenated intermediates by UV-vis and Mössbauer spectroscopy, proposed structures from DFT and QM/MM computational studies, and elucidated chemical steps involved in dioxygen activation through the kinetic studies of T201peroxo formation. In the current study, we investigated the kinetics of T201peroxo decay to explore the reaction mechanism of the oxygenated intermediates following O2 activation. The decay rates of T201peroxo were monitored in the absence and presence of external (phenol) or internal (tryptophan residue in an I100W variant) substrates under pre-steady-state conditions. Three possible reaction pathways were evaluated and the results demonstrate that T201peroxo is on the pathway of arene oxidation and appears to be in equilibrium with ToMOHperoxo. PMID:21595439

  8. JOURNAL DE PHYSIQUE Colloque C5, supplment au n 11, Tome 37., Novembre 1976, page C5-177 INTERMEDIATE STRUCTURE IN LIGHT ION REACTIONS

    E-print Network

    Paris-Sud XI, Université de

    -177 INTERMEDIATE STRUCTURE IN LIGHT ION REACTIONS H. Feshbach Massachusetts Institute of Technology, Cambridge and doorway states which have been discovered in the reactions induced by collision of the light ions 12 C-sections for the colli- sion of light ions is presented. This paper will present a review of the inter- mediate structure

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

    PubMed

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

    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

  10. Energetics of intermediates and reaction steps involved in the hydroformylation reaction catalyzed by HCo(CO)/sub 4/. A theoretical study based on density functional theory

    SciTech Connect

    Versluis, L.; Ziegler, T.; Baerends, E.J.; Ravenek, W.

    1989-03-15

    A theoretical study based on density functional theory has been carried out on the CO dissociation of HCo(CO)/sub 4/ and the migratory insertion reaction RCo(CO)/sub 4/ /yields/ RC(O)Co(CO)/sub 3/ for R = H and R = CH/sub 3/, respectively. RCo(CO)/sub 4/ was shown to form two stable isomers of trigonal-bipyramidal geometry. The configuration with R in axial position was lower in energy (63 kJ mol/sup /minus/1/ for R = H and 42 kJ mol/sup /minus/1/ for R = CH/sub 3/) than the corresponding isomer with R along the basal axis. The Co-CO dissociation energy of HCo(CO)/sub 4/ was found to be 186 kJ mol/sup /minus/1/. The resulting intermediate HCo(CO)/sub 3/ had as its most stable conformation a butterfly structure with the hydride in apical position. The migratory insertion of CO into the Co-CH/sub 3/ bond affords a coordinatively unsaturated acyl intermediate CH/sub 3/C(O)Co(CO)/sub 3/ that was found to form several stable isomers, with the ones that have the acyl oxygen facing the vacant site lowest in energy due to the formation of stable /eta//sup 2/ interactions. The reaction profile of the migration process was investigated by a linear transit procedure. The methyl 1,2-shift reaction to a cis-carbonyl group was found to have a low activation barrier and a reaction enthalpy of not more than 70 kJ mol/sup /minus/1/, whereas the direct insertion of a CO ligand into the Co-CH/sub 3/ bond was disfavored by an activation barrier of /approx/ 200 kJ mol/sup /minus/1/. The corresponding hydride migration to a neighboring CO group was considerably more endothermic and did not produce stable formyl intermediates on the Hartree-Fock-Slater energy surface. The alternative isomers with the formyl oxygen pointing toward the empty site were found to be stable but high in energy.

  11. 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

  12. 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.

  13. Vector and tensor analysing powers in deuteron-proton breakup reactions at intermediate energies

    E-print Network

    D. Chiladze; J. Carbonell; S. Dymov; V. Glagolev; M. Hartmann; V. Hejny; A. Kacharava; I. Keshelashvili; A. Khoukaz; H. R. Koch; V. Komarov; P. Kulessa; A. Kulikov; G. Macharashvili; Y. Maeda; T. Mersmann; S. Merzliakov; S. Mikirtytchiants; A. Mussgiller; M. Nioradze; H. Ohm; F. Rathmann; R. Schleichert; H. J. Stein; H. Stroeher; Yu. Uzikov; S. Yaschenko; C. Wilkin

    2006-03-15

    Vector and tensor analysing powers of the d(pol)p->(pp)n (charge-exchange) and d(pol)p->(pn)p (non-charge-exchange) breakup reactions have been measured with the ANKE spectrometer at the COSY ring at a deuteron beam energy of 1170 MeV for small momentum transfers to the low excitation energy (pp) or (pn) systems. A quantitative understanding of the values of A_xx and A_yy for the charge-exchange reaction is provided by impulse approximation calculations. The data suggest that spin-flip isospin-flip transitions, which dominate the charge-exchange breakup of the deuteron, are also important in the non-charge-exchange reaction.

  14. Emission of high-energy, light particles from intermediate-energy heavy-ion reactions

    SciTech Connect

    Ball, J.B.; Auble, R.L.

    1982-01-01

    One of the early surprises in examining reaction products from heavy ion reactions at 10 MeV/nucleon and above was the large yield of light particles emitted and the high energies to which the spectra of these particles extended. The interpretation of the origin of the high energy light ions has evolved from a picture of projectile excitation and subsequent evaporation to one of pre-equilibrium (or nonequilibrium) emission. The time scale for particle emission has thus moved from one that occurs following the initial collision to one that occurs at the very early stages of the collision. Research at ORNL on this phenomenon is reviewed. (WHK)

  15. Identification of reaction products and intermediates of aromatic-amine dehydrogenase by 15N and 13C NMR.

    PubMed

    Bishop, G R; Zhu, Z; Whitehead, T L; Hicks, R P; Davidson, V L

    1998-03-15

    13C- and 15N-NMR studies of the reaction of aromatic amine dehydrogenase (AADH) with methylamine demonstrated that the products of the reductive half-reaction are an equivalent of formaldehyde hydrate and a reduced aminoquinol form of the tryptophan tryptophylquinone (TTQ) cofactor which contains covalently bound substrate-derived N. These data are consistent with the Ping Pong kinetic mechanism and aminotransferase-type chemical reaction mechanism which have been previously proposed for AADH. Comparison of the 15N-NMR spectra of the aminoquinol TTQ intermediates of AADH and methylamine dehydrogenase (MADH) revealed that the substrate-derived aminoquinol N of AADH and MADH exhibited distinct 15N chemical shifts which are separated by approx. 7 p.p.m. In each case, the signal for the substrate-derived aminoquinol N appears optimally with short pulse delay and exhibits a relaxation time and chemical shift which are consistent with 15N covalently bound to an aromatic ring (i.e. aminoquinol) which is attached to a rigid protein matrix. The aminoquinol of AADH is less stable against reoxidation than that of MADH. These data suggest that differences in the active-site mediated electrostatic environments of the aminoquinol N in the respective enzymes may influence both the observed 15N chemical shift and the relative reactivities of the TTQ aminoquinols towards oxygen. These data also demonstrate the utility of 13C- and 15N-NMR spectroscopy as a tool for monitoring the intermediates and products of enzyme-catalysed transformations. PMID:9494080

  16. 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

  17. Trapping Conformational Intermediate States in the Reaction Center Protein from Photosynthetic Bacteria

    E-print Network

    Gunner, Marilyn

    +, and reduced QB -, return to the ground state at cryogenic temperature in a conformation that allows a high yield of QB reduction. Thus, RCs frozen under illumination are found to be trapped above the ground 16 ( 3 meV. Thus, there are several conformational substates along the reaction coordinate

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

    E-print Network

    Frenkel, Anatoly

    -structure data isolated by PCA. The method is demonstrated using reduction and reoxidation of Cu-doped ceria metal oxides CuO,1 Cu-ceria,2 Au-ceria,3 and Cu­MoO2 Ref. 4 in water-gas- shift reactions. Another area

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

    E-print Network

    C. A. Bertulani P. G. Hansen

    2004-08-15

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

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

    PubMed Central

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

    1994-01-01

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

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

    SciTech Connect

    Balasi, K. G.; Kosmas, T. S.; Divari, P. C.; Chasioti, V. C. [Theoretical Physics Section, University of Ioannina, GR 45110 Ioannina (Greece)

    2008-01-24

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

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

    SciTech Connect

    Groh, D. E.; Pinter, J. S.; Mantica, P. F. [Department of Chemistry, Michigan State University, East Lansing, Michigan 48824 (United States); National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824 (United States); Mertzimekis, T. J. [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824 (United States); Stuchbery, A. E. [Department of Nuclear Physics, Research School for Physical Sciences and Engineering, Australian National University, Canberra, ACT 0200 (Australia); Khoa, D. T. [Institute for Nuclear Science and Technique, VAEC, P. O. Box 5T-160, Nghia Do, Hanoi, (Viet Nam)

    2007-11-15

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

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

    E-print Network

    Xu, Jun; Shen, Wen-Qing; Xia, Yin

    2015-01-01

    It is well known that non-central nuclear forces, such as the spin-orbital coupling and the tensor force, play important roles in understanding many interesting features of nuclear structures. However, their dynamical effects in nuclear reactions are poorly known since only the spin-averaged observables are normally studied both experimentally and theoretically. Realizing that spin-sensitive observables in nuclear reactions may carry useful information about the in-medium properties of non-central nuclear interactions, besides earlier studies using the time-dependent Hartree-Fock approach to understand effects of spin-orbital coupling on the threshold energy and spin polarization in fusion reactions, some efforts have been made recently to explore dynamical effects of non-central nuclear forces in intermediate-energy heavy-ion collisions using transport models. The focuses of these studies have been on investigating signatures of the density and isospin dependence of the form factor in the spin-dependent sing...

  4. {sup 16}O({gamma},{ital n}) reaction at intermediate energy

    SciTech Connect

    Andersson, B.; Adler, J.; Bulychjev, S.A.; Isaksson, L.; Ruijter, H.; Schroder, B. [Institute of Physics, University of Lund, Soelvegatan 14, S-22362 Lund (Sweden)] [Institute of Physics, University of Lund, Soelvegatan 14, S-22362 Lund (Sweden); Annand, J.R.M.; Crawford, G.I.; Harty, P.D.; McGeorge, J.C.; Miller, G.J. [Department of Physics and Astronomy, University of Glasgow, G12 8QQ (United Kingdom)] [Department of Physics and Astronomy, University of Glasgow, G12 8QQ (United Kingdom); Ryckebusch, J. [Institute for Nuclear Physics, Proeftuinstraat 86, B-9000 Gent (Belgium)] [Institute for Nuclear Physics, Proeftuinstraat 86, B-9000 Gent (Belgium)

    1995-05-01

    Measurements of the reaction {sup 16}O({gamma},{ital n}), made with tagged photons at {ital E}{sub {gamma}}{similar_to}58 MeV, are presented. Neutron energy determination was by time of flight, giving a resolution of {similar_to}2 MeV which enabled the ground-state excitation in {sup 15}O to be resolved from states at 5.2 and 6.2 MeV. Differential cross sections were measured in the angular range 30{degree}--110{degree} and are compared with the predictions of a microscopic, self-consistent Hartree-Fock, random phase approximation model of ({gamma},{ital N}) reactions. The implications for the theoretical description are discussed, notably the dependence of the ({gamma},{ital n}) cross section on meson exchange currents and final-state rescattering.

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

    SciTech Connect

    Halabi, Ghina M.; El Eid, Mounib [American University of Beirut, Department of Physics, P.O. Box 11-0236, Riad El-Solh, Beirut (Lebanon)

    2012-11-20

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

  6. Identification and Quantitation of Reaction Intermediates and Residuals in Lipase-Catalyzed Transesterified Oils by HPLC

    Microsoft Academic Search

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

    A high-performance liquid chromatography (HPLC) unit equipped with size exclusion column and a refractive index detector was\\u000a used for simultaneous monitoring, identification, and quantitation of the reaction components from lipase-catalyzed transesterification\\u000a of three oils. The procedure simultaneously separated and detected the unreacted triacylglycerols (TAG), diacyl-, and monoacyl-glycerol\\u000a (DAG and MAG) co-products, residual alcohol as well as free fatty acid (FFA)

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

    PubMed

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

    2010-08-01

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

  8. Anionic ligand effect on the nature of epoxidizing intermediates in iron porphyrin complex-catalyzed epoxidation reactions.

    PubMed

    Nam, Wonwoo; Jin, Sook Won; Lim, Mi Hee; Ryu, Ju Yeon; Kim, Cheal

    2002-07-15

    We have studied an anionic ligand effect in iron porphyrin complex-catalyzed competitive epoxidations of cis- and trans-stilbenes by various terminal oxidants and found that the ratios of cis- to trans-stilbene oxide products formed in competitive epoxidations were markedly dependent on the ligating nature of the anionic ligands. The ratios of cis- to trans-stilbene oxides obtained in the reactions of Fe(TPP)X (TPP = meso-tetraphenylporphinato dianion and X(-) = anionic ligand) and iodosylbenzene (PhIO) were 14 and 0.9 when the X(-) of Fe(TPP)X was Cl(-) and CF(3)SO(3)(-), respectively. An anionic ligand effect was also observed in the reactions of an electron-deficient iron(III) porphyrin complex containing a number of different anionic ligands, Fe(TPFPP)X [TPFPP = meso-tetrakis(pentafluorophenyl)porphinato dianion and X(-) = anionic ligand], and various terminal oxidants such as PhIO, m-chloroperoxybenzoic acid (m-CPBA), tetrabutylammonium oxone (TBAO), and H(2)O(2). While high ratios of cis- to trans-stilbene oxides were obtained in the reactions of iron porphyrin catalysts containing ligating anionic ligands such as Cl(-) and OAc(-), the ratios of cis- to trans-stilbene oxide were low in the reactions of iron porphyrin complexes containing nonligating or weakly ligating anionic ligands such as SbF(6)(-), CF(3)SO(3)(-), and ClO(4)(-). When the anionic ligand was NO(3)(-), the product ratios were found to depend on terminal oxidants and olefin concentrations. We suggest that the dependence of the product ratios on the anionic ligands of iron(III) porphyrin catalysts is due to the involvement of different reactive species in olefin epoxidation reactions. That is, high-valent iron(IV) oxo porphyrin cation radicals are generated as a reactive species in the reactions of iron porphyrin catalysts containing nonligating or weakly ligating anionic ligands such as SbF(6)(-), CF(3)SO(3)(-), and ClO(4)(-), whereas oxidant-iron(III) porphyrin complexes are the reactive intermediates in the reactions of iron porphyrin catalysts containing ligating anionic ligands such as Cl(-) and OAc(-). PMID:12099867

  9. Interaction of phosphonate analogues of the tetrahedral reaction intermediate with 5-enolpyruvylshikimate-3-phosphate synthase in atomic detail.

    PubMed

    Priestman, Melanie A; Healy, Martha L; Becker, Andreas; Alberg, David G; Bartlett, Paul A; Lushington, Gerald H; Schönbrunn, Ernst

    2005-03-01

    The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the penultimate step of the shikimate pathway and is the target of the broad-spectrum herbicide glyphosate. Since the functionality of the shikimate pathway is vital not only for plants but also for microorganisms, EPSPS is considered a prospective target for the development of novel antibiotics. We have kinetically analyzed and determined the crystal structures of Escherichia coli EPSPS inhibited by (R)- and (S)-configured phosphonate analogues of the tetrahedral reaction intermediate. Both diastereomers are competitive inhibitors with respect to the substrates of the EPSPS reaction, shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP). Remarkably, the (S)-phosphonate (K(iS3P) = 750 nM), whose configuration corresponds to that of the genuine tetrahedral intermediate, is a much weaker inhibitor than the (R)-phosphonate analogue (K(iS3P) = 16 nM). The crystal structures of EPSPS liganded with the (S)- and (R)-phosphonates, at 1.5 and 1.9 A resolution, respectively, revealed that binding of the (R)-phosphonate induces conformational changes of the strictly conserved residues Arg124 and Glu341 within the active site. This appears to give rise to substantial structural alterations in the amino-terminal globular domain of the enzyme. By contrast, binding of the (S)-phosphonate renders the enzyme structure unchanged. Thus, EPSPS may facilitate the tight binding of structurally diverse ligands through conformational flexibility. Molecular docking calculations did not explain why the (R)-phosphonate is the better inhibitor. Therefore, we propose that the structural events during the open-closed transition of EPSPS are altered as a result of inhibitor action. PMID:15736934

  10. 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.

  11. 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

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

    SciTech Connect

    Calaza, Florencia [Max Planck Society, Fritz Haber Institute; Chen, Tsung-Liang [ORNL; Mullins, David R [ORNL; Xu, Ye [Louisiana State University; Overbury, Steven {Steve} H [ORNL

    2015-01-01

    Adsorption and reaction of acetic acid on a CeO2(1 1 1) surface was studied by a combination of ultra-highvacuum based methods including temperature desorption spectroscopy (TPD), soft X-ray photoelectronspectroscopy (sXPS), near edge X-ray absorption spectroscopy (NEXAFS) and reflection absorption IRspectroscopy (RAIRS), together with density functional theory (DFT) calculations. TPD shows that thedesorption products are strongly dependent upon the initial oxidation state of the CeO2surface, includingselectivity between acetone and acetaldehyde products. The combination of sXPS and NEXAFS demon-strate that acetate forms upon adsorption at low temperature and is stable to above 500 K, above whichpoint ketene, acetone and acetic acid desorb. DFT and RAIRS show that below 500 K, bridge bondedacetate coexists with a moiety formed by adsorption of an acetate at an oxygen vacancy, formed bywater desorption.

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

    SciTech Connect

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

    1984-10-01

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

  14. Development of a 4{pi} neutron detector for intermediate-energy-ion reaction studies

    SciTech Connect

    Zhao, X.; Baldwin, S.P.; Schroder, W.U. [and others

    1993-04-01

    An advanced, segmented 4{pi} Neutron Multiplicity Meter (NMM) is under development at University of Rochester. The NMM consists of three approximately cylindrical middle segments and two spherical end segments, with a total volume of 17.2m{sup 3}, and is filled with gadolinium-loaded liquid scintillator. The NMM covers 98% of the solid angle and contains a 51 inches long x 36 inches diameter cylindrical scattering chamber. The NMM can be operated in conjunction with 4{pi} charged-particle detectors, providing full coverage of all light particles emitted in a nuclear reaction, as well as a coarse angular distribution of these quantities. General design and performance characteristics of the NMM are discussed, and the results of simulation calculations are presented.

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

    PubMed Central

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

    2015-01-01

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

  16. 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.

  17. Differential inhibition of class I and class II 5-enolpyruvylshikimate-3-phosphate synthases by tetrahedral reaction intermediate analogues.

    PubMed

    Funke, Todd; Healy-Fried, Martha L; Han, Huijong; Alberg, David G; Bartlett, Paul A; Schönbrunn, Ernst

    2007-11-20

    The shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSP synthase or EPSPS) is best known as the target of the herbicide glyphosate. EPSPS is also considered an attractive target for the development of novel antibiotics since the pathogenicity of many microorganisms depends on the functionality of the shikimate pathway. Here, we have investigated the inhibitory potency of stable fluorinated or phosphonate-based analogues of the tetrahedral reaction intermediate (TI) in a parallel study utilizing class I (glyphosate-sensitive) and class II (glyphosate-tolerant) EPSPS. The (R)-difluoromethyl and (R)-phosphonate analogues of the TI are the most potent inhibitors of EPSPS described to date. However, we found that class II EPSPS are up to 400 times less sensitive to inhibition by these TI analogues. X-ray crystallographic data revealed that the conformational changes of active site residues observed upon inhibitor binding to the representative class I EPSPS from Escherichia coli do not occur in the prototypical class II enzyme from Agrobacterium sp. strain CP4. It appears that because the active sites of class II EPSPS do not possess the flexibility to accommodate these TI analogues, the analogues themselves undergo conformational changes, resulting in less favorable inhibitory properties. Since pathogenic microorganisms such as Staphylococcus aureus utilize class II EPSPS, we conclude that the rational design of novel EPSPS inhibitors with potential as broad-spectrum antibiotics should be based on the active site structures of class II EPSP synthases. PMID:17958399

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

    SciTech Connect

    Isied, Stephan S.

    2003-03-11

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

  19. 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

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

    NASA Astrophysics Data System (ADS)

    Carraher, Jack McCaslin

    Reactive species like high-valent metal-oxo complexes and carbon and oxygen centered radicals are important intermediates in enzymatic systems, atmospheric chemistry, and industrial processes. Understanding the pathways by which these intermediates form, their relative reactivity, and their fate after reactions is of the utmost importance. Herein are described the mechanistic detail for the generation of several reactive intermediates, synthesis of precursors, characterization of precursors, and methods to direct the chemistry to more desirable outcomes yielding 'greener' sources of commodity chemicals and fuels. High-valent Chromium from Hydroperoxido-Chromium(III). The decomposition of pentaaquahydroperoxido chromium(III) ion (hereafter Cr aqOOH2+) in acidic aqueous solutions is kinetically complex and generates mixtures of products (Craq3+, HCrO 4-, H2O2, and O2). The yield of high-valent chromium products (known carcinogens) increased from a few percent at pH 1 to 70 % at pH 5.5 (near biological pH). Yields of H 2O2 increased with acid concentration. The reproducibility of the kinetic data was poor, but became simplified in the presence of H2O2 or 2,2?-azinobis(3-ethylbenzothiazoline-6-sulfonate) dianion (ABTS2-). Both are capable of scavenging strongly oxidizing intermediates). The observed rate constants (pH 1, [O2] ? 0.03 mM) in the presence of these scavengers are independent of [scavenger] and within the error are the same (k,ABTS2- = (4.9 +/- 0.2) x 10-4 s-1 and kH2O2 = (5.3 +/- 0.7) x 10-4 s-1); indicating involvement of the scavengers in post-rate determining steps. In the presence of either scavenger, decomposition of CrOOH2+ obeyed a two-term rate law, k obs / s-1 = (6.7 +/- 0.7) x 10-4 + (7.6 +/- 1.1) x 10-4 [H+]. Effect of [H+] on the kinetics and the product distribution, cleaner kinetics in the presence of scavengers, and independence of kobs on [scavenger] suggest a dual-pathway mechanism for the decay of Craq OOH2+. The H+-catalyzed path leads to the dissociation of H2O2 from Cr(III), while in the H+-independent reaction, CraqOOH2+ is transformed to Cr(V). Both scavengers rapidly remove Cr(V) and simplify both the kinetics and products by impeding formation of Cr(IV, V, VI). Syntheses, Reactivity, and Thermodynamic Considerations LRhR2+. Macrocyclic rhodium(II) complexes LRh(H 2O)2+ (L = L1= cyclam and L2 = meso-Me6-cyclam) react with alkyl hydroperoxides R(CH3)2COOH to generate the corresponding rhodium(III) alkyls LRh(H2O)R2+ (R = CH3, C2 H5, PhCH2). Methyl and benzyl complexes can also be prepared by bimolecular group transfer from alkyl cobaloximes (dmgX) 2(H2O)CoR (where R = CH3, CH2Ph and dmgX is either dimethylglyoxime or a BF2-capped derivative of dmg) to LRh(H2O)2+. When R = C2H5, C3H7 or C4H9, the mechanism changes from group transfer to hydrogen atom abstraction from the coordinated alkyl and produces LRh(H2O)H2+ and an a-olefin. The new LRh(H2O)R2+ complexes were characterized by solution NMR and by crystal structure analysis. They exhibit great stability in aqueous solution at room temperature, but undergo efficient Rh-C bond cleavage upon photolysis. 'Green' Model for Decarboxylation of Biomass Derived Acids via Photolysis of in situ formed Metal-Carboxylate Complexes. Photolysis of aqueous solutions containing propionic acid and Fe 3+ aq in the absence of oxygen generates a mixture of hydrocarbons (ethane, ethylene and butane), carbon dioxide, and Fe2+. Photolysis in the presence of O2 yields catalytic amounts of hydrocarbon products. When halide ions are present during photolysis; nearly quantitative yields of ethyl halides are produced via extraction of a halide atom from FeX2+ by ethyl radical. The rate constants for ethyl radical reactions with FeCl2+ (k = 4.0 (+/- 0.5) x 106 M-1s-1) and with FeBr 2+ (k = 3.0 (+/- 0.5) x 107 M-1s -1) were determined via competition reactions. Irradiation of solutions containing aqueous Cu2+ salts and linear carboxylic acids yield alpha-olefins selectively. This process is made catalytic by the introduction of O2. Photochemical decarboxylation of

  1. Heterogeneous Reactions of Epoxides in Acidic Media

    E-print Network

    Lal, Vinita

    2012-02-14

    Epoxides have been recently identified as one of the intermediate species in the gas phase oxidation of alkenes. This study investigates the reaction of isoprene oxide and alpha-pinene oxide with sulfuric acid to identify the potential of epoxides...

  2. Nuclear modification factor for identified hadrons at forward rapidity in Au+Au reactions at 200 GeV

    E-print Network

    Nuclear modification factor for identified hadrons at forward rapidity in Au+Au reactions at 200 Ge University, Reymonta 4, Krak´ow 30-059, Poland Herewith we present the production of identified hadrons in Au at the same energy [1]. High pT hadrons are primarily produced from the fragmentation of the hard- scattered

  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. 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

  6. Molybdopterin Biosynthesis: Trapping of Intermediates for the MoaA-Catalyzed Reaction Using 2?-DeoxyGTP and 2?-ChloroGTP as Substrate Analogues.

    PubMed Central

    2015-01-01

    MoaA is a radical S-adenosylmethionine (AdoMet) enzyme that catalyzes a complex rearrangement of guanosine-5'-triphosphate (GTP) in the first step of molybdopterin biosynthesis. In this paper, we provide additional characterization of the MoaA reaction product, describe the use of 2?-chloroGTP to trap the GTP C3? radical, generated by hydrogen atom transfer to the 5?-deoxyadenosyl radical, and the use of 2?-deoxyGTP to block a late step in the reaction sequence. These probes, coupled with the previously reported trapping of an intermediate in which C3? of the ribose is linked to C8 of the purine, allow us to propose a plausible mechanism for the MoaA-catalyzed reaction. PMID:24955657

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

    PubMed Central

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

    2009-01-01

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

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

    SciTech Connect

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

    2009-01-01

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

  9. 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.

    Organic Chemistry Jasperse Acid-Base Practice Problems A. Identify each chemical as either an "acid" 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 reaction

  10. Reaction pathways in the electrochemical degradation of thiocarbamate herbicides in NaCl solution

    Microsoft Academic Search

    FERENC MOGYORÓDY

    2006-01-01

    We have identified the intermediates and end products which are formed during the electrolytic degradation of thiocarbamate pesticides in aqueous NaCl solutions and investigated how the intermediate and end product volumes and ratios depend on reaction conditions. Further, we have defined both the reaction pathways leading to intermediate and end product formation and the methods affecting this process. The degradation

  11. 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

  12. Effects of Stabilized Criegee Intermediate and OH Radical Scavengers on Aerosol Formation from Reactions of ?-Pinene with O 3

    Microsoft Academic Search

    Kenneth S. Docherty; Paul J. Ziemann

    2003-01-01

    The formation of secondary organic aerosol (SOA) from reactions of O 3 with g -pinene, an exocyclic monoterpene prominent in the ambient atmosphere, was studied in an environmental chamber using a thermal desorption particle beam mass spectrometer for chemical analysis and a scanning mobility particle sizer for aerosol yield measurements. Potential reaction pathways for SOA formation were investigated in a

  13. Kinetics of and intermediates in a photocycle branching reaction of the photoactive yellow protein from Ectothiorhodospira halophila

    E-print Network

    van Stokkum, Ivo

    that absorption of a blue photon leads to cisCCtrans isomerization of the 4-hydroxy-cinnamyl chromophore of PYP Abstract We have studied the kinetics of the blue light-induced branching reaction in the photocycle/Vis spectroscopy. As compared to the parallel dark recovery reaction of the presumed blue-shifted signaling state p

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

    NASA Astrophysics Data System (ADS)

    Breton, Gary W.

    1997-01-01

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

  15. 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.

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

    E-print Network

    Butler, Laurie J.

    role in combustion chemistry, especially low temperature com- bustion where the nearly barrierless in the O+allyl bimolecular reaction. The data include velocity map imaging and molecular beam scattering

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

    PubMed

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

    2015-07-27

    LiFePO4 is an important cathode material for lithium-ion batteries. Regardless of the biphasic reaction between the insulating end members, Lix FePO4 , x?0 and x?1, optimization of the nanostructured architecture has substantially improved the power density of positive LiFePO4 electrode. The charge transport that occurs in the interphase region across the biphasic boundary is the primary stage of solid-state electrochemical reactions in which the Li concentrations and the valence state of Fe deviate significantly from the equilibrium end members. Complex interactions among Li ions and charges at the Fe sites have made understanding stability and transport properties of the intermediate domains difficult. Long-range ordering at metastable intermediate eutectic composition of Li2/3 FePO4 has now been discovered and its superstructure determined, which reflected predominant polaron crystallization at the Fe sites followed by Li(+) redistribution to optimize the Li?Fe interactions. PMID:26074480

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

    ERIC Educational Resources Information Center

    Zhou, Shaona; Zhang, Chunbin; Xiao, Hua

    2015-01-01

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

  19. 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

  20. 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.

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

    E-print Network

    Gao-Feng Wei

    2015-06-26

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

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

    E-print Network

    Wei, Gao-Feng

    2015-01-01

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

  3. A novel fault-tree approach for identifying potential causes of satellite reaction wheel failure

    Microsoft Academic Search

    A. Barua; P. Sinha; K. Khorasani; S. Tafazoli

    2005-01-01

    Due to unforeseen circumstances and naturally occurring faults, it is desired that an on-board fault-diagnosis system of a space vehicle be capable of detecting, isolating, identifying or classifying faults in the system. In this paper, a novel approach is proposed which strengthens existing efficient fault-detection mechanisms with an additional ability to classify different types of faults to effectively determine potential

  4. Reaction Kinetics and Intermediate Determination of Solid Acid Catalysed Liquid-phase Hydrolysis Reactions: A Real-time in situ ATR FT-IR Study

    Microsoft Academic Search

    Gerben M. Hamminga; Guido Mul; Jacob A. Moulijn

    2006-01-01

    The appearance of catalyst–reactant interactions observed in on-line ATR FT-IR spectra of Nafion\\/silica catalysed esterification\\u000a and etherification reactions of 1-octanol was investigated. It was assessed by variation of catalyst and solvent that the\\u000a catalyst–reactant band is a result of the reaction of silica with 1-octanol, yields Si–O–R functionalities. Based on off-line\\u000a TPD-MS and TGA characterisation of the used solid catalyst

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

    PubMed

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

    2014-01-01

    The degradation of 230 mL of a 0.6-mM sulfanilamide solution in 0.05 M 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

  6. Measuring Rate Constants for Reactions of the Simplest Criegee Intermediate (CH2OO) by Monitoring the OH Radical

    NASA Astrophysics Data System (ADS)

    liu, Y.; Bayes, K. D.; Sander, S. P.

    2013-12-01

    While generating the CH2OO molecule by reacting CH2I with O2, significant amounts of the OH radical were observed by laser induced fluorescence (LIF). At least two different processes formed OH; a fast process was probably due to a reaction of vibrationally hot CH2I radicals. The second process appeared to be associated with the decay of the CH2OO molecule. The addition of molecules known to react with CH2OO increased the observed decay rates of the OH signal. Using the OH signals as a proxy for the CH2OO concentration, the rate constant for the reaction of hexafluoroacetone with CH2OO was determined to be (3.33 × 0.27) x 10-11 cm3 molecule-1 s-1, in good agreement with the value measured by Taatjes et al.1 The rate constant for the reaction of SO2 with CH2OO, (3.53 × 0.29) x 10-11 cm3 molecule-1 s-1, showed no pressure dependence over the range of 50 to 200 Torr and was in agreement with the value at 4 Torr reported by Welz et al.2 This lack of a pressure dependence shows that SO2 + CH2OO is almost certainly a two-body reaction forming SO3 + CH2O and not a three-body stabilization.

