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Sample records for identify reaction intermediate

  1. A reaction landscape identifies the intermediates critical for self-assembly of virus capsids and other polyhedral structures

    PubMed Central

    Endres, Dan; Miyahara, Masaki; Moisant, Paul; Zlotnick, Adam

    2005-01-01

    The capsids of spherical viruses may contain from tens to hundreds of copies of the capsid protein(s). Despite their complexity, these particles assemble rapidly and with high fidelity. Subunit and capsid represent unique end states. However, the number of intermediate states in these reactions can be enormous—a situation analogous to the protein folding problem. Approaches to accurately model capsid assembly are still in their infancy. In this paper, we describe a sailshaped reaction landscape, defined by the number of subunits in each species, the predicted prevalence of each species, and species stability. Prevalence can be calculated from the probability of synthesis of a given intermediate and correlates well with the appearance of intermediates in kinetics simulations. In these landscapes, we find that only those intermediates along the leading edge make a significant contribution to assembly. Although the total number of intermediates grows exponentially with capsid size, the number of leading-edge intermediates grows at a much slower rate. This result suggests that only a minute fraction of intermediates needs to be considered when describing capsid assembly. PMID:15930000

  2. Intermediate energy heavy ion reactions

    NASA Astrophysics Data System (ADS)

    Grégoire, C.; Tamain, B.

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

  3. Characterization of reaction intermediates by ion spectroscopy.

    PubMed

    Roithová, Jana

    2012-01-21

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

  4. Reaction plane dispersion at intermediate energies

    E-print Network

    J. Lukasik; W. Trautmann

    2006-03-29

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

  5. Transfer and breakup reactions at intermediate energies

    SciTech Connect

    Stokstad, R.G.

    1986-04-01

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

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

    ERIC Educational Resources Information Center

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

    2009-01-01

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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1989-05-01

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

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

    PubMed

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

    2015-12-01

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

  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.

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

    E-print Network

    Chen, Peng

    reaction. For both nanocatalysts, the distributions of the microscopic reaction time from a single catalystSingle-Molecule Kinetics Reveals a Hidden Surface Reaction Intermediate in Single and characterizing reaction inter- mediates is not only important and powerful for elucidating reaction mechanisms

  13. Photocyclization and Photoaddition Reactions of Arylphenols via Intermediate Quinone Methides.

    PubMed

    Lukeman, Matthew; Simon, Hilary; Wan, Peter; Wang, Yu-Hsuan

    2015-11-20

    A series of five benzannelated derivatives of 2-phenylphenol were prepared, and their photochemistry was investigated. Two of these (3-phenyl-2-naphthol, 10, and 1-phenyl-2-naphthol, 11) were photoinert. For 2-(1-naphthyl)phenol (12) and 1-(1-naphthyl)-2-naphthol (13), ESPT took place to either the 2'-position or the 7'-position of the naphthalene ring to give quinone methides (QMs) that underwent either reverse proton transfer (RPT) or electrocyclic ring closure to give dihydrobenzoxanthenes. The intermediate QMs for 12 and 13 were detected and characterized by laser flash photolysis. For 2-(9-phenanthryl)phenol (14), ESPT took place either to the 5'-position to give a QM that underwent quantitative electrocyclic ring closure to give the corresponding benzoxanthene or to the 10'-position to give a QM that underwent RPT. If the solution contained methanol, the QM produced on ESPT to the 10'-position in 14 could be trapped as the photoaddition product. The compounds studied in this work demonstrate three possible reactions of QMs produced following ESPT to aromatic carbon atoms: (1) reverse proton transfer (RPT) to regenerate starting material; (2) addition of hydroxylic solvents to give the photoaddition product; and (3) electrocyclic ring closure to give benzoxanthene derivatives. PMID:26496171

  14. Spectroscopic features of cytochrome P450 reaction intermediates

    PubMed Central

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

    2010-01-01

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

  15. 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...

  16. Recent Developments in Methods for Identifying Reaction Coordinates

    E-print Network

    Li, Wenjin

    2015-01-01

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

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

    PubMed Central

    Stack, Douglas E.

    2015-01-01

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

  18. 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.

  19. An oxocarbenium-ion intermediate of a ribozyme reaction indicated by kinetic isotope effects

    E-print Network

    Bartel, David

    An oxocarbenium-ion intermediate of a ribozyme reaction indicated by kinetic isotope effects Peter the formation of a pyrimidine nucleotide. Primary and secondary kinetic isotope ef- fects indicate isotope effect of 1.002 0.003 indicates that the reaction is likely to be less concerted than

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

    SciTech Connect

    Hoffman, M.Z.

    1992-07-31

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

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

    NASA Astrophysics Data System (ADS)

    Hoffman, M. Z.

    1992-07-01

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

  2. 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…

  3. 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.

  4. 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.

  5. Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome

    SciTech Connect

    Yang, Xiaojing; Ren, Zhong; Kuk, Jane; Moffat, Keith

    2012-03-27

    Light is a fundamental signal that regulates important physiological processes such as development and circadian rhythm in living organisms. Phytochromes form a major family of photoreceptors responsible for red light perception in plants, fungi and bacteria. They undergo reversible photoconversion between red-absorbing (Pr) and far-red-absorbing (Pfr) states, thereby ultimately converting a light signal into a distinct biological signal that mediates subsequent cellular responses. Several structures of microbial phytochromes have been determined in their dark-adapted Pr or Pfr states. However, the structural nature of initial photochemical events has not been characterized by crystallography. Here we report the crystal structures of three intermediates in the photoreaction of Pseudomonas aeruginosa bacteriophytochrome (PaBphP). We used cryotrapping crystallography to capture intermediates, and followed structural changes by scanning the temperature at which the photoreaction proceeded. Light-induced conformational changes in PaBphP originate in ring D of the biliverdin (BV) chromophore, and E-to-Z isomerization about the C{sub 15} = C{sub 16} double bond between rings C and D is the initial photochemical event. As the chromophore relaxes, the twist of the C{sub 15} methine bridge about its two dihedral angles is reversed. Structural changes extend further to rings B and A, and to the surrounding protein regions. These data indicate that absorption of a photon by the Pfr state of PaBphP converts a light signal into a structural signal via twisting and untwisting of the methine bridges in the linear tetrapyrrole within the confined protein cavity.

  6. The reaction of Fe and Ni at intermediate energies 

    E-print Network

    Liddick, Sean Nicholas

    2013-02-22

    VrIVERSITY UNDERGRADUATE RESEARCH FEI LOtVS April 2001 Group. Physical Sciences THE REACTION OF Fe AND Vi AT IlvTFRMEDIATE ENERGIFS A Senior Honors Thesis B& SEAN NICHOLAS I. IDDICK Submitted to the Office of Honors Progran & Academic Scholarships Texas Ak. %1... Undergraduate Research Competition Presentations for Honors Thesis Group, Physical Sciences Texas A&. M University Student Research Week Poster Presentation at 2001 Spring ACS National Meeting ...

  7. Detection of the reaction intermediates catalyzed by a copper amine oxidase.

    PubMed

    Kataoka, Misumi; Oya, Hiroko; Tominaga, Ayuko; Otsu, Masayuki; Okajima, Toshihide; Tanizawa, Katsuyuki; Yamaguchi, Hiroshi

    2011-01-01

    To reveal the chemical changes and geometry changes of active-site residues that cooperate with a reaction is important for understanding the functional mechanism of proteins. Consecutive temporal analyses of enzyme structures have been performed during reactions to clarify structure-based reaction mechanisms. Phenylethylamine oxidase from Arthrobacter globiformis (AGAO) contains a copper ion and topaquinone (TPQ(ox)). The catalytic reaction of AGAO catalyzes oxidative deaminations of phenylethylamine and consists of reductive and oxidative half-reactions. In the reduction step, TPQ(ox) reacts with a phenylethylamine (PEA) substrate giving rise to a topasemiquinone (TPQ(sq)) formed Schiff-base and produces phenylacetaldehyde. To elucidate the mechanism of the reductive half-reaction, an attempt was made to trap the reaction intermediates in order to analyze their structures. The reaction proceeded within the crystals when AGAO crystals were soaked in a PEA solution and freeze-trapped in liquid nitrogen. The reaction stage of each crystal was confirmed by single-crystal microspectrometry, before X-ray diffraction measurements were made of four reaction intermediates. The structure at 15 min after the onset of the reaction was analyzed at atomic resolution, and it was shown that TPQ(ox) and some residues in the substrate channel were alternated via catalytic reductive half-reactions. PMID:21169693

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

    E-print Network

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

    2015-08-16

    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 single-nucleon potential. Interestingly, some useful probes were identified in the model studies while so far there is still no data to compare with. In this brief review, we summarize the main physics motivations as well as the recent progress in understanding the spin dynamics and identifying spin-sensitive observables in heavy-ion reactions at intermediate energies. We hope the interesting, important, and new physics potentials identified in the spin dynamics of heavy-ion collisions will stimulate more experimental work in this direction.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    PubMed

    Li, Fei; Liu, Jun; Rozovsky, Sharon

    2014-11-01

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

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

    PubMed Central

    Li, Fei; Liu, Jun; Rozovsky, Sharon

    2014-01-01

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

  12. $dd\\to {^3}He n$ reaction at intermediate energies

    E-print Network

    N. B. Ladygina

    2012-03-21

    The $dd\\to ^3He n$ reaction is considered at the energies between 200 MeV and 520 MeV. The Alt-Grassberger-Sandhas equations are iterated up to the lowest order terms over the nucleon-nucleon t-matrix. The parameterized ${^3He}$ 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.