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

    NASA Technical Reports Server (NTRS)

    Opila, Elizabeth J.

    1997-01-01

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

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

    PubMed Central

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

    2015-01-01

    Validation of claims-based algorithms to identify serious hypersensitivity reactions and osteonecrosis of the jaw has not been performed in large osteoporosis populations. The objective of this project is to estimate the positive predictive value of the claims-based algorithms in older women with osteoporosis enrolled in Medicare. Using the 2006-2008 Medicare 5% sample data, we identified potential hypersensitivity and osteonecrosis of the jaw cases based on ICD-9 diagnosis codes. Potential hypersensitivity cases had a 995.0, 995.2, or 995.3 diagnosis code on emergency department or inpatient claims. Potential osteonecrosis of the jaw cases had ?1 inpatient or outpatient physician claim with a 522.7, 526.4, 526.5, or 733.45 diagnosis code or ?2 claims of any type with a 526.9 diagnosis code. All retrieved records were redacted and reviewed by experts to determine case status: confirmed, not confirmed, or insufficient information. We calculated the positive predictive value as the number of confirmed cases divided by the total number of retrieved records with sufficient information. We requested 412 potential hypersensitivity and 304 potential osteonecrosis of the jaw records and received 174 (42%) and 84 (28%) records respectively. Of 84 potential osteonecrosis of the jaw cases, 6 were confirmed, resulting in a positive predictive value (95% CI) of 7.1% (2.7, 14.9). Of 174 retrieved potential hypersensitivity records, 95 were confirmed. After exclusion of 25 records with insufficient information for case determination, the overall positive predictive value (95% CI) for hypersensitivity reactions was 76.0% (67.5, 83.2). In a random sample of Medicare data, a claim-based algorithm to identify serious hypersensitivity reactions performed well. An algorithm for osteonecrosis of the jaw did not, partly due to the inclusion of diagnosis codes that are not specific for osteoporosis of the jaw. PMID:26161858

  9. [Use of polymerase chain reaction for identifying helminth DNA from the species Trichinella, Fasciola, Echinococcus, Nematodirus, Taenia].

    PubMed

    Romanova, E A; Semenova, S K; Benediktov, I I; Ryskov, A P

    1997-01-01

    We have used the polymerase chain reaction (PCR) and random amplified polymorphic DNA (RAPD) method to identify DNA polymorphism in three classes of helminths, Cestoda, Nematoda and Trematoda. In this study, RAPD markers have been used for a description of the genetic variability between the families, genera, species and isolates of helminths. We optimized the conditions of the RAPD analysis and revealed the genetic variability of helminths belonging to different taxonomic groups. These results show that the RAPD-PCR method can be considered as a suitable technic for a phylogenetic study of helminths. The problem of an age variability and most specificity of RAPDs markers is discussed. PMID:9297179

  10. 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.

  11. 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.

  12. The determination of the kinetics and the products from the reactions between intermediate chlorine and bromine compounds in water treatment

    Microsoft Academic Search

    Christopher Scott Furman

    1998-01-01

    Multiwavelength spectrophotometric analysis of 32 wavelengths, over the range of 240-400 nm, has resolved the decay of HOCl from a multicomponent solution. It has been found that HOBr catalyzes the decomposition of HOCl under identical experimental conditions, where the decay of HOCl by itself is otherwise slow $\\\\rm({\\\\ll}10\\\\sp{-5}\\\\ s\\\\sp{-1}).$ To a first approximation, the rate-determining step is the 1:1 reaction

  13. Light charged particle and intermediate mass fragment cross-sections in GeV proton-induced reactions

    Microsoft Academic Search

    V. Bollini; A. Bubak; A. Budzanowski; J. Cugnon; D. Filges; F. Goldenbaum; A. Heczko; H. Hodde; L. Jarczyk; B. Kamys; M. Kistryn; A. Kowalczyk; P. Kulessa; H. Machner; A. Magiera; W. Migdal; K. Nünighoff; N. Paul; B. Piskor-Ignatowicz; K. Pysz; Z. Rudy; R. Siudak; M. Wojciechowski; E. Kozik

    2006-01-01

    As an international collaboration PISA (Proton Induced SpAllation) has initiated measurements of total and double differential cross-sections for products of spallation reactions at the proton accelerator COSY in Jülich (Germany) in order to study secondary particle production created in structural, window, and target materials by proton beams up to 2.5GeV incident kinetic energy. In the framework of Spallation Neutron Sources

  14. Infrared Spectroscopy of OH··CH3OH: Hydrogen-Bonded Intermediate Along the Hydrogen Abstraction Reaction Path.

    PubMed

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

    2015-07-23

    Substantial non-Arrhenius behavior has been previously observed in the low temperature reaction between the hydroxyl radical and methanol. This behavior can be rationalized assuming the stabilization of an association adduct in the entrance channel of the reaction, from which barrier penetration via quantum mechanical tunneling produces the CH3O radical and H2O. Helium nanodroplet isolation and a serial pick-up technique are used to stabilize the hydrogen bonded prereactive OH··CH3OH complex. Mass spectrometry and infrared spectroscopy are used to confirm its production and probe the OH stretch vibrations. Stark spectroscopy reveals the magnitude of the permanent electric dipole moment, which is compared to ab initio calculations that account for wide-amplitude motion in the complex. The vibrationally averaged structure has Cs symmetry with the OH moiety hydrogen bonded to the hydroxyl group of methanol. Nevertheless, the zero-point level of the complex exhibits a wave function significantly delocalized over a bending coordinate leading to the transition state of the CH3O producing reaction. PMID:26135615

  15. Characterization of nanoparticles of LiMn2O4 synthesized by a one-step intermediate-temperature solid-state reaction.

    PubMed

    Guo, Z P; Ahn, J H; Liu, H K; Dou, S X

    2004-01-01

    Nanoparticles of lithium manganese oxide (LiMn2O4) with a spinel structure have been synthesized by a one-step intermediate temperature solid-state reaction. The influence of the molar ratio of citric acid to the metal ions on the physicochemical properties of LiMn2O4 powders in air has been analyzed by means of X-ray diffraction and electron microscope techniques. The electrochemical behavior of the material has been examined by charge/discharge tests and cyclic voltammetry. Test results reveal that LiMn2O4 particles with lower molar ratios of citric acid to metal ions (1:2) are highly crystalline and highly electrochemically reversible, with better cycle capabilities when compared with a sample with a higher molar ratio (2:1). The LiMn2O4 powders obtained by this method have a uniform morphology with a narrow size distribution. PMID:15112561

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

    PubMed

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

    2015-05-28

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

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

    SciTech Connect

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

    2008-03-21

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

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

    PubMed Central

    Su, Jia; Groves, John T.

    2009-01-01

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

  19. Discussions of Ambiguities on Current Operators in Exclusive (e,e'p) Reactions for Intermediate Electron Energy

    NASA Astrophysics Data System (ADS)

    Cheoun, Myung Ki; Kim, K. S.

    2004-08-01

    Possible ambiguities in the theoretical interpretation of exclusive (e,e'p) reactions are discussed on the basis of realistic model calculations. Gauge ambiguity, medium effects, and contribution of the ? current are evaluated in distorted wave Born approximation (DWBA) where the four momentum transfer square |q?|2 is less than 0.5 (GeV/c)2. The gauge ambiguity effects are shown to be about 10% in the small missing momentum region and about 20% maximally in the high missing momentum region. Medium effects of about 6-10% appear mainly in the small missing momentum region. The ?-resonance current influences the high missing momentum region by about 10% maximally.

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

    PubMed

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

    2013-04-01

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

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

    PubMed

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

    2014-08-19

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

  2. 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

  3. 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

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

    SciTech Connect

    Salowe, S.P.; Krol, W.J.; Iwata-Reuyl, D.; Townsend, C.A. (Johns Hopkins Univ., Baltimore, MD (United States))

    1991-02-26

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

  5. Measurement of the 8He(p,n)8Li Reaction at Intermediate Energy in Inverse Kinematics

    NASA Astrophysics Data System (ADS)

    Kobayashi, Motoki; Yako, Kentaro; Shimoura, Susumu; Dozono, Masanori; Kawase, Shoichiro; Kisamori, Keiichi; Kubota, Yuki; Lee, CheongSoo; Michimasa, Shinichiro; Miya, Hiroyuki; Ota, Shinsuke; Sakai, Hideyuki; Sasano, Masaki; Takaki, Motonobu

    We performed the first measurement of the 8He(p,n)8Li reaction at a beam energy of 190A MeV in inverse kinematics at the RIKEN RI Beam Factory in order to study the spin-isospin response of a neutron-rich nucleus 8He. The excitation energy spectrum of the residual 8Li was obtained by tagging the channels decaying to Li isotopes. In addition to a peak which is assigned to the 1+ state at 0.98 MeV, a peak with a large transition strength is observed at around 8 MeV, which is likely to be populated by Gamow-Teller transitions.

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

    PubMed

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

    2009-12-14

    For the double exponential fluorescence decays of the locally excited (LE) and intramolecular charge transfer (ICT) states of 4-(dimethylamino)benzonitrile (DMABN) in acetonitrile (MeCN) the same times tau(1) and tau(2) are observed. This means that the reversible LE<==>ICT reaction, starting from the initially excited LE state, can be adequately described by a two state mechanism. The most important factor responsible for the sometimes experimentally observed differences in the nanosecond decay time, with tau(1)(LE)intermediate in the ICT reaction of DMABN are discussed. From the appearance of an excited state absorption (ESA) band in the spectral region between 700 and 800 nm in MeCN for N,N-dimethylanilines with CN, Br, F, CF(3), and C(=O)OC(2)H(2) p-substituents, it is concluded that this ESA band cannot be attributed to a pisigma( *) state, as only the C-C[Triple Bond]N group can undergo the required 120 degrees bending. PMID:20001042

  7. Ability of non-high-density lipoprotein cholesterol and calculated intermediate-density lipoprotein to identify nontraditional lipoprotein subclass risk factors in dialysis patients

    Microsoft Academic Search

    Sharina S Belani; Anne C Goldberg; Daniel W Coyne

    2004-01-01

    Background: Non-high-density lipoprotein cholesterol (non-HDL-C) and calculated intermediate-density lipoprotein cholesterol (IDL-C) have been proposed as surrogate markers to estimate apolipoprotein B-containing lipoproteins. The purpose of this study was to determine the validity of non-HDL-C and calculated IDL-C to predict nontraditional lipoprotein risk factors among dialysis patients and to compare the prevalence of these nontraditional risk factors between dialysis modalities. Methods:

  8. 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.

    Organic Chemistry Jasperse Acid-Base Practice Problems A. Identify each chemical as either an "acid" or a "base" in the following reactions, and identify "conjugate" relationships. -You should have one acid the More Acidic for Each of the Following Pairs: Single Variable Problems 16. 17. 18. 19. 20. 21. O O O OH

  9. Photo- and electroluminescence spectra from an n-TiO/sub 2/ semiconductor electrode as related to the intermediates of the photoxidation reaction of water

    SciTech Connect

    Nakato, Y.; Tsumura, A.; Tsubomura, H.

    1983-06-23

    Photo- and electroluminescence spectra of an n-type TiO/sub 2/ electrode in aqueous solutions were measured as functions of the electrode potential and the solution pH, together with the current-potential curves. The photoluminescence spectrum showed a relatively sharp band peaked at 1.47 eV. From quenching of the photoluminescence by reductants in solution, this band was concluded to arise from an oxidative surface species, called X/sub 1.47/, acting as an intermediate of the photoxidation reaction of water. It was shown that the species X/sub 1.47/ is orginally absent at an n-TiO/sub 2/ surface, but produced and accumulated by illumination under anodic bias. It was also suggested, from a comparison of the electroluminescence spectra in H/sub 2/O solutions with those in S/sub 2/O/sub 8//sup 2 -/ solutions, that the species X/sub 1.47/ can be assigned to a kind of OH. radical surface adduct. The origins of other luminescence bands peaked at higher energies appearing in the electroluminescence spectra are also discussed.

  10. A new modular phosphite-pyridine ligand library for asymmetric Pd-catalyzed allylic substitution reactions: a study of the key Pd-?-allyl intermediates.

    PubMed

    Mazuela, Javier; Pàmies, Oscar; Diéguez, Montserrat

    2013-02-11

    A library of phosphite-pyridine ligands L1-L12?a-g has been successfully applied for the first time in the Pd-catalyzed allylic substitution reactions of several di- and trisubstituted substrates by using a wide range of C, N and O nucleophiles, among which are the little studied ?-substituted malonates, ?-diketones, and alkyl alcohols. The highly modular nature of this ligand library enables the substituents/configuration at the ligand backbone, and the substituents/configurations at the biaryl phosphite moiety to be easily and systematically varied. We found that the introduction of an enantiopure biaryl phosphite moiety played an essential role in increasing the versatility of the Pd-catalytic systems. Enantioselectivities were therefore high for several hindered and unhindered di- and trisubstituted substrates by using a wide range of C, N and O nucleophiles. Of particular note were the high enantioselectivities (up to>99%?ee) and high activities obtained for the trisubstituted substrates S6 and S7, which compare favorably with the best that have been reported in the literature. We have also extended the use of these new catalytic systems in alternative environmentally friendly solvents such as propylene carbonate and ionic liquids. Studies on the Pd-?-allyl intermediates provide a deeper understanding of the effect of ligand parameters on the origin of enantioselectivity. PMID:23297053

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

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

    SciTech Connect

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

    1987-02-04

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

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

    PubMed Central

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

    2011-01-01

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

  14. Atomic Description of an Enzyme Reaction Dominated by Proton Tunneling

    Microsoft Academic Search

    Laura Masgrau; Anna Roujeinikova; Linus O. Johannissen; Parvinder Hothi; Jaswir Basran; Kara E. Ranaghan; Adrian J. Mulholland; Michael J. Sutcliffe; Nigel S. Scrutton; David Leys

    2006-01-01

    We present an atomic-level description of the reaction chemistry of an enzyme-catalyzed reaction dominated by proton tunneling. By solving structures of reaction intermediates at near-atomic resolution, we have identified the reaction pathway for tryptamine oxidation by aromatic amine dehydrogenase. Combining experiment and computer simulation, we show proton transfer occurs predominantly to oxygen O2 of Asp128beta in a reaction dominated by

  15. Interactions of plant acetohydroxy acid isomeroreductase with reaction intermediate analogues: correlation of the slow, competitive, inhibition kinetics of enzyme activity and herbicidal effects.

    PubMed Central

    Dumas, R; Cornillon-Bertrand, C; Guigue-Talet, P; Genix, P; Douce, R; Job, D

    1994-01-01

    N-Hydroxy-N-isopropyloxamate (IpOHA) is known to inhibit extremely tightly (Ki of 22 pM) the bacterial acetohydroxy acid isomeroreductase (EC 1.1.1.86) [Aulabaugh and Schloss (1990) Biochemistry 29, 2824-2830], the second enzyme of the branched-chain-amino-acid-biosynthetic pathway. Yet, although the same pathway exists in plant cells, this compound presents only very poor herbicidal action. Towards the goal of gaining a better understanding of this behaviour, we have studied the mechanism of interaction of this compound with a highly purified acetohydroxy acid isomeroreductase of plant origin, i.e. the spinach (Spinacia oleracea) chloroplast enzyme. IpOHA behaved as a nearly irreversible inhibitor of the enzyme. Encounter complex formation was very slow (association rate constant 1.9 x 10(3) M-1.s-1) and involved a single bimolecular step. Since inhibition was competitive with respect to acetohydroxy acid substrates, the time needed to achieve substantial (90%) inhibition in vitro of enzyme activity in the simultaneous presence of substrates and inhibitors was extremely long (for example of the order of hours at 1 microM IpOHA and 100 microM acetohydroxy acid substrates). Thus, under in vivo conditions, binding of the inhibitor may be so slow that it may delay considerably the time required for inhibition of the target enzyme. Simialr kinetic behaviour was observed with another reaction intermediate analogue described by Schulz, Spönemann, Köcher and Wengenmayer [(1988) FEBS Lett. 238, 375-378], 2-dimethyl-phosphinoyl-2-hydroxyacetic acid (Hoe 704), which displays a higher herbicide activity than IpOHA. The herbicidal potency of these two compounds appeared to be correlated with their rates of association with the plant acetohydroxy acid isomeroreductase, since the bimolecular rate constant for Hoe 704 (2.2 x 10(4) M-1.s-1) was higher than that for IpOHA. PMID:8053906

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

    SciTech Connect

    Lee, Jai Young (KAIST, Republic of Korea); Muller, Richard Partain; Kang, Jeung Ku (KAIST, Republic of Korea); Goddard, William A., III (California Institute of Technology, Pasadena, CA)

    2005-06-01

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

  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)]+ (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.

  18. Advanced oxidation and reduction process chemistry of methyl tert-butyl ether (MTBE) reaction intermediates in aqueous solution: 2Methoxy2-methyl-propanal, 2-methoxy-2-methyl-propanol, and 2-methoxy-2-methyl-propanoic acid

    Microsoft Academic Search

    Stephen P. Mezyk; D. Rance Hardison; Weihua Song; Kevin E. O’Shea; David M. Bartels; William J. Cooper

    2009-01-01

    Absolute rate constants for the reaction of three important degradation products of methyl-tert-butyl ether (MTBE) with the hydroxyl radical, hydrated electron and hydrogen atom were determined in aqueous solution at room temperature. These three intermediate species; 2-methoxy-2-methyl propanal (MMP), 2-methoxy-2-methyl-propanol (MMP-OH) and 2-methoxy-2-methyl-propionic acid (MMP-acid), are formed in the degradation of MTBE under advanced oxidation and reduction process conditions. The

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

    PubMed Central

    2014-01-01

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

  20. 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

  1. Reactions of dioxygen difluoride with neptunium oxides and fluorides

    Microsoft Academic Search

    P. Gary Eller; Larned B. Asprey; Scott A. Kinkead; Basil I. Swanson; Richard J. Kissane

    1998-01-01

    Neptunium dioxide and tetrafluoride are converted in essentially quantitative yield to volatile neptunium hexafluoride by dioxygen difluoride (O2F2), both in gas–solid reactions at ambient temperatures and in liquid anhydrous hydrogen fluoride at ?78°C. Neptunium dioxydifluoride was identified by Raman spectroscopy as a dominant reaction intermediate in the neptunium dioxide reaction. Direct reaction of NpF4 with liquid O2F2 resulted in violent

  2. Reactions of 2,7-Dimethyloxepin with Dimethyldioxirane and Methyl(trifluoromethyl)dioxirane: Ring Opening and Probable Observation of the Intermediate “2,3-Epoxyoxepin”

    Microsoft Academic Search

    Arthur Greenberg; Aviv Ozari; Clifford M. Carlin

    1998-01-01

    The reactions of dimethyldioxirane (7) and methyl(trifluoromethyl)dioxirane (8) with 2,7-dimethyloxepin (4) both yielded Z,Z-3,5-octadiene-2,7-dione (Z,Z-6) as their initial stable products. This is the first published reaction of a dioxirane with an isolable pure oxepin. Reaction of the dienedione Z,Z-6 with one mole equivalent of either 7 or 8 yielded the corresponding monoepoxide. Treatment of this monoepoxide with another equivalent of

  3. INVESTIGATION OF A N-BUTYL-N-(2-NITROXYETHYL)NITRAMINE (BUNENA) PROCESS: IDENTIFICATION OF PROCESS INTERMEDIATES, BY-PRODUCTS AND REACTION PATHWAYS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A process for N-butyl-N-(2-nitroxyethyl)nitramine (BuNENA) was investigated: Step 1 involves N-butyl-ethanolamine addition to 98% HNO3 to form a salt mixture; Step 2 is addition of acetic anhydride/acetyl chloride catalyst to the salt mixture. A number of potential intermediates, by-products, and ...

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

    PubMed Central

    2015-01-01

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

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

    PubMed

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

    2014-07-01

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

  6. 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

  7. Browning inhibition mechanisms by cysteine, ascorbic acid and citric acid, and identifying PPO-catechol-cysteine reaction products.

    PubMed

    Ali, Hussein M; El-Gizawy, Ahmed M; El-Bassiouny, Rawia E I; Saleh, Mahmoud A

    2015-06-01

    The titled compounds were examined as PPO inhibitors and antibrowning agents; their various mechanisms were investigated and discussed. All compounds reduced significantly both the browning process and PPO activity. Browning index gave strong correlation with PPO activity (r(2)?=?0.96, n?=?19) indicating that the browning process is mainly enzymatic. Ascorbic acid could reduce the formed quinone instantly to the original substrate (catechol) at high concentration (>1.5 %) while at lower concentrations acted as competitive inhibitor (KI?=?0.256?±?0.067 mM). Cysteine, at higher concentrations (?1.0 %), reacted with the resulted quinone to give a colorless products while at the low concentrations, cysteine worked as competitive inhibitor (KI?=?1.113?±?0.176 mM). Citric acid acted only as PPO non-competitive inhibitor with KI?=?2.074?±?0.363 mM. The products of PPO-catechole-cysteine reaction could be separation and identification by LC-ESI-MS. Results indicated that the product of the enzymatic oxidation of catechol, quinone, undergoes two successive nucleophilic attacks by cysteine thiol group. Cysteine was condensed with the resulted mono and dithiocatechols to form peptide side chains. PMID:26028748

  8. 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.

  9. An ion source with which ions produced by electrospray can be subjected to ion/molecule reactions at intermediate pressures (10-100 Torr). Deprotonation of polyprotonated peptides

    NASA Astrophysics Data System (ADS)

    Ikonomou, Michael G.; Kebarle, Paul

    1992-09-01

    Ions produced by electrospray at 1 atm pressure are transferred by means of a small bore capillary to a cylindrical reaction chamber of [approximate] 5 cm length which is attached to the inlet of a triple quadrupole mass spectrometer. The reaction chamber pressure can be maintained between 10 and 100 Torr and reagent gases can be introduced in flow through the chamber. When protonated bases BH+ are produced by electrospray, proton transfer to a stronger reagent gas base such as tributylamine (TBA) can be initiated in the reaction chamber. Also, polyprotonated peptides such as polyprotonated cytochrome C can be partially deprotonated in the presence of TBA. The intensities of the mass-analyzed ions after reactive changes are still very high, up to 5 × 105 counts s-1, and therefore the reaction chamber is very useful for reactive preparation of ions which are to be studied by collision-induced dissociation. The chamber is less well suited for studies of reaction rates and equilibria but the present preliminary design provides information on flow conditions inside the reactor and required changes that would make rate and equilibria studies possible. The question regarding the dependence of the rate constant, k, for proton transfer from multiply protonated peptides on the number of protons present is examined.

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

    NASA Astrophysics Data System (ADS)

    Onderwaater, Jacobus; ALICE Collaboration

    2015-05-01

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

  11. Radical intermediates generated in the reactions of L-arginine with hydroxyl radical and sulfate radical anion: A pulse radiolysis study

    NASA Astrophysics Data System (ADS)

    Ito, Takeo; Morimoto, Shota; Fujita, Shin-ichi; Nishimoto, Sei-ichi

    2009-04-01

    Reactions of L-arginine (Arg) with hydroxyl radical ( rad OH) and sulfate radical anion (SO 4- rad ) were kinetically investigated by the pulse radiolysis technique. Hydrogen abstraction from Arg by rad OH afforded redox chemically oxidizing, neutral, and reducing carbon-centered Arg radicals. Kinetic properties of the radicals indicated that the reducing species might include the ?-C-centered Arg radical and CO 2 radical anion. Similar transient spectra were observed in the SO 4- rad reaction with Arg, suggesting direct oxidation at the guanidino group is less likely.

  12. 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.

    -powered vehicles. To reduce this problem, among the alternatives commercially available today, liquid hydrogen has a good potential of be- coming the hydrogen fuel for vehicle transport in that it has a high mass densityHydrogen storage in LiAlH4 : Predictions of the crystal structures and reaction mechanisms

  13. Intermediates in reactions of copper(I) complexes with N-oxides: from the formation of stable adducts to oxo transfer.

    PubMed

    Hong, Sungjun; Gupta, Aalo K; Tolman, William B

    2009-07-20

    Reactions of copper(I) complexes of bidentate N-donor supporting ligands with pyridine- and trimethylamine-N-oxides or PhIO were explored. Key results include the identification of novel copper(I) N-oxide adducts, aryl substituent hydroxylation, and bis(mu-oxo)dicopper complex formation via a route involving oxo transfer. PMID:19425587

  14. Intermediate inputs and economic productivity.

    PubMed

    Baptist, Simon; Hepburn, Cameron

    2013-03-13

    Many models of economic growth exclude materials, energy and other intermediate inputs from the production function. Growing environmental pressures and resource prices suggest that this may be increasingly inappropriate. This paper explores the relationship between intermediate input intensity, productivity and national accounts using a panel dataset of manufacturing subsectors in the USA over 47 years. The first contribution is to identify sectoral production functions that incorporate intermediate inputs, while allowing for heterogeneity in both technology and productivity. The second contribution is that the paper finds a negative correlation between intermediate input intensity and total factor productivity (TFP)--sectors that are less intensive in their use of intermediate inputs have higher productivity. This finding is replicated at the firm level. We propose tentative hypotheses to explain this association, but testing and further disaggregation of intermediate inputs is left for further work. Further work could also explore more directly the relationship between material inputs and economic growth--given the high proportion of materials in intermediate inputs, the results in this paper are suggestive of further work on material efficiency. Depending upon the nature of the mechanism linking a reduction in intermediate input intensity to an increase in TFP, the implications could be significant. A third contribution is to suggest that an empirical bias in productivity, as measured in national accounts, may arise due to the exclusion of intermediate inputs. Current conventions of measuring productivity in national accounts may overstate the productivity of resource-intensive sectors relative to other sectors. PMID:23359736

  15. Studies with Flavin Analogs Provide Evidence That a Protonated Reduced FMN Is the Substrate-induced Transient Intermediate in the Reaction of Escherichia coli Chorismate Synthase

    Microsoft Academic Search

    S. Bornemann; Sandro Ghislai; Roger N. F. Thorneley

    1996-01-01

    Chorismate synthase catalyzes the 1,4-elimination of phosphate and the C-(6-pro-R) hydrogen from 5-enol- pyruvylshikimate 3-phosphate (EPSP) to generate cho- rismate. Although this reaction does not involve an overall change in redox state, the enzyme requires re- duced FMN. To investigate the role of the flavin in ca- talysis we have employed chemically modified flavins: 1- and 5-deaza-, 2- and 4-thio-,

  16. Implications of far-side dominance for the disagreement between distorted wave theory and well-matched intermediate energy (d, p) reactions

    Microsoft Academic Search

    E. J. Stephenson; R. C. Johnson; J. A. Tostevin; V. R. Cupps; J. D. Brown; C. C. Foster; J. A. Gering; W. P. Jones; D. A. Low; D. W. Miller; H. Nann; C. Olmer; A. K. Opper; P. Schwandt; J. W. Seubert; S. W. Wissink

    1986-01-01

    Distorted wave calculations of large ln-transfer (d, p) reactions near 90 MeV indicate that far-side dominance reduces the number of effective amplitudes at large angles to two or three, making many spin observables redundant. Comparisons of Ay with Ayy data for 116Sn(d, p)117Sn, and Ayy with py data for 66Zn(d, p)67Zn, do not confirm this expectation.

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

    PubMed

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

    2014-11-01

    Kinetic and DFT results for the carbonate catalysed Co(H2O)6(2+) + H2O2 Fenton-like reaction suggest a mechanism involving the formation of a cyclic transient, cyclic-(CO4)Co(II)(OOH)(H2O)2(-) that decomposes into Co(II)(H2O)(OOH)(OH)2 + CO3?(-), i.e. no OH? radicals are involved. Plausible biological implications are pointed out. PMID:25223650

  18. 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.

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

    SciTech Connect

    Sakai, H.; Yako, K. [University of Tokyo, Department of Physics, Hongo 7-3-1, Bunkyo, Tokyo 113-0033 (Japan)

    2009-08-26

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

  20. Proteomics of endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membranes from brefeldin A-treated HepG2 cells identifies ERGIC-32, a new cycling protein that interacts with human Erv46.

    PubMed

    Breuza, Lionel; Halbeisen, Regula; Jenö, Paul; Otte, Stefan; Barlowe, Charles; Hong, Wanjin; Hauri, Hans-Peter

    2004-11-01

    Cycling proteins play important roles in the organization and function of the early secretory pathway by participating in membrane traffic and selective transport of cargo between the endoplasmic reticulum (ER), the intermediate compartment (ERGIC), and the Golgi. To identify new cycling proteins, we have developed a novel procedure for the purification of ERGIC membranes from HepG2 cells treated with brefeldin A, a drug known to accumulate cycling proteins in the ERGIC. Membranes enriched 110-fold over the homogenate for ERGIC-53 were obtained and analyzed by mass spectrometry. Major proteins corresponded to established and putative cargo receptors and components mediating protein maturation and membrane traffic. Among the uncharacterized proteins, a 32-kDa protein termed ERGIC-32 is a novel cycling membrane protein with sequence homology to Erv41p and Erv46p, two proteins enriched in COPII vesicles of yeast. ERGIC-32 localizes to the ERGIC and partially colocalizes with the human homologs of Erv41p and Erv46p, which mainly localize to the cis-Golgi. ERGIC-32 interacts with human Erv46 (hErv46) as revealed by covalent cross-linking and mistargeting experiments, and silencing of ERGIC-32 by small interfering RNAs increases the turnover of hErv46. We propose that ERGIC-32 functions as a modulator of the hErv41-hErv46 complex by stabilizing hErv46. Our novel approach for the isolation of the ERGIC from BFA-treated cells may ultimately lead to the identification of all proteins rapidly cycling early in the secretory pathway. PMID:15308636

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

    SciTech Connect

    Oganessian, Yu. Ts.; Abdullin, F. Sh.; Dmitriev, S. N.; Itkis, M. G.; Lobanov, Yu. V.; Mezentsev, A. N.; Polyakov, A. N.; Sagaidak, R. N.; Shirokovsky, I. V.; Subbotin, V. G.; Sukhov, A. M.; Tsyganov, Yu. S.; Utyonkov, V. K.; Voinov, A. A.; Vostokin, G. K. [Joint Institute for Nuclear Research, RU-141980 Dubna (Russian Federation); Bailey, P. D.; Benker, D. E.; Ezold, J. G.; Porter, C. E.; Riley, F. D. [Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States)

    2011-05-15

    The heaviest isotopes of elements Z=117 to Z=105, {sup 294}117, {sup 293}117, {sup 290}115, {sup 289}115, {sup 286}113, {sup 285}113, {sup 282}Rg, {sup 281}Rg, {sup 278}Mt, {sup 274}Bh, and {sup 270}Db, were identified by means of the Dubna gas-filled recoil separator among the products of the {sup 249}Bk + {sup 48}Ca reaction. The details of the observed six decay chains, indicating the production and decay of isotopes {sup 293}117 and {sup 294}117, are presented and discussed. The decay energies and resulting half-lives of these new nuclei show a strong rise of stability with increasing neutron number, validating the concept of the island of enhanced stability for superheavy nuclei [Oganessian et al., Phys. Rev. Lett. 104, 142502 (2010)].

  2. Intermediate uveitis.

    PubMed

    Lai, Wico W; Pulido, Jose S

    2002-09-01

    The cause of intermediate uveitis remains unknown. It is important to rule out other causes of the condition before initiating therapy. Many patients presenting with a mild form of the disease and who have good visual acuity may not require treatment. Those with decreased vision because of inflammation or cystoid macular edema may require periocular injections or systemic administration of corticosteroids (Fig. 2). Those who develop recalcitrant disease and those who experience severe side effects from the steroid therapy may require other immunosuppressive agents. Close monitoring of systemic side effects is required. Laser photocoagulation or cryotherapy of the peripheral retina is useful in patients who develop neovascularization of the vitreous base, in those who are not responsive to periocular injections, and in those who develop severe side effects from corticosteroids. This should be considered before starting systemic immunosuppressive agents. Pars plana vitrectomy with or without cryotherapy or laser photocoagulation is indicated in patients with marked vitreous debris, cystoid macular edema, and in those who develop a vitreous hemorrhage. PMID:12434479

  3. One-electron transfer reactions of diquat radical to different reduction intermediates of oxygen. Formation of hydroxyl radical and electronically excited states

    SciTech Connect

    Mira, D.; Brunk, U.; Boveris, A.; Cadenas, E. (Univ. of Linkoeping (Sweden))

    1988-01-01

    The one-electron transfer activation of DQ++ by microsomal fractions comprises an aerobic phase and an anaerobic phase. The aerobic phase is characterized by O2 consumption, formation of electronically excited states with main emission below 600 nm, and H2O2 formation. The anaerobic phase is characterized by H2O2 consumption, DQ+ accumulation, HO. formation, and also electronically excited state formation with main emission beyond 600 nm. Superoxide dismutase abolishes the photoemission during the aerobic phase, whereas it has no effect on the photoemission originating during the anaerobic phase. The hydroxylation products of the aromatic compound salicylate, mainly 2,3- and 2,5-dihydroxybenzoic acids--indicative of the occurrence of HO.-, were detected by h.p.l.c. with oxidative electrochemical detection during the anaerobic phase, but not during the aerobic phase. Neither H2O2 consumption nor HO. are prevented by desferrioxamine. These experimental observations are interpreted on the grounds of two main electron-transfer reactions of DQ.+: under aerobic conditions, two one-electron transfer steps to molecular O2 and O2.- to yield H2O2. Under anaerobic conditions, one-electron transfer step to contaminating iron or any ferrioxamine formed to a ferrous complex which can support a Fenton-like reduction of H2O2 with formation of HO.. The toxicological relevance for the occurrence of such reactions is also discussed in terms of the formation of electronically excited states.

  4. Tetraphosphabenzenes Obtained via a Triphosphacyclobutadiene Intermediate

    E-print Network

    Cummins, Christopher C.

    An acyl triphosphirene ligand transfers an O?atom to Nb to liberate the putative triphosphacyclobutadiene intermediate [RCP3{W(CO)5}2], which engages in [2+4]-cycloaddition reactions with an organic diene and a phosphaalkyne ...

  5. 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.

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

    PubMed

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

    2012-11-29

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

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

    SciTech Connect

    Halabi, Ghina M.; El Eid, Mounib F. [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.

  8. Intermediate mass fragment production in intermediate energy nuclear reactions

    SciTech Connect

    Fields, D.E.

    1992-01-01

    A systematic study of two systems was performed over a large range of bombarding energy. The systems [sup 14]N + [sup nat]Ag and [sup 14]N + [sup 197]Au were examined by measuring inclusive IMF energy spectra, angular distributions and absolute cross-sections with projectile energies from 20 MeV/A to 100 MeV/A. The experiments were performed at the National Superconducting Cyclotron Laboratory at Michigan State Univ. and analyzed at the Indiana Univ. Cyclotron Facility. The experiments showed three distinguishable sources of IMF emission: (1) emission from an equilibrated source with temperatures and velocities near those of a fusion-like residue, (2) emission on a fast time scale resulting in energy spectra with harder slopes than expected and having a strongly forward peaked angular distribution, and (3) emission from a projectile-like source for fragments near or below the projectile mass and charge with energy spectra peaked near the beam velocity and important only inside the grazing angle of the beam. In order to tag IMFs with information about their source, an experiment was performed at the Indiana Univ. Cyclotron Facility with [sup 3]He beams of 270 MeV incident energy on a [sup 232]Th target. Two detection systems were employed to gather the necessary information: (1) two arrays of segmented silicon detectors were placed on either side of the beam to detect the angle, energy, and time-of-flight of coincident fission fragments, and (2) eight ion-chamber/silicon/scintillator telescopes were distributed at angles from 20[degrees] to 160[degrees] in the plane of the fission-fragment detectors to detect coincident IMFs and low energy light charged particles. The author has determined the amount of linear momentum transferred to the emitting source and can deduce the amount of excitation energy deposited in the system of interest. This information can give new insight into the mechanism for complex fragment emission and the decay of hot nuclear matter.

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2001-03-01

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

  11. Light induced radical pair intermediates in photosynthetic reaction centres in contact with an observer spin label: spin dynamics and effects on transient EPR spectra

    NASA Astrophysics Data System (ADS)

    Salikhov, Kev M.; Zech, Stephan G.; Stehlik, Dietmar

    A novel strategy is discussed using site directed spin labelling to study the electron transfer process in photosynthetic reaction centres. An algorithm is presented for numerical simulations of the time resolved EPR spectra of radical pair states in the presence of an observer spin label. This algorithm accounts for spin dynamics, charge recombination and relaxation processes. It is shown that satisfactory agreement between experimental and simulated EPR spectra of the first stabilized radical pair state in photosystem I is achieved for various microwave frequencies. Transient EPR spectra for the radical pair state P •+Q •- in photosystem I were simulated for various distances and positions of the observer spin label with respect to the acceptor quinone molecule. It is shown that distances up to more than 20 Å give rise to observable changes in the transient EPR spectra. Both the additional spin-spin coupling between the quinone radical and the label and the polarization transfer processes contribute to the changes. Furthermore, the shape and intensity of the EPR spectrum of the spin label is altered by the coupling with the radical pair spins for distances up to 25 Å. Experiments on site directed spin labelled photosystem I are thus expected to provide valuable information on the dynamics of electron transfer in photosystem I.

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

    SciTech Connect

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

    1987-03-26

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

  13. 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

  14. 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

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

    2013-12-01

    Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason-Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the ?-phosphate site. Phosphorus-31 NMR spectroscopy ((31)P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue ?,?-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

  15. 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

  16. Propene oxidation at low and intermediate temperatures

    SciTech Connect

    Wilk, R.D.; Cernansky, N.P. (Drexel Univ., Philadelphia, PA (USA). Dept. of Mechanical Engineering); Pitz, W.J.; Westbrook, C.K. (Lawrence Livermore National Lab., CA (USA))

    1989-08-01

    A detailed chemical kinetic mechanism for propene oxidation is developed and used to model reactions in a static reactor at temperatures of 530-740 {Kappa}, equivalence ratios of 0.8-2.0, and a pressure of 600 torr. Modeling of hydrocarbon oxidation in this temperature range is important for the validation of detailed models to be used for performing calculations related to automotive engine knock. The model predicted induction periods and species concentrations for all the species and all conditions measured experimentally in the static reactor. Overall, the calculated concentrations of carbon monoxide and acetaldehyde agreed well with those measured. The calculated concentrations of ethene are low compared to the experimental measurements, and the calculated concentrations of the formaldehyde are high. Agreement for concentrations of carbon dioxide, methane, methanol, acrolein, and propene oxide is mixed. The characteristic s-shape of the fuel concentration history is well predicted. Modeling calculations identified some of the key reaction steps at the present conditions. Addition of OH to propene and H-atom abstraction by OH from propene are important steps in determining the subsequent distributions of intermediate products, such as acetaldehyde, acrolein and formaldehyde. Allyl radicals are very abundant in propene oxidation, and the primary steps found to be responsible for their consumption are reaction with HO/sub 2/ and CH/sub 3/O/sub 2/.

  17. Degradation of methyl bromide and methyl chloride in soil microcosms: Use of stable C isotope fractionation and stable isotope probing to identify reactions and the responsible microorganisms

    NASA Astrophysics Data System (ADS)

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

    2004-08-01

    Bacteria in soil microcosm experiments oxidized elevated levels of methyl chloride (MeCl) and methyl bromide (MeBr), the former compound more rapidly than the latter. MeBr was also removed by chemical reactions while MeCl was not. Chemical degradation dominated the early removal of MeBr and accounted for more than half of its total loss. Fractionation of stable carbon isotopes during chemical degradation of MeBr resulted in a kinetic isotope effect (KIE) of 59 ± 7‰. Soil bacterial oxidation dominated the later removal of MeBr and MeCl and was characterized by different KIEs for each compound. The KIE for MeBr oxidation was 69 ± 9‰ and the KIE for MeCl oxidation was 49 ± 3‰. Stable isotope probing revealed that different populations of soil bacteria assimilated added 13C-labeled MeBr and MeCl. The identity of the active MeBr and MeCl degrading bacteria in soil was determined by analysis of 16S rRNA gene sequences amplified from 13C-DNA fractions, which identified a number of sequences from organisms not previously thought to be involved in methyl halide degradation. These included Burkholderia, the major clone type in the 13C-MeBr fraction, and Rhodobacter, Lysobacter and Nocardioides the major clone types in the 13C-MeCl fraction. None of the 16S rRNA gene sequences for methyl halide oxidizing bacteria currently in culture (including Aminobacter strain IMB-1 isolated from fumigated soil) were identified. Functional gene clone types closely related to Aminobacter spp. were identified in libraries containing the sequences for the cmuA gene, which codes for the enzyme known to catalyze the initial step in the oxidation of MeBr and MeCl. The cmuA gene was limited to members of the alpha-Proteobacteria whereas the greater diversity demonstrated by the 16S rRNA gene may indicate that other enzymes catalyze methyl halide oxidation in different groups of bacteria.

  18. 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.

  19. 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.

  20. Unraveling curcumin degradation: autoxidation proceeds through spiroepoxide and vinylether intermediates en route to the main bicyclopentadione.

    PubMed

    Gordon, Odaine N; Luis, Paula B; Sintim, Herman O; Schneider, Claus

    2015-02-20

    Curcumin is a dietary anti-inflammatory and chemopreventive agent consisting of two methoxyphenol rings connected by a conjugated heptadienedione chain. Curcumin is unstable at physiological pH and rapidly degrades in an autoxidation reaction to a major bicyclopentadione product in which the 7-carbon chain has undergone oxygenation and double cyclization. Early degradation products (but not the final bicyclopentadione) mediate topoisomerase poisoning and possibly many other activities of curcumin, but it is not known how many and what autoxidation products are formed, nor their mechanism of formation. Here, using [(14)C2]curcumin as a tracer, seven novel autoxidation products, including two reaction intermediates, were isolated and identified using one- and two-dimensional NMR and mass spectrometry. The unusual spiroepoxide and vinylether reaction intermediates are precursors to the final bicyclopentadione product. A mechanism for the autoxidation of curcumin is proposed that accounts for the addition and exchange of oxygen that have been determined using (18)O2 and H2(18)O. Several of the by-products are formed from an endoperoxide intermediate via reactions that are well precedented in lipid peroxidation. The electrophilic spiroepoxide intermediate formed a stable adduct with N-acetylcysteine, suggesting that oxidative transformation is required for biological effects mediated by covalent adduction to protein thiols. The spontaneous autoxidation distinguishes curcumin among natural polyphenolic compounds of therapeutic interest; the formation of chemically diverse reactive and electrophilic products provides a novel paradigm for understanding the polypharmacological effects of curcumin. PMID:25564617

  1. 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

  2. Hybrid-polymerase chain reaction to identify novel target genes of miR-134 in paclitaxel resistant human ovarian carcinoma cells

    PubMed Central

    SHUANG, TING; WANG, MIN; CHANG, SHUANG

    2015-01-01

    Increasing evidence has shown that miR-134 is involved in the promotion of tumorigenesis and chemoresistance. However, whether miR-134 participates in ovarian cancer chemoresistance and its functional targets still remains unclear. The objective of this study was to apply hybrid-polymerase chain reaction (PCR) to screen target genes of miR-134 in ovarian carcinoma paclitaxel resistant SKOV3-TR30 cells, and to provide a number of novel targets of miR-134 for further study of ovarian cancer paclitaxel resistance. The current study found that miR-134 was decreased in SKOV3-TR30 cells compared with the parental SKOV3 cell line. By applying hybrid-PCR, 8 putative target genes of miR-134 in SKOV3-TR30 cells were identified, including C16orf72, PNAS-105, SRM, VIM, F-box protein 2, GAPDH, PRPF6 and RPL41. Notably, the target sites of VIM and PRPF6 were not located in 3?untranslated region, but rather in the coding sequence region. By conducting a luciferase reporter assay, miR-134 was demonstrated to recognize the putative binding sites of these target genes including VIM and PRPF6. Transfecting SKOV3-TR30 cells with miR-134 mimic and performing reverse transcription-PCR in addition to western blot analysis confirmed that miR-134 regulates vimentin expression at a post transcriptional level. This finding provides a novel perspective for studying the mechanism of miR-134/mRNA interaction. In conclusion, this study was the first to apply an effective method of hybrid-PCR to screen putative target mRNAs of miR-134 in paclitaxel resistant SKOV3-TR30 cells and indicate that miR-134 may contribute to the induction of SKOV3-TR30 paclitaxel resistance by targeting these genes. PMID:26137169

  3. Some Intermediate-Level Violin Concertos.

    ERIC Educational Resources Information Center

    Abramson, Michael

    1997-01-01

    Contends that many violin students attempt difficult concertos before they are technically or musically prepared. Identifies a variety of concertos at the intermediate and advanced intermediate-level for students to study and master before attempting the advanced works by Bach and Mozart. Includes concertos by Vivaldi, Leclair, Viotti, Haydn,…

  4. 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.

  5. Membrane Fusion Intermediates via Directional and Full Assembly of the SNARE Complex

    PubMed Central

    Hernandez, Javier M.; Stein, Alexander; Behrmann, Elmar; Riedel, Dietmar; Cypionka, Anna; Farsi, Zohreh; Walla, Peter J.; Raunser, Stefan; Jahn, Reinhard

    2013-01-01

    Cellular membrane fusion is thought to proceed through intermediates including docking of apposed lipid bilayers, merging of proximal leaflets to form a hemifusion diaphragm, and fusion pore opening. A membrane-bridging four-helix complex of soluble N-ethylmaleimide–sensitive factor attachment protein receptors (SNAREs) mediates fusion. However, how assembly of the SNARE complex generates docking and other fusion intermediates is unknown. Using a cell-free reaction we identified intermediates visually and then arrested the SNARE fusion machinery when fusion was about to begin. Partial and directional assembly of SNAREs tightly docked bilayers, but efficient fusion and an extended form of hemifusion required assembly beyond the core complex to the membrane-connecting linkers. We propose that straining of lipids at the edges of an extended docking zone initiates fusion. PMID:22653732

  6. 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

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  8. 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

  9. 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.

  10. Using metal-catalyzed oxidation reactions and mass spectrometry to identify amino acid residues within 10 Å of the metal in Cu-binding proteins

    Microsoft Academic Search

    Juma D. Bridgewater; Jihyeon Lim; Richard W. Vachet

    2006-01-01

    Metal-catalyzed oxidation (MCO) reactions and mass spectrometry (MS) can be used together to determine the amino acids bound\\u000a to Cu in a metalloprotein. Selective oxidation of only amino acids bound to Cu during the MCO\\/MS approach relies on proper\\u000a choice of the types and concentrations of the reducing and oxidizing agents. We show here that if these MCO reagent concentrations

  11. rpoB Gene Mutations in Rifampin-Resistant Mycobacterium tuberculosis Identified by Polymerase Chain Reaction Single-Stranded Conformational Polymorphism

    Microsoft Academic Search

    Miriam Bobadilla-del-Valle; Alfredo Ponce-de-Leon; Catalina Arenas-Huertero; Gilberto Vargas-Alarcon; Midori Kato-Maeda; Peter M. Small; Patricia Couary; Guillermo M. Ruiz-Palacios; Jose Sifuentes-Osornio

    2001-01-01

    The use of polymerase chain reaction-single-stranded conformational poly- morphism (PCR-SSCP) to study rpoB gene mutations in rifampin-resistant (RIFr) Mycobacterium tuberculosis has yielded contradictory results. To determine the sensitivity of this method, we analyzed 35 RIFr strains and 11 rifampin-susceptible (RIFs) strains, using the DNA sequencing of the core region of rpoB for comparison. Of the RIFr, 24 had a PCR-SSCP

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

    PubMed

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

    1993-04-01

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

  13. 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.

  14. Intermediates in the Formation of Aromatics in Hydrocarbon Combustion

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  15. 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

  16. Intermediate band solar cells

    Microsoft Academic Search

    Antonio Marti

    2010-01-01

    Intermediate band (IB)solar cells aim to exploit the energy of below bandgap energy photons in solar cells. They are based in a material that, in addition to the conventional conduction and valence bands, have an electronic band (named intermediate band) located inside the bandgap and separated from the conduction and valence band by a null density of states. The theoretical

  17. Versatile Electrochemical C?H Amination via Zincke Intermediates.

    PubMed

    Waldvogel, Siegfried R; Möhle, Sabine

    2015-05-26

    Simply by applying electricity, the amination reaction of a broad variety of arenes, heteroarenes, and benzylic substrates is achieved. Pyridine serves as the nitrogen source and the intermediate cationic species are well-protected from over-oxidation. PMID:25967883

  18. GC-MS Method for the Quantitation of Carbohydrate Intermediates in Glycation Systems.

    PubMed

    Milkovska-Stamenova, Sanja; Schmidt, Rico; Frolov, Andrej; Birkemeyer, Claudia

    2015-07-01

    Glycation is a ubiquitous nonenzymatic reaction of carbonyl compounds with amino groups of peptides and proteins, resulting in the formation of advanced glycation end-products (AGEs) and thereby affecting the properties and quality of thermally processed foods. In this context, mechanisms of the Maillard reaction of proteins need to be understood; that is, glycation products and intermediates (?-dicarbonyls and sugars) need to be characterized. Although the chemical analysis of proteins, peptides, and ?-dicarbonyls is well established, sensitive and precise determination of multiple sugars in glycation mixtures is still challenging. This paper presents a gas chromatography-mass spectrometry (GC-MS) method for absolute quantitation of 22 carbohydrates in the model of phosphate-buffered glycation systems. The approach relied on the removal of the phosphate component by polymer-based ion exchange solid phase extraction (SPE) followed by derivatization of carbohydrates and subsequent GC-MS analysis. Thereby, baseline separation for most of the analytes and detection limits of up to 10 fmol were achieved. The method was successfully applied to the analysis of in vitro glycation reactions. Thereby, at least seven sugar-related Maillard reaction intermediates could be identified and quantified. The most abundant reaction product was d-fructose, reaching 2.70 ± 0.12 and 2.38 ± 0.66 mmol/L after 120 min of incubation in the absence and presence of the model peptide, respectively. PMID:26043919

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

    PubMed

    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

  20. 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

  1. 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

  2. Epidemiology of Imported Cutaneous Leishmaniasis at the Hospital for Tropical Diseases, London, United Kingdom: Use of Polymerase Chain Reaction to Identify the Species

    PubMed Central

    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

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

    PubMed

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

    2012-01-01

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

  4. Multifragmentation in intermediate energy heavy ion collisions

    SciTech Connect

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

    1986-04-14

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

  5. Long-lived glycosyl-enzyme intermediate mimic produced by formate re-activation of a mutant endoglucanase lacking its catalytic nucleophile.

    PubMed Central

    Viladot, J L; Canals, F; Batllori, X; Planas, A

    2001-01-01

    The mutant E134A 1,3-1,4-beta-glucanase from Bacillus licheniformis, in which the catalytic nucleophilic residue has been removed by mutation to alanine, has its hydrolytic activity rescued by exogenous formate in a concentration-dependent manner. A long-lived alpha-glycosyl formate is detected and identified by (1)H-NMR and matrix-assisted laser desorption ionization-time-of-flight-MS. The intermediate is kinetically competent, since it is, at least partially, enzymically hydrolysed, and able to act as a glycosyl donor in transglycosylation reactions. This transient compound represents a true covalent glycosyl-enzyme intermediate mimic of the proposed covalent intermediate in the reaction mechanism of retaining glycosidases. PMID:11256951

  6. 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...

  7. 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

  8. Intermediate phase evolution in YBCO thin films grown by the TFA process

    Microsoft Academic Search

    K. Zalamova; A. Pomar; A. Palau; T. Puig; X. Obradors

    2010-01-01

    The YBCO thin film growth process from TFA precursors involves a complex reaction path which includes several oxide, fluoride and oxyfluoride intermediate phases, and the final microstructure and properties of the films are strongly influenced by the morphological and chemical evolution of these intermediate phases. In this work we present a study of the evolution of the intermediate phases involved

  9. METHODS TO IDENTIFY YEAST

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Yeasts are commonly identified from either phenotype or, more recently, from diagnostic gene sequences. Methods based on phenotype include fermentation reactions on a select set of sugars and growth responses on various carbon and nitrogen sources or on other diagnostic compounds. Isolates are fur...

  10. Lens Intermediate Filaments

    PubMed Central

    2009-01-01

    The ocular lens assembles two separate Intermediate Filament systems sequentially with differentiation. Canonical 8–11 nm IFs composed of Vimentin are assembled in lens epithelial cells and younger fiber cells, while the fiber cell-specific Beaded Filaments are switched on as fiber cell elongation initiates. Some of the key features of both filament systems are reviewed. PMID:19071112

  11. 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…

  12. MATERIALS FOR INTERMEDIATE TELUGU.

    ERIC Educational Resources Information Center

    KELLEY, GERALD B.

    ONE OF THE FOUR DRAVIDIAN LANGUAGES RECOGNIZED BY THE INDIAN CONSTITUTION OF 1950 AS OFFICIAL LANGUAGES OF THE COUNTRY, TELUGU IS SPOKEN BY 42 MILLION PEOPLE IN ANDHRA PRADESH. THESE INSTRUCTIONAL MATERIALS ARE DESIGNED FOR THE INTERMEDIATE STUDENT OF TELUGU AND ARE DIVIDED INTO NEWSPAPER READINGS AND DIALOGUES OF EVERYDAY CONVERSATION. SUBJECTS…

  13. Intermediate Pashto. Teachers' Manual.

    ERIC Educational Resources Information Center

    Tegey, Habibullah; Robson, Barbara

    The teachers' guide to the "Intermediate Pashto" textbook (FL 019 797) contains notes for the teacher on each of the fourteen units and sub-sections of the textbook. Unit and section headings are in English and Pashto; virtually all text is in Pashto. (MSE)

  14. Station Identifier

    Microsoft Academic Search

    J. Stepan

    1968-01-01

    This paper describes an end office tributary identifier which sends to a toll center the calling subscriber's directory number. It is arranged to interface with the Bell System's centralized automatic message accounting (CAMA) centers. The electronic identifier operates on either a terminal per line, a terminal per station, or mixed basis. In operating, it feeds an ac signal on the

  15. Intermediates in serine recombinase-mediated site-specific recombination.

    PubMed

    Marshall Stark, W; Boocock, Martin R; Olorunniji, Femi J; Rowland, Sally-J

    2011-04-01

    Site-specific recombinases are enzymes that promote precise rearrangements of DNA sequences. They do this by cutting and rejoining the DNA strands at specific positions within a pair of target sites recognized and bound by the recombinase. One group of these enzymes, the serine recombinases, initiates strand exchange by making double-strand breaks in the DNA of the two sites, in an intermediate built around a catalytic tetramer of recombinase subunits. However, these catalytic steps are only the culmination of a complex pathway that begins when recombinase subunits recognize and bind to their target sites as dimers. To form the tetramer-containing reaction intermediate, two dimer-bound sites are brought together by protein dimer-dimer interactions. During or after this initial synapsis step, the recombinase subunit and tetramer conformations change dramatically by repositioning of component subdomains, bringing about a transformation of the enzyme from an inactive to an active configuration. In natural serine recombinase systems, these steps are subject to elaborate regulatory mechanisms in order to ensure that cleavage and rejoining of DNA strands only happen when and where they should, but we and others have identified recombinase mutants that have lost dependence on this regulation, thus facilitating the study of the basic steps leading to catalysis. We describe how our studies on activated mutants of two serine recombinases, Tn3 resolvase and Sin, are providing us with insights into the structural changes that occur before catalysis of strand exchange, and how these steps in the reaction pathway are regulated. PMID:21428950

  16. 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

  17. 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...

  18. 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.

  19. Measurements of the {sup 116}Cd(p,n) and {sup 116}Sn(n,p) reactions at 300 MeV for studying Gamow-Teller transition strengths in the intermediate nucleus of the {sup 116}Cd double-{beta} decay

    SciTech Connect

    Sasano, M.; Kuboki, H.; Sekiguchi, K. [RIKEN Nishina Center, Wako, Saitama 351-0198 (Japan); Sakai, H.; Yako, K.; Miki, K.; Noji, S. [Department of Physics, University of Tokyo, Bunkyo, Tokyo 113-0033 (Japan); Wakasa, T.; Dozono, M.; Fujita, K. [Department of Physics, Kyushu University, Higashi, Fukuoka 812-8581 (Japan); Greenfield, M. B. [Department of Physics, International Christian University, Mitaka, Tokyo 181-8585 (Japan); Hatanaka, K.; Okamura, H.; Tamii, A. [Research Center for Nuclear Physics (RCNP), Osaka university, Ibaraki, Osaka 567-0047 (Japan); Kawabata, T. [Department of Physics, Kyoto University, Sakyo, Kyoto 605-8502 (Japan); Maeda, Y. [Department of Applied Physics, University of Miyazaki, Gakuen Kibanadai-nishi, Miyazaki, 889-2192 Japan (Japan); Sakemi, Y. [Cyclotron and Radioisotope Center, Tohoku University, Aoba-ku, Sendai 980-8578 (Japan); Shimizu, Y.; Uesaka, T.; Sasamoto, Y. [Center for Nuclear Study, University of Tokyo, Bunkyo, Tokyo 113-0033 (Japan)] (and others)

    2009-11-09

    The double differential cross sections for the {sup 116}Cd(p,n) and {sup 116}Sn(n,p) reactions at 300 MeV have been measured over a wide excitation-energy region including Gamow-Teller (GT) giant resonance (GTGR) for studying GT transition strengths in the intermediate nucleus of the {sup 116}Cd double-{beta} decay, namely {sup 116}In. A large amount of the strengths in the {beta}{sup +} direction has been newly found in the energy region up to 30 MeV, which may imply that the GT strengths in the GTGR region contribute to the nuclear matrix element of the two-neutrino double-{beta} decay.

  20. A Mechanochemical Switch to Control Radical Intermediates

    PubMed Central

    2015-01-01

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

  1. Coke formation and minimisation during steam reforming reactions

    Microsoft Academic Search

    D. L. Trimm

    1997-01-01

    The formation of coke during the steam reforming of light hydrocarbons results mainly from catalytic reactions. It is believed that the process is endemic to steam reforming in that the same intermediates are involved in the main reaction as are involved in coking. As a result, control of coking depends on the control of the kinetics of intermediate reactions. On

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

    SciTech Connect

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

    2008-01-01

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

  3. Pyrolysis of 9-methylenespiro(3. 5)nona-5,7-diene: A route to benzo-2-hexene-1,6-diyl, a putative intermediate in the retro-Diels-Alder reaction of tetralin

    SciTech Connect

    Gajewski, J.J.; Paul, G.C. (Indiana Univ., Bloomington (United States))

    1990-07-20

    A precursor to the 1,6-biradical potentially formed in the retro-Diels-Alder reaction of tetralin, namely, 5-methylenespiro(bicyclo(2.2.1)hept-2-ene-6,1{prime}-cyclobutan)-7-one (9) has been prepared and found to give tetralin and o-allyltoluene upon pyrolysis in solution below 100C and upon flash vacuum pyrolysis around 250C. The product ratio changes from 1:1 to 6:1 at higher temperatures. Rate-determining loss of CO from 9 to give 9-methylenespiro(3.5)nona-5,7-diene, 2, has been demonstrated by trapping the triene with N-methyl- and N-phenyltriazolinedione in a reaction whose rate is independent of trapping agent concentration. The kinetics for loss of ketone, 9, gave log k (s{sup {minus}1}) = 14.628 {plus minus} 0.038-(30.554 {plus minus} 0.064)/2.3RT. Pyrolysis of cis-cyn(to methylene)- and trans-1,2-dimethyl-9-methylenespiro(3.5)nona-5,7-diene gives the vinylcyclobutane rearrangement product, 2,3-dimethyltetralin, with a 4:1 and 2.7:1, respectively, preference for retention over inversion at the migrating carbon. Hydrogen shift products are also formed and by highly ordered transition states. One of these hydrogen shifts involves an unprecedented shift from the carbon remote from the vinyl group.

  4. Reaction coordinates for electron transfer reactions

    SciTech Connect

    Rasaiah, Jayendran C. [Department of Chemistry, University of Maine, Orono, Maine 04469 (United States); Zhu Jianjun [Department of Chemistry, State University of New York, Stonybrook, New York 11790 (United States) and Department of Chemistry, Henan Normal University, Xinxiang, Henan (China)

    2008-12-07

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

  5. 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.

  6. 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!

  7. Identify Symmetry

    NSDL National Science Digital Library

    Mrs. Neubert

    2011-03-03

    This unit will teach you how to identify symmetry in everyday objects and mathematical shapes in lines and rotational symmetry. What is line symmetry? Click on the link to find out: Line Symmetry Here is a line activity to see if you understand it: Line Symmetry Class Zone See if you understand the concepts by doing the following quiz: Line Symmetry Work Now for rotational symmetry: Rotational Symmetry See if you understand rotational symmetry by taking this quiz: Rotational Symmetry Work ...

  8. 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

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

    2010-09-01

    Acetyl-CoA synthase (ACS) catalyzes the synthesis of acetyl-CoA from CO, coenzyme A (CoA), and a methyl group from the CH(3)-Co(3+) site in the corrinoid iron-sulfur protein (CFeSP). These are the key steps in the Wood-Ljungdahl pathway of anaerobic CO and CO(2) 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 [Fe(4)S(4)](2+)-(Ni(p)(+)-CO)-(Ni(d)(2+)), where Ni(p) and Ni(d) represent the Ni centers in the A-cluster that are proximal and distal to the [Fe(4)S(4)](2+) cluster, respectively. This well-characterized Ni(p)(+)-CO intermediate is often called the NiFeC species. Photolysis of the Ni(p)(+)-CO state generates a novel Ni(p)(+) species (A(red)*) with a rhombic electron paramagnetic resonance spectrum (g values of 2.56, 2.10, and 2.01) and an extremely low (1 kJ/mol) barrier for recombination with CO. We suggest that the photolytically generated A(red)* species is (or is similar to) the Ni(p)(+) species that binds CO (to form the Ni(p)(+)-CO species) and the methyl group (to form Ni(p)-CH(3)) in the ACS catalytic mechanism. The results provide support for a binding site (an "alcove") for CO near Ni(p), indicated by X-ray crystallographic studies of the Xe-incubated enzyme. We propose that, during catalysis, a resting Ni(p)(2+) state predominates over the active Ni(p)(+) species (A(red)*) that is trapped by the coupling of a one-electron transfer step to the binding of CO, which pulls the equilibrium toward Ni(p)(+)-CO formation. PMID:20669901

  9. Learning to Predict Chemical Reactions

    PubMed Central

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

    2011-01-01

    Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles respectively are not high-throughput, are not generalizable or scalable, or lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry dataset consisting of 1630 full multi-step reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval, problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of non-productive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system is generalizable, making reasonable predictions over reactants and conditions which the rule-based expert does not handle. A web interface to the machine learning based mechanistic reaction predictor is accessible through our chemoinformatics portal (http://cdb.ics.uci.edu) under the Toolkits section. PMID:21819139

  10. 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

  11. Surface intermediates in selective olefin oxidation and ammoxidation

    SciTech Connect

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

    1983-02-01

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

  12. 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

  13. Identifying Species

    NSDL National Science Digital Library

    Michael DiSpezio

    This two part activity will allow students to investigate biological diversity in the area of their school. They will first prepare a taxonomic key to distinguish between the four insects or spiders that they have selected. All of the keys are combined and students then perform a transect study of a neighborhood field or school playing ground. Finally as a class students will compile a list of the animals and plants that are found within a mile of their school. They may need to use field guides, local resources, taxonomic keys, and species lists to help identify these organisms. Once they have compiled their list they will organize the species into the taxonomic groups they have studied.