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

    PubMed

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

    2008-12-21

    We present a robust data analysis method of time-resolved x-ray absorption spectroscopy experiments suitable for chemical speciation and structure determination of reaction intermediates. Chemical speciation is done by principal component analysis (PCA) of the time-resolved x-ray absorption near-edge structure data. Structural analysis of intermediate phases is done by theoretical modeling of their extended x-ray absorption fine-structure data isolated by PCA. The method is demonstrated using reduction and reoxidation of Cu-doped ceria catalysts where we detected reaction intermediates and measured fine details of the reaction kinetics. This approach can be directly adapted to many time-resolved x-ray spectroscopy experiments where new rapid throughput data collection and analysis methods are needed. PMID:19102533

  14. 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

  15. A Model for the 3He(\\vec d, p)4He Reaction at Intermediate Energies

    E-print Network

    H. Kamada; W. Gloeckle; H. Witala; S. Gojuki

    2000-02-02

    Polarization correlation coefficients have been measured atRIKEN for the \\vec 3He(\\vec d,p)4He reaction at intermediate energies. We propose a model for the (\\vec d, p) reaction mechanism using the pd elastic scattering amplitude which is rigorously determined by a Faddeev calculation and using modern NN forces. Our theoretical predictions for deuteron polarization observables A_y, A_{yy}, A_{xx} and A_{xz} at E_d=140, 200 and 270 MeV agree qualitatively in shape with the experimental data for the reaction 3He(\\vec d,p)4He.

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

    SciTech Connect

    Hoffman, M.Z.

    1991-12-31

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

  17. LC/MS/MS structure elucidation of reaction intermediates formed during the TiO2 photocatalysis of microcystin-LR

    EPA Science Inventory

    Microcystin-LR (MC-LR), a cyanotoxin and emerging drinking water contaminant, was treated with TiO(2) photocatalysts immobilized on stainless steel plates as an alternative to nanoparticles in slurry. The reaction intermediates of MC-LR were identified with mass spectrometry (MS)...

  18. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Jackels, C. F.

    1985-01-01

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

  1. 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

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

    PubMed Central

    2015-01-01

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

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

    SciTech Connect

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

    2012-02-27

    The biosynthetic shikimate pathway consists of seven enzymes that catalyze sequential reactions to generate chorismate, a critical branch point in the synthesis of the aromatic amino acids. The third enzyme in the pathway, dehydroquinate dehydratase (DHQD), catalyzes the dehydration of 3-dehydroquinate to 3-dehydroshikimate. We present three crystal structures of the type I DHQD from the intestinal pathogens Clostridium difficile and Salmonella enterica. Structures of the enzyme with substrate and covalent pre- and post-dehydration reaction intermediates provide snapshots of successive steps along the type I DHQD-catalyzed reaction coordinate. These structures reveal that the position of the substrate within the active site does not appreciably change upon Schiff base formation. The intermediate state structures reveal a reaction state-dependent behavior of His-143 in which the residue adopts a conformation proximal to the site of catalytic dehydration only when the leaving group is present. We speculate that His-143 is likely to assume differing catalytic roles in each of its observed conformations. One conformation of His-143 positions the residue for the formation/hydrolysis of the covalent Schiff base intermediates, whereas the other conformation positions the residue for a role in the catalytic dehydration event. The fact that the shikimate pathway is absent from humans makes the enzymes of the pathway potential targets for the development of non-toxic antimicrobials. The structures and mechanistic insight presented here may inform the design of type I DHQD enzyme inhibitors.

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

    SciTech Connect

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

    2013-06-01

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

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

    PubMed Central

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

    1997-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2015-06-23

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

  8. A Computational Re-examination of the Criegee Intermediate-Sulfur Dioxide Reaction.

    PubMed

    Kuwata, Keith T; Guinn, Emily J; Hermes, Matthew R; Fernandez, Jenna A; Mathison, Jon M; Huang, Ke

    2015-10-15

    The atmospheric oxidation of sulfur dioxide by the parent and dimethyl Criegee intermediates (CIs) may be an important source of sulfuric acid aerosol, which has a large impact on radiative forcing and therefore upon climate. A number of computational studies have considered how the CH2OOS(O)O heteroozonide (HOZ) adduct formed in the CI + SO2 reaction converts SO2 to SO3. In this work we use the CBS-QB3 quantum chemical method along with equation-of-motion spin-flip CCSD(dT) and MCG3 theories to reveal new details regarding the formation and decomposition of the endo and exo conformers of the HOZ. Although ?75% of the parent CI + SO2 reaction is initiated by formation of the exo HOZ, hyperconjugation preferentially stabilizes many of the endo intermediates and transition structures by 1-5 kcal mol(-1). Our quantum chemical calculations, in conjunction with statistical rate theory models, predict a rate coefficient for the parent CI + SO2 reaction of 3.68 × 10(-11) cm(3) molecule(-1) s(-1), in good agreement with recent experimental measurements. RRKM/master equation simulations based on our quantum chemical data predict a prompt carbonyl + SO3 yield of >95% for the reaction of both the parent and dimethyl CI with SO2. The existence of concerted cycloreversion transition structures 10-15 kcal mol(-1) higher in energy than the HOZ accounts for most of the predicted SO3 formation. PMID:26397164

  9. 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.

  10. 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

  11. Intermediate trapping on a mutant retaining alpha-galactosyltransferase identifies an unexpected aspartate residue.

    PubMed

    Lairson, Luke L; Chiu, Cecilia P C; Ly, Hoa D; He, Shouming; Wakarchuk, Warren W; Strynadka, Natalie C J; Withers, Stephen G

    2004-07-01

    Lipopolysaccharyl-alpha-1,4-galactosyltransferase C (LgtC), a glycosyltransferase family 8 alpha-1,4-galactosyltransferase from Neisseria meningitidis, catalyzes the transfer of galactose from UDP galactose to terminal lactose-containing acceptor sugars with net retention of anomeric configuration. To investigate the potential role of discrete nucleophilic catalysis suggested by the double displacement mechanism generally proposed for retaining glycosyltransferases, the side chain amide of Gln-189, which is suitably positioned to act as the catalytic nucleophile of LgtC, was substituted with the more nucleophilic carboxylate-containing side chain of glutamate in the hope of accumulating a glycosyl-enzyme intermediate. The resulting mutant was subjected to kinetic, mass spectrometric, and x-ray crystallographic analysis. Although the K(m) for UDP-galactose is not significantly altered, the k(cat) was reduced to 3% that of the wild type enzyme. Electrospray mass spectrometric analysis revealed that a steady state population of the Q189E variant contains a covalently bound galactosyl moiety. Liquid chromatographic/mass spectrometric analysis of fragmented proteolytic digests identified the site of labeling not as Glu-189 but, surprisingly, as the sequentially adjacent Asp-190. However, the side chain carboxylate of Asp-190 is located 8.9 A away from the donor substrate in the available crystal structure. Kinetic analysis of a D190N mutant at this position revealed a k(cat) value 3000-fold lower than that of the wild type enzyme. A 2.6-A crystal structure of the Q189E mutant with bound uridine 5'-diphospho-2-deoxy-2-fluoro-alpha-d-galactopyranose revealed no significant perturbation of the mode of donor sugar binding nor of active site configuration. This is the first trapping of an intermediate in the active site of a retaining glycosyltransferase and, although not conclusive, implicates Asp-190 as an alternative candidate catalytic nucleophile, thereby rekindling a longstanding mechanistic debate. PMID:15075344