  14. Stabilizing the Hammick intermediate.

    PubMed

    Hollóczki, Oldamur; Nyulászi, László

    2008-07-01

    The possible stabilization of pyridine-2-ylidene has been investigated at B3LYP/6-31+G* and B3LYP/6-311+G** levels of theory. The aromaticity of this compound is a significant contributor to its stability (ISE(c) = 24-27 kcal mol(-1), Bird index = 77, NICS(0) = -6.8 ppm, NICS(1) = -9.1 ppm; all about 80% of those for the H-shift isomer pyridine). The stabilization energy of the carbene (measured by an appropriate isodesmic reaction) can be influenced by the substitution at nitrogen with bulky groups, and at the carbon atom by amino groups. Considering possible competitive deprotonation reactions of the most likely synthetic route, 1j, 1k, and 1L are suggested as synthesizeable new stable carbenes. PMID:18543975

  15. 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.

  16. The Bicyclic Intermediate Structure Provides Insights into the Desuccinylation Mechanism of Human Sirtuin 5 (SIRT5)*

    PubMed Central

    Zhou, Yeyun; Zhang, Hongmin; He, Bin; Du, Jintang; Lin, Hening; Cerione, Richard A.; Hao, Quan

    2012-01-01

    Sirtuins are pivotal regulators in various cellular processes, including transcription, DNA repair, genome stability, and energy metabolism. Their functions have been generally attributed to NAD-dependent deacetylase activity. However, human SIRT5 (sirtuin 5), which has been reported to exhibit little deacetylase activity, was recently identified as an NAD-dependent demalonylase and desuccinylase. Biochemical studies suggested that the mechanism of SIRT5-catalyzed demalonylation and desuccinylation is similar to that of deacetylation catalyzed by other sirtuins. Previously, we solved the crystal structure of a SIRT5-succinyl-lysine peptide-NAD complex. Here, we present two more structures: a binary complex of SIRT5 with an H3K9 succinyl peptide and a binary complex of SIRT5 with a bicyclic intermediate obtained by incubating SIRT5-H3K9 thiosuccinyl peptide co-crystals with NAD. To our knowledge, this represents the first bicyclic intermediate for a sirtuin-catalyzed deacylation reaction that has been captured in a crystal structure, thus providing unique insights into the reaction mechanism. The structural information should benefit the design of specific inhibitors for SIRT5 and help in exploring the therapeutic potential of targeting sirtuins for treating human diseases. PMID:22767592

  17. Microsurgical intermediate subinguinal varicocelectomy.

    PubMed

    Lee, Joo Yong; Yu, Ho Song; Ham, Won Sik; Kang, Dong Hyuk; Kim, Kyu Hyun; Chung, Doo Yong; Cho, Kang Su

    2014-01-01

    This study was conducted to introduce a simple modification that can facilitate microsurgical subinguinal varicocelectomy (MSV) especially for surgeons inexperienced in microsurgical technique. A single surgeon performed microsurgical intermediate subinguinal varicocelectomy (MISV) on 52 patients with 61 cases between September 2010 and August 2012. Patient age, varicocele grade, operation time, intraoperative findings, postoperative complications, and 3-month follow-up results were analyzed. Patient mean age was 28 years (range, 15-69 years), and there were 9 bilateral cases. The mean operative time was 51 minutes (range, 34-109 minutes). We compared the first 31 cases to the second 30 cases, to assess investigator experience on operating times. The mean number of ligated veins was 5 (range, 3-10) in internal spermatic vein, 1 (range, 0-4) in external spermatic vein, and 1 (range, 0-3) in gubernacular vein. In 28 patients, the average postoperative sperm concentration at the 3-month follow-up was significantly higher than the preoperative sperm concentration (28.5±18.2×10(6)/mL versus 10.5±23.0×10(6)/mL; P=0.003). Mean motility improved after MSIV (65.7%±18.2% versus 47.2%±21.7%; P=0.004). In conclusion, MISV appears comparable with MSV in terms of the high success rate, low complication rate, and low postoperative pain; and it can be easily accomplished by inexperienced surgeons. PMID:25058772

  18. Microsurgical Intermediate Subinguinal Varicocelectomy

    PubMed Central

    Lee, Joo Yong; Yu, Ho Song; Ham, Won Sik; Kang, Dong Hyuk; Kim, Kyu Hyun; Chung, Doo Yong; Cho, Kang Su

    2014-01-01

    This study was conducted to introduce a simple modification that can facilitate microsurgical subinguinal varicocelectomy (MSV) especially for surgeons inexperienced in microsurgical technique. A single surgeon performed microsurgical intermediate subinguinal varicocelectomy (MISV) on 52 patients with 61 cases between September 2010 and August 2012. Patient age, varicocele grade, operation time, intraoperative findings, postoperative complications, and 3-month follow-up results were analyzed. Patient mean age was 28 years (range, 15–69 years), and there were 9 bilateral cases. The mean operative time was 51 minutes (range, 34–109 minutes). We compared the first 31 cases to the second 30 cases, to assess investigator experience on operating times. The mean number of ligated veins was 5 (range, 3–10) in internal spermatic vein, 1 (range, 0–4) in external spermatic vein, and 1 (range, 0–3) in gubernacular vein. In 28 patients, the average postoperative sperm concentration at the 3-month follow-up was significantly higher than the preoperative sperm concentration (28.5 ± 18.2 × 106/mL versus 10.5 ± 23.0 × 106/mL; P = 0.003). Mean motility improved after MSIV (65.7% ± 18.2% versus 47.2% ± 21.7%; P = 0.004). In conclusion, MISV appears comparable with MSV in terms of the high success rate, low complication rate, and low postoperative pain; and it can be easily accomplished by inexperienced surgeons. PMID:25058772

  19. Reaction efficiency effects on binary chemical reactions.

    PubMed

    Lazaridis, Filippos; Savara, Aditya; Argyrakis, Panos

    2014-09-14

    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. PMID:25217900

  20. Structural relations for time-dependent intermediate shocks

    NASA Technical Reports Server (NTRS)

    Wu, C. C.; Kennel, C. F.

    1992-01-01

    A quantitative description of time-dependent (MHD) intermediate shocks is formulated. In non-coplanar Riemann problems, time-dependent 2 yields 3 intermediate shocks evolve in time as a localized self-similar structure whose strength decreases as 1/sq rt t, and whose width expands as sq rt t. We derive structural relations, similar to Rankine-Hugoniot relations, between the plasma properties and the magnitude of the transverse magnetic field, which we hope can help identify time-dependent 2 yields 3 intermediate shocks at the magnetopause, in the solar wind, and elsewhere in space. The analytic forms of the structural relations agree with our numerical results.

  1. Masonry. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Thompson, Moses

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

  2. Controlling reaction specificity in pyridoxal phosphate enzymes.

    PubMed

    Toney, Michael D

    2011-11-01

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

  3. Controlling reaction specificity in pyridoxal phosphate enzymes

    PubMed Central

    Toney, Michael D.

    2012-01-01

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

  4. Reaction specificity in pyridoxal phosphate enzymes.

    PubMed

    Toney, Michael D

    2005-01-01

    Pyridoxal phosphate enzymes catalyze a wide variety of reaction types on amines and amino acids, generally by stabilizing carbanionic intermediates. This makes them very useful in cellular metabolism, but it also creates problems in controlling the reaction pathway that a given enzyme follows, i.e., in controlling reaction specificity. Stereoelectronic effects have been proposed to play a major role in determining the bond to Calpha that gets broken in the external aldimine intermediate that is common to all PLP enzymes. Here, we discuss our work on dialkylglycine decarboxylase aimed at providing direct evidence for stereoelectronic control of external aldimine reactivity. Once a bond to Calpha has been broken to form the carbanionic intermediate, enzymes must also carefully control the fate of this reactive species. Our studies with alanine racemase suggest that the enzyme selectively destabilizes the carbanionic quinonoid intermediate to promote higher racemization specificity by avoiding transamination side reactions. PMID:15581583

  5. Use of high-pressure/variable-temperature infrared flow cell to examine the reaction kinetics of the migratory insertion intermediate ({eta}{sup 5}-C{sub 5}H{sub 5})Fe(CO)C(O)CH{sub 3} by time-resolved spectroscopy

    SciTech Connect

    Massick, S.M.; Ford, P.C.

    1999-10-11

    The reactive intermediate CpFe(CO)C(O)CH{sub 3} (1; Cp = {eta}{sup 5}-C{sub 5}H{sub 5}) was prepared by flash photolysis of CpFe(CO){sub 2}C(O)CH{sub 3} (A) in cyclohexane solutions and its reaction kinetics interrogated by time-resolved infrared spectroscopy in a flow system designed to allow equilibration of photolysis solutions at elevated temperatures and high carbon monoxide pressures. The high CO pressures (P{sub CO} {le} 28 atm) allowed for the measurement of the previously undetermined second-order rate constant (k{sub CO}) of CO trapping of 1 to regenerate A, which under these conditions occurs in competition with migration of the methyl group from the carbonyl carbon to the iron (K{sub M}). These rates were also measured over the temperature range 25--45 C, which allowed the determination of the activation parameters for methyl migration ({Delta}H{double{underscore}dagger}) = 44 {+-} 2 kJ mol{sup {minus}1}, {Delta}S{double{underscore}dagger} = {minus}5 {+-} 8 J K{sup {minus}1} mol{sup {minus}1} and for reaction with CO ({Delta} H{double{underscore}dagger} = 34 {+-} 2 kJ mol{sup {minus}1}, {Delta}S{double{underscore}dagger} = {minus}28 {+-} 6 J K{sup {minus}1}mol{sup {minus}1}). The mechanistic implications of these results are discussed. Details regarding the design of the high-pressure/variable-temperature TRIR flow cell are also discussed.

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

    SciTech Connect

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

    2014-09-01

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

  7. Radical Intermediates in the Addition of OH to Propene: Photolytic Precursors and Angular Momentum E ects

    E-print Network

    Butler, Laurie J.

    Radical Intermediates in the Addition of OH to Propene: Photolytic Precursors and Angular Momentum Supporting Information ABSTRACT: We investigate the photolytic production of two radical intermediates in the reaction of OH with propene, one from addition of the hydroxyl radical to the terminal carbon and the other

  8. 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.

  9. Racemization in Prins Cyclization Reactions

    PubMed Central

    Jasti, Ramesh

    2008-01-01

    Isotopic labeling experiments were performed in order to elucidate a new mechanism for racemization in Prins cyclization reactions. The loss in optical activity for these reactions was shown to occur by 2-oxonia-Cope rearrangements by way of a (Z)-oxocarbenium ion intermediate. Reaction conditions such as solvent, temperature, and the nucleophile employed played a critical role in whether an erosion in enantiomeric excess was observed. Additionally, certain structural features of Prins cyclization precursors were also shown to be important for preserving optical purity in these reactions. PMID:17031979

  10. ChemTeacher: Decomposition 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 Decomposition Reactions page includes resources for teaching students about identifying and predicting decomposition reactions.

  11. 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.

  12. Fenton Oxidation Kinetics and Intermediates of Nonylphenol Ethoxylates

    PubMed Central

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

    2014-01-01

    Abstract Removal of nonylphenol ethoxylates (NPEOs) in aqueous solution by Fenton oxidation process was studied in a laboratory-scale batch reactor. Operating parameters, including initial pH temperature, hydrogen peroxide, and ferrous ion dosage, were thoroughly investigated. Maximum NPEOs reduction of 84% was achieved within 6?min, under an initial pH of 3.0, 25°C, an H2O2 dosage of 9.74×10?3 M, and a molar ratio of [H2O2]/[Fe2+] of 3. A modified pseudo-first-order kinetic model was found to well represent experimental results. Correlations of reaction rate constants and operational parameters were established based on experimental data. Results indicated that the Fenton oxidation rate and removal efficiency were more dependent on the dosage of H2O2 than Fe2+, and the apparent activation energy (?E) was 17.5?kJ/mol. High-performance liquid chromatography and gas chromatograph mass spectrometer analytical results indicated degradation of NPEOs obtained within the first 2?min stepwise occurred by ethoxyl (EO) unit shortening. Long-chain NPEOs mixture demonstrated a higher degradation rate than shorter-chain ones. Nonylphenol (NP), short-chain NPEOs, and NP carboxyethoxylates were identified as the primary intermediates, which were mostly further degraded. PMID:24868141

  13. Mechanism of Ethane Destruction in Dielectric Barrier Discharge in Air: Detailed Elementary Reaction Model and Experiment

    NASA Astrophysics Data System (ADS)

    Krasnoperov, Lev; Modenese, Camila; Krishtopa, Larisa

    2006-10-01

    Free radical destruction mechanism was extended by inclusion of reactions of excited and ionic species. The mechanism consists of 935 reactions of 85 neutral species, 9 excited states and 38 ions. The reactions include 9 initiation processes in streamers, 66 processes involving excited states and 83 reactions involving ions. The reactant, the final products as well as the major intermediates of the destruction of ethane in air in corona discharge were identified and quantified Carbon dioxide (CO2), water (H2O), formaldehyde (H2CO), acetaldehyde (CH3CHO), methanol (CH3OH), ethanol (C2H5OH), formic acid (HCOOH), acetic acid (CH3COOH), methyl nitrate (CH3ONO2) and ethyl nitrate (C2H5ONO2) were identified among the major destruction products. The destruction efficiency predicted by the mechanism is in good agreement with the experiment, the major contribution is being due to the ionization transfer reactions. Reactions of excited species play but only a minor role. The product spectrum is consistent with the subsequent low temperature free radical reactions complicated by the presence of ozone and nitrogen oxides. The generic reaction mechanism for other organic as well as inorganic compounds is discussed.

  14. Ozonation and peroxone oxidation of benzophenone-3 in water: effect of operational parameters and identification of intermediate products.

    PubMed

    Gago-Ferrero, Pablo; Demeestere, Kristof; Silvia Díaz-Cruz, M; Barceló, Damià

    2013-01-15

    The goal of this study was to bring forward new data and insights with respect to the effect of operational variables and reaction pathways during ozonation and peroxone oxidation of the UV filter compound benzophenone-3 (BP3) in water. A systematic parameter study, investigating the effect of the ozone inlet concentration, temperature, pH, H(2)O(2) and t-butanol addition in a lab-scale bubble reactor, showed the promising potential of ozonation towards BP3 degradation. pH showed to be a major process parameter, with half-life times (5.1-15.0 min) being more than two times shorter at pH10 compared to neutral and acid conditions. This indicates the important role of hydroxyl radicals as supported by the addition of H(2)O(2) and t-butanol as HO promoter and scavenger, respectively. Ozonation intermediate products were identified by liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry (HPLC-QqTOF-MS/MS). Demethylation and non-selective HO attack proved to be the major reaction mechanisms. Where available, identified intermediates were confirmed using analytical standards, and concentration profiles along the ozonation process were determined through selective targeted MS/MS analysis. Benzophenone-1 (BP1), also being a UV-filter compound, and 2,2'-dihydroxy-4-methoxybenzophenone (DHMB) revealed to be the major BP3 degradation products, showing a maximum concentration at about the half-life time of BP3. PMID:23186632

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

    E-print Network

    Kinney, Jerry Neal

    1970-01-01

    (Mallinckrodt reagent) was stored over calcium hydride prior to use. Tetraphenyllead, triphenyllead chloride, and diphenyllead di- chloride were obtained from Alfa Inorganics, Inc. Bromobenzene (Fisher reagent) and iodomethane (Aldrich) were dried over...

  16. The reaction of Fe and Ni at intermediate energies 

    E-print Network

    Liddick, Sean Nicholas

    2013-02-22

    at the Texas A&M University Cyclotron Institute. Differing beams of the above materials were created and impinged on the different targets. The resulting fragments were detected in combinations of cesium iodide detectors, silicon detectors and the neutron...

  17. Correlations in intermediate energy two-proton removal reactions.

    PubMed

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

    2012-11-16

    We report final-state-exclusive measurements of the light charged fragments in coincidence with (26)Ne residual nuclei following the direct two-proton removal from a neutron-rich (28)Mg secondary beam. A Dalitz-plot analysis and comparisons with simulations show that a majority of the triple-coincidence events with two protons display phase-space correlations consistent with the (two-body) kinematics of a spatially correlated pair-removal mechanism. The fraction of such correlated events, 56(12)%, is consistent with the fraction of the calculated cross section, 64%, arising from spin S=0 two-proton configurations in the entrance-channel (shell-model) (28)Mg ground state wave function. This result promises access to an additional and more specific probe of the spin and spatial correlations of valence nucleon pairs in exotic nuclei produced as fast secondary beams. PMID:23215478

  18. 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...

  19. Synchrotron Photoionization Study of Mesitylene Oxidation Initiated by Reaction with Cl((2)P) or O((3)P) Radicals.

    PubMed

    Ng, Martin Y; Nelson, Jordan; Taatjes, Craig A; Osborn, David L; Meloni, Giovanni

    2014-05-15

    This work studies the oxidation of mesitylene (1,3,5-trimethylbenzene) initiated by O((3)P) or Cl((2)P) atoms. The O((3)P) initiated mesitylene oxidation was investigated at room temperature and 823 K, whereas the Cl-initiated reaction was carried out at room temperature only. Products were probed by a multiplexed chemical kinetics photoionization mass spectrometer using the synchrotron radiation produced at the Advanced Light Source (ALS) of Lawrence Berkeley National Laboratory. Reaction products and intermediates are identified on the basis of their time behavior, mass-to-charge ratio, ionization energies, and photoionization spectra. Branching yields are derived for the O-initiated reaction at 823 K and the Cl-initiated reaction at room temperature. Reaction schematics are proposed and presented. PMID:24766093

  20. Non-genomic regulation of intermediate conductance potassium channels by aldosterone in human colonic crypt cells

    PubMed Central

    Bowley, K A; Morton, M J; Hunter, M; Sandle, G I

    2003-01-01

    Background: Aldosterone has a rapid, non-genomic, inhibitory effect on macroscopic basolateral K+ conductance in the human colon, reducing its capacity for Cl? secretion. The molecular identity of the K+ channels constituting this aldosterone inhibitable K+ conductance is unclear. Aim: To characterise the K+ channel inhibited by aldosterone present in the basolateral membrane of human colonic crypt cells. Methods: Crypts were isolated from biopsies of healthy sigmoid colon obtained during colonoscopy. The effect of aldosterone on basolateral K+ channels, and the possible involvement of Na+:H+ exchange, were studied by patch clamp techniques. Total RNA from isolated crypts was subjected to reverse transcriptase-polymerase chain reaction (RT-PCR) using primers specific to intermediate conductance K+ channels (KCNN4) previously identified in other human tissues. Results: In cell attached patches, 1 nmol/l aldosterone significantly decreased the activity of intermediate conductance (27 pS) K+ channels by 31%, 53%, and 54% after 1, 5 and 10, minutes, respectively. Increasing aldosterone concentration to 10 nmol/l produced a further 56% decrease in channel activity after five minutes. Aldosterone 1–10 nmol/l had no effect on channel activity in the presence of 20 ?mol/l ethylisopropylamiloride, an inhibitor of Na+:H+ exchange. RT-PCR identified KCNN4 mRNA, which is likely to encode the 27 pS K+ channel inhibited by aldosterone. Conclusion: Intermediate conductance K+ channels (KCNN4) present in the basolateral membranes of human colonic crypt cells are a target for the non-genomic inhibitory effect of aldosterone, which involves stimulation of Na+:H+ exchange, thereby reducing the capacity of the colon for Cl? secretion. PMID:12740342

  1. Intermediate ions in the atmosphere

    NASA Astrophysics Data System (ADS)

    Tammet, Hannes; Komsaare, Kaupo; Hõrrak, Urmas

    2014-01-01

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

  2. A Putative Fe2+-bound Persulfenate Intermediate in Cysteine Dioxygenase

    PubMed Central

    Simmons, Chad R.; Krishnamoorthy, Kalyanaraman; Granett, Spencer L.; Schuller, David J.; Dominy, John E.; Begley, Tadhg P.; Stipanuk, Martha H.; Karplus, P. Andrew

    2008-01-01

    The common reactions of dioxygen, superoxide and hydroperoxides with thiolates are thought to proceed via persulfenate intermediates, yet these have never been visualized. Here we report a 1.4 Å resolution crystal structure of the Fe2+-dependent enzyme cysteine dioxygenase (CDO) containing this putative intermediate trapped in its active site pocket. The complex raises the possibility that, distinct from known dioxygenases and proposed CDO mechanisms, the Fe-proximal oxygen atom may be involved in the primary oxidation event to yield a unique three-membered Fe-S-O cyclic intermediate. A non-polar environment of the distal oxygen would facilitate isomerization of the persulfenate to the sulfinate product. PMID:18847220

  3. Gas–solid reaction model for a shrinking spherical particle with unreacted shrinking core

    Microsoft Academic Search

    Shunji Homma; Shinji Ogata; Jiro Koga; Shiro Matsumoto

    2005-01-01

    A heterogeneous reaction model is developed to represent the gas–solid reaction consisting of two-step reactions: formation of a solid intermediate on the core of unreacted solid and consumption of the solid intermediate. The presented model takes into account the shrinkage of both the unreacted core and the solid particle itself. The model successfully represents the fluorination of uranium dioxide where

  4. Propene oxidation at low and intermediate temperatures: A detailed chemical kinetic study

    SciTech Connect

    Wilk, R.D.; Cernansky, N.P.; Pitz, W.J.; Westbrook, C.K.

    1987-03-24

    A detailed chemical kinetic mechanism for propene oxidation is developed and used to model reactions in a static reactor at temperatures of 575-715 K, equivalence ratios of 0.8 - 2.0, and a pressure of 600 torr. Modeling of hydrocarbon oxidation in this temperature range is important for the validation of detailed models to be used for performing calculations related to automotive engine knock. The model predicted induction periods and species concentrations for all the species and all conditions measured experimentally in the static reactor. Overall, the calculated concentrations of carbon monoxide, acetaldehyde, acrolein, and propane oxide agreed well with those measured. The calculated concentrations of ethane are low compared to the experimental measurements, and the calculated concentrations of formaldehyde are high. Agreement for concentrations of carbon dioxide, methane, and methanol is mixed. The characteristic s-shape of the fuel concentration history is well predicted. Modeling calculations identified some of the key reaction steps at the present conditions. Addition of OH to propene and H atom abstraction by OH from propene are important steps in determining the subsequent distributions of intermediate products, such as acetaldehyde, acrolein and formaldehyde. Allyl radicals are very abundant in propene oxidation, and the primary steps found to be responsible for their consumption are reaction with CH/sub 3/O/sub 2/ and HO/sub 2/. 37 refs., 5 figs., 1 tab.

  5. Propene oxidation at low and intermediate temperatures: A detailed chemical kinetic study

    SciTech Connect

    Wilk, R.D.; Gernansky, N.P.; Pitz, W.J.; Westbrook, C.K.

    1987-01-01

    A detailed chemical kinetic mechanism for propene oxidation is developed and used to model reactions in a static reactor at temperatures of 575-715 K, equivalence ratios of 0.8 - 2.0, and a pressure of 600 torr. Modeling of hydrocarbon oxidation in this temperature range is important for the validation of detailed models to be used for performing calculations related to automotive engine knock. The model predicted induction periods and species concentrations for all the species and all conditions measured experimentally in the static reactor. Overall, the calculated concentrations of carbon monoxide, acetaldehyde, acrolein, and propene oxide agreed well with those measured. The calculated concentrations of ethene are low compared to the experimental measurements, and the calculated concentrations of formaldehyde are high. Agreement for concentrations of carbon dioxide, methane, and methanol is mixed. The characteristic s-shape of the fuel concentration history is well predicted. Modeling calculations identified some of the key reaction steps at the present conditions. Addition of OH to propene and H atom abstraction by OH from propene are important steps in determining the subsequent distributions of intermediate products, such as acetaldehyde, acrolein and formaldehyde. Allyl radicals are very abundant in propene oxidation, and the primary steps found to be responsible for their consumption are reaction with CH/sub 3/O/sub 2/ and HO/sub 2/.

  6. Ketonic decarboxylation reaction mechanism: a combined experimental and DFT study.

    PubMed

    Pulido, Angeles; Oliver-Tomas, Borja; Renz, Michael; Boronat, Mercedes; Corma, Avelino

    2013-01-01

    The ketonic decarboxylation of carboxylic acids has been carried out experimentally and studied theoretically by DFT calculations. In the experiments, monoclinic zirconia was identified as a good catalyst, giving high activity and high selectivity when compared with other potential catalysts, such as silica, alumina, or ceria. It was also shown that it could be used for a wide range of substrates, namely, for carboxylic acids with two to eighteen carbon atoms. The reaction mechanism for the ketonic decarboxylation of acetic acid over monoclinic zirconia was investigated by using a periodic DFT slab model. A reaction pathway with the formation of a ?-keto acid intermediate was considered, as well as a concerted mechanism, involving simultaneous carbon-carbon bond formation and carbon dioxide elimination. DFT results showed that the mechanism with the ?-keto acid was the kinetically favored one and this was further supported by an experiment employing a mixture of isomeric (linear and branched) pentanoic acids. PMID:23203990

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

    PubMed

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

    2015-01-01

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

  8. Intermediate polars in low states

    E-print Network

    Brian Warner

    2003-10-09

    Although no intermediate polar (IP) has been observed in recent years to descend into a state of low rate of mass transfer, there are candidate stars that appear to be already in intermediate and low states. V709 Cas is probably an intermediate state IP; NSV 2872 appears to be a low state IP, and will probably resemble the long orbital period IP V1072 Tau if it returns to a high state. The enigmatic V407 Vul, which has had many interpretations as an ultra-short period binary, has many resemblances to the pre-cataclysmic variable V471 Tau, and may therefore be an IP precursor of quite long orbital period, and not yet a fully fledged cataclysmic variable.

  9. 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

  10. Intermediate tax sanctions: an overview.

    PubMed

    Peregrine, M W

    1997-07-01

    New federal tax law applies intermediate tax sanctions when tax-exempt organizations enter into so-called excess benefit transactions with corporate insiders. The sanctions take the form of a two-tiered penalty excise tax, which is assessed not on the tax-exempt organization itself but on the insider who receives the excess benefit and the organizational managers and board members who knowingly participate in an improper transaction. The intermediate tax sanctions, therefore, present tax-planning challenges for tax-exempt hospitals and integrated delivery systems as well as for 501(c)(4) HMOs. Forthcoming treasury regulations are expected to add clarity to the new law. PMID:10168439

  11. Tracing Traffic through Intermediate Hosts that Repacketize Flows

    Microsoft Academic Search

    Young June Pyun; Young Hee Park; Xinyuan Wang; Douglas S. Reeves; Peng Ning

    2007-01-01

    Tracing interactive traffic that traverses stepping stones (i.e., intermediate hosts) is challenging, as the packet headers, lengths, and contents can all be changed by the stepping stones. The traffic timing has therefore been studied as a means of tracing traffic. One such technique uses traffic timing as a side channel into which a watermark, or identifying tag, can be embedded

  12. Intermediate Educational Units and Their Promise for Rural Education.

    ERIC Educational Resources Information Center

    Benson, Charles W.; Barber, R. Jerry

    The document discussed the functions of intermediate educational units their relation to rural schools, and the unique needs of rural schools. Chapter I traced the development of the American school system from its inception in colonial America to contemporary times. Characteristics of America's rural population were identified and briefly…

  13. Methanogenic toluene metabolism: community structure and intermediates.

    PubMed

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

    2012-03-01

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

  14. A Unified Theory of Chemical Reactions

    E-print Network

    Aubry, S

    2014-01-01

    We propose a new and general formalism for elementary chemical reactions where quantum electronic variables are used as reaction coordinates. This formalism is in principle applicable to all kinds of chemical reactions ionic or covalent. Our theory reveals the existence of an intermediate situation between ionic and covalent which may be almost barrierless and isoenegetic and which should be of high interest for understanding biochemistry.

  15. Cestina pro Pokrocile (Intermediate Czech).

    ERIC Educational Resources Information Center

    Kabat, Grazyna; And Others

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

  16. Learning through Literature: Geography, Intermediate.

    ERIC Educational Resources Information Center

    Sterling, Mary Ellen

    This resource book provides specific strategies and activities for integrating the intermediate geography curriculum with related children's literature selections. The book includes the following sections: (1) "World Geography Overview"; (2) "Oceans"; (3) "Polar Regions"; (4) "Islands"; (5) "Rain Forests"; (6) "Mountains"; (7) "Forests"; (8)…

  17. Intermediate Temperature Solid Oxide Fuel Cell Development

    SciTech Connect

    S. Elangovan; Scott Barnett; Sossina Haile

    2008-06-30

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

  18. Cytochrome P450-catalysed arene-epoxidation of the bioactive tea tree oil ingredient p-cymene: indication for the formation of a reactive allergenic intermediate?

    PubMed

    Meesters, R J W; Duisken, M; Hollender, J

    2009-09-01

    1. The cytochrome P450-mediated metabolism of the tea tree oil ingredient p-cymene (p-isopropyltoluene) was studied by the application of in vitro enzymatic assays using different recombinant human cytochrome P450 enzymes. 2. In total, four enzymatic products were identified by gas chromatography-mass spectrometry. The enzymatic products identified were: thymol (2-isopropyl-5-methylphenol), p-isopropylbenzyl alcohol, p,alpha,alpha-trimethylbenzyl alcohol, and p-isopropylbenzaldehyde. 3. The enzymatic products of p-cymene resulted from catalysed enzymatic arene-epoxidation and hydroxylation reactions by the studied cytochrome P450 enzymes. 4. An in vivo study could only confirm the formation of one enzymatic product, namely thymol. Thymol was identified after enzymatic hydrolysis of glucuronide and sulphate conjugates in collected blood and urine samples. 5. The obtained results may help to increase the understanding of cases where skin sensitization and irritation by tea tree oil-containing products that are involved with allergic reactions of users of these products. The results also indicate that skin sensitization and irritation reactions not only can be explained by the frequently in literature reported auto-oxidation of tea tree resulting in bioactive oxidized products, but also now by the formation of epoxide intermediates resulting from catalysed arene-epoxidation reactions by selected human cytochrome P450 enzymes which are also located in different organs in humans. PMID:19480554

  19. Molecular dynamics of the Diels-Alder reactions of tetrazines with alkenes and N2 extrusions from adducts.

    PubMed

    Törk, Lisa; Jiménez-Osés, Gonzalo; Doubleday, Charles; Liu, Fang; Houk, K N

    2015-04-15

    The cycloadditions of tetrazines with cyclopropenes and other strained alkenes have become among the most valuable bioorthogonal reactions. These reactions lead to bicyclic Diels-Alder adducts that spontaneously lose N2. We report quantum mechanical (QM) and quasiclassical trajectory simulations on a number of these reactions, with special attention to stereoelectronic and dynamic effects on spontaneous N2 loss from these adducts. QM calculations show that the barrier to N2 loss is low, and molecular dynamics calculations show that the intermediate is frequently bypassed dynamically. There is a large preference for N2 loss anti to the cyclopropane moiety rather than syn from adducts formed from reactions with cyclopropenes. This is explained by the interactions of the Walsh orbitals of the cyclopropane group with the breaking C-N bonds in N2 loss. Dynamical effects opposing the QM preferences have also been discovered involving the coupling of vibrations associated with the formation of the new C-C bonds in the cycloaddition step, and those of the breaking C-N bonds during subsequent N2 loss. This dynamic matching leads to pronounced nonstatistical effects on the lifetimes of Diels-Alder intermediates. An unusual oscillatory behavior of the intermediate decay rate has been identified and attributed to specific vibrational coupling. PMID:25726899

  20. 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.

  1. 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

  2. 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.

  3. Evidence for a population of beamed radio intermediate quasars

    E-print Network

    Tinggui Wang; Hongyan Zhou; Junxian Wang; Youjun Lu; Yu Lu

    2006-03-19

    Whether radio intermediate quasars possess relativistic jets as radio-loud quasars is an important issue in the understanding of the origin of radio emission in quasars. In this letter, using the two-epoch radio data obtained during Faint Image of Radio Sky at Twenty centimeter sky (FIRST) and NOAO VLA Sky Survey (NVSS), we identify 89 radio variable sources in the Sloan Digital Sky Survey. Among them, more than half are radio intermediate quasars (RL=f2cm/f2500A<250). For all objects with available multiple band radio observations, the radio spectra are either flat or inverted. The brightness temperature inferred from the variability is larger than the synchrotron-self Compton limit for a stationary source in 87 objects, indicating of relativistic beaming. Considering the sample selection and viewing angle effect, we conclude that relativistic jets probably exist in a substantianl fraction of radio intermediate quasars.

  4. Multiple intermediate valence in plutonium

    Microsoft Academic Search

    A. V. Mirmelstein; E. S. Clementyev; O. V. Kerbel

    2009-01-01

    On the basis of the concepts of an intermediate-valence (IV) regime, an empirical model is proposed that quantitatively describes\\u000a the magnetic susceptibility, specific heat, and effective atomic volume of the low-temperature ? phase and the gallium or\\u000a aluminum-stabilized face-centered cubic (fcc) ? phase of plutonium metal. The results of the paper allow one to estimate the\\u000a entropy change associated with

  5. 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

  6. 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

  7. DXRD studies of sodium nickel ferrocyanide reactions with equimolar nitrate/nitrite salts

    SciTech Connect

    Dodds, J.N.; Thomson, W.J. (Washington State Univ., Pullman, WA (United States))

    1994-05-01

    Dynamic X-ray diffraction (DXRD) has been used to identify and quantify the solid-state reactions that take place between sodium nickel ferrocyanide, Na[sub 2]NiFe(CN)[sub 6], and equimolar concentrations of sodium nitrate/nitrite, reactions of interest to the continued environmental safety of certain waste storage tanks at the Hanford site in eastern Washington. The results are supportive of previous work that indicated that endothermic dehydration and melting of the nitrates take place prior to the occurrence of exothermic reactions, which begin about 300[degree]C. The DXRD results show that a major reaction set at these temperatures is the occurrence of a series reaction which produces sodium cyanate, NaCNO, as an intermediate in a mildly exothermic first step. In the presence of gaseous oxygen, NaCNO subsequently reacts exothermally and at a faster rate to form metal oxides. Measurements of the rate of this reaction are used to estimate the heat release, and comparisons of this with heat-transfer rates from a hypothetical [open quotes]hot spot[close quotes] show that, even in a worse case scenario, the heat-transfer rates are approximately eight times higher than the rate of energy release from the exothermic reactions. 20 refs., 7 figs., 3 tabs.

  8. A detailed investigation on electro-Fenton treatment of propachlor: Mineralization kinetic and degradation intermediates.

    PubMed

    Gençten, Metin; Özcan, Ali

    2015-10-01

    In this study, electrochemical removal of propachlor from water has been investigated by electro-Fenton process which provides continuous electrochemical production of hydroxyl radical which is a highly oxidizing agent. This radical can react with propachlor unselectively and can oxidize it into carbon dioxide and water. Effects of applied current, catalyst (Fe2(SO4)3) and supporting electrolyte (Na2SO4) concentrations on the degradation rate of propachlor have been examined and determined as 200mA, 0.20mM and 25mM, respectively. The oxidation reaction showed a second-order reaction kinetic with an absolute rate constant value of (3.6±0.2)×10(9)M(-1)s(-1) which was determined by competition kinetic experiments. Total organic carbon analysis was employed to follow the mineralization of propachlor. The total mineralization was completed in a seven-hour electrolysis at 300mA indicating that the electro-Fenton process is very effective in the mineralization of propachlor in water. Oxidation of propachlor with hydroxyl radical led to the formation of intermediate species. Some of these species were detected and quantified by chromatographic and spectroscopic methods such as HPLC, GC-MS and IC. A plausible mineralization pathway for the electrochemical removal of propachlor was proposed based on the identified by-products. PMID:25989604

  9. 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

  10. 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.

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

    PubMed Central

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

    2010-01-01

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

  12. Identification of a key catalytic intermediate demonstrates that nitrogenase is activated by the reversible exchange of N? for H?.

    PubMed

    Lukoyanov, Dmitriy; Yang, Zhi-Yong; Khadka, Nimesh; Dean, Dennis R; Seefeldt, Lance C; Hoffman, Brian M

    2015-03-18

    Freeze-quenching nitrogenase during turnover with N2 traps an S = ½ intermediate that was shown by ENDOR and EPR spectroscopy to contain N2 or a reduction product bound to the active-site molybdenum-iron cofactor (FeMo-co). To identify this intermediate (termed here EG), we turned to a quench-cryoannealing relaxation protocol. The trapped state is allowed to relax to the resting E0 state in frozen medium at a temperature below the melting temperature; relaxation is monitored by periodically cooling the sample to cryogenic temperature for EPR analysis. During -50 °C cryoannealing of EG prepared under turnover conditions in which the concentrations of N2 and H2 ([H2], [N2]) are systematically and independently varied, the rate of decay of EG is accelerated by increasing [H2] and slowed by increasing [N2] in the frozen reaction mixture; correspondingly, the accumulation of EG is greater with low [H2] and/or high [N2]. The influence of these diatomics identifies EG as the key catalytic intermediate formed by reductive elimination of H2 with concomitant N2 binding, a state in which FeMo-co binds the components of diazene (an N-N moiety, perhaps N2 and two [e(-)/H(+)] or diazene itself). This identification combines with an earlier study to demonstrate that nitrogenase is activated for N2 binding and reduction through the thermodynamically and kinetically reversible reductive-elimination/oxidative-addition exchange of N2 and H2, with an implied limiting stoichiometry of eight electrons/protons for the reduction of N2 to two NH3. PMID:25741750

  13. ChemTeacher: Double Replacement 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 Double Replacement Reactions page includes resources for teaching students about identifying and predicting double replacement reactions.

  14. 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.

  15. Copper-Catalyzed Oxidative Heck Reactions between Alkyltrifluoroborates and Vinylarenes

    PubMed Central

    Liwosz, Timothy W.; Chemler, Sherry R.

    2013-01-01

    We report herein that potassium alkyltrifluoroborates can be utilized in oxidative Heck-type reactions with vinyl arenes. The reaction is catalyzed by a Cu(OTf)2/1,10-phenanthroline with MnO2 as the stoichiometric oxidant. In addition to the alkyl Heck, amination, esterification and dimerization reactions of alkyltrifluoroborates are demonstrated under analogous reaction conditions. Evidence for an alkyl radical intermediate is presented. PMID:23734764

  16. 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.

  17. 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

  18. Silica hydride intermediate for octadecylsilica and phenyl bonded phase preparation via heterogeneous hydrosilation in supercritical carbon dioxide.

    PubMed

    Scully, N M; Ashu-Arrah, B A; Nagle, A P; Omamogho, J O; O'Sullivan, G P; Friebolin, V; Dietrich, B; Albert, K; Glennon, J D

    2011-04-15

    Investigations into the preparation of silica hydride intermediate in supercritical carbon dioxide (sc-CO(2)) that avoids the use of organic solvents such as toluene or dioxane are described. The effects of reaction temperature, pressure and time on the surface coverage of the supercritical fluid generated silica hydride intermediate were studied. Under optimised supercritical conditions of 120°C, 483 bar and 3 h reaction time, silica hydride (Si-H) conversion efficiencies of ca. 40% were achieved for the hydride intermediate prepared from a monofunctional silane reagent (dimethylmethoxysilane). Si-H conversion efficiencies (as determined from (29)Si CP-MAS NMR spectral analysis) for the hydride intermediate prepared from triethoxysilane (TES) in sc-CO(2) were found to be comparable to those obtained using a TES silanisation approach in an organic solvent. (13)C and (29)Si CP-MAS-NMR spectroscopy was employed to provide a complete structural assignment of the silica hydride intermediates. Furthermore, supercritical CO(2) was subsequently employed as a reaction medium for the heterogenous hydrosilation of silica hydride with octadecene and with styrene, in the presence of a free radical initiator. These supercritical fluid generated reversed-phase materials were prepared in a substantially reduced reaction time (3 h) compared to organic solvent based methods (100 h reaction time). Silica functionalisation in sc-CO(2) presents an efficient and clean alternative to organic solvent based methods for the preparation of important silica hydride intermediate and silica bonded stationary phases via a hydrosilation approach. PMID:21353227

  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. Stochastic operator-splitting method for reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Choi, TaiJung; Maurya, Mano Ram; Tartakovsky, Daniel M.; Subramaniam, Shankar

    2012-11-01

    Many biochemical processes at the sub-cellular level involve a small number of molecules. The local numbers of these molecules vary in space and time, and exhibit random fluctuations that can only be captured with stochastic simulations. We present a novel stochastic operator-splitting algorithm to model such reaction-diffusion phenomena. The reaction and diffusion steps employ stochastic simulation algorithms and Brownian dynamics, respectively. Through theoretical analysis, we have developed an algorithm to identify if the system is reaction-controlled, diffusion-controlled or is in an intermediate regime. The time-step size is chosen accordingly at each step of the simulation. We have used three examples to demonstrate the accuracy and robustness of the proposed algorithm. The first example deals with diffusion of two chemical species undergoing an irreversible bimolecular reaction. It is used to validate our algorithm by comparing its results with the solution obtained from a corresponding deterministic partial differential equation at low and high number of molecules. In this example, we also compare the results from our method to those obtained using a Gillespie multi-particle (GMP) method. The second example, which models simplified RNA synthesis, is used to study the performance of our algorithm in reaction- and diffusion-controlled regimes and to investigate the effects of local inhomogeneity. The third example models reaction-diffusion of CheY molecules through the cytoplasm of Escherichia coli during chemotaxis. It is used to compare the algorithm's performance against the GMP method. Our analysis demonstrates that the proposed algorithm enables accurate simulation of the kinetics of complex and spatially heterogeneous systems. It is also computationally more efficient than commonly used alternatives, such as the GMP method.

  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. Reaction Time

    NSDL National Science Digital Library

    New York Hall of Science

    1999-01-01

    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.

  3. Reaction studies of hot silicon and germanium radicals. Progress report, September 1, 1979-August 31, 1980

    SciTech Connect

    Gaspar, P.P.

    1980-08-31

    The experimental approach to attaining the goals of this research program is briefly outlined and the progress made in the last year is reviewed in sections entitled: (a) primary steps in the reaction of recoiling silicon and germanium atoms and the identification of reactive intermediates in the recoil reactions; (b) thermally induced silylene and germylene reactions; (c) ion-molecule reaction studies.

  4. In situ mid-infrared analyses of reactive gas-phase intermediates in TEOS/Ozone SAPCVD

    SciTech Connect

    Whidden, Thomas K.; Doiron, Sarah [Xylaur enterprises, Fredericton, New Brunswick, E3B 6C2 (Canada)

    1998-11-24

    In this report, we present in situ characterizations of chemical vapour deposition (CVD) reactors used in silicon dioxide thin film depositions. The characterizations are based on Fourier transform infrared spectroscopy. The infrared absorption data are interpreted within the context of process and thin film properties and the bearing of the spectroscopic data upon the chemical mechanisms extant in the deposition reaction. The relevance of the interpretations to real-time process control is discussed. The process under study in this work is TEOS/ozone-based deposition of silicon dioxide thin films at subatmospheric pressures. This process exhibits many desirable properties but has fundamental problems that may be solvable by reaction control based on in situ analyses and the real-time manipulation of reagent concentrations and process conditions. Herein we discuss our preliminary data on characterizations of TEOS/ozone chemistries in commercial reactor configurations. Reaction products and reactive intermediate species are detected and identified. Quantitative in situ measurements of the reagent materials are demonstrated. Preliminary correlations of these data with process and thin film properties are discussed.

  5. [CuO](+) and [CuOH](2+) Complexes: Intermediates in Oxidation Catalysis?

    PubMed

    Gagnon, Nicole; Tolman, William B

    2015-07-21

    Characterization of monocopper intermediates in enzymes and other catalysts that attack strong C-H bonds is important for unraveling oxidation catalysis mechanisms and, ultimately, designing new, more efficient catalytic systems. Because initially formed 1:1 Cu/O2 adducts resulting from reactions of Cu(I) sites with O2 react relatively sluggishly with substrates with strong C-H bonds, it has been suggested that reductive O-O bond scission might occur instead to yield more reactive [CuO](+) or protonated [CuOH](2+) cores. Experimental and theoretical studies of [CuO](+) species in the gas phase have provided key insights into the possible reactivity of these species, but detailed information is lacking for discrete complexes with the [CuO](+) or [CuOH](2+) core in solution or the solid state. We describe herein our recent efforts to address this issue through several disparate approaches. In one strategy based on precedent from studies of enzymes and synthetic compounds with iron-?-ketocarboxylate motifs, reactions of O2 with Cu(I)-?-ketocarboxylate complexes were explored, with the aim of identifying reaction pathways that would implicate the intermediacy of a [CuO](+) species. A second approach focused on the reaction of N-oxides with Cu(I) complexes, with the goal being to elicit O-N bond heterolysis to yield [CuO](+) complexes. For both strategies, the course of the reactions depended on the nature of the supporting bidentate N-donor ligand, and indirect evidence in support of the sought-after [CuO](+) intermediates was obtained in some instances. In the final approach discussed herein, strongly electron donating and sterically encumbered pyridine-dicarboxamide ligands (L) enabled the synthesis of [LCu(II)OH](-) complexes, which upon one-electron oxidation formed complexes with the [CuOH](2+) core that were characterized in solution. Rapid hydrogen atom abstraction (HAT) from dihydroanthracene (DHA) was observed, yielding LCu(II)OH2. The O-H bond dissociation enthalpy (BDE) of ?90 kcal/mol for this complex was determined through evaluation of its pKa (?19) and the [LCu(II)OH](-)/LCu(III)OH reduction potential (approximately -0.08 V vs Fc/Fc(+)). Thus, the poor oxidizing power of the complex is offset by the high basicity of the hydroxide moiety to yield a strong O-H bond. This high BDE provided a thermodynamic rationale for the rapid HAT rate from DHA and suggested that stronger C-H bonds could be attacked. Indeed, using an inert solvent (1,2-difluorobenzene), substrates with C-H bond strengths as high as 99 kcal/mol were shown to react with the [CuOH](2+) complex, and a linear log k vs C-H BDE plot supported similar HAT pathways across the series. Importantly, these results provided key evidence in favor of the possible intermediacy of this core in oxidation catalysis, and we suggest that because it is a more energetically accessible intermediate than the [CuO](+) moiety, it should be considered as an alternative in proposed mechanisms for oxidations by enzymes and other synthetic systems. PMID:26075312

  6. 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 ...

  7. Biocatalytic synthesis of chiral intermediates for antiviral and antihypertensive drugs

    Microsoft Academic Search

    Ramesh N. Patel; Bristol-Myers Squibb

    1999-01-01

    The chiral intermediate (1S,2R) [3-chloro-2-hydroxy-1-(phenylmethyl)propyl] carbamic acid, 1,1-dimethylethyl ester 2a was prepared for the total synthesis of a human immunodeficiency virus protease inhibitor, BMS-186318. The stereoselective\\u000a reduction of (1S) [3-chloro-2-oxo-1(phenylmethyl)propyl] carbamic acid, 1,1-dimethylethyl ester 1 was carried out using microbial cultures, among which Streptomyces nodosus SC 13149 efficiently reduced 1 to 2a. A reaction yield of 80%, enantiomeric excess (e.e.)

  8. Evidence for intermediate-like filaments in a heterotrichous ciliate.

    PubMed

    Mohr, M; Ruthmann, A; Eichenlaub-Ritter, U; Kühn, S; Traub, P

    1990-03-01

    In the heterotrichous ciliate Nyctotherus ovalis, a meshwork of 10 nm filaments present in the cell cortex surrounds cytostome and cytoproct and is connected by thin strands to a perinuclear coat. Like intermediate filaments (If) of higher organisms the filaments are insoluble in non-ionic detergent, and paracrystals can be formed after dissolution in 8 M urea. The cross-reactions of these filaments with monoclonal anti-vimentin and anti-cytokeratin antibodies suggest that they share common epitopes with both types of If proteins. PMID:23195973

  9. Detection and Identification of the Keto-Hydroperoxide (HOOCH2OCHO) and Other Intermediates during Low-Temperature Oxidation of Dimethyl Ether.

    PubMed

    Moshammer, Kai; Jasper, Ahren W; Popolan-Vaida, Denisia M; Lucassen, Arnas; Diévart, Pascal; Selim, Hatem; Eskola, Arkke J; Taatjes, Craig A; Leone, Stephen R; Sarathy, S Mani; Ju, Yiguang; Dagaut, Philippe; Kohse-Höinghaus, Katharina; Hansen, Nils

    2015-07-16

    In this paper we report the detection and identification of the keto-hydroperoxide (hydroperoxymethyl formate, HPMF, HOOCH2OCHO) and other partially oxidized intermediate species arising from the low-temperature (540 K) oxidation of dimethyl ether (DME). These observations were made possible by coupling a jet-stirred reactor with molecular-beam sampling capabilities, operated near atmospheric pressure, to a reflectron time-of-flight mass spectrometer that employs single-photon ionization via tunable synchrotron-generated vacuum-ultraviolet radiation. On the basis of experimentally observed ionization thresholds and fragmentation appearance energies, interpreted with the aid of ab initio calculations, we have identified HPMF and its conceivable decomposition products HC(O)O(O)CH (formic acid anhydride), HC(O)OOH (performic acid), and HOC(O)OH (carbonic acid). Other intermediates that were detected and identified include HC(O)OCH3 (methyl formate), cycl-CH2-O-CH2-O- (1,3-dioxetane), CH3OOH (methyl hydroperoxide), HC(O)OH (formic acid), and H2O2 (hydrogen peroxide). We show that the theoretical characterization of multiple conformeric structures of some intermediates is required when interpreting the experimentally observed ionization thresholds, and a simple method is presented for estimating the importance of multiple conformers at the estimated temperature (?100 K) of the present molecular beam. We also discuss possible formation pathways of the detected species: for example, supported by potential energy surface calculations, we show that performic acid may be a minor channel of the O2 + ?H2OCH2OOH reaction, resulting from the decomposition of the HOOCH2O?HOOH intermediate, which predominantly leads to the HPMF. PMID:25695304

  10. Sequential fission process observed in the reaction (16.7 MeV/u) 238U + nat.Au using mica as dielectric track detector

    NASA Astrophysics Data System (ADS)

    Shahzad, Muhammad Ikram; Qureshi, Imtinan Elahi; Manzoor, Shahid; Khan, Hameed Ahmed

    1999-01-01

    The evidence of sequential fission has been found in the heavy-ion reaction (16.7 MeV/u) 238U + nat.Au , using muscovite mica as Dielectric Track Detector (DTD) placed in a 2?-geometry configuration. The reaction products originating from the interactions of 238U ions with the atoms of gold were registered in the detector in the form of tracks and identified for performing a detailed kinematical analysis. For this purpose the spherical polar coordinates of the correlated tracks of the multipronged events have been analyzed on an event-by-event basis. Automatic, semi-automatic and manual measuring methods have been employed to collect and manipulate the track data. The known characteristics of binary and ternary events observed in the reaction have been used for the calibration of the detectors. The computed masses, Q-values and relative velocities of the reaction products determined in this analysis are compared with theoretical predictions based on sequential fission process. Agreement within one standard deviation with respect to the experimental values has been found for the majority of analyzed events. Therefore, it is concluded that three particles in the exit channel of the reaction are produced in two successive steps. In the first step of the reaction, two intermediate nuclei are formed as a result of an inelastic collision between projectile and target atoms while in the second step the fission of one of the intermediate nuclei of the previous step takes place. Furthermore no proximity effects have been observed.

  11. 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

  12. Numerical modeling of intermediate band solar cells

    NASA Astrophysics Data System (ADS)

    Tobías, I.; Luque, A.; Martí, A.

    2011-01-01

    The performance of intermediate band solar cells under concentrated sunlight is analyzed by means of computer simulation. The continuity equations for electrons and holes and the Poisson equation are numerically solved in one dimension under steady-state conditions. Two situations are considered for a given density of intermediate band centers and optical cross sections. In the first situation, the intermediate band is undoped and a large capture coefficient links conduction and intermediate bands; a large short circuit current enhancement with respect to a conventional cell is obtained, but at the price of strong voltage and efficiency degradation. In the second, the intermediate band is partially filled by doping and there is little thermal contact with the semiconductor bands. The potential of the intermediate band concept is then realized with significant efficiency improvement under highly concentrated illumination. The analysis also reveals that the approximation of flat quasi-Fermi levels is not appropriate.

  13. 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.

  14. HS 0943+1404, a true intermediate polar

    NASA Astrophysics Data System (ADS)

    Rodríguez-Gil, P.; Gänsicke, B. T.; Hagen, H.-J.; Nogami, D.; Torres, M. A. P.; Lehto, H.; Aungwerojwit, A.; Littlefair, S.; Araujo-Betancor, S.; Engels, D.

    2005-09-01

    We have identified a new intermediate polar, HS 0943+1404, as part of our ongoing search for cataclysmic variables in the Hamburg Quasar Survey. The orbital and white dwarf spin periods determined from time-resolved photometry and spectroscopy are Porb ? 250 min and Pspin= 69.171 ± 0.001 min, respectively. The combination of a large ratio Pspin/Porb?0.3 and a long orbital period is very unusual compared to the other known intermediate polars. The magnetic moment of the white dwarf is estimated to be ?1˜1034 G cm3, which is in the typical range of polars. Our extensive photometry shows that HS 0943+1404 enters into deep (~3 mag) low states, which are also a characteristic feature of polars. We therefore suggest that the system is a true "intermediate" polar that will eventually synchronise, that is, a transitional object between intermediate polars and polars. The optical spectrum of HS 0943+1404 also exhibits a number of unusual emission lines, most noticeably NII?5680, which is likely to reflect enhanced nitrogen abundances in the envelope of the secondary.

  15. Spring loading a pre-cleavage intermediate for hairpin telomere formation.

    PubMed

    Lucyshyn, Danica; Huang, Shu Hui; Kobryn, Kerri

    2015-07-13

    The Borrelia telomere resolvase, ResT, forms the unusual hairpin telomeres of the linear Borrelia replicons in a process referred to as telomere resolution. Telomere resolution is a DNA cleavage and rejoining reaction that proceeds from a replicated telomere intermediate in a reaction with mechanistic similarities to that catalyzed by type IB topoisomerases. Previous reports have implicated the hairpin-binding module, at the end of the N-terminal domain of ResT, in distorting the DNA between the scissile phosphates so as to promote DNA cleavage and hairpin formation by the catalytic domain. We report that unwinding the DNA between the scissile phosphates, prior to DNA cleavage, is a key cold-sensitive step in telomere resolution. Through the analysis of ResT mutants, rescued by substrate modifications that mimic DNA unwinding between the cleavage sites, we show that formation and/or stabilization of an underwound pre-cleavage intermediate depends upon cooperation of the hairpin-binding module and catalytic domain. The phenotype of the mutants argues that the pre-cleavage intermediate promotes strand ejection to favor the forward reaction and that subsequent hairpin capture is a reversible reaction step. These reaction features are proposed to promote hairpin formation over strand resealing while allowing reversal back to substrate of aborted reactions. PMID:26007659

  16. Intermediate-grade squamous intraepithelial lesion may be a valid diagnostic/interpretive category.

    PubMed

    Ravinsky, Esther; Baker, Patricia

    2009-02-01

    We undertook this study to assess the characteristics of smears with features intermediate between high-grade squamous intraepithelial lesion (HSIL) and low-grade squamous intraepithelial lesion (ISIL). We also wanted to determine how these smears correlate with high risk biopsy diagnosis and to compare this with the biopsy correlation of LSIL and HSIL. Seventy-four squamous intraepithelial lesion (SIL) smears were identified as intermediate-grade SIL smears taken at colposcopy in a 1 year period. They were correlated with concurrent colposcopically guided biopsies. Thirty-five percent of cases with intermediate-grade SIL smears had a biopsy diagnosis of moderate dysplasia or higher as compared with 12% for LSIL 74% for HSIL. This confirmed our hypothesis that intermediate-grade SIL smears have a rate of biopsy diagnosis of moderate dysplasia or higher intermediate to that of LSIL and HSIL. PMID:19021235

  17. 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

  18. Peripherality of breakup reactions

    NASA Astrophysics Data System (ADS)

    Capel, P.; Nunes, F. M.

    2007-05-01

    The sensitivity of elastic breakup to the interior of the projectile wave function is analyzed. Breakup calculations of loosely bound nuclei (B8 and Be11) are performed with two different descriptions of the projectile. The descriptions differ strongly in the interior of the wave function, but exhibit identical asymptotic properties, namely the same asymptotic normalisation coefficient, and phase shifts. Breakup calculations are performed at intermediate energies (40 70 MeV/nucleon) on lead and carbon targets as well as at low energy (26 MeV) on a nickel target. No dependence on the projectile description is observed. This result confirms that breakup reactions are peripheral in the sense that they probe only the external part of the wave function. These measurements are thus not directly sensitive to the total normalization of the wave function, i.e., spectroscopic factor.

  19. Base-Mediated Intermolecular sp2 C-H Bond Arylation via Benzyne Intermediates

    PubMed Central

    Truong, Thanh; Daugulis, Olafs

    2011-01-01

    A transition-metal-free method for arylation of heterocycle and arene carbon-hydrogen bonds by aryl chlorides and fluorides has been developed. The reactions proceed via aryne intermediates and are highly regioselective with respect to the C-H bond coupling component. PMID:21384889

  20. Double NN scattering effects in the ion-ion interaction at intermediate energies

    SciTech Connect

    Rego, R.A.; Hussein, M.S.

    1986-06-01

    The double scattering correction to the ion-ion double folding interaction is calculated for the /sup 12/C+/sup 12/C system. The multiple scattering theory was employed for the purpose. The effect of this correction on the total reaction cross section at intermediate energies (approx.100 MeV/nucleon) was found to be less than 10%.

  1. Unveiling New Degradation Intermediates/Pathways from the Photocatalytic Degradation of Microcystin-LR

    EPA Science Inventory

    This study focuses on the identification of reaction intermediates formed during the photocatalytic degradation of the cyanotoxin microcystin-LR with immobilized TiO2 Tphotocatalysts at neutral pH. To differentiate between impurities already existing in the MC-LR stand...

  2. Signal interactions between nitric oxide and reactive oxygen intermediates in the plant hypersensitive disease resistance response

    Microsoft Academic Search

    Massimo Delledonne; Jürgen Zeier; Adriano Marocco; Chris Lamb

    2001-01-01

    Nitric oxide (NO) and reactive oxygen intermediates (ROIs) play key roles in the activation of disease resistance mechanisms both in animals and plants. In animals NO cooperates with ROIs to kill tumor cells and for macrophage killing of bacteria. Such cytotoxic events occur because unregulated NO levels drive a diffusion-limited reaction with O2 to generate peroxynitrite (ONOO), a mediator of

  3. Total syntheses of (?)-vallesamidine and related Aspidosperma and Hunteria type indole alkaloids from the common intermediate

    Microsoft Academic Search

    Hideo Tanino; Kazuhisa Fukuishi; Mina Ushiyama; Kunisuke Okada

    2004-01-01

    A new synthetic method of (?)-vallesamidine, including a unique 2,2,3-trialkylindoline skeleton, was developed by reductive radical cyclization reaction from the 2,3-dialkylindole derivative, which has been known to be an intermediate for the synthesis of aspidospermidine.

  4. 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.

  5. 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

  6. Deconstruction of vulnerability to complex diseases: enhanced effect sizes and power of intermediate phenotypes.

    PubMed

    Goldman, David; Ducci, Francesca

    2007-01-01

    The deconstruction of vulnerability to complex disease with the help of intermediate phenotypes, including the heritable and disease-associated endophenotypes, is a legacy of Henri Begleiter. Systematic searches for genes influencing complex disorders, including bipolar disorder, have recently been completed using whole genome association (WGA), identifying a series of validated loci. Using this information, it is possible to compare effect sizes of disease loci discovered in very large samples to the effect sizes of replicated functional loci determining intermediate phenotypes that are of essential interest in psychiatric disorders. It is shown that the genes influencing intermediate phenotypes tend to have a larger effect size. Furthermore, the WGA results reveal that the number of loci of large effect size for complex diseases is limited, and yet multiple functional loci have already been identified for intermediate phenotypes relevant to psychiatric diseases, and without the benefit of WGA. PMID:17982585

  7. Electrocatalysis of hydrogen peroxide reactions on perovskite oxides: experiment versus kinetic modeling.

    PubMed

    Poux, T; Bonnefont, A; Ryabova, A; Kéranguéven, G; Tsirlina, G A; Savinova, E R

    2014-07-21

    Hydrogen peroxide has been identified as a stable intermediate of the electrochemical oxygen reduction reaction on various electrodes including metal, metal oxide and carbon materials. In this article we study the hydrogen peroxide oxidation and reduction reactions in alkaline medium using a rotating disc electrode (RDE) method on oxides of the perovskite family (LaCoO3, LaMnO3 and La0.8Sr0.2MnO3) which are considered as promising electrocatalytic materials for the cathode of liquid and solid alkaline fuel cells. The experimental findings, such as the higher activity of Mn-compared to that of Co-perovskites, the shape of RDE curves, and the influence of the H2O2 concentration, are rationalized with the help of a microkinetic model. PMID:24643772

  8. Infrared matrix isolation study of the reaction between trichloromethane and oxygen atoms

    NASA Astrophysics Data System (ADS)

    Schriver, L.; Gauthier-Roy, B.; Carrère, D.; Schriver, A.; Abouaf-Marguin, L.