  12. Near-threshold absolute photoionization cross-sections of some reaction intermediates in combustion

    NASA Astrophysics Data System (ADS)

    Wang, Juan; Yang, Bin; Cool, Terrill A.; Hansen, Nils; Kasper, Tina

    2008-02-01

    The use of photoionization mass spectrometry for the development of quantitative kinetic models for the complex combustion chemistry of both conventional hydrocarbon fuels and oxygenated biofuels requires near-threshold measurements of absolute photoionization cross-sections for numerous reaction intermediates. Near-threshold absolute cross-sections for molecular and dissociative photoionization for 20 stable reaction intermediates (methane, ethane, propane, n-butane, cyclopropane, methylcyclopentane, 1-butene, cis-2-butene, isobutene, 1-pentene, cyclohexene, 3,3-dimethyl-1-butene, 1,3-hexadiene, 1,3-cyclohexadiene, methyl acetate, ethyl acetate, tetrahydrofuran, propanal, 1-butyne, 2-butyne) are presented. Previously measured total photoionization cross-sections for 9 of these molecules are in good agreement with the present results. The measurements are performed with photoionization mass spectrometry (PIMS) using a monochromated VUV synchrotron light source with an energy resolution of 40 meV (fwhm) comparable to that used for flame-sampling molecular beam PIMS studies of flame chemistry and reaction kinetics.

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

    NASA Astrophysics Data System (ADS)

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

    1996-02-01

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

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

    PubMed

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

    2013-05-01

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

  15. Two-Step Contribution to Intermediate Energy (p,p') and (p,n) Reactions

    E-print Network

    Y. Nakaoka; M. Ichimura

    1999-11-20

    We calculate the two-step contribution to (p,p') and (p,n) reactions at intermediate energy. We describe the motion of the incident nucleon with plane wave and compare the contribution from the two-step processes with that from the one-step processes. To describe the two-step processes, we extende the response functions into the nondiagonal ones with respect to the momentum transfer q. We performed a numerical calculation for the cross sections of the $^{12}$C, $^{40}$Ca(p,p') scatterings and the spin longitudinal and the spin transverse cross sections of the $^{12}$C,$^{40}$Ca(p,n) reactions at 346 MeV and 494 MeV. We found that the two-step contribution is appreciable in comparison with the one-step processes in higher energy transfer region for the spin longitudinal and the spin transverse (p,n) reactions. We also found that the two-step processes give larger contribution to the spin transverse (p,n) reaction than to the spin longitudinal reaction. This finding is very encouraging to interpret the discrepancy between the DWIA calculation and the experimental results of the spin longitudinal and the spin transverse cross sections.

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

    SciTech Connect

    Kerby, Leslie M.; Mashnik, Stepan G.

    2015-05-14

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

  17. Gold-Catalyzed Reactions via Cyclopropyl Gold Carbene-like Intermediates

    PubMed Central

    2015-01-01

    Cycloisomerizations of 1,n-enynes catalyzed by gold(I) proceed via electrophilic species with a highly distorted cyclopropyl gold(I) carbene-like structure, which can react with different nucleophiles to form a wide variety of products by attack at the cyclopropane or the carbene carbons. Particularly important are reactions in which the gold(I) carbene reacts with alkenes to form cyclopropanes either intra- or intermolecularly. In the absence of nucleophiles, 1,n-enynes lead to a variety of cycloisomerized products including those resulting from skeletal rearrangements. Reactions proceeding through cyclopropyl gold(I) carbene-like intermediates are ideally suited for the bioinspired synthesis of terpenoid natural products by the selective activation of the alkyne in highly functionalized enynes or polyenynes. PMID:26061916

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

    DOE PAGESBeta

    Kerby, Leslie M.; Mashnik, Stepan G.

    2015-05-14

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

  19. 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.

  20. 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.

  1. 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

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

    SciTech Connect

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

    2009-04-22

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

  3. Radical intermediates in photoinduced reactions on TiO2 (an EPR spin trapping study).

    PubMed

    Dvoranová, Dana; Barbieriková, Zuzana; Brezová, Vlasta

    2014-01-01

    The radical intermediates formed upon UVA irradiation of titanium dioxide suspensions in aqueous and non-aqueous environments were investigated applying the EPR spin trapping technique. The results showed that the generation of reactive species and their consecutive reactions are influenced by the solvent properties (e.g., polarity, solubility of molecular oxygen, rate constant for the reaction of hydroxyl radicals with the solvent). The formation of hydroxyl radicals, evidenced as the corresponding spin-adducts, dominated in the irradiated TiO2 aqueous suspensions. The addition of 17O-enriched water caused changes in the EPR spectra reflecting the interaction of an unpaired electron with the 17O nucleus. The photoexcitation of TiO2 in non-aqueous solvents (dimethylsulfoxide, acetonitrile, methanol and ethanol) in the presence of 5,5-dimethyl-1-pyrroline N-oxide spin trap displayed a stabilization of the superoxide radical anions generated via electron transfer reaction to molecular oxygen, and various oxygen- and carbon-centered radicals from the solvents were generated. The character and origin of the carbon-centered spin-adducts was confirmed using nitroso spin trapping agents. PMID:25353381

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    SciTech Connect

    Nathan, A.M.; Sandorfi, A.M.

    1992-10-01

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

  6. 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

  7. 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.

  8. Total Reaction Cross Sections in CEM and MCNP6 at Intermediate Energies

    E-print Network

    Leslie M. Kerby; Stepan G. Mashnik

    2015-05-04

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

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

    NASA Astrophysics Data System (ADS)

    Kerby, Leslie M.; Mashnik, Stepan G.

    2015-08-01

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

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

    PubMed Central

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

    2015-01-01

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

  11. 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

  12. Oligomer Formation Reactions of Criegee Intermediates in the Ozonolysis of Small Unsaturated Hydrocarbons

    NASA Astrophysics Data System (ADS)

    Sakamoto, Y.; Inomata, S.; Hirokawa, J.

    2013-12-01

    Secondary organic aerosol (SOA) constitutes a substantial fraction of atmospheric fine particulate matters and has an effect on visibility, climate and human health. One of the major oxidizing processes leading to SOA formation is an ozonolysis of unsaturated hydrocarbons (UHCs).[1] Despite of its importance, the contribution of the ozonolysis of UHCs to the SOA formation in the troposphere is not sufficiently understood due to a lack of information on reaction pathways to produce low volatile compounds. While many studies have previously been focused on SOA formation from the ozonolysis of large UHCs, SOA formation from the ozonolysis of UHCs with less than six carbon atoms have been rarely investigated because their products are expected to be too volatile to contribute to the SOA formation. Very recently, a few studies have reported the SOA formation from the ozonolysis of such small UHCs but chemical mechanisms are still unclear. [2-4] In order to understand SOA formation from the ozonolysis of the small UHCs, this study investigated gas- and particle-phase products in laboratory experiments with a Teflon bag using a negative ion chemical ionization mass spectrometry (NI-CIMS) with chloride ion transfer for chemical ionization. This technique is suitable for analysis of compounds such as carboxylic acids and hydroperoxides expected to be produced in the ozonolysis of UHCs with less fragmentation, high selectivity, and high sensitivity. In the particle-phase analysis, SOAs collected on a PTFE filter were heated, and thermally desorbed compounds were analyzed. In the gas-phase analysis, series of peaks with an interval of a mass-to-charge ratio equal to the molecular weight of a Criegee intermediate formed in their ozonolysis were observed. These peaks were attributed to oligomeric hydroperoxides composed of Criegee intermediates as a chain unit. These oligomeric hydroperoxides were also observed in the particle-phase analysis, indicating that the oligomeric hydroperoxides of low volatility formed in the gas phase are partitioned into the particle phase to contribute to the SOA formation. Here, we propose a new oligomer formation mechanism including sequential addition of Criegee intermediates to hydroperoxides. REFERENCE: (1)Kroll, J. H.; Seinfeld, J. H. Chemistry of Secondary Organic Aerosol: Formation and Evolution of Low-Volatility Organics in the Atmosphere. Atmos. Environ. 2008, 42, 3593-3624. (2)Sadezky, A.; Chaimbault, P.; Mellouki, A.; Roempp, A.; Winterhalter, R.; Le Bras, G.; Moortgat, G. K. Formation of Secondary Organic Aerosol and Oligomers from the Ozonolysis of Enol Ethers. Atmos. Chem. Phys. 2006, 6, 5009-5024. (3)Sadezky, A.; Winterhalter, R.; Kanawati, B.; Roempp, A.; Spengler, B.; Mellouki, A.; Le Bras, G.; Chaimbault, P.; Moortgat, G. K. Oligomer Formation during Gas-Phase Ozonolysis of Small Alkenes and Enol Ethers: New Evidence for the Central Role of the Criegee Intermediate as Oligomer Chain Unit. Atmos. Chem. Phys. 2008, 8, 2667-2699. (4)Klotz, B.; Barnes, I.; Imamura, T. Product Study of the Gas-Phase Reactions of O3, OH and NO3 Radicals with Methyl Vinyl Ether. Phys. Chem. Chem. Phys. 2004, 6, 1725-1734.