    1992-07-01

    The reactions of CHCl 3 with both excited and ground state oxygen atoms have been investigated in argon matrices at 12 K by Fourier transform IR spectroscopy. Ozone was employed as photolytic oxygen atoms source. Products were identified by using 18O 3 precursor and deuterium substitution in the CH bond. Two major pathways are observed for the CHCl 3+O( 1D) reaction and lead, respectively, to complexed phosgene and formylchloride as primary products. With O( 3P) the second pathway is forbidden. No evidence is obtained for the formation of an intermediate species. Appearance of CO⋯HCl complexes is attributed to a secondary photolysis decomposition of primary products. A change in the primary products distribution is observed with CDCl 3 and confirmed by relative kinetic studies of the products growth.

  9. Characterization of Onthophagus sellatus as the major intermediate host of the dog esophageal worm Spirocerca lupi in Israel

    Microsoft Academic Search

    Yuval Gottlieb; Alex Markovics; Eyal Klement; Shachar Naor; Michael Samish; Itamar Aroch; Eran Lavy

    2011-01-01

    Spirocerca lupi is a parasitic nematode of dogs, that causes significant morbidity and mortality. Its intermediate hosts in Israel have never been described. The aim of this study was therefore to identify the intermediate hosts of S. lupi in Israel and to describe their abundance and annual infection rate with the nematode, in different microenvironments (i.e., the effects of irrigation

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

    ERIC Educational Resources Information Center

    Lang, Thomas

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

  11. 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…

  12. Transient folding intermediates characterized by protein engineering

    Microsoft Academic Search

    Andreas Matouschek; James T. Kellis; Luis Serrano; Mark Bycroft; Alan R. Fersht

    1990-01-01

    Kinetic experiments on engineered mutants of barnase detect an intermediate on the folding pathway and allow the mapping of the tertiary interactions of the side chains and their energetics. Many of the interactions present in the final folded state tend to be either fully formed or not formed at all in the intermediate or subsequent transition state for folding, but

  13. 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.

  14. 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.…

  15. 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

  16. 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

  17. Business Machine Maintenance. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    McMinn, Robert

    Several intermediate performance objectives and corresponding criterion measures are listed for each of 28 terminal objectives presented in this guide for an intermediate business machine maintenance course at the secondary level. (For the basic course guide see CE 010 949.) Titles of the 28 terminal objective sections are Career Opportunities,…

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

    ERIC Educational Resources Information Center

    Jones, Marion

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

  19. Diesel Mechanics. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Tidwell, Joseph

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

  20. Remote recondenser with intermediate temperature heat sink

    Microsoft Academic Search

    Bartlett

    1989-01-01

    A cryogenic recondenser is described for recondensing cryogen retained in a storage vessel having a radiation shield, the recondenser comprising: cooling means positioned outside of the storage vessel, the cooling means having a mechanical refrigerator and precooling a volume of working gas; an intermediate transfer line leading from an intermediate portion of the cooling means into the storage vessel; an

  1. Imports of intermediate inputs and plant survival

    Microsoft Academic Search

    Ricardo A. López

    2006-01-01

    Previous studies have analyzed the effect of exporting on plant survival. No work has been done examining the role of importing intermediate inputs on survival. Using plant-level data from Chile we find that importing intermediate inputs increases the probability of survival.

  2. A smoke screen theory of financial intermediation

    E-print Network

    Boyer, Edmond

    mitigating the underlying ap- propriability problem. Keywords : financial intermediation, informational rent of signaling information1. In contrast, we develop in this paper a theory of financial intermediation where investors care about the appropriability of the information they produce when they engage

  3. 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.

  4. A multistep screening method to identify genes using evolutionary transcriptome of plants.

    PubMed

    Kim, Chang-Kug; Lim, Hye-Min; Na, Jong-Kuk; Choi, Ji-Weon; Sohn, Seong-Han; Park, Soo-Chul; Kim, Young-Hwan; Kim, Yong-Kab; Kim, Dool-Yi

    2014-01-01

    We introduced a multistep screening method to identify the genes in plants using microarrays and ribonucleic acid (RNA)-seq transcriptome data. Our method describes the process for identifying genes using the salt-tolerance response pathways of the potato (Solanum tuberosum) plant. Gene expression was analyzed using microarrays and RNA-seq experiments that examined three potato lines (high, intermediate, and low salt tolerance) under conditions of salt stress. We screened the orthologous genes and pathway genes involved in salinity-related biosynthetic pathways, and identified nine potato genes that were candidates for salinity-tolerance pathways. The nine genes were selected to characterize their phylogenetic reconstruction with homologous genes of Arabidopsis thaliana, and a Circos diagram was generated to understand the relationships among the selected genes. The involvement of the selected genes in salt-tolerance pathways was verified by reverse transcription polymerase chain reaction analysis. One candidate potato gene was selected for physiological validation by generating dehydration-responsive element-binding 1 (DREB1)-overexpressing transgenic potato plants. The DREB1 overexpression lines exhibited increased salt tolerance and plant growth when compared to that of the control. Although the nine genes identified by our multistep screening method require further characterization and validation, this study demonstrates the power of our screening strategy after the initial identification of genes using microarrays and RNA-seq experiments. PMID:24812480

  5. A Multistep Screening Method to Identify Genes Using Evolutionary Transcriptome of Plants

    PubMed Central

    Kim, Chang-Kug; Lim, Hye-Min; Na, Jong-Kuk; Choi, Ji-Weon; Sohn, Seong-Han; Park, Soo-Chul; Kim, Young-Hwan; Kim, Yong-Kab; Kim, Dool-Yi

    2014-01-01

    We introduced a multistep screening method to identify the genes in plants using microarrays and ribonucleic acid (RNA)-seq transcriptome data. Our method describes the process for identifying genes using the salt-tolerance response pathways of the potato (Solanum tuberosum) plant. Gene expression was analyzed using microarrays and RNA-seq experiments that examined three potato lines (high, intermediate, and low salt tolerance) under conditions of salt stress. We screened the orthologous genes and pathway genes involved in salinity-related biosynthetic pathways, and identified nine potato genes that were candidates for salinity-tolerance pathways. The nine genes were selected to characterize their phylogenetic reconstruction with homologous genes of Arabidopsis thaliana, and a Circos diagram was generated to understand the relationships among the selected genes. The involvement of the selected genes in salt-tolerance pathways was verified by reverse transcription polymerase chain reaction analysis. One candidate potato gene was selected for physiological validation by generating dehydration-responsive element-binding 1 (DREB1)-overexpressing transgenic potato plants. The DREB1 overexpression lines exhibited increased salt tolerance and plant growth when compared to that of the control. Although the nine genes identified by our multistep screening method require further characterization and validation, this study demonstrates the power of our screening strategy after the initial identification of genes using microarrays and RNA-seq experiments. PMID:24812480

  6. Highly Diastereoselective Alkylation of a Pyroglutamate Derivative with an Electrophile Obtained from Indole. Synthesis of a Potential Intermediate for the Preparation of the Natural Sweetener (-)-Monatin

    Microsoft Academic Search

    Davi de Jesus Oliveira; Femando Coelho

    2000-01-01

    The synthesis of a potential intermediate for the preparation of the very intensive sweetening agent (-)-Monatin is described. The synthesis is based on a highly diastereoselective alkylation reaction of a pyroglutamate derivative with an electrophile obtained from indole.

  7. 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

  8. 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

  9. New possible ionic structures in Wittig reaction: Analysis of stability and rotation barriers by semiempirical PM3 method

    NASA Astrophysics Data System (ADS)

    Mracec, Maria; Pascariu, Aurelia; Berger, Stefan; Mracec, Mircea

    For the Wittig reaction between butylidentriphenylphosphorane and benzaldehyde studied previously using NMR spectroscopy, three ionic intermediates have been proposed in order to explain the ?stereochemical drift? (different ratio in oxaphosphetane stereoisomers compared with the ratio of the final Z/E olefins). In this paper, the PM3 semiempirical MO method was applied on the proposed ionic intermediates. Two of the ionic intermediates could lead to a shift of the reaction towards the final products, olefins and phosphine oxide, while the third intermediate could be implicated in a retro-Wittig reaction.

  10. Global reaction route mapping of isomerization pathways of exotic C{sub 6}H molecular species

    SciTech Connect

    Vikas,, E-mail: qlabspu@pu.ac.in, E-mail: qlabspu@yahoo.com; Kaur, Gurpreet [Quantum Chemistry Group, Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh 160 014 (India)] [Quantum Chemistry Group, Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh 160 014 (India)

    2013-12-14

    C{sub 6}H radical is known to exist in the astrophysical environment in linear form; however, it may originate from nonlinear isomeric forms. Potential energy surface of C{sub 6}H is explored to search isomers of C{sub 6}H and transition states connecting them. This work reports first-ever identification of reaction pathways for isomerization of C{sub 6}H. The reaction route search is performed through global reaction route mapping method, which utilizes an uphill walking technique based on an anharmonic downward distortion following approach to search intermediates and transition states. The computations performed at the CASSCF/aug-cc-pVTZ, CCSD(T)/6-311++G(d,p)//DFT/B3LYP/6-311++G(d,p), and DFT/B3LYP/aug-cc-pVTZ levels of the theory identified 14 isomers (including 8 new isomeric forms of C{sub 6}H) and 28 transition states. Most of the identified isomers are found to have significant multireference character. The kinetic stability and natural bond orbital analysis of the identified isomers is also investigated. The isomeric forms are further characterized using spectral analysis involving rotational constants, vibrational frequencies, and Raman scattering activities as well as analyzing the effect of isotopic substitution of hydrogen on the spectral features. This study proposes that the linear-C{sub 6}H can readily isomerize to a six-member ring isomer.

  11. Remote recondenser with intermediate temperature heat sink

    SciTech Connect

    Bartlett, A.J.

    1989-01-10

    A cryogenic recondenser is described for recondensing cryogen retained in a storage vessel having a radiation shield, the recondenser comprising: cooling means positioned outside of the storage vessel, the cooling means having a mechanical refrigerator and precooling a volume of working gas; an intermediate transfer line leading from an intermediate portion of the cooling means into the storage vessel; an end of the intermediate transfer line in the storage vessel being in thermal communication with but out of physical contact with the radiation shield of the storage vessel, partially pre-cooled gas being transferred in the intermediate transfer line from the intermediate portion of the cooling means to the end of the intermediate transfer line and back to the cooling means for further cooling, the transferring being in a manner such that the end of the intermediate transfer line through the partially pre-cooled gas removes heat from the radiation shield; and a final transfer line removeably leading into the storage vessel from the cooling means, an end of the final transfer line in the storage vessel being in heat exchange relation with boil-off from the cryogen retained in the storage vessel, pre-cooled gas being transferred in the final transfer line from the cooling means to the end of the final transfer line in the storage vessel in a manner which cools and recondenses the boil-off.

  12. Degradation of thiamethoxam and metoprolol by UV, O3 and UV/O3 hybrid processes: Kinetics, degradation intermediates and toxicity

    NASA Astrophysics Data System (ADS)

    Šoji?, D.; Despotovi?, V.; Or?i?, D.; Szabó, E.; Arany, E.; Armakovi?, S.; Illés, E.; Gajda-Schrantz, K.; Dombi, A.; Alapi, T.; Sajben-Nagy, E.; Palágyi, A.; Vágvölgyi, Cs.; Manczinger, L.; Bjelica, L.; Abramovi?, B.

    2012-11-01

    SummaryA comprehensive study of the degradation of thiamethoxam (THIA) and metoprolol (MET) was conducted by using UV-induced photolysis (? = 254 nm), ozonation, and a combination of these methods. In order to investigate how molecular structure of the substrate influences the rate of its degradation, we compared these three processes for the insecticide THIA and the drug MET (a ?1-blocker). Of the three treatments applied, the UV photolysis and the combination of UV/O3 were found to be most effective in the degradation of THIA, while the UV/O3 process appeared to be the most efficient in terms of MET decay. The degradation kinetics was monitored by LC-DAD, and spectrophotometry, while the mineralization of the substrates was studied by TOC analysis. Reaction intermediates were studied in detail and a number of them were identified using LC-MS (ESI+/ESI-). Both parent compounds showed slight toxic effects towards algae Pseudokirchneriella subcapitata and bacteria Vibrio fischeri. However, the toxicity of the solutions containing also the degradation intermediates appeared to be much higher for all the test organisms. The inhibition/mortality rates were reduced most efficiently by the UV/O3 procedure. Ames test and Comet assay were used to follow the genotoxicity during the degradation of the studied compounds. Genotoxic intermediates were frequently detected in the case of MET in the UV treatment alone or in the presence of ozone. Treatments of THIA samples resulted less frequently in genotoxic intermediates. To our best knowledge, this work is the first genotoxicological investigation dealing with the photolytic degradation process of the studied compounds.

  13. Novel Approaches for the Accumulation of Oxygenated Intermediates to Multi-Millimolar Concentrations

    PubMed Central

    Krebs, Carsten; Dassama, Laura M. K.; Matthews, Megan L.; Jiang, Wei; Price, John C.; Korboukh, Victoria; Li, Ning; Bollinger, J. Martin

    2012-01-01

    Metalloenzymes that utilize molecular oxygen as a co-substrate catalyze a wide variety of chemically difficult oxidation reactions. Significant insight into the reaction mechanisms of these enzymes can be obtained by the application of a combination of rapid kinetic and spectroscopic methods to the direct structural characterization of intermediate states. A key limitation of this approach is the low aqueous solubility (< 2 mM) of the co-substrate, O2, which undergoes further dilution (typically by one-third or one-half) upon initiation of reactions by rapid-mixing. This situation imposes a practical upper limit on [O2] (and therefore on the concentration of reactive intermediate(s) that can be rapidly accumulated) of ?1-1.3 mM in such experiments as they are routinely carried out. However, many spectroscopic methods benefit from or require significantly greater concentrations of the species to be studied. To overcome this problem, we have recently developed two new approaches for the preparation of samples of oxygenated intermediates: (1) direct oxygenation of reduced metalloenzymes using gaseous O2 and (2) the in situ generation of O2 from chlorite catalyzed by the enzyme chlorite dismutase (Cld). Whereas the former method is applicable only to intermediates with half lives of several minutes, owing to the sluggishness of transport of O2 across the gas-liquid interface, the latter approach has been successfully applied to trap several intermediates at high concentration and purity by the freeze-quench method. The in situ approach permits generation of a pulse of at least 5 mM O2 within ? 1 ms and accumulation of O2 to effective concentrations of up to ? 11 mM (i.e. ? 10-fold greater than by the conventional approach). The use of these new techniques for studies of oxygenases and oxidases is discussed. PMID:24368870

  14. 19-electron intermediates in the Ligand Substitution of CpW(CO)3with a Lewis Base

    SciTech Connect

    Cahoon, James F.; Kling, Matthias F.; Sawyer, Karma R.; Frei,Heinz; Harris, Charles B.

    2005-12-14

    Odd electron species are important intermediates in organometallic chemistry, participating in a variety of catalytic and electron-transfer reactions which produce stable even-electron products. While electron deficient 17-electron (17e) radicals have been well characterized, the possible existence of short-lived 19-electron (19e) radicals has been a subject of continuing investigation. 19e radicals have been postulated as intermediates in the photochemical ligand substitution and disproportionation reactions of organometallic dimers containing a single metal-metal bond, yet the reactions of these intermediates on diffusion-limited time scales (ns-{micro}s) have never been directly observed. This study resolves the 19e dynamics in the ligand substitution of 17e radicals CpW(CO){sub 3}{sup {sm_bullet}} (Cp = C{sub 5}H{sub 5}) with the Lewis base P(OMe){sub 3}, providing the first complete description 19e reactivity.

  15. Dynamic flexibility in the light reactions of photosynthesis governed by both electron and proton transfer reactions

    Microsoft Academic Search

    David M. Kramer; Thomas J. Avenson; Gerald E. Edwards

    2004-01-01

    Plant photosynthesis performs the remarkable feat of converting light energy into usable chemical forms, which involves taming highly reactive intermediates without harming plant cells. This requires an apparatus that is not only efficient and robust but also flexible in its responses to changing environmental conditions. It also requires that the output of the energy-storing reactions be matched with the demands

  16. Aromatic Monomers by in Situ Conversion of Reactive Intermediates in the Acid-Catalyzed Depolymerization of Lignin.

    PubMed

    Deuss, Peter J; Scott, Martin; Tran, Fanny; Westwood, Nicholas J; de Vries, Johannes G; Barta, Katalin

    2015-06-17

    Conversion of lignin into well-defined aromatic chemicals is a highly attractive goal but is often hampered by recondensation of the formed fragments, especially in acidolysis. Here, we describe new strategies that markedly suppress such undesired pathways to result in diverse aromatic compounds previously not systematically targeted from lignin. Model studies established that a catalytic amount of triflic acid is very effective in cleaving the ?-O-4 linkage, most abundant in lignin. An aldehyde product was identified as the main cause of side reactions under cleavage conditions. Capturing this unstable compound by reaction with diols and by in situ catalytic hydrogenation or decarbonylation lead to three distinct groups of aromatic compounds in high yields acetals, ethanol and ethyl aromatics, and methyl aromatics. Notably, the same product groups were obtained when these approaches were successfully extended to lignin. In addition, the formation of higher molecular weight side products was markedly suppressed, indicating that the aldehyde intermediates play a significant role in these processes. The described strategy has the potential to be generally applicable for the production of interesting aromatic compounds from lignin. PMID:26001165

  17. Identification of a Discrete Intermediate in the Assembly\\/Disassembly of Physalis Mottle Tymovirus through Mutational Analysis

    Microsoft Academic Search

    Mira Sastri; D. Srihari Reddy; S. Sri Krishna; M. R. N. Murthy; H. S. Savithri

    1999-01-01

    Assembly intermediates of icosahedral viruses are usually transient and are difficult to identify. In the present investigation, site-specific and deletion mutants of the coat protein gene of physalis mottle tymovirus (PhMV) were used to delineate the role of specific amino acid residues in the assembly of the virus and to identify intermediates in this process. N-terminal 30, 34, 35 and

  18. Gang Identifiers and Terminology.

    ERIC Educational Resources Information Center

    Cantrell, Mary Lynn

    1992-01-01

    Provides lists of gang identifiers and terminology. Suggests that, to find out names and associated identifiers of local gangs, readers should talk to their local police. Included in listing are descriptions of gang-related symbols, physical signals, graffiti, slogans, right-left rules, colors, clothing, jewelry, hair styles, and fingernails. Also…

  19. Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach

    PubMed Central

    Kotera, Masaaki; Tabei, Yasuo; Yamanishi, Yoshihiro; Muto, Ai; Moriya, Yuki; Tokimatsu, Toshiaki; Goto, Susumu

    2014-01-01

    Motivation: Metabolic pathway analysis is crucial not only in metabolic engineering but also in rational drug design. However, the biosynthetic/biodegradation pathways are known only for a small portion of metabolites, and a vast amount of pathways remain uncharacterized. Therefore, an important challenge in metabolomics is the de novo reconstruction of potential reaction networks on a metabolome-scale. Results: In this article, we develop a novel method to predict the multistep reaction sequences for de novo reconstruction of metabolic pathways in the reaction-filling framework. We propose a supervised approach to learn what we refer to as ‘multistep reaction sequence likeness’, i.e. whether a compound–compound pair is possibly converted to each other by a sequence of enzymatic reactions. In the algorithm, we propose a recursive procedure of using step-specific classifiers to predict the intermediate compounds in the multistep reaction sequences, based on chemical substructure fingerprints/descriptors of compounds. We further demonstrate the usefulness of our proposed method on the prediction of enzymatic reaction networks from a metabolome-scale compound set and discuss characteristic features of the extracted chemical substructure transformation patterns in multistep reaction sequences. Our comprehensively predicted reaction networks help to fill the metabolic gap and to infer new reaction sequences in metabolic pathways. Availability and implementation: Materials are available for free at http://web.kuicr.kyoto-u.ac.jp/supp/kot/ismb2014/ Contact: goto@kuicr.kyoto-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24931980

  20. Unconventional actin conformations localize on intermediate filaments in mitosis

    SciTech Connect

    Hubert, Thomas; Vandekerckhove, Joel; Gettemans, Jan, E-mail: jan.gettemans@vib-ugent.be

    2011-03-04

    Research highlights: {yields} Unconventional actin conformations colocalize with vimentin on a cage-like structure in metaphase HEK 293T cells. {yields} These conformations are detected with the anti-actin antibodies 1C7 ('lower dimer') and 2G2 ('nuclear actin'), but not C4 (monomeric actin). {yields} Mitotic unconventional actin cables are independent of filamentous actin or microtubules. {yields} Unconventional actin colocalizes with vimentin on a nocodazole-induced perinuclear dense mass of cables. -- Abstract: Different structural conformations of actin have been identified in cells and shown to reside in distinct subcellular locations of cells. In this report, we describe the localization of actin on a cage-like structure in metaphase HEK 293T cells. Actin was detected with the anti-actin antibodies 1C7 and 2G2, but not with the anti-actin antibody C4. Actin contained in this structure is independent of microtubules and actin filaments, and colocalizes with vimentin. Taking advantage of intermediate filament collapse into a perinuclear dense mass of cables when microtubules are depolymerized, we were able to relocalize actin to such structures. We hypothesize that phosphorylation of intermediate filaments at mitosis entry triggers the recruitment of different actin conformations to mitotic intermediate filaments. Storage and partition of the nuclear actin and antiparallel 'lower dimer' actin conformations between daughter cells possibly contribute to gene transcription and transient actin filament dynamics at G1 entry.

  1. Synthetic Routes to Methylerythritol Phosphate Pathway Intermediates and Downstream Isoprenoids

    PubMed Central

    Jarchow-Choy, Sarah K; Koppisch, Andrew T; Fox, David T

    2014-01-01

    Isoprenoids constitute the largest class of natural products with greater than 55,000 identified members. They play essential roles in maintaining proper cellular function leading to maintenance of human health, plant defense mechanisms against predators, and are often exploited for their beneficial properties in the pharmaceutical and nutraceutical industries. Most impressively, all known isoprenoids are derived from one of two C5-precursors, isopentenyl diphosphate (IPP) or dimethylallyl diphosphate (DMAPP). In order to study the enzyme transformations leading to the extensive structural diversity found within this class of compounds there must be access to the substrates. Sometimes, intermediates within a biological pathway can be isolated and used directly to study enzyme/pathway function. However, the primary route to most of the isoprenoid intermediates is through chemical catalysis. As such, this review provides the first exhaustive examination of synthetic routes to isoprenoid and isoprenoid precursors with particular emphasis on the syntheses of intermediates found as part of the 2C-methylerythritol 4-phosphate (MEP) pathway. In addition, representative syntheses are presented for the monoterpenes (C10), sesquiterpenes (C15), diterpenes (C20), triterpenes (C30) and tetraterpenes (C40). Finally, in some instances, the synthetic routes to substrate analogs found both within the MEP pathway and downstream isoprenoids are examined. PMID:25009443

  2. Intermediated Technology Use in Developing Communities

    E-print Network

    Narasayya, Vivek

    Methods Field Work Participant observation Semi-structured interviews Surveys Photo diaries Personas Landscape Infrastructure Discontinuous, unstable Usage Communication Entertainment Devices Nokia 2600 phone!" [Mythili, 30] Proximate translation #12;Designing for intermediation · Concerns: Accuracy, Storage

  3. The Italian Intermediate School: Knowledge and Control

    ERIC Educational Resources Information Center

    Steedman, Hilary

    1974-01-01

    Author explored certain aspects of B. Bernstein's thesis concerning educational knowledge and social control by applying his model of collection and integrated codes and their power and control components to an examination of the Italian intermediate school. (Author/RK)

  4. Intermediate/Advanced Research Design and Statistics

    NASA Technical Reports Server (NTRS)

    Ploutz-Snyder, Robert

    2009-01-01

    The purpose of this module is To provide Institutional Researchers (IRs) with an understanding of the principles of advanced research design and the intermediate/advanced statistical procedures consistent with such designs

  5. Cu-catalyzed cross-coupling reactions of epoxides with organoboron compounds.

    PubMed

    Lu, Xiao-Yu; Yang, Chu-Ting; Liu, Jing-Hui; Zhang, Zheng-Qi; Lu, Xi; Lou, Xin; Xiao, Bin; Fu, Yao

    2015-02-11

    A copper-catalyzed cross-coupling reaction of epoxides with arylboronates is described. This reaction is not limited to aromatic epoxides, because aliphatic epoxides are also suitable substrates. In addition, N-sulfonyl aziridines can be successfully converted into the products. This reaction provides convenient access to ?-phenethyl alcohols, which are valuable synthetic intermediates. PMID:25564373

  6. 29 CFR 452.81 - Rights in intermediate body elections.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...false Rights in intermediate body elections. 452.81 Section...81 Rights in intermediate body elections. While the literal language in section 401(c) relating...provisions also apply to intermediate bodies. 42 The Department of...

  7. 29 CFR 452.81 - Rights in intermediate body elections.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...false Rights in intermediate body elections. 452.81 Section...81 Rights in intermediate body elections. While the literal language in section 401(c) relating...provisions also apply to intermediate bodies. 42 The Department of...

  8. 29 CFR 452.81 - Rights in intermediate body elections.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...false Rights in intermediate body elections. 452.81 Section...81 Rights in intermediate body elections. While the literal language in section 401(c) relating...provisions also apply to intermediate bodies. 42 The Department of...

  9. 29 CFR 452.81 - Rights in intermediate body elections.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...false Rights in intermediate body elections. 452.81 Section...81 Rights in intermediate body elections. While the literal language in section 401(c) relating...provisions also apply to intermediate bodies. 42 The Department of...

  10. 29 CFR 452.81 - Rights in intermediate body elections.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...false Rights in intermediate body elections. 452.81 Section...81 Rights in intermediate body elections. While the literal language in section 401(c) relating...provisions also apply to intermediate bodies. 42 The Department of...

  11. Intermediate-Frequency-to-Video-Band Converter

    NASA Technical Reports Server (NTRS)

    Ham, N. C.; Chavez, V. M.; Chen, V. S.; Sato, T.

    1986-01-01

    Analog and digital circuits combined to frequency-convert from intermediate frequencies directly to video-band frequencies to meet stringent requirements. IF-to-video-band converter operates on principle of signal-band cancellation in phase-quadrature circuits. Downconverts intermediate frequencies directly to video-band frequencies to near-zero frequency with good image-band rejection and low phase variation within passband.

  12. Composite particle production in intermediate-energy heavy ion collisions

    SciTech Connect

    Curtin, M.W.

    1986-01-01

    Experimental and theoretical studies of composite fragment production in intermediate energy heavy ion collisions presented. Inclusive yield measurements were undertaken to differentiate between the various theoretical approaches. The reaction /sup 14/N + /sup nat/Ag at incident energies of 20A, 30 A, and 35 A MeV leading to complex fragments in the range 3 less than or equal to 7 less than or equal to 24 was examined. Theoretical studies had suggested that the production cross sections of such complex fragments might provide evidence for the occurrence of a liquid-gas phase transition in nuclear systems. Since other reactions mechanisms also lead to complex fragment production, these processes were also investigated. The experimental data indicate that further experiments are required before a definitive conclusion can be reached regarding the occurrence of critical phenomena such as predicted in the phase transition theories. Results suggest that further experiments on heavy ion reactions are necessary in the energy range 40A MeV less than or equal to E/sub inc/ less than or equal to 100A MeV.

  13. Initialization effect in heavy-ion collisions at intermediate energies

    SciTech Connect

    Yong Gaochan; Zuo Wei; Zhang Xunchao [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Gao Yuan [School of Information Engineering, Hangzhou Dianzi University, Hangzhou 310018 (China)

    2011-09-15

    Based on the isospin-dependent Boltzmann-Uehling-Uhlenbeck transport model plus the Skyrme force parameters, the initialization effect is studied in heavy-ion collisions at intermediate energies. We find that there are moderate initialization effects in the following observables: free neutron to proton ratio (n/p), {pi}{sup -}/{pi}{sup +} ratio, and neutron to proton differential flow (F{sub n-p}{sup x}). Effects of initialization are larger for charged {pi}{sup -}/{pi}{sup +} ratios than for n/p ratios. And the effects of initialization are more evident in nuclear reactions at lower incident beam energies. We do not see large effects of initialization for light reaction systems or large asymmetric (neutron-richer) reaction systems. We also see relatively large effects of initialization on the neutron to proton differential flow at relatively lower incident beam energies or with large impact parameters. These results may be useful for the delicate studies of the equation of state of asymmetric nuclear matter.

  14. Arenium ions are not obligatory intermediates in electrophilic aromatic substitution

    PubMed Central

    Galabov, Boris; Koleva, Gergana; Simova, Svetlana; Hadjieva, Boriana; Schaefer, Henry F.; Schleyer, Paul von Ragué

    2014-01-01

    Our computational and experimental investigation of the reaction of anisole with Cl2 in nonpolar CCl4 solution challenges two fundamental tenets of the traditional SEAr (arenium ion) mechanism of aromatic electrophilic substitution. Instead of this direct substitution process, the alternative addition–elimination (AE) pathway is favored energetically. This AE mechanism rationalizes the preferred ortho and para substitution orientation of anisole easily. Moreover, neither the SEAr nor the AE mechanisms involve the formation of a ?-complex (Wheland-type) intermediate in the rate-controlling stage. Contrary to the conventional interpretations, the substitution (SEAr) mechanism proceeds concertedly via a single transition state. Experimental NMR investigations of the anisole chlorination reaction course at various temperatures reveal the formation of tetrachloro addition by-products and thus support the computed addition–elimination mechanism of anisole chlorination in nonpolar media. The important autocatalytic effect of the HCl reaction product was confirmed by spectroscopic (UV-visible) investigations and by HCl-augmented computational modeling. PMID:24972792

  15. Higher order antibunching in intermediate states

    E-print Network

    A Verma; N K Sharma; A Pathak

    2007-06-05

    Since the introduction of binomial state as an intermediate state, different intermediate states have been proposed. Different nonclassical effects have also been reported in these intermediate states. But till now higher order antibunching or higher order subpoissonian photon statistics is predicted only in one type of intermediate state, namely shadowed negative binomial state. Recently we have shown the existence of higher order antibunching in some simple nonlinear optical processes to establish that higher order antibunching is not a rare phenomenon (J. Phys. B 39 (2006) 1137). To establish our earlier claim further, here we have shown that the higher order antibunching can be seen in different intermediate states, such as binomial state, reciprocal binomial state, hypergeometric state, generalized binomial state, negative binomial state and photon added coherent state. We have studied the possibility of observing the higher order subpoissonian photon statistics in different limits of intermediate states. The effect of different control parameters have also been studied in this connection and it has been shown that the depth of nonclassicality can be tuned by controlling various physical parameters.

  16. Pyrite formation via kinetic intermediates through low-temperature solid-state metathesis.

    PubMed

    Martinolich, Andrew J; Neilson, James R

    2014-11-01

    The preparation of materials with limited phase stabilities yet high kinetic activation barriers is challenging. Knowledge of their possible formation pathways aids in addressing these challenges. Metathesis reactions present an approach to circumvent these barriers; however, solid-state metathesis reactions are often too rapid from extensive self-heating to understand the reaction. The stoichiometric reaction of MCl2 salts (M = Mn, Fe, Co, Ni, Cu, Zn) with Na2S2 enables the formation of pyrite (FeS2), CoS2, and NiS2 at low temperatures (250-350 °C). Na2S2 has the same polyanionic dimer as found in the pyrite structure, which would suggest the possibility of a facile ion-exchange reaction. However, from high-resolution synchrotron X-ray diffraction and differential scanning calorimetry, the energetic driving force does not appear to result solely from NaCl formation but also from formation of intermediate and pyrite phases. It is apparent that the reaction proceeds through polyanionic disproportionation and formation of a low-density alkali-rich intermediate, followed by anionic comproportionation and atomic rearrangement into the pyrite phase. These results have profound implications for the use of low-temperature metathesis in achieving materials by design. PMID:25313440

  17. [Investigation of cytokeratin and vimentin intermediate filaments in polycystic ovaries (PCOS) -- presence and specific structure of Balbiani body in primordial follicles].