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    PubMed

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

    2015-01-01

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

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

    SciTech Connect

    Lin, M.C.

    1994-04-01

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

  17. The genome sequence of the emerging common midwife toad virus identifies an evolutionary intermediate within ranaviruses.

    PubMed

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

    2012-04-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Foong, Chow Ming; Sani, Norrakiah Abdullah

    2013-11-01

    Meat has been widely consumed as an important protein source in daily life of human. Furthermore, with busy and intense urban lifestyle, processed food is now one of the main protein sources of one's diet. Consumers rely on the food labeling to decide if the meat product purchased is safe and reliable. Therefore, it is important to ensure the food labeling is done in a correct manner to avoid consumer fraud. More consumers are now concern about the food quality and safety as compared to before. This study described the meat species identification and detection method using Polymerase Chain Reaction (PCR) in 8 types of meats (cattle, buffalo, goat, sheep, chicken, duck, pork and horse). The objective of this study is to decide on the specificity of oligonucleotide sequences obtained from previous study. There were 5 proposed oligonucleotide primer in this study. The main important finding in this work is the specificity of oligonucleotide primers to raw meats. It if found that the oligonucleotide primers proposed were not specific to the local raw meat species. Therefore, further study is needed to obtain a species-specific oligonucletide primers for PCR, in order to be applied in food product testing.

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

    SciTech Connect

    Foong, Chow Ming; Sani, Norrakiah Abdullah

    2013-11-27

    Meat has been widely consumed as an important protein source in daily life of human. Furthermore, with busy and intense urban lifestyle, processed food is now one of the main protein sources of one’s diet. Consumers rely on the food labeling to decide if the meat product purchased is safe and reliable. Therefore, it is important to ensure the food labeling is done in a correct manner to avoid consumer fraud. More consumers are now concern about the food quality and safety as compared to before. This study described the meat species identification and detection method using Polymerase Chain Reaction (PCR) in 8 types of meats (cattle, buffalo, goat, sheep, chicken, duck, pork and horse). The objective of this study is to decide on the specificity of oligonucleotide sequences obtained from previous study. There were 5 proposed oligonucleotide primer in this study. The main important finding in this work is the specificity of oligonucleotide primers to raw meats. It if found that the oligonucleotide primers proposed were not specific to the local raw meat species. Therefore, further study is needed to obtain a species-specific oligonucletide primers for PCR, in order to be applied in food product testing.

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

    PubMed

    Fukutome, Asuka; Kawamoto, Haruo; Saka, Shiro

    2015-07-01

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

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

    PubMed

    McWhirter, R B; Hille, R

    1991-12-15

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

  3. Spectroscopically Identified Intermediate Age Stars at 0.5 - 3 pc Distance from Sgr A*

    E-print Network

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

    2015-01-01

    Nuclear star clusters (NSCs) at the dynamical center of galaxies appear to have a complex star formation history. This suggests repeated star formation even in the influence of the strong tidal field from supermassive black holes. In our previous study, we have detected 31 so far unknown early-type star candidates throughout the Galactic NSC (at 0.5 - 3 pc from Sgr A*; Nishiyama and Schoedel 2013). The aim of this study is a confirmation of the spectral type for the candidates. We have carried out NIR spectroscopic observations of the candidates using Subaru/IRCS/AO188/LGS. K-band spectra for 20 out of the 31 candidates were obtained. By determining an equivalent width, EW(CO), of the 12CO absorption feature at 2.294 um, we have derived an effective temperature and a bolometric magnitude for each candidate, and then constructed an HR diagram. No young (~ Myr), massive stars are included in the 20 candidates we observed; however, 13 candidates are most likely intermediate-age giants (50 - 500 Myr). Two oth...

  4. The GC-MS Observation of Intermediates in a Stepwise Grignard Addition Reaction

    ERIC Educational Resources Information Center

    Latimer, Devin

    2007-01-01

    Preparation of phenylmagnesium bromide described by Eckert, addition of three equivalents of Grignard reagent to diethyl carbonate to form triphenylmethanol and a series of GC-MS procedures that form intermediates. The analysis is consistent with a gas chromatogram and mass spectrum for each of the expected intermediates and final product of the…

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

    SciTech Connect

    Kovaleva, Elena G.; Lipscomb, John D.

    2009-02-16

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

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

    PubMed

    Draksharapu, Apparao; Codolà, Zoel; Gómez, Laura; Lloret-Fillol, Julio; Browne, Wesley R; Costas, Miquel

    2015-11-16

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

  7. Characterization of a paramagnetic, mononuclear Pt(III)-alkyl complex intermediate in carbon-halogen bond coupling reactions.

    PubMed

    Rivada-Wheelaghan, Orestes; Ortuño, Manuel A; Díez, Josefina; García-Garrido, Sergio E; Maya, Celia; Lledós, Agustí; Conejero, Salvador

    2012-09-19

    Addition of Br(2) or I(2) to 14-electron, cationic Pt(II)-alkyl complexes led to the formation of the corresponding carbon-halogen Pt(II) coupling products. Low temperature experiments with Br(2) allowed us to isolate and characterize crystallographically a very unusual mononuclear, paramagnetic Pt(III)-alkyl intermediate with a seesaw structure that can be further oxidized to a transient Pt(IV) species before reductive carbon-halogen coupling reaction takes place. PMID:22934962

  8. Automatic Method for Identifying Reaction Coordinates in Complex Systems Ao Ma and Aaron R. Dinner*

    E-print Network

    Dinner, Aaron

    Automatic Method for Identifying Reaction Coordinates in Complex Systems Ao Ma and Aaron R. Dinner-derived electrostatic torque around one of the main-chain bonds, and the collective, long-ranged nature of this interaction accounts for previous failures to characterize this reaction. 1. Introduction Simulations

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

    PubMed

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

    2006-12-01

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

  10. Photocatalytic degradation of methylene blue on nanocrystalline TiO2: Surface mass spectrometry of reaction intermediates

    NASA Astrophysics Data System (ADS)

    Gnaser, Hubert; Savina, Michael R.; Calaway, Wallis F.; Tripa, C. Emil; Veryovkin, Igor V.; Pellin, Michael J.

    2005-08-01

    Photocatalytic degradation reactions of methylene blue on nanocrystalline TiO2 (nc-TiO2) films were studied in situ by surface mass spectrometric techniques including secondary ion mass spectrometry, laser desorption direct ion mass spectrometry, and laser desorption/laser photoion mass spectrometry. The parent ion of methylene blue and/or its reduced form leucomethylene blue was observed with little fragmentation by all methods prior to ultraviolet exposure. The surface composition changed upon ultraviolet (UV) irradiation in air, an observation ascribed to photocatalytic reactions induced by UV photons: the parent molecule signal diminished and intermediate reaction products such as sulfoxides and sulfones were detected from the TiO2 surface. After prolonged UV irradiation these species also vanished and the methylene blue appeared to be almost completely mineralized.