    PubMed

    Zhivkova, R; Panevska, M; Delimitreva, S; Markova, M; Nikolova, V; Chakarova, I; Tenev, T; Hadzhinesheva, V; Mainhard, K; Vatev, I

    2013-01-01

    Despite of the importance of cytoskeletal proteins for ovarian function and pathology, very few studies have addressed the presence and distribution of these proteins in polycystic ovaries. We investigated sections of human polycystic ovarian tissue for vimentin and a set of cytokeratins by epifluorescence. The studied proteins showed strong colocalization. Positive reaction was detected in two main ovarian compartments: with weak intensity in follicular cells and very strong in perinuclear position in oocytes of primordial follicles. Epifluorescent study of the oocytes from primordial follicles allowed us to identify the immunopositive structure in oocytes as Balbiani body, a transient organelle responsible for establishing oocyte polarity and ooplasm gradients in nonmammalian vertebrates. Our results suggest functional interaction of different types of cytoplasmic intermediate filament proteins in polycystic ovaries and a possible importance of the Balbiani body for human oogenesis in norm and pathology. PMID:24505633

  18. Identifying the Acoustic Neuroma

    MedlinePLUS

    ... Search ANAUSA.org Connect with us! Identifying the Acoustic Neuroma Advances in medicine have made possible the identification of small acoustic neuromas (those still confined to the internal auditory ...

  19. Dry Molten Globule Intermediates and the Mechanism of Protein Unfolding

    PubMed Central

    Baldwin, Robert L.; Frieden, Carl; Rose, George D.

    2010-01-01

    New experimental results show that either gain or loss of close packing can be observed as a discrete step in protein folding or unfolding reactions. This finding poses a significant challenge to the conventional two-state model of protein folding. Results of interest involve dry molten globule intermediates, an expanded form of the protein that lacks appreciable solvent. When an unfolding protein expands to the dry molten globule state, side chains unlock and gain conformational entropy, while liquid-like van der Waals interactions persist. Four unrelated proteins are now known to form dry molten globules as the first step of unfolding, suggesting that such an intermediate may well be commonplace in both folding and unfolding. Data from the literature show that peptide amide protons are protected in the dry molten globule, indicating that backbone structure is intact despite loss of side chain close packing. Other complementary evidence shows that secondary structure formation provides a major source of compaction during folding. In our model, the major free-energy barrier separating unfolded from native states usually occurs during the transition between the unfolded state and the dry molten globule. The absence of close packing at this barrier provides an explanation for why ?-values, derived from a Brønsted-Leffler plot, depend primarily on structure at the mutational site and not on specific side chain interactions. The conventional two-state folding model breaks down when there are dry molten globule intermediates, a realization that has major implications for future experimental work on the mechanism of protein folding. PMID:20635344

  20. Kinetic intermediates en route to the final serpin-protease complex: studies of complexes of ?1-protease inhibitor with trypsin.

    PubMed

    Maddur, Ashoka A; Swanson, Richard; Izaguirre, Gonzalo; Gettins, Peter G W; Olson, Steven T

    2013-11-01

    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

  1. The intermediate line region of QSOs

    NASA Technical Reports Server (NTRS)

    Brotherton, M. S.; Wills, Beverley J.; Francis, Paul J.; Steidel, Charles C.

    1994-01-01

    Our recent statistical investigations of broad UV lines of luminous quasars (QSOs) suggest that the traditional broadline region (BLR) consists of two components-one of width approximately 2000 km/s FWHM with the peak within a few hundred kilometers per second of the systemic redshift, and another very broad component of width greater than or equal to 7000 km/s FWHM and blueshifted by greater than or equal to 1000 km/s. Differences in the relative strengths of these components account for much of the diversity of broad-line profiles, as well as relations among line strength, line width, asymmetry, and peak blueshift. We have suggested that the narrower component arises in a distinct intermediate-line region (ILR) that is an inner extension of the narrow-line region (NLR). We form spectra of the ILR and very broad line region (VBLR) in two complementary ways. First, using a small sample of high-quality spectra, we difference two composite spectra, one with FWHM (sub C IV) approximately 3000 km/s, the other with FWHM (sub C IV) approximately 7000 km/s (essentially a VBLR spectrum)-revealing a narrower line spectrum with FWHM approximately 2000 km/s. Second, we use a principal component analysis of 200 low signal-to-noise ratio spectra from the Large Bright Quasar Survey. The ILR is identified with the first principal component-that component accounting for most of the spectrum-to-spectrum variation. The VBLR spectrum is derived by subtracting this ILR from the mean spectrum. The two methods yield similar results, and the spectra of the ILR and VBLR are very different. Additional support for the existence of two component is the lack of a correlation between the equivalent widths of the ILR and VBLR. We discuss the relationships between the VBLR, the ILR, and the traditional NLR. The ILR line intensity ratios are distinctly different from those of the VBLR, with (relative to C IV lambda 1549) stronger Lyman alpha and weaker N v lambda 1240, lambda 1400 feature, He II lambda 1640, O III lambda 1663, and Al III lambda 1860. Comparison with other active galactic nuclei (AGN) emission-line regions shows that the ILR spectrum tends to be intermediate between that of the VBLR and that of gas more distant from the ionizing continuum, such as the NLR and extended Lyman alpha nebulosity. Comparison of the spectra with results from photoionization models suggests that, compared with the VBLR, the ILR is about 10 times more distant from the ionizing continuum (approximately 1 pc), 100 to 1000 times less dense (10(exp 10)/cu cm), and has a smaller covering factor (less than or approximately 3%, compared with approximately 24% for the VBLR).

  2. Oxidation intermediates of ?-glucosyl rutin by pulse radiolysis

    NASA Astrophysics Data System (ADS)

    Nakata, Kunihiko; Morita, Naofumi; Horii, Hideo; Chubachi, Mitsuo

    1997-11-01

    Transient intermediates generated in the reaction of ?-glucosyl rutin (G-rutin) with the OH radical or the azide radical were investigated by pulse radiolysis. The OH radical reacted with G-rutin to produce the OH-adduct radical, followed by deprotonation in neutral and acidic solutions. In alkaline solutions, the OH-adduct di-anion radical formed from the di-anions of G-rutin were dehydrated to the phenoxyl radical. On the other hand, G-rutin was oxidized to one-electron oxidized cation radical by the azide radical. The pK a values of the OH radical adduct were found to be 6.83 ± 0.10 and 8.87 ± 0.13. While, the pK a values of the phenoxyl radical of G-rutin were found to be 7.52 ± 0.11 and 9.95 ± 0.13.

  3. Investigation of transverse collective flow of intermediate mass fragments

    SciTech Connect

    Kohley, Z.; May, L. W.; Wuenschel, S.; Soisson, S. N.; Stein, B. C.; Yennello, S. J. [Chemistry Department, Texas A and M University, College Station, Texas 77843 (United States); Cyclotron Institute, Texas A and M University, College Station, Texas 77843 (United States); Bonasera, A. [Cyclotron Institute, Texas A and M University, College Station, Texas 77843 (United States); Laboratori Nazionali del Sud, Istituto Nazionale di Fisica Nucleare, I-95123 Catania (Italy); Hagel, K.; Tripathi, R.; Wada, R.; Shetty, D. V.; Galanopoulos, S.; Smith, W. B. [Cyclotron Institute, Texas A and M University, College Station, Texas 77843 (United States); Souliotis, G. A. [Cyclotron Institute, Texas A and M University, College Station, Texas 77843 (United States); Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens GR-15771 (Greece); Mehlman, M. [Cyclotron Institute, Texas A and M University, College Station, Texas 77843 (United States); Physics and Astronomy Department, Texas A and M University, College Station, Texas 77843 (United States)

    2010-12-15

    The transverse flow of intermediate mass fragments (IMFs) has been investigated for the 35 MeV/u {sup 70}Zn+{sup 70}Zn, {sup 64}Zn+{sup 64}Zn, and {sup 64}Ni+{sup 64}Ni systems. A transition from the IMF transverse flow strongly depending on the mass of the system, in the most violent collisions, to a dependence on the charge of the system, for the peripheral reactions, is shown. This transition was shown to be sensitive to the density dependence of the symmetry energy using the antisymmetrized molecular-dynamics model. The results present an observable, the IMF transverse flow, that can be used to probe the nuclear equation of state. Comparison with the simulation demonstrated a preference for a stiff density dependence of the symmetry energy.

  4. MATERIALS SYSTEM FOR INTERMEDIATE TEMPERATURE SOLID OXIDE FUEL CELL

    SciTech Connect

    Uday B. Pal; Srikanth Gopalan

    2004-02-15

    AC complex impedance spectroscopy studies were conducted on symmetrical cells of the type [gas, electrode/LSGM electrolyte/electrode, gas]. The electrode materials were slurry-coated on both sides of the LSGM electrolyte support. The electrodes selected for this investigation are candidate materials for SOFC electrodes. Cathode materials include La{sub 1-x}Sr{sub x}MnO{sub 3} (LSM), LSCF (La{sub 1-x}Sr{sub x}Co{sub y}Fe{sub 1-y}O{sub 3}), a two-phase particulate composite consisting of LSM + doped-lanthanum gallate (LSGM), and LSCF + LSGM. Pt metal electrodes were also used for the purpose of comparison. Anode material investigated was the Ni + GDC composite. The study revealed important details pertaining to the charge-transfer reactions that occur in such electrodes. The information obtained can be used to design electrodes for intermediate temperature SOFCs based on LSGM electrolyte.

  5. Formamidine Reactions

    E-print Network

    Griffin, E. L.

    1913-05-15

    of Hantzsch. (1), and the method of Uhlenhuth (2) was found to be not very much more satisfactory owing to the fact that the methyl lsoxazolon broKe down too much on heating Better results were obtained when the oxime of acetoacetic ester was obtained...,C ~ CH RNrOM-SHR = CH.C - C::CHHKR * li , II I H-0- CO U-0- CO * E2sTHx since methyl lsoxazolon is made by the reaction of hydroxylamine hydrochlorid on acetoacetic ester, it was thought that it might be possible to maKe the amldo methylene...

  6. Copolymerization of carbon dioxide and butadiene via a lactone intermediate.

    PubMed

    Nakano, Ryo; Ito, Shingo; Nozaki, Kyoko

    2014-04-01

    Although carbon dioxide has attracted broad interest as a renewable carbon feedstock, its use as a monomer in copolymerization with olefins has long been an elusive endeavour. A major obstacle for this process is that the propagation step involving carbon dioxide is endothermic; typically, attempted reactions between carbon dioxide and an olefin preferentially yield olefin homopolymerization. Here we report a strategy to circumvent the thermodynamic and kinetic barriers for copolymerizations of carbon dioxide and olefins by using a metastable lactone intermediate, 3-ethylidene-6-vinyltetrahydro-2H-pyran-2-one, which is formed by the palladium-catalysed condensation of carbon dioxide and 1,3-butadiene. Subsequent free-radical polymerization of the lactone intermediate afforded polymers of high molecular weight with a carbon dioxide content of 33 mol% (29 wt%). Furthermore, the protocol was applied successfully to a one-pot copolymerization of carbon dioxide and 1,3-butadiene, and one-pot terpolymerizations of carbon dioxide, butadiene and another 1,3-diene. This copolymerization technique provides access to a new class of polymeric materials made from carbon dioxide. PMID:24651200

  7. Copolymerization of carbon dioxide and butadiene via a lactone intermediate

    NASA Astrophysics Data System (ADS)

    Nakano, Ryo; Ito, Shingo; Nozaki, Kyoko

    2014-04-01

    Although carbon dioxide has attracted broad interest as a renewable carbon feedstock, its use as a monomer in copolymerization with olefins has long been an elusive endeavour. A major obstacle for this process is that the propagation step involving carbon dioxide is endothermic; typically, attempted reactions between carbon dioxide and an olefin preferentially yield olefin homopolymerization. Here we report a strategy to circumvent the thermodynamic and kinetic barriers for copolymerizations of carbon dioxide and olefins by using a metastable lactone intermediate, 3-ethylidene-6-vinyltetrahydro-2H-pyran-2-one, which is formed by the palladium-catalysed condensation of carbon dioxide and 1,3-butadiene. Subsequent free-radical polymerization of the lactone intermediate afforded polymers of high molecular weight with a carbon dioxide content of 33 mol% (29 wt%). Furthermore, the protocol was applied successfully to a one-pot copolymerization of carbon dioxide and 1,3-butadiene, and one-pot terpolymerizations of carbon dioxide, butadiene and another 1,3-diene. This copolymerization technique provides access to a new class of polymeric materials made from carbon dioxide.

  8. ?-Terpineol reactions with the nitrate radical: Rate constant and gas-phase products

    NASA Astrophysics Data System (ADS)

    Jones, Brian T.; Ham, Jason E.

    The bimolecular rate constant of k rad +?-terpineol (16 ± 4) × 10 -12 cm 3 molecule -1 s -1 was measured using the relative rate technique for the reaction of the nitrate radical (NO 3rad ) with ?-terpineol (2-(4-methyl-1-cyclohex-3-enyl)propan-2-ol) at 297 ± 3 K and 1 atmosphere total pressure. To more clearly define part of ?-terpineol's indoor environment degradation mechanism, the products of ?-terpineol + NO 3rad reaction were investigated. The identified reaction products were: acetone, glyoxal (HC( dbnd O)C( dbnd O)H), and methylglyoxal (CH 3C( dbnd O)C( dbnd O)H). The use of derivatizing agents O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine (PFBHA) and N, O-bis(trimethylsilyl) trifluoroacetamide (BSTFA) were used to propose the other major reaction products: 6-hydroxyhept-5-en-2-one, 4-(1-hydroxy-1-methylethyl)-1-methyl-2-oxocyclohexyl nitrate, 5-(1-hydroxy-1-methylethyl)-2-oxocyclohexyl nitrate, 1-formyl-5-hydroxy-4-(hydroxymethyl)-1,5-dimethylhexyl nitrate, and 1,4-diformyl-5-hydroxy-1,5-dimethylhexyl nitrate. The elucidation of these products was facilitated by mass spectrometry of the derivatized reaction products coupled with plausible ?-terpineol + NO 3rad reaction mechanisms based on previously published volatile organic compound + NO 3rad gas-phase mechanisms. The additional gas-phase products (2,6,6-trimethyltetrahydro-2 H-pyran-2,5-dicarbaldehyde and 2,2-dimethylcyclohexane-1,4-dicarbaldehyde) are proposed to be the result of cyclization through a reaction intermediate.

  9. MOMDIS: a Glauber model computer code for knockout reactions

    NASA Astrophysics Data System (ADS)

    Bertulani, C. A.; Gade, A.

    2006-09-01

    A computer program is described to calculate momentum distributions in stripping and diffraction dissociation reactions. A Glauber model is used with the scattering wavefunctions calculated in the eikonal approximation. The program is appropriate for knockout reactions at intermediate energy collisions ( 30 MeV?E/nucleon?2000 MeV). It is particularly useful for reactions involving unstable nuclear beams, or exotic nuclei (e.g., neutron-rich nuclei), and studies of single-particle occupancy probabilities (spectroscopic factors) and other related physical observables. Such studies are an essential part of the scientific program of radioactive beam facilities, as in for instance the proposed RIA (Rare Isotope Accelerator) facility in the US. Program summaryTitle of program: MOMDIS (MOMentum DIStributions) Catalogue identifier:ADXZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXZ_v1_0 Computers: The code has been created on an IBM-PC, but also runs on UNIX or LINUX machines Operating systems: WINDOWS or UNIX Program language used: Fortran-77 Memory required to execute with typical data: 16 Mbytes of RAM memory and 2 MB of hard disk space No. of lines in distributed program, including test data, etc.: 6255 No. of bytes in distributed program, including test data, etc.: 63 568 Distribution format: tar.gz Nature of physical problem: The program calculates bound wavefunctions, eikonal S-matrices, total cross-sections and momentum distributions of interest in nuclear knockout reactions at intermediate energies. Method of solution: Solves the radial Schrödinger equation for bound states. A Numerov integration is used outwardly and inwardly and a matching at the nuclear surface is done to obtain the energy and the bound state wavefunction with good accuracy. The S-matrices are obtained using eikonal wavefunctions and the "t- ??" method to obtain the eikonal phase-shifts. The momentum distributions are obtained by means of a Gaussian expansion of integrands. Main integrals are performed with the Simpson's method. Typical running time: Almost all CPU time is consumed by calculations of integrals, specially for transverse momentum distributions which involves multiple integral loops. It takes up to 30 min on a 2 GHz Intel P4-processor machine.

  10. Crystal structure of Mycobacterium tuberculosis polyketide synthase 11 (PKS11) reveals intermediates in the synthesis of methyl-branched alkylpyrones.

    PubMed

    Gokulan, Kuppan; O'Leary, Seán E; Russell, William K; Russell, David H; Lalgondar, Mallikarjun; Begley, Tadhg P; Ioerger, Thomas R; Sacchettini, James C

    2013-06-01

    PKS11 is one of three type III polyketide synthases (PKSs) identified in Mycobacterium tuberculosis. Although many PKSs in M. tuberculosis have been implicated in producing complex cell wall glycolipids, the biological function of PKS11 is unknown. PKS11 has previously been proposed to synthesize alkylpyrones from fatty acid substrates. We solved the crystal structure of M. tuberculosis PKS11 and found the overall fold to be similar to other type III PKSs. PKS11 has a deep hydrophobic tunnel proximal to the active site Cys-138 to accommodate substrates. We observed electron density in this tunnel from a co-purified molecule that was identified by mass spectrometry to be palmitate. Co-crystallization with malonyl-CoA (MCoA) or methylmalonyl-CoA (MMCoA) led to partial turnover of the substrate, resulting in trapped intermediates. Reconstitution of the reaction in solution confirmed that both co-factors are required for optimal activity, and kinetic analysis shows that MMCoA is incorporated first, then MCoA, followed by lactonization to produce methyl-branched alkylpyrones. PMID:23615910

  11. Structure and Reaction of Oxametallacycles Derived from Styrene Oxide on Ag(110).

    SciTech Connect

    Lukaski, Adrienne C.; Enever, Michael C.; Barteau, Mark A.

    2007-08-15

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Styrene oxide forms a strongly bound oxametallacycle intermediate via activated adsorption on the Ag(110) surface. The oxametallacycle species derived from styrene oxide on Ag(110) fits well with the family of oxametallacycles identified previously in studies of nonallylic epoxides with unsaturated substituent groups on silver. Temperature-programmed reaction experiments demonstrate that styrene oxide ring opens at the substituted carbon, and Density Functional Theory calculations indicate that the phenyl ring of the resulting oxametallacycle is oriented nearly parallel to the Ag(110) surface. Interaction of the phenyl group with the silver surface stabilizes this intermediate relative to that derived from the mono-olefin epoxide, ethylene oxide. During temperature-programmed reaction, the oxametallacycle undergoes ring-closure to reform styrene oxide and isomerization to phenylacetaldehyde at 505 K on Ag(11 0). Styrene oxide-derived oxametallacycles exhibit similar ring-closure behavior on the Ag(111) surface.

  12. Substrate dependent reaction channels of the Wolff–Kishner reduction reaction: A theoretical study

    PubMed Central

    Zeng, Guixiang; Guan, Wei; Sakaki, Shigeyoshi

    2014-01-01

    Summary Wolff–Kishner reduction reactions were investigated by DFT calculations for the first time. B3LYP/6-311+G(d,p) SCRF=(PCM, solvent = 1,2-ethanediol) optimizations were carried out. To investigate the role of the base catalyst, the base-free reaction was examined by the use of acetone, hydrazine (H2N–NH2) and (H2O)8. A ready reaction channel of acetone ? acetone hydrazine (Me2C=N–NH2) was obtained. The channel involves two likely proton-transfer routes. However, it was found that the base-free reaction was unlikely at the N2 extrusion step from the isopropyl diimine intermediate (Me2C(H)–N=N–H). Two base-catalyzed reactions were investigated by models of the ketone, H2N–NH2 and OH?(H2O)7. Here, ketones are acetone and acetophenone. While routes of the ketone ? hydrazone ? diimine are similar, those from the diimines are different. From the isopropyl diimine, the N2 extrusion and the C–H bond formation takes place concomitantly. The concomitance leads to the propane product concertedly. From the (1-phenyl)ethyl substituted diimine, a carbanion intermediate is formed. The para carbon of the phenyl ring of the anion is subject to the protonation, which leads to a 3-ethylidene-1,4-cyclohexadiene intermediate. Its [1,5]-hydrogen migration gives the ethylbenzene product. For both ketone substrates, the diimines undergoing E2 reactions were found to be key intermediates. PMID:24605145

  13. Greigite: a true intermediate on the polysulfide pathway to pyrite

    PubMed Central

    Hunger, Stefan; Benning, Liane G

    2007-01-01

    The formation of pyrite (FeS2) from iron monosulfide precursors in anoxic sediments has been suggested to proceed via mackinawite (FeS) and greigite (Fe3S4). Despite decades of research, the mechanisms of pyrite formation are not sufficiently understood because solid and dissolved intermediates are oxygen-sensitive and poorly crystalline and therefore notoriously difficult to characterize and quantify. In this study, hydrothermal synchrotron-based energy dispersive X-ray diffraction (ED-XRD) methods were used to investigate in situ and in real-time the transformation of mackinawite to greigite and pyrite via the polysulfide pathway. The rate of formation and disappearance of specific Bragg peaks during the reaction and the changes in morphology of the solid phases as observed with high resolution microscopy were used to derive kinetic parameters and to determine the mechanisms of the reaction from mackinawite to greigite and pyrite. The results clearly show that greigite is formed as an intermediate on the pathway from mackinawite to pyrite. The kinetics of the transformation of mackinawite to greigite and pyrite follow a zero-order rate law indicating a solid-state mechanism. The morphology of greigite and pyrite crystals formed under hydrothermal conditions supports this conclusion and furthermore implies growth of greigite and pyrite by oriented aggregation of nanoparticulate mackinawite and greigite, respectively. The activation enthalpies and entropies of the transformation of mackinawite to greigite, and of greigite to pyrite were determined from the temperature dependence of the rate constants according to the Eyring equation. Although the activation enthalpies are uncharacteristic of a solid-state mechanism, the activation entropies indicate a large increase of order in the transition state, commensurate with a solid-state mechanism. PMID:17376247

  14. The quaternary hemoglobin conformation regulates the formation of the nitrite-induced bioactive intermediate and the dissociation of nitric oxide from this intermediate

    PubMed Central

    Rifkind, Joseph M.; Nagababu, Enika; Ramasamy, Somasundaram

    2011-01-01

    Deoxyhemoglobin reduces nitrite to nitric oxide (NO). In order to study the effect of the hemoglobin quaternary conformation on the nitrite reaction, we compared T-state deoxyhemoglobin with R-state deoxyhemoglobin produced by reacting hemoglobin with carboxypeptidase-A prior to deoxygenation. The nitrite reaction with deoxyhemoglobin was followed by chemiluminescence, electron paramagnetic resonance and visible spectroscopy. The initial steps in this reaction involve the binding of nitrite to deoxyhemoglobin followed by the formation of an electron delocalized metastable intermediate that retains potential NO bioactivity. This reaction is shown by visible spectroscopy to occur 5.6 times faster in the R-state than in the T-state. However, the dissociation of NO from the delocalized intermediate is shown to be facilitated by the T-quaternary conformation with a 9.6 fold increase in the rate constant. The preferred NO-release in the T-state, which has a higher affinity for the membrane, can result in the NO diffusing out of the RBC and being released to the vasculature at low partial pressures of oxygen. PMID:21236353

  15. ?2-Triterpenes: Early intermediates in the diagenesis of terrigenous triterpenoids

    NASA Astrophysics Data System (ADS)

    ten Haven, H. L.; Peakman, T. M.; Rullkötter, J.

    1992-05-01

    A series of ?2-triterpenoids (oleana-2,12-diene, oleana-2,13(18)-diene, oleana-2,18-diene, ursa-2, 12-diene, and taraxera-2,14-diene) has been identified in Holocene buried mangrove sediments (Florida, USA) by comparison of the mass spectra of and by co-injections with authentic standards. In the Oligocene Brandon lignite (Vermont, USA) oleana-2,12-diene and oleana-2,13(18)-diene were also identified, along with two A-ring contracted amyrin derivatives. By comparison with the sedimentary occurrence of related analogues of oxyallobetulin and betulin and the demonstrated diagenetic formation of lup-2-ene from lupan-3-one, these novel terrigenous biological markers are considered diagenetic products formed by dehydration of precursor molecules, such as ?- and ?-amyrin, and taraxerol. The identification of these early intermediates brings us one step closer to the full understanding of the diagenetic fate of terrigenous triterpenoids.

  16. 40 CFR 721.10212 - 1,2-Ethanediol, reaction products with epichlorohydrin.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...Uses for Specific Chemical Substances ...2-Ethanediol, reaction products with epichlorohydrin. (a) Chemical substance and...reporting. (1) The chemical substance identified...2-ethanediol, reaction products...

  17. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...Uses for Specific Chemical Substances § 721...rosin amidoamine reaction product (generic). (a) Chemical substance and significant...reporting. (1) The chemical substance identified...rosin amidoamine reaction product...

  18. 40 CFR 721.10212 - 1,2-Ethanediol, reaction products with epichlorohydrin.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...Uses for Specific Chemical Substances ...2-Ethanediol, reaction products with epichlorohydrin. (a) Chemical substance and...reporting . (1) The chemical substance identified...2-ethanediol, reaction products...

  19. 40 CFR 721.3805 - Formaldehyde, reaction products with 1,3-benzenedimethanamine and bisphenol A.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...Uses for Specific Chemical Substances ...Formaldehyde, reaction products with...bisphenol A. (a) Chemical substance and...reporting. (1) The chemical substance identified as formaldehyde, reaction products...

  20. 40 CFR 721.3805 - Formaldehyde, reaction products with 1,3-benzenedimethanamine and bisphenol A.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...Uses for Specific Chemical Substances ...Formaldehyde, reaction products with...bisphenol A. (a) Chemical substance and...reporting. (1) The chemical substance identified as formaldehyde, reaction products...

  1. 40 CFR 721.10212 - 1,2-Ethanediol, reaction products with epichlorohydrin.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...Uses for Specific Chemical Substances ...2-Ethanediol, reaction products with epichlorohydrin. (a) Chemical substance and...reporting . (1) The chemical substance identified...2-ethanediol, reaction products...

  2. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...Uses for Specific Chemical Substances § 721...rosin amidoamine reaction product (generic). (a) Chemical substance and significant...reporting. (1) The chemical substance identified...rosin amidoamine reaction product...

  3. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...Uses for Specific Chemical Substances § 721...rosin amidoamine reaction product (generic). (a) Chemical substance and significant...reporting. (1) The chemical substance identified...rosin amidoamine reaction product...

  4. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...Uses for Specific Chemical Substances § 721...rosin amidoamine reaction product (generic). (a) Chemical substance and significant...reporting. (1) The chemical substance identified...rosin amidoamine reaction product...

  5. 40 CFR 721.10212 - 1,2-Ethanediol, reaction products with epichlorohydrin.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...Uses for Specific Chemical Substances ...2-Ethanediol, reaction products with epichlorohydrin. (a) Chemical substance and...reporting . (1) The chemical substance identified...2-ethanediol, reaction products...

  6. 40 CFR 721.3805 - Formaldehyde, reaction products with 1,3-benzenedimethanamine and bisphenol A.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...Uses for Specific Chemical Substances ...Formaldehyde, reaction products with...bisphenol A. (a) Chemical substance and...reporting. (1) The chemical substance identified as formaldehyde, reaction products...

  7. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...Uses for Specific Chemical Substances § 721...rosin amidoamine reaction product (generic). (a) Chemical substance and significant...reporting. (1) The chemical substance identified...rosin amidoamine reaction product...

  8. Hydrolysis of peptides by carboxypeptidase A: equilibrium trapping of the ES2 intermediate.

    PubMed

    Geoghegan, K F; Galdes, A; Hanson, G; Holmquist, B; Auld, D S; Vallee, B L

    1986-08-12

    The cobalt absorption and electron paramagnetic resonance (EPR) spectra of cobalt carboxypeptidase undergo unique variations on formation of catalytic peptide and ester intermediates as previously recorded in cryoenzymologic experiments employing rapid-scanning spectroscopy and cryotrapping [Geoghegan, K. F., Galdes, A., Martinelli, R. A., Holmquist, B., Auld, D.S., & Vallee, B. L. (1983) Biochemistry 22, 2255-2262]. We here describe a means of stabilizing these intermediates, which we have termed "equilibrium trapping". It allows peptide intermediates to be observed for longer periods (much greater than 1 min) at ambient as well as subzero temperatures. The reaction intermediate with the rapidly turned over peptide substrate Dns-Ala-Ala-Phe is trapped when the cobalt enzyme (greater than 10 microM) has catalyzed the attainment of chemical equilibrium between high concentrations of the hydrolysis products Dns-Ala-Ala, 10 mM, and L-phenylalanine, 50 mM, and the product of their coupling Dns-Ala-Ala-Phe. Under these conditions, Dns-Ala-Ala-Phe is present in the equilibrated substrate-product reaction mixture at a level that exceeds the one predicted on the basis of K'eq for hydrolysis of this substrate and is close to the enzyme concentration. Other pairs of peptide hydrolysis products yield similar results. Visible absorption and EPR spectra of the cobalt enzyme show that the synthesized peptide binds to the active site in the mode previously recognized as the ES2 catalytic intermediate in peptide hydrolysis. Equilibrium trapping of the ES2 intermediate allows analysis of its physicochemical properties by methods that could not be employed readily under cryoenzymological conditions, e.g., circular dichroic and magnetic circular dichroic spectra.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:3021197

  9. Nuclear disassembly in violent central collisions at intermediate energies: (65-115)A MeV 40Ar+Cu, Ag, Au

    NASA Astrophysics Data System (ADS)

    Colin, E.; Sun, Rulin; Ajitanand, N. N.; Alexander, John M.; Barton, M. A.; Deyoung, P. A.; Drake, K. L.; Elmaani, A.; Gelderloos, C. J.; Gualtieri, E. E.; Guinet, D.; Hannuschke, S.; Jaasma, J. A.; Kowalski, L.; Lacey, Roy A.; Lauret, J.; Norbeck, E.; Pak, R.; Peaslee, G. F.; Stern, M.; Stone, N. T.; Sundbeck, S. D.; Vander Molen, A. M.; Westfall, G. D.; Yang, L. B.; Yee, J.

    2000-06-01

    Nuclear disassembly into light and intermediate mass ejectiles is searched for in 40Ar + Cu, Ag, Au reactions of 17-115 A MeV. Distributions in fragment mass versus velocity show that such nuclear disassembly does occur for 65-115 A MeV. However, it is very rare, with much less abundance than reactions leading to a massive residual nucleus.