  11. Detailed mechanism of the CH?I + O? reaction: yield and self-reaction of the simplest Criegee intermediate CH?OO.

    PubMed

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

    2014-09-14

    The application of a new reaction scheme using CH2I + O2 to generate the simplest Criegee intermediate, CH2OO, has stimulated lively research; the Criegee intermediates are extremely important in atmospheric chemistry. The detailed mechanism of CH2I + O2 is hence important in understanding kinetics involving CH2OO. We employed ultraviolet absorption to probe simultaneously CH2I2, CH2OO, CH2I, and IO in the reaction system of CH2I + O2 upon photolysis at 248 nm of a flowing mixture of CH2I2, O2, and N2 (or SF6) in the pressure range 7.6-779 Torr to investigate the reaction kinetics. With a detailed mechanism to model the observed temporal profiles of CH2I, CH2OO, and IO, we found that various channels of the reaction CH2I + O2 and CH2OO + I play important roles; an additional decomposition channel of CH2I + O2 to form products other than CH2OO or ICH2OO becomes important at pressure less than 60 Torr. The pressure dependence of the derived rate coefficients of various channels of reactions of CH2I + O2 and CH2OO + I has been determined. We derived a rate coefficient also for the self-reaction of CH2OO as k = (8 ± 4) × 10(-11) cm(3) molecule(-1) s(-1) at 295 K. The yield of CH2OO from CH2I + O2 was found to have a pressure dependence on N2 and O2 smaller than in previous reports; for air under 1 atm, the yield of ~30% is about twice of previous estimates. PMID:25217917

  12. 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}).

  13. 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}).

  14. 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.

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2008-01-01

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

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

    PubMed

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

    2012-11-12

    Polyhydroxyalkanoate (PHA) synthase from Aeromonas caviae FA440 (PhaC(Ac), BAA21815) is one of the most valuable PHA synthase, because of its function to synthesize a practical bioplastic, poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)]. However, biochemical activity and active intermediates of PhaC(Ac) have not been clarified until now. In the present study, a gene of PhaC(Ac) was cloned and overexpressed by a cell-free protein expression system. Both the polymerization activity and oligomerization behavior of the purified PhaC(Ac) were characterized in order to clarify the active intermediates of PhaC(Ac) based on the hydrodynamic diameters and specific activities of PhaC(Ac). The influences of a substrate, (R)-3-hydroxybutyryl-CoA (3HB-CoA), on the oligomerization of PhaC(Ac) (7.5 ?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

  18. Synthesis of Y1BaCu3O(x) superconducting powders by intermediate phase reactions

    NASA Technical Reports Server (NTRS)

    Moure, C.; Fernandez, J. F.; Tartaj, J.; Recio, P.; Duran, P.

    1991-01-01

    A procedure for synthesizing Y1Ba2Cu3O(x) by solid state reactions was developed. The method is based on the use of barium compounds, previously synthesized, as intermediate phases for the process. The reaction kinetics of this procedure were established between 860 C and 920 C. The crystal structure and the presence of second phases were studied by means of XRD. The sintering behavior and ceramic parameters were also determined. The orthorhombic type-I structure was obtained on the synthesized bodies after a cooling cycle in an air atmosphere. Superconducting transition took place at 91 K. Sintering densities higher than 95 percent D sub th were attained at temperatures below 940 C.

  19. Characterization of the Peroxidase Mechanism upon Reaction of Prostacyclin Synthase with Peracetic Acid. Identification of a Tyrosyl Radical Intermediate

    PubMed Central

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

    2010-01-01

    Prostacyclin synthase (PGIS) is a membrane-bound class III cytochrome P450 that catalyzes an isomerization of prostaglandin H2, an endoperoxide, to prostacyclin. We report here the characterization of the PGIS intermediates in reactions with other peroxides, peracetic acid (PA), and iodosylbenzene. Rapid-scan stopped-flow experiments revealed an intermediate with an absorption spectrum similar to that of compound ES (Cpd ES), which is an oxo–ferryl (Fe(IV)=O) plus a protein-derived radical. Cpd ES, formed upon reaction with PA, has an X-band (9 GHz) EPR signal of g = 2.0047 and a half-saturation power, P1/2, of 0.73 mW. High-field (130 GHz) EPR reveals the presence of two species of tyrosyl radicals in Cpd ES with their g-tensor components (gx, gy, gz) of 2.00970, 2.00433, 2.00211 and 2.00700, 2.00433, 2.00211 at a 1:2 ratio, indicating that one is involved in hydrogen bonding and the other is not. The line width of the g = 2 signal becomes narrower, while its P1/2 value becomes smaller as the reaction proceeds, indicating migration of the unpaired electron to an alternative site. The rate of electron migration (~0.2 s?1) is similar to that of heme bleaching, suggesting the migration is associated with the enzymatic inactivation. Moreover, a g = 6 signal that is presumably a high-spin ferric species emerges after the appearance of the amino acid radical and subsequently decays at a rate comparable to that of enzymatic inactivation. This loss of the g = 6 species thus likely indicates another pathway leading to enzymatic inactivation. The inactivation, however, was prevented by the exogenous reductant guaiacol. The studies of PGIS with PA described herein provide a mechanistic model of a peroxidase reaction catalyzed by the class III cytochromes P450. PMID:19187034

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

    DOEpatents

    Maya, Leon (Oak Ridge, TN)

    1988-05-24

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

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

    DOEpatents

    Maya, Leon (Oak Ridge, TN)

    1991-01-01

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

  2. Energy-loss cross sections for inclusive charge-exchange reactions at intermediate energies

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Townsend, Lawrence W.; Dubey, Rajendra R.

    1993-01-01

    Charge-exchange reactions for scattering to the continuum are considered in a high-energy multiple scattering model. Calculations for (p,n) and (He-3,H-3) reactions are made and compared with experimental results for C-12, O-16, and Al-27 targets. Coherent effects are shown to lead to an important role for inelastic multiple scattering terms when light projectiles are considered.

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

    E-print Network

    Gent, Universiteit

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

  4. 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.

  5. Freezeout concept and dynamical transport model in intermediate-energy heavy-ion reactions

    NASA Astrophysics Data System (ADS)

    Liu, X.; Lin, W.; Huang, M.; Wada, R.; Wang, J.; Chen, Z.; Wang, Q.; Ren, P.; Yang, Y.; Jin, S.; Ma, P.; Ma, J.; Bai, Z.; Hu, Q.

    2015-07-01

    For the central collision events of 40Ca +40Ca , generated by an antisymmetrized molecular dynamics model in the intermediate energy range of 35 to 300 MeV/nucleon, the density and temperature of a fragmenting source have been extracted using a self-consistent method with the modified Fisher model. Rather flat density values, ? /?0˜0.65 to 0.7, are evaluated at the incident energies studied, even though the maximum density of the system achieved during the collisions increases monotonically from ? /?0˜1.3 at 35 MeV/nucleon to 1.8 at 300 MeV/nucleon. Flat temperature values of T ˜5.9 to 6.5 MeV are also extracted in this incident energy range. These extracted values indicate that, in average, intermediate mass fragments are formed at a later stage when the hot nuclear matter reaches at a "freezeout" volume by the expansion, which is not assumed in any transport models, but assumed generally in statistical multifragmentation models. This is the first time to demonstrate quantitatively a direct connection between the freezeout concept and transport model simulations in a multifragmenting regime of heavy ion collisions.

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

    SciTech Connect

    Hoffman, M.Z.

    1992-07-31

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

  7. 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

  8. 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

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

    PubMed

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

    2015-12-01

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

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

    SciTech Connect

    Nathan, A.M.; Sandorfi, A.M.

    1992-01-01

    This report contains papers on the following topics: The proton compton effect: Recent measurements of the electric and magnetic polorizabilities of the proton; experiments on the electric polarizability of the neutron; chiral symmetry and nucleon polarizabilities; chiral model predictions for electromagnetic polarizabilities of the nucleon, a consumer report; the polarizabilities of bound nucleons; nucleon polarizability in free space and in nuclear matter; mechanisms of photon scattering on nucleons at intermediate energies; pion polarizabilities in chiral perturbation theory; pion polarizabilities and the shielding of [sigma](700)-meson exchange in [gamma][gamma][yields][pi][pi] processes; pion and kaon polarizabilities in the quark confinement model; radiative pion photoproduction and pion polarizabilities; pion and sigma polarizabilities and radiative transitions; the quadrupole amplitude in the [gamma][Nu]-[Delta] transition; pion photoproduction and the [gamma][Nu]-[Delta] amplitudes; effective- lagrangians, Watson's theorem, and the E2/M1 mixing ratio in the excitation of the delta resonance; new measurements of the p([rvec [gamma

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

    SciTech Connect

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

    2007-11-15

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

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

    PubMed

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

    2015-12-15

    The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and ?-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solved NgTet1-5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH2-) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH2 towards the metal-ligand water molecule, where a dioxygen O2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably because the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate. PMID:26323320

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

    PubMed Central

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

    2015-01-01

    The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and ?-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solved NgTet1–5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH2-) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH2 towards the metal-ligand water molecule, where a dioxygen O2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably because the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate. PMID:26323320

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

    DOE PAGESBeta

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

    2015-08-31

    The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and ?-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solvedmore »NgTet1–5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH2-) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH2 towards the metal-ligand water molecule, where a dioxygen O2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably due to the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate.« less

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

    SciTech Connect

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

    1981-01-01

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

  16. 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...

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

    PubMed

    Aceituno, Mónica; Stalikas, Constantine D; Lunar, Loreto; Rubio, Soledad; Pérez-Bendito, Dolores

    2002-08-01

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

  18. 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.

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

    PubMed

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

    2009-02-10

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

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

    PubMed

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

    2014-10-01

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

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

    PubMed Central

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

    2015-01-01

    The copper-catalyzed 1,3-dipolar cycloaddition of an azide to a terminal alkyne (CuAAC) is one of the most popular chemical transformations, with applications ranging from material to life sciences. However, despite many mechanistic studies, direct observation of key components of the catalytic cycle is still missing. Initially, mononuclear species were thought to be the active catalysts, but later on, dinuclear complexes came to the front. We report the isolation of both a previously postulated ?,?-bis(copper) acetylide and a hitherto never-mentioned bis(metallated) triazole complex. We also demonstrate that although mono- and bis-copper complexes promote the CuAAC reaction, the dinuclear species are involved in the kinetically favored pathway. PMID:26601202

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

    SciTech Connect

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

    2015-01-01

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

  3. 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.

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

    SciTech Connect

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

    2015-03-28

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

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

    E-print Network

    Nottingham, University of

    Choice reaction times for identifying the direction of first-order motion and different varieties of the human visual system by measuring forced-choice reaction times for dis- criminating the drift direction of stimulus modulation depths. In general, reaction times for all types of second-order motion were slower

  6. Understanding the reaction mechanism and intermediate stabilization in mammalian serine racemase using multiscale quantum-classical simulations.

    PubMed

    Nitoker, Neta; Major, Dan Thomas

    2015-01-20

    Serine racemase (SerR) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme catalyzing the racemization of l-Ser to d-Ser. In mammals, d-Ser is an endogenous coagonist required for the activation of N-methyl-d-aspartate receptors (NMDARs), thus making SerR a promising pharmaceutical target. However, mechanistic studies of SerR are scarce, and the details of the enzymatic racemization reaction are not fully understood. In the current study we elucidate the catalytic mechanism in SerR by employing combined multiscale classical/quantum simulations. The free energy profile of a model SerR racemization reaction is first calculated in the gas phase and in aqueous solution. To obtain the free energy profile for the enzymatic reaction, hybrid quantum mechanics/molecular mechanics molecular dynamics simulations in conjunction with umbrella sampling are performed. The results suggest that in SerR, similarly to the related enzyme alanine racemase, the unprotonated PLP-substrate intermediate is stabilized mostly due to solvation effects contributed by water molecules and active-site residues, as well as long-range electrostatic interactions with the enzyme environment. In addition to a deeper understanding of the racemization mechanism in SerR, based on our simulations we propose specific mutations, which might shift the SerR equilibrium in favor of either l-Ser or d-Ser. Finally, the current studies have produced catalytically competent forms of the rat and human enzymes, which may serve as targets for future docking studies and drug design. PMID:25493718

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

    NASA Astrophysics Data System (ADS)

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

    2004-05-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

  9. 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-Heterocyclic the heterocyclic moiety is retained in the product 5 (eq 1). With an appropriately substituted carbohydrate precursor this could lead to N-heterocyclic glycosides8 of 2-amino- or C2-branched sugars.9 Additionally

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

    E-print Network

    Butler, Laurie J.

    Unimolecular dissociation of the propargyl radical intermediate of the CH+C2H2 and C+C2H3 reactions examines the unimolecular dissociation of propargyl HCCCH2 radicals over a range of internal energies/mol as the lowest barrier to dissociation of the radical. This barrier is significantly lower than predictions

  11. Multifragmentation and Isospin Dependence of Reaction Mechanism at Intermediate Energy D. V. Shetty, A. Keksis, E. Martin, A. Ruangma, G. Souliotis, M. Veselsky, E. M. Winchester,

    E-print Network

    Yennello, Sherry

    Multifragmentation and Isospin Dependence of Reaction Mechanism at Intermediate Energy D. V. Shetty established, the role of entrance channel dynamics and isospin asymmetry in determining conditions leading of effects which are sensitive to the isospin dependence of the symmetry potential of the mean field

  12. 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.

    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.

  13. Atmospheric isoprene ozonolysis: impacts of stabilised Criegee intermediate reactions with SO2, H2O and dimethyl sulfide

    NASA Astrophysics Data System (ADS)

    Newland, M. J.; Rickard, A. R.; Vereecken, L.; Muñoz, A.; Ródenas, M.; Bloss, W. J.

    2015-08-01

    Isoprene is the dominant global biogenic volatile organic compound (VOC) emission. Reactions of isoprene with ozone are known to form stabilised Criegee intermediates (SCIs), which have recently been shown to be potentially important oxidants for SO2 and NO2 in the atmosphere; however the significance of this chemistry for SO2 processing (affecting sulfate aerosol) and NO2 processing (affecting NOx levels) depends critically upon the fate of the SCIs with respect to reaction with water and decomposition. Here, we have investigated the removal of SO2 in the presence of isoprene and ozone, as a function of humidity, under atmospheric boundary layer conditions. The SO2 removal displays a clear dependence on relative humidity, confirming a significant reaction for isoprene-derived SCIs with H2O. Under excess SO2 conditions, the total isoprene ozonolysis SCI yield was calculated to be 0.56 (±0.03). The observed SO2 removal kinetics are consistent with a relative rate constant, k(SCI + H2O) / k(SCI + SO2), of 3.1 (±0.5) × 10-5 for isoprene-derived SCIs. The relative rate constant for k(SCI decomposition) / k(SCI+SO2) is 3.0 (±3.2) × 1011 cm-3. Uncertainties are ±2? and represent combined systematic and precision components. These kinetic parameters are based on the simplification that a single SCI species is formed in isoprene ozonolysis, an approximation which describes the results well across the full range of experimental conditions. Our data indicate that isoprene-derived SCIs are unlikely to make a substantial contribution to gas-phase SO2 oxidation in the troposphere. We also present results from an analogous set of experiments, which show a clear dependence of SO2 removal in the isoprene-ozone system as a function of dimethyl sulfide concentration. We propose that this behaviour arises from a rapid reaction between isoprene-derived SCIs and dimethyl sulfide (DMS); the observed SO2 removal kinetics are consistent with a relative rate constant, k(SCI + DMS) / k(SCI + SO2), of 3.5 (±1.8). This result suggests that SCIs may contribute to the oxidation of DMS in the atmosphere and that this process could therefore influence new particle formation in regions impacted by emissions of unsaturated hydrocarbons and DMS.

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

    PubMed

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

    2009-04-01

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

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

    PubMed Central

    Skerry, Amy E.; Spelke, Elizabeth S.

    2014-01-01

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

  16. 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

  17. 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.