  10. Metal alloy identifier

    DOEpatents

    Riley, William D. (Avondale, MD); Brown, Jr., Robert D. (Avondale, MD)

    1987-01-01

    To identify the composition of a metal alloy, sparks generated from the alloy are optically observed and spectrographically analyzed. The spectrographic data, in the form of a full-spectrum plot of intensity versus wavelength, provide the "signature" of the metal alloy. This signature can be compared with similar plots for alloys of known composition to establish the unknown composition by a positive match with a known alloy. An alternative method is to form intensity ratios for pairs of predetermined wavelengths within the observed spectrum and to then compare the values of such ratios with similar values for known alloy compositions, thereby to positively identify the unknown alloy composition.

  11. Experimental and theoretical studies of OH-initiated reactions of isoprene

    E-print Network

    Zhang, Dan

    2001-01-01

    -flow reactor coupled to chemical ionization mass spectrometry (CIMS) detection. Intermediate species such as OH-isoprene adduct and hydroxy-isoprene peroxy radical were detected directly with the CIMS method. Bimolecular reaction rate constants were determined...

  12. Dynamics of Radical Ion Pairs following Photoinduced Electron Transfer in Solvents with Low and Intermediate Polarities.

    PubMed

    Mentel, Kamila K; Nunes, Rui M D; Serpa, Carlos; Arnaut, Luis G

    2015-06-18

    Fluorescence quenching of p-xylene, naphthalene, or pyrene by fumaronitrile in apolar solvents and in solvents of intermediate polarities leads to weakly fluorescent radical ion pairs. This emission is assigned to ion pairs in close contact on the basis of their solvent polarity dependence, kinetics, and thermodynamics. The temperature-dependence of the intensity and fluorescence emission maxima of ion pairs in methyl acetate reveals that they have decay channels competitive with their thermal equilibration. The results presented in this work are consistent with the direct formation of contact ion pairs in weakly polar solvents and in solvents of intermediate polarities as the result of bimolecular photoinduced electron transfer reactions between aromatic hydrocarbons and nitriles. The implications of these findings in free-energy relationships of electron transfer reactions are discussed. PMID:25588979

  13. Characterizing millisecond intermediates in hemoproteins using rapid-freeze-quenched resonance Raman spectroscopy

    PubMed Central

    Matsumura, Hirotoshi; Moënne-Loccoz, Pierre

    2014-01-01

    Summary The combination of rapid-freeze-quenching (RFQ) technique and resonance Raman (RR) spectroscopy represents a unique tool to investigate the nature of short-lived intermediates formed during the enzymatic reaction of metalloproteins. Commercially available equipment allows trapping of intermediates within the millisecond to second timescale for low-temperature RR analysis and direct detection of metal-ligand vibrations and porphyrin skeletal vibrations in hemoproteins. This chapter briefly discusses previous RFQ-RR studies carried-out in our laboratory, and presents as a practical example protocols for the preparation of RFQ samples of the reaction of metmyoglobin with nitric oxide (NO) which requires anaerobic conditions. We also describe important controls and practical procedure for the analysis of these samples by low-temperature RR spectroscopy. PMID:24639256

  14. Degradation of Hyaluronic Acid, Poly and MonoSaccharides, and Model Compounds by Hypochlorite: Evidence for Radical Intermediates and Fragmentation

    Microsoft Academic Search

    Clare L. Hawkins; Michael J. Davies

    1998-01-01

    Degradation of hyaluronic acid by oxidants such as HO· and HOCl\\/ClO? is believed to be important in the progression of rheumatoid arthritis. While reaction of hyaluronic acid with HO· has been investigated extensively, reaction with HOCl\\/ClO? is less well defined. Thus, little is known about the site(s) of HOCl\\/ClO? attack, the intermediates formed, or the mechanism(s) of polymer degradation. In

  15. Does P450-type catalysis proceed through a peroxo-iron intermediate? A review of studies with microperoxidase.

    PubMed

    Veeger, Cees

    2002-07-25

    Recent stopped-flow kinetics demonstrated the existence of an intermediate before the occurrence of the final product of the reaction of both iron-containing microperoxidase-8 (Fe(III)MP-8) and manganese-containing microperoxidase-8 (Mn(III)MP-8) with H(2)O(2). The intermediate was assigned to be (hydro)peroxo-iron. With both mini-catalysts the final state obtained after 30-40 ms showed a resemblance to PorM(IV)MP-8[double bond]O(R(+)*); (R(+)*) is a radical located at the peptide. Quantum mechanical calculations indicate that hydroperoxo-iron is inactive as a catalytic intermediate in cytochrome P450 (P450)-type catalysis. Instead, the calculations suggest that peroxo-iron acts as the catalytic intermediate in P450-type catalysis. In addition, the calculations demonstrate that, although less likely, the possibility that oxenoid-iron acts as a catalytic intermediate in P450 catalysis cannot be fully excluded. An interesting aspect of the reactions catalysed by MP-8 is the possibility that, in view of the reversibility of the reactions between (hydro)peroxo-iron and oxenoid-iron, H(2)O plays a decisive role, at least in some cytochromes P450, in the removal of halogens, avoiding the production of compounds hazardous to the organism. PMID:12121760

  16. Probing the Catalytic Mechanism of S-Ribosylhomocysteinase (LuxS) with Catalytic Intermediates and Substrate Analogues

    SciTech Connect

    Gopishetty, Bhaskar; Zhu, Jinge; Rajan, Rakhi; Sobczak, Adam J.; Wnuk, Stanislaw F.; Bell, Charles E.; Pei, Dehua; (OSU); (FIU)

    2009-05-12

    S-Ribosylhomocysteinase (LuxS) cleaves the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine (Hcys) and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of the type II bacterial quorum sensing molecule (AI-2). The catalytic mechanism of LuxS comprises three distinct reaction steps. The first step involves carbonyl migration from the C1 carbon of ribose to C2 and the formation of a 2-ketone intermediate. The second step shifts the C=O group from the C2 to C3 position to produce a 3-ketone intermediate. In the final step, the 3-ketone intermediate undergoes a {beta}-elimination reaction resulting in the cleavage of the thioether bond. In this work, the 3-ketone intermediate was chemically synthesized and shown to be chemically and kinetically competent in the LuxS catalytic pathway. Substrate analogues halogenated at the C3 position of ribose were synthesized and reacted as time-dependent inhibitors of LuxS. The time dependence was caused by enzyme-catalyzed elimination of halide ions. Examination of the kinetics of halide release and decay of the 3-ketone intermediate catalyzed by wild-type and mutant LuxS enzymes revealed that Cys-84 is the general base responsible for proton abstraction in the three reaction steps, whereas Glu-57 likely facilitates substrate binding and proton transfer during catalysis.

  17. Identifying Technical Vocabulary

    ERIC Educational Resources Information Center

    Chung, Teresa Mihwa; Nation, Paul

    2004-01-01

    This study compared four different approaches to identifying technical words in an anatomy text. The first approach used a four step rating scale, and was used as the comparison for evaluating the other three approaches. It had a high degree of reliability. The least successful approach was that using clues provided by the writer such as labels in…

  18. Identifying Critical Job Tasks.

    ERIC Educational Resources Information Center

    Burkhart, Jennifer

    This guide, which is intended for project directors, coordinators, and other professional staff involved in developing and delivering workplace education programs, explains the implications of identifying critical job tasks and details a process by which educational partners can facilitate identification of critical job tasks. First, critical job…

  19. Paramagnetic Intermediates Generated by Radical S-Adenosylmethionine (SAM) Enzymes

    PubMed Central

    2015-01-01

    Conspectus A [4Fe–4S]+ cluster reduces a bound S-adenosylmethionine (SAM) molecule, cleaving it into methionine and a 5?-deoxyadenosyl radical (5?-dA•). This step initiates the varied chemistry catalyzed by each of the so-called radical SAM enzymes. The strongly oxidizing 5?-dA• is quenched by abstracting a H-atom from a target species. In some cases, this species is an exogenous molecule of substrate, for example, l-tyrosine in the [FeFe] hydrogenase maturase, HydG. In other cases, the target is a proteinaceous residue as in all the glycyl radical forming enzymes. The generation of this initial radical species and the subsequent chemistry involving downstream radical intermediates is meticulously controlled by the enzyme so as to prevent unwanted reactions. But the manner in which this control is exerted is unknown. Electron paramagnetic resonance (EPR) spectroscopy has proven to be a valuable tool used to gain insight into these mechanisms. In this Account, we summarize efforts to trap such radical intermediates in radical SAM enzymes and highlight four examples in which EPR spectroscopic results have shed significant light on the corresponding mechanism. For lysine 2,3-aminomutase, nearly each possible intermediate, from an analogue of the initial 5?-dA• to the product radical l-?-lysine, has been explored. A paramagnetic intermediate observed in biotin synthase is shown to involve an auxiliary [FeS] cluster whose bridging sulfide is a co-substrate for the final step in the biosynthesis of vitamin B7. In HydG, the l-tyrosine substrate is converted in unprecedented fashion to a 4-oxidobenzyl radical on the way to generating CO and CN– ligands for the [FeFe] cluster of hydrogenase. And finally, EPR has confirmed a mechanistic proposal for the antibiotic resistance protein Cfr, which methylates the unactivated sp2-hybridized C8-carbon of an adenosine base of 23S ribosomal RNA. These four systems provide just a brief survey of the ever-growing set of radical SAM enzymes. The diverse chemistries catalyzed by these enzymes make them an intriguing target for continuing study, and EPR spectroscopy, in particular, seems ideally placed to contribute to our understanding. PMID:24991701

  20. Paramagnetic intermediates generated by radical S-adenosylmethionine (SAM) enzymes.

    PubMed

    Stich, Troy A; Myers, William K; Britt, R David

    2014-08-19

    A [4Fe-4S](+) cluster reduces a bound S-adenosylmethionine (SAM) molecule, cleaving it into methionine and a 5'-deoxyadenosyl radical (5'-dA(•)). This step initiates the varied chemistry catalyzed by each of the so-called radical SAM enzymes. The strongly oxidizing 5'-dA(•) is quenched by abstracting a H-atom from a target species. In some cases, this species is an exogenous molecule of substrate, for example, L-tyrosine in the [FeFe] hydrogenase maturase, HydG. In other cases, the target is a proteinaceous residue as in all the glycyl radical forming enzymes. The generation of this initial radical species and the subsequent chemistry involving downstream radical intermediates is meticulously controlled by the enzyme so as to prevent unwanted reactions. But the manner in which this control is exerted is unknown. Electron paramagnetic resonance (EPR) spectroscopy has proven to be a valuable tool used to gain insight into these mechanisms. In this Account, we summarize efforts to trap such radical intermediates in radical SAM enzymes and highlight four examples in which EPR spectroscopic results have shed significant light on the corresponding mechanism. For lysine 2,3-aminomutase, nearly each possible intermediate, from an analogue of the initial 5'-dA(•) to the product radical L-?-lysine, has been explored. A paramagnetic intermediate observed in biotin synthase is shown to involve an auxiliary [FeS] cluster whose bridging sulfide is a co-substrate for the final step in the biosynthesis of vitamin B7. In HydG, the L-tyrosine substrate is converted in unprecedented fashion to a 4-oxidobenzyl radical on the way to generating CO and CN(-) ligands for the [FeFe] cluster of hydrogenase. And finally, EPR has confirmed a mechanistic proposal for the antibiotic resistance protein Cfr, which methylates the unactivated sp(2)-hybridized C8-carbon of an adenosine base of 23S ribosomal RNA. These four systems provide just a brief survey of the ever-growing set of radical SAM enzymes. The diverse chemistries catalyzed by these enzymes make them an intriguing target for continuing study, and EPR spectroscopy, in particular, seems ideally placed to contribute to our understanding. PMID:24991701

  1. Transient response of propionaldehyde formation during CO/H{sub 2}/C{sub 2}H{sub 4} reaction on Rh/SiO{sub 2}

    SciTech Connect

    Balakos, M.W.; Chuang, S.S.C. [Univ. of Akron, OH (United States)] [Univ. of Akron, OH (United States)

    1995-02-01

    The transient response of propionaldehyde formation during ethylene hydroformylation over Rh/SiO{sub 2} has been studied by transient isotopic methods combined with in situ infrared spectroscopy at 0.1-0.5 MPa and 503 K. The transient methods used in this study involved pulsing {sup 13}CO into the CO feed flow and switching from CO to {sup 13}CO flow. The C{sub 2}H{sub 5}{sup 13}CHO response to the {sup 13}CO step input was found to be equivalent to the integration of the C{sub 2}H{sub 5}{sup 13}CHO response to the pulse input with respect to time. The pulse method allows the economical use of costly isotope to obtain the transient information that is commonly acquired from the step method. Analysis of the transient response reveals that the propionaldehyde may be formed via (i) the insertion of CO into adsorbed ethyl species to form the acyl intermediate, (ii) hydrogenation of the acyl intermediate to produce adsorbed propionaldehyde, and (iii) desorption of adsorbed propionaldehyde. Increasing the total reaction pressure (i.e, increasing all partial pressures in the same ratios) increases the rate constant for hydrogenation of the acyl intermediate which has been identified as the rate-determining step for propionaldehyde formation at 0.1 MPa. Increasing the pressure also increases the coverage, but decreases the residence time of intermediates leading to propionaldehyde. Steady-state rate measurements show that increasing reaction pressure decreased the overall activation energy and increased both rate and selectivity for propionaldehyde. The increase in the rate constant for hydrogenation of acyl intermediate can be related to the decrease in the overall activation energy for propionaldehyde formation. Rate constant analysis of the propionaldehyde response shows that the rate constant for propionaldehyde formation exhibits a sharp single distribution. 52 refs., 13 figs., 3 tabs.

  2. Synthesis of prostaglandin analogues, latanoprost and bimatoprost, using organocatalysis via a key bicyclic enal intermediate.

    PubMed

    Prévost, Sébastien; Thai, Karen; Schützenmeister, Nina; Coulthard, Graeme; Erb, William; Aggarwal, Varinder K

    2015-02-01

    Two antiglaucoma drugs, bimatoprost and latanoprost, which are analogues of the prostaglandin, PGF2?, have been synthesized in just 7 and 8 steps, respectively. The syntheses employ an organocatalytic aldol reaction that converts succinaldehyde into a key bicyclic enal intermediate, which is primed for attachment of the required lower and upper side chains. By utilizing the crystalline lactone, the drug molecules were prepared in >99% ee. PMID:25582321

  3. Glycerol electro-oxidation on a carbon-supported platinum catalyst at intermediate temperatures

    NASA Astrophysics Data System (ADS)

    Ishiyama, Keisuke; Kosaka, Fumihiko; Shimada, Iori; Oshima, Yoshito; Otomo, Junichiro

    2013-03-01

    The electro-oxidation of glycerol on a carbon-supported platinum catalyst (Pt/C) in combination with a reaction products analysis was investigated at intermediate temperatures (235-260 °C) using a single cell with a CsH2PO4 proton conducting solid electrolyte. A high current density was achieved. The main products were H2, CO2 and CO but the formation of C2 compounds, such as glycolic acid and ethane, was also observed. In addition, several C3 compounds were detected as minor products. A reaction products analysis revealed that the C-C bond dissociation ratio of glycerol was 70-80% at both low and high potentials (>200 mV vs. reversible hydrogen electrode) at 250 °C, suggesting that rapid dissociation occurs on Pt/C. The reaction products analysis also suggested that hydrogen production via thermal decomposition and/or steam reforming of glycerol (indirect path) and direct electro-oxidation of glycerol (direct path) proceed in parallel. More detailed reaction paths involving C1, C2 and C3 reaction products are discussed as well as the possible rate-determining step in glycerol electro-oxidation at intermediate temperatures.

  4. Phenol destruction by photocatalysis on TiO 2: an attempt to solve the reaction mechanism

    Microsoft Academic Search

    Andrzej Sobczy?ski; ?ukasz Duczmal; Wojciech Zmudzi?ski

    2004-01-01

    Six hydroxylated aromatic compounds, p-benzoquinone and four aliphatic compounds were detected as intermediates of the reaction of phenol photocatalytic oxidation in the presence of illuminated TiO2. The concentration of catechol, hydroquinone and p-benzoquinone was determined quantitatively along with that of phenol in the course of the photoreaction. The reactions of TiO2-photooxidation of phenol and its primary intermediates—dihydroxybenzenes show 1st order

  5. The azomethine ylide route to amine C-H functionalization: redox-versions of classic reactions and a pathway to new transformations.

    PubMed

    Seidel, Daniel

    2015-02-17

    Conspectus Redox-neutral methods for the functionalization of amine ?-C-H bonds are inherently efficient because they avoid external oxidants and reductants and often do not generate unwanted byproducts. However, most of the current methods for amine ?-C-H bond functionalization are oxidative in nature. While the most efficient variants utilize atmospheric oxygen as the terminal oxidant, many such transformations require the use of expensive or toxic oxidants, often coupled with the need for transition metal catalysts. Redox-neutral amine ?-functionalizations that involve intramolecular hydride transfer steps provide viable alternatives to certain oxidative reactions. These processes have been known for some time and are particularly well suited for tertiary amine substrates. A mechanistically distinct strategy for secondary amines has emerged only recently, despite sharing common features with a range of classic organic transformations. Among those are such widely used reactions as the Strecker, Mannich, Pictet-Spengler, and Kabachnik-Fields reactions, Friedel-Crafts alkylations, and iminium alkynylations. In these classic processes, condensation of a secondary amine with an aldehyde (or a ketone) typically leads to the formation of an intermediate iminium ion, which is subsequently attacked by a nucleophile. The corresponding redox-versions of these transformations utilize identical starting materials but incorporate an isomerization step that enables ?-C-H bond functionalization. Intramolecular versions of these reactions include redox-neutral amine ?-amination, ?-oxygenation, and ?-sulfenylation. In all cases, a reductive N-alkylation is effectively combined with an oxidative ?-functionalization, generating water as the only byproduct. Reactions are promoted by simple carboxylic acids and in some cases require no additives. Azomethine ylides, dipolar species whose usage is predominantly in [3 + 2] cycloadditions and other pericyclic processes, have been identified as common intermediates. Extension of this chemistry to amine ?,?-difunctionalization has been shown to be possible by way of converting the intermediate azomethine ylides into transient enamines. This Account details the evolution of this general strategy and the progress made to date. Further included is a discussion of related decarboxylative reactions and transformations that result in the redox-neutral aromatization of (partially) saturated cyclic amines. These processes also involve azomethine ylides, reactive intermediates that appear to be far more prevalent in condensation chemistry of amines and carbonyl compounds than previously considered. In contrast, as exemplified by some redox transformations that have been studied in greater detail, iminium ions are not necessarily involved in all amine/aldehyde condensation reactions. PMID:25560649

  6. Studying Ozonolysis Reactions of 2-BUTENES Using Cavity Ring-Down Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wang, Liming; Liu, Yingdi; Campos-Pineda, Mixtli; Priest, Chad; Zhang, Jingsong

    2014-06-01

    Ozonolysis reactions of alkenes are important oxidation pathways of alkenes in the atmosphere, and they are also significant sources of tropospheric hydroxyl radicals. In this work, ozone reactions with trans- and cis-2-butene are studied using cavity ring-down spectroscopy (CRDS). Vinoxy (CH2CHO) radical, a proposed co-product of OH from dissociation of Criegee intermediates following the primary ozonolysis of 2-butenes, is directly observed. The vinoxy formation is found to decrease with increasing pressure. Formaldehyde (HCHO), a side-product in the ozonolysis reactions, is also monitored. Chemical kinetic modeling has been performed to illustrate the reaction mechanisms and to quantify the reactive intermediate and product yields.

  7. General Biology 1, Reactions 1 CHEMICAL REACTIONS *

    E-print Network

    Prestwich, Ken

    General Biology 1, Reactions 1 CHEMICAL REACTIONS * Note: This is the first of a two-part set of notes. This set will review chemical reactions and the next will overview enzymes. What you learn and ribozymes. At their heart, organisms are complex chemical engines. However, many of the chemical reactions

  8. Intro Biology, Reactions 1 CHEMICAL REACTIONS *

    E-print Network

    Prestwich, Ken

    Intro Biology, Reactions 1 CHEMICAL REACTIONS * Note: This is the first of a two-part set of notes. This set will review chemical reactions and the next will overview enzymes. What you learn in these two and ribozymes. At their heart, organisms are complex chemical engines. However, many of the chemical reactions

  9. Risk factors for nosocomial sepsis in newborn intensive and intermediate care units

    Microsoft Academic Search

    M. L. Moro; A. De Toni; I. Stolfi; M. P. Carrieri; M. Braga; C. Zunin

    1996-01-01

    A multicentre prospective study was performed to estimate the incidence of hospital infections and to identify the most relevant risk fac- tors for sepsis in a large and unse- lected population of high-risk new- borns. The study involved 49 neona- tal intensive care units and 17 neona- tal intermediate care units in Italy. Newborns were followed up from admittance to

  10. Intermediate linkages in the relationship between job satisfaction and employee turnover

    Microsoft Academic Search

    William H. Mobley

    1977-01-01

    The relationship between job satisfaction and turnover is significant and consistent, but not particularly strong. A more complete understanding of the psychology of the withdrawal decision process requires investigation beyond the replication of the satisfaction–turnover relationship. Toward this end, a heuristic model of the employee withdrawal decision process, which identifies possible intermediate linkages in the satisfaction–turnover relationship, is presented. Previous

  11. Evaluating EFL Intermediate Teachers' Performance in the Light of Quality Standards in Saudi Arabia

    ERIC Educational Resources Information Center

    Al-Thumali, Amani Dakheel Allah

    2011-01-01

    The present research aimed at four points: First, Identifying the most appropriate standards of EFL Saudi teachers' performance in the light of quality standards. Second, designing an objective and comprehensive evaluation rubric based on quality standards to evaluate EFL Saudi intermediate teachers' performance. Third, determining to what extent…

  12. HIV-1 DIS stem loop forms an obligatory bent kissing intermediate in the dimerization pathway

    PubMed Central

    Mundigala, Hansini; Michaux, Jonathan B.; Feig, Andrew L.; Ennifar, Eric; Rueda, David

    2014-01-01

    The HIV-1 dimerization initiation sequence (DIS) is a conserved palindrome in the apical loop of a conserved hairpin motif in the 5?-untranslated region of its RNA genome. DIS hairpin plays an important role in genome dimerization by forming a ‘kissing complex’ between two complementary hairpins. Understanding the kinetics of this interaction is key to exploiting DIS as a possible human immunodeficiency virus (HIV) drug target. Here, we present a single-molecule Förster resonance energy transfer (smFRET) study of the dimerization reaction kinetics. Our data show the real-time formation and dissociation dynamics of individual kissing complexes, as well as the formation of the mature extended duplex complex that is ultimately required for virion packaging. Interestingly, the single-molecule trajectories reveal the presence of a previously unobserved bent intermediate required for extended duplex formation. The universally conserved A272 is essential for the formation of this intermediate, which is stabilized by Mg2+, but not by K+ cations. We propose a 3D model of a possible bent intermediate and a minimal dimerization pathway consisting of three steps with two obligatory intermediates (kissing complex and bent intermediate) and driven by Mg2+ ions. PMID:24813449

  13. HIV-1 DIS stem loop forms an obligatory bent kissing intermediate in the dimerization pathway.

    PubMed

    Mundigala, Hansini; Michaux, Jonathan B; Feig, Andrew L; Ennifar, Eric; Rueda, David

    2014-06-01

    The HIV-1 dimerization initiation sequence (DIS) is a conserved palindrome in the apical loop of a conserved hairpin motif in the 5'-untranslated region of its RNA genome. DIS hairpin plays an important role in genome dimerization by forming a 'kissing complex' between two complementary hairpins. Understanding the kinetics of this interaction is key to exploiting DIS as a possible human immunodeficiency virus (HIV) drug target. Here, we present a single-molecule Förster resonance energy transfer (smFRET) study of the dimerization reaction kinetics. Our data show the real-time formation and dissociation dynamics of individual kissing complexes, as well as the formation of the mature extended duplex complex that is ultimately required for virion packaging. Interestingly, the single-molecule trajectories reveal the presence of a previously unobserved bent intermediate required for extended duplex formation. The universally conserved A272 is essential for the formation of this intermediate, which is stabilized by Mg(2+), but not by K(+) cations. We propose a 3D model of a possible bent intermediate and a minimal dimerization pathway consisting of three steps with two obligatory intermediates (kissing complex and bent intermediate) and driven by Mg(2+) ions. PMID:24813449

  14. Diamond Deposition on WC/Co Alloy with a Molybdenum Intermediate Layer

    NASA Astrophysics Data System (ADS)

    Liu, Sha; Yu, Zhi-Ming; Yi, Dan-Qing

    It is known that in the condition of chemical vapor deposition (CVD) diamond process, molybdenum is capable of forming carbide known as the "glue" which promotes growth of the CVD diamond, and aids its adhesion by (partial) relief of stresses at the interface. Furthermore, the WC grains are reaction bonded to the Mo2C phase. Therefore, molybdenum is a good candidate material for the intermediate layer between WC-Co substrates and diamond coatings. A molybdenum intermediate layer of 1-3 ?m thickness was magnetron sputter-deposited on WC/Co alloy prior to the deposition of diamond coatings. Diamond films were deposited by hot filament chemical vapor deposition (HFCVD). The chemical quality, morphology, and crystal structure of the molybdenum intermediate layer and the diamond coatings were characterized by means of SEM, EDX, XRD and Raman spectroscopy. It was found that the continuous Mo intermediate layer emerged in spherical shapes and had grain sizes of 0.5-1.5 ?m after 30 min sputter deposition. The diamond grain growth rate was slightly slower as compared with that of uncoated Mo layer on the WC-Co substrate. The morphologies of the diamond films on the WC-Co substrate varied with the amount of Mo and Co on the substrate. The Mo intermediate layer was effective to act as a buffer layer for both Co diffusion and diamond growth.

  15. Following the transient reactions in lithium-sulfur batteries using an in situ nuclear magnetic resonance technique.

    PubMed

    Xiao, Jie; Hu, Jian Zhi; Chen, Honghao; Vijayakumar, M; Zheng, Jianming; Pan, Huilin; Walter, Eric D; Hu, Mary; Deng, Xuchu; Feng, Ju; Liaw, Bor Yann; Gu, Meng; Deng, Zhiqun Daniel; Lu, Dongping; Xu, Suochang; Wang, Chongmin; Liu, Jun

    2015-05-13

    A fundamental understanding of electrochemical reaction pathways is critical to improving the performance of Li-S batteries, but few techniques can be used to directly identify and quantify the reaction species during disharge/charge cycling processes in real time. Here, an in situ (7)Li NMR technique employing a specially designed cylindrical microbattery was used to probe the transient electrochemical and chemical reactions occurring during the cycling of a Li-S system. In situ NMR provides real time, semiquantitative information related to the temporal evolution of lithium polysulfide allotropes during both discharge/charge processes. This technique uniquely reveals that the polysulfide redox reactions involve charged free radicals as intermediate species that are difficult to detect in ex situ NMR studies. Additionally, it also uncovers vital information about the (7)Li chemical environments during the electrochemical and parasitic reactions on the Li metal anode. These new molecular-level insights about transient species and the associated anode failure mechanism are crucial to delineating effective strategies to accelerate the development of Li-S battery technologies. PMID:25785550

  16. Adsorption, Coadsorption and Reaction of Acetaldehyde and NO? on Na-Y,FAU: an in situ FTIR Investigation

    SciTech Connect

    Szanyi, Janos; Kwak, Ja Hun; Moline, Ryan A.; Peden, Charles HF

    2004-11-04

    The adsorption of acetaldehyde and its co-adsorption and reaction with NO? were investigated on a Na-Y, FAU zeolite using in situ FTIR spectroscopy. Acetaldehyde adsorbs strongly over Na-Y and desorbs molecularly at around 400K with very limited extent of condensation or polymerization. Reaction between CH?CHO and NO? takes place in co-adsorption experiments even at 300K. In the initial step, acetaldehyde is oxidized to acetic acid accompanied by the formation of NO, which can be observed as N2O? formed via a further reaction between NO and NO?. The key intermediates in the overall NOx reduction in this process are nitro- and nitrosomethane, which form in the next step. Their decomposition and further reaction with adsorbed NOx species lead to the formation of HCN, HNCO, N?O, CO? and organic nitrile species identified by their characteristic IR vibrational signatures. At 473K, the reaction between adsorbed CH?CHO and NO? is very fast. The results seem to suggest a mechanism in which N-N bond formation takes place among ionic nitrogen containing species (NO? and CN? or NCO?). No evidence has been found to suggest the participation of NHx?NOy? type species in the N?N bond formation under the experimental conditions of this study.

  17. Effect of intermediate compounds and products on wet oxidation and biodegradation rates of pharmaceutical compounds.

    PubMed

    Collado, Sergio; Laca, Adriana; Diaz, Mario

    2013-06-01

    Kinetics of pure compounds in batch agitated reactors are useful data to clarify the characteristics of a given reaction, but they frequently do not provide the required information to design industrial mixed continuous processes because in this case the final and intermediate products interact with the reaction of interest, due to backmixing effects. Simultaneously, the presence and transformations of other compounds, frequent in industrial wastewater treatments, adds more complexity to these types of interactions, whose effect can be different, favorable or unfavorable, for chemical or biological reactions. In this work, batch laboratory reactor data were obtained for the wet oxidation and biodegradation of four phenolic compounds present in a pharmaceutical wastewater and then compared with those collected from industrial continuous stirred tank reactors. For wet oxidation, batch laboratory degradation rates were significantly lower than those found in industrial continuous stirred operation. This behavior was explained by a different distribution of intermediate compounds in lab and industrial treatments, caused by the degree of backmixing and the synergistic effects between phenolic compounds (matrix effects). On the other hand, the specific utilization rates during aerobic biodegradation in the continuous industrial operation were lower than those measured in the laboratory, due to the simultaneous presence of the four pollutants in the industrial process (matrix effects) increasing the inhibitory effects of these compounds and its intermediates. PMID:23582709

  18. Photosynthesis-The Light Reactions

    Microsoft Academic Search

    K. Sauer

    1979-01-01

    During the past three or four years there has been a substantial advance in our knowledge of the light reactions in photosynthesis. This comes at a time of heightened interest in sunlight as a source of energy for our daily needs. The exploration of potential practical applications in this area will be helped by identifying the common features of the

  19. Identifying Effective School Principals 

    E-print Network

    Fernandez, Kandyce; Flores, Santa; Huang, Emily; Igwe, Carolyn; McDonald, Leslie; Stroud, Ryan; Willis, Rebecca; Dugat, Amber

    2007-01-01

    METHODOLOGY Evaluating geostatistical m p ir e p cases that occurs within a group of people in a geographic area over a defined period of time. The Centers for Disease first step because of a failure to identify a critically small p-value [2..., is usually a statistical evaluation of the likelihood of the disease distribution. Commonly the state health agency examines its health registry data and performs statistical testing comparing in- cidence rates among arbitrary geographic areas [1]. Once a...

  20. Hunting Icebergs: Identifying Icebergs

    NSDL National Science Digital Library

    2012-08-03

    This self-paced, interactive tutorial guides learners through the decision-making process in locating data that will enable the identification of tabular icebergs, including: selecting the appropriate satellite orbit, and identifying the optimal solar and infrared wavelength values to discriminate between water and ice in remotely-sensed images. This resource is part of the tutorial series, Satellite Observations in Science Education, and is the first of three modules in the tutorial, Hunting Icebergs. (Note: requires Java plug-in)