  18. Methodological framework to identify possible adverse drug reactions using population-based administrative data

    PubMed Central

    Sauer, Brian; Nebeker, Jonathan; Shen, Shuying; Rupper, Randall; West, Suzanne; Shinogle, Judith A.; Xu, Wu; Lohr, Kathleen N.; Samore, Matthew

    2014-01-01

    Purpose: We present a framework for detecting possible adverse drug reactions (ADRs) using the Utah Medicaid administrative data. We examined four classes of ADRs associated with treatment of dementia by acetylcholinesterase inhibitors (AChEIs): known reactions (gastrointestinal, psychological disturbances), potential reactions (respiratory disturbance), novel reactions (hepatic, hematological disturbances), and death. Methods: Our cohort design linked drug utilization data to medical claims from Utah Medicaid recipients. We restricted the analysis to 50 years-old and older beneficiaries diagnosed with dementia-related diseases. We compared patients treated with AChEI to patients untreated with anti-dementia medication therapy. We attempted to remove confounding by establishing propensity-score-matched cohorts for each outcome investigated; we then evaluated the effects of drug treatment by conditional multivariable Cox-proportional-hazard regression. Acute and transient effects were evaluated by a crossover design using conditional logistic regression. Results: Propensity-matched analysis of expected reactions revealed that AChEI treatment was associated with gastrointestinal episodes (Hazard Ratio [HR]: 2.02; 95%CI: 1.28-3.2), but not psychological episodes, respiratory disturbance, or death. Among the unexpected reactions, the risk of hematological episodes was higher (HR: 2.32; 95%CI: 1.47-3.6) in patients exposed to AChEI. AChEI exposure was not associated with an increase in hepatic episodes. We also noted a trend, identified in the case-crossover design, toward increase odds of experiencing acute hematological events during AChEI exposure (Odds Ratio: 3.0; 95% CI: 0.97 - 9.3). Conclusions: We observed an expected association between AChEIs treatment and gastrointestinal disturbances and detected a signal of possible hematological ADR after treatment with AChEIs in this pilot study. Using this analytic framework may raise awareness of potential ADEs and generate hypotheses for future investigations. Early findings, or signal detection, are considered hypothesis generating since confirmatory studies must be designed to determine if the signal represents a true drug safety problem. PMID:26180631

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

    SciTech Connect

    Hoffman, M.Z.

    1991-12-31

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

    2015-01-01

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

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

    PubMed

    Nosrati, Geoffrey R; Houk, K N

    2012-05-01

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

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

    SciTech Connect

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

    2011-01-01

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

  5. 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...

  6. Density functional theory calculation of cyclic carboxylic phosphorus mixed anhydrides as possible intermediates in biochemical reactions: implications for the Pro-Tide approach.

    PubMed

    Ricci, Antonio; Brancale, Andrea

    2012-04-15

    Cyclic acyl phosphoramidates (CAPAs) are important components in several fundamental biological reactions such as protein synthesis and phosphorylation. These structures are particularly interesting in the nucleotide pro-drug approach, Pro-Tide, since they are putative intermediates in one of the hydrolysis steps required for activation. The central role played by the amino acid carboxylate function suggests first the formation of a cyclic mixed phosphorus anhydride, rapidly followed by water attack. To investigate such speculations, we performed quantum mechanical calculations using the B3LYP/6-311+G** level of theory for the plausible mechanisms of action considered. In the five-membered ring case, transition state theory demonstrated how the overall, gas-phase, mechanism of action could be split into two in-line addition-elimination (A-E) steps separated by a penta-coordinate phosphorane intermediate. The difference between five-membered and six-membered ring first A-E was also explored, revealing a single step, unimolecular reaction for the six-membered ring A-E profile. Implicit solvent contribution further confirmed the importance of CAPAs as reactive intermediates in such kind of reactions. Lastly, the second A-E pathway was analyzed to understand the complete pathway of the reaction. This analysis is the first attempt to clarify the putative mechanism of action involved in the activation of Pro-Tides and casts light also on the possible mechanism of action involved in primordial protein syntheses, strengthening the hypothesis of a common cyclic mixed phosphorus anhydride species as a common intermediate. PMID:22318882

  7. DETECTION OF SPIRORCHIID TREMATODES IN GASTROPOD TISSUES BY POLYMERASE CHAIN REACTION: PRELIMINARY IDENTIFICATION OF AN INTERMEDIATE HOST OF

    E-print Network

    Florida, University of

    . Jacobson College of Veterinary Medicine, University of Florida, P.O. Box 100136, Gainesville, Florida 32610 unsuccessful (Greiner et al., 1980; Dailey et al., 1992). Classical parasitological methods for intermediate

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

    PubMed Central

    Wilks, A F

    1989-01-01

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

  9. Kinetics and Spectroscopic Evidence that the Cu(I) ? Semiquinone Intermediate Reduces Molecular Oxygen in the Oxidative Half-Reaction of Arthrobacter globiformis Amine Oxidase†

    PubMed Central

    Shepard, Eric M.; Okonski, Kristina M.; Dooley, David M.

    2009-01-01

    The role of copper during the reoxidation of substrate-reduced amine oxidases by O2 has not yet been definitively established. Both outer-sphere and inner-sphere pathways for the reduction of O2 to H2O2 have been proposed. A key step in the inner-sphere mechanism is the reaction of O2 directly with the Cu(I) center of a [Cu(I) ? semiquinone] intermediate. To thoroughly examine this possibility, we have measured the spectral changes associated with single-turnover reoxidation by O2 of substrate-reduced Arthrobacter globiformis amine oxidase (AGAO) under a wide range of conditions. We have previously demonstrated that the internal electron-transfer reaction [Cu(II) ? TPQAMQ ? Cu(I) ? TPQSQ] (where TPQAMQ is the aminoquinol form of reduced TPQ and TPQSQ is the semiquinone form) occurs at a rate that could permit the reaction of O2 with both species to be observed on the stopped-flow time scale (Shepard EM and Dooley DM (2006) JBIC 11:1039-1048). The transient absorption spectra observed for the reaction of O2 with substrate-reduced AGAO provide compelling support for the reaction of the Cu(I) ? TPQSQ form. Further, global analysis of the kinetics and the transient absorption spectra are fully consistent with an inner-sphere reaction of the Cu(I)-semiquinone intermediate with O2 and are inconsistent with an outer-sphere mechanism for the reaction of the reduced enzyme with O2. PMID:19053231

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

    NASA Astrophysics Data System (ADS)

    Lee, Yuan-Pern

    2015-07-01

    The Criegee intermediates, carbonyl oxides proposed by Criegee in 1949 as key intermediates in the ozonolysis of alkenes, play important roles in many aspects of atmospheric chemistry. Because direct detection of these gaseous intermediates was unavailable until recently, previous understanding of their reactions, derived from indirect experimental evidence, had great uncertainties. Recent laboratory detection of the simplest Criegee intermediate CH2OO and some larger members, produced from ultraviolet irradiation of corresponding diiodoalkanes in O2, with various methods such as photoionization, ultraviolet absorption, infrared absorption, and microwave spectroscopy opens a new door to improved understanding of the roles of these Criegee intermediates. Their structures and spectral parameters have been characterized; their significant zwitterionic nature is hence confirmed. CH2OO, along with other products, has also been detected directly with microwave spectroscopy in gaseous ozonolysis reactions of ethene. The detailed kinetics of the source reaction, CH2I + O2, which is critical to laboratory studies of CH2OO, are now understood satisfactorily. The kinetic investigations using direct detection identified some important atmospheric reactions, including reactions with NO2, SO2, water dimer, carboxylic acids, and carbonyl compounds. Efforts toward the characterization of larger Criegee intermediates and the investigation of related reactions are in progress. Some reactions of CH3CHOO are found to depend on conformation. This perspective examines progress toward the direct spectral characterization of Criegee intermediates and investigations of the associated reaction kinetics, and indicates some unresolved problems and prospective challenges for this exciting field of research.

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

    PubMed

    Lee, Yuan-Pern

    2015-07-14

    The Criegee intermediates, carbonyl oxides proposed by Criegee in 1949 as key intermediates in the ozonolysis of alkenes, play important roles in many aspects of atmospheric chemistry. Because direct detection of these gaseous intermediates was unavailable until recently, previous understanding of their reactions, derived from indirect experimental evidence, had great uncertainties. Recent laboratory detection of the simplest Criegee intermediate CH2OO and some larger members, produced from ultraviolet irradiation of corresponding diiodoalkanes in O2, with various methods such as photoionization, ultraviolet absorption, infrared absorption, and microwave spectroscopy opens a new door to improved understanding of the roles of these Criegee intermediates. Their structures and spectral parameters have been characterized; their significant zwitterionic nature is hence confirmed. CH2OO, along with other products, has also been detected directly with microwave spectroscopy in gaseous ozonolysis reactions of ethene. The detailed kinetics of the source reaction, CH2I + O2, which is critical to laboratory studies of CH2OO, are now understood satisfactorily. The kinetic investigations using direct detection identified some important atmospheric reactions, including reactions with NO2, SO2, water dimer, carboxylic acids, and carbonyl compounds. Efforts toward the characterization of larger Criegee intermediates and the investigation of related reactions are in progress. Some reactions of CH3CHOO are found to depend on conformation. This perspective examines progress toward the direct spectral characterization of Criegee intermediates and investigations of the associated reaction kinetics, and indicates some unresolved problems and prospective challenges for this exciting field of research. PMID:26178082

  12. 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

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

    PubMed Central

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

    2014-01-01

    Pharmacovigilance involves continually monitoring drug safety after drugs are put to market. To aid this process; algorithms for the identification of strongly correlated drug/adverse drug reaction (ADR) pairs from data sources such as adverse event reporting systems or Electronic Health Records have been developed. These methods are generally statistical in nature, and do not draw upon the large volumes of knowledge embedded in the biomedical literature. In this paper, we investigate the ability of scalable Literature Based Discovery (LBD) methods to identify side effects of pharmaceutical agents. The advantage of LBD methods is that they can provide evidence from the literature to support the plausibility of a drug/ ADR association, thereby assisting human review to validate the signal, which is an essential component of pharmacovigilance. To do so, we draw upon vast repositories of knowledge that has been extracted from the biomedical literature by two Natural Language Processing tools, MetaMap and SemRep. We evaluate two LBD methods that scale comfortably to the volume of knowledge available in these repositories. Specifically, we evaluate Reflective Random Indexing (RRI), a model based on concept-level co-occurrence, and Predication-based Semantic Indexing (PSI), a model that encodes the nature of the relationship between concepts to support reasoning analogically about drug-effect relationships. An evaluation set was constructed from the Side Effect Resource 2 (SIDER2), which contains known drug/ADR relations, and models were evaluated for their ability to “rediscover” these relations. In this paper, we demonstrate that both RRI and PSI can recover known drug-adverse event associations. However, PSI performed better overall, and has the additional advantage of being able to recover the literature underlying the reasoning pathways it used to make its predictions. PMID:25046831

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

    SciTech Connect

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

    1991-05-01

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

  15. Elimination-addition mechanism for nucleophilic substitution reaction of cyclohexenyl iodonium salts and regioselectivity of nucleophilic addition to the cyclohexyne intermediate.

    PubMed

    Fujita, Morifumi; Kim, Wan Hyeok; Sakanishi, Yuichi; Fujiwara, Koji; Hirayama, Sayaka; Okuyama, Tadashi; Ohki, Yasuhiro; Tatsumi, Kazuyuki; Yoshioka, Yasunori

    2004-06-23

    The reaction of 4-substituted cyclohex-1-enyl(phenyl)iodonium tetrafluoroborate with tetrabutylammonium acetate gives both the ipso and cine acetate-substitution products in aprotic solvents. The isomeric 5-substituted iodonium salt also gives the same mixture of the isomeric acetate products. The reaction is best explained by an elimination-addition mechanism with 4-substituted cyclohexyne as a common intermediate. The cyclohexyne formation was confirmed by deuterium labeling and trapping to lead to [4 + 2] cycloadducts and a platinum-cyclohexyne complex. Cyclohexyne can also be generated in the presence of some other mild bases such as fluoride ion, alkoxides, and amines, though amines are less effective bases for the elimination. Kinetic deuterium isotope effects show that the anionic bases induce the E2 elimination (k(H)/k(D) > 2), while the amines allow formation of a cyclohexenyl cation in chloroform to lead to E1 as well as S(N)1 reactions (k(H)/k(D) approximately 1). Bases are much less effective in methanol, and methoxide was the only base to efficiently afford the cyclohexyne intermediate. Nucleophiles react with the cyclohexyne to give regioisomeric products in the ratio dependent on the ring substituent. The observed regioselectivity of nucleophilic addition to substituted cyclohexynes is rationalized from calculated LUMO populations, which are governed by the bond angles at the acetylenic carbons: The less deformed carbon has a higher LUMO population and is preferentially attacked by the nucleophile. PMID:15198602

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

    PubMed

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

    2013-10-16

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

  17. Identifying the Structure of the Intermediate, Li2/3CoPO4, Formed during Electrochemical Cycling of LiCoPO4

    PubMed Central

    2014-01-01

    In situ synchrotron diffraction measurements and subsequent Rietveld refinements are used to show that the high energy density cathode material LiCoPO4 (space group Pnma) undergoes two distinct two-phase reactions upon charge and discharge, both occurring via an intermediate Li2/3(Co2+)2/3(Co3+)1/3PO4 phase. Two resonances are observed for Li2/3CoPO4 with intensity ratios of 2:1 and 1:1 in the 31P and 7Li NMR spectra, respectively. An ordering of Co2+/Co3+ oxidation states is proposed within a (a × 3b × c) supercell, and Li+/vacancy ordering is investigated using experimental NMR data in combination with first-principles solid-state DFT calculations. In the lowest energy configuration, both the Co3+ ions and Li vacancies are found to order along the b-axis. Two other low energy Li+/vacancy ordering schemes are found only 5 meV per formula unit higher in energy. All three configurations lie below the LiCoPO4–CoPO4 convex hull and they may be readily interconverted by Li+ hops along the b-direction. PMID:25960604

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2001-07-01

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

  20. 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

  1. Origin of product selectivity in a prenyl transfer reaction from the same intermediate: exploration of multiple FtmPT1-catalyzed prenyl transfer pathways.

    PubMed

    Pan, Li-Li; Yang, Yue; Merz, Kenneth M

    2014-09-30

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

  2. 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

  3. 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.

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

    NASA Astrophysics Data System (ADS)

    Wei, Gao-Feng

    2015-07-01

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

  5. 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.

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

    SciTech Connect

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

    1996-10-01

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

  7. 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

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

    E-print Network

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

    2007-03-05

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

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

    SciTech Connect

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

    2015-08-31

    The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and ?-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solved NgTet1–5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH2-) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH2 towards the metal-ligand water molecule, where a dioxygen O2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably due to the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  11. A density functional theory study of hydroxyl and the intermediate in the water formation reaction on Pt

    E-print Network

    Alavi, Ali

    on Pt A. Michaelides and P. Hu Citation: The Journal of Chemical Physics 114, 513 (2001); doi: 10://scitation.aip.org/content/aip/journal/jcp/114/1?ver=pdfcov Published by the AIP Publishing Articles you may be interested in Reaction dynamics of Pt atoms is 0.1 eV. This low barrier coupled with H bonding between neighboring OH groups indicates

  12. Spectroscopic study of reaction intermediates and mechanisms in nitramine decomposition and combustion. Final report, 20 March 1992-19 March 1995

    SciTech Connect

    Jacox, M.B.

    1995-05-20

    The infrared spectra of reaction intermediates trapped in solid neon were studied in order to support the development of diagnostics for short-lived species which are reaction carriers in nitramine decomposition and combustion and to derive information about reactions which are important in the condensed-phase decomposition of nitramines. Nitromethane and monomethylnitramine were used as model compounds in these studies. Evidence was obtained for the formation of water complexes with both of these species. The results support the water-catalyzed decomposition mechanism for nitramines that was proposed by Melius. Studies of the photodecomposition of isotopically substituted monomethylnitramine demonstrate that four different groups of products are formed. Tentative spectral assignments are made for the aci-isomer of monomethylnitramine and for CH3NHONO. The final photodecomposition products are CH4, NO, CH3OH, and N20. Other studies have provided evidence for the formation of a weakly bonded complex of H2 with H20, as well as spectral data for the HCC free radical and for the H20+, N02+, NO(2-), and NO(3-), molecular ions.

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

    SciTech Connect

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

    1994-12-31

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

  14. 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…

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

    E-print Network

    Gent, Universiteit

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

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

    PubMed Central

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

    2009-01-01

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

  17. 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

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

    SciTech Connect

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

    2008-03-21

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

  19. 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

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

    PubMed

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

    2001-02-13

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

  1. Catalytic hydrotreatment studies with model compounds. Quarterly report, April 1-June 30, 1986. [Hydrodeoxygenation of reaction intermediates of dibenzofuran - 2 phenylphenol, 2-cyclohexylphenol, trans-2-phenylhexanol, and 2-cyclohexylcyclohexanol

    SciTech Connect

    Satterfield, C.N.; LaVopa, V.

    1986-01-01

    Studies of the hydrodeoxygenation (HDO) of dibenzofuran continued. To help clarify the reaction network four possible reaction intermediates were studied in detail: 2 phenyl phenol, 2-cyclohexylphenol, trans-2-phenyl-cyclohexanol, and 2-cyclohexylcyclohexanol. All four intermediates are more reactive than dibenzofuran itself. The most detailed study previously reported on the HDO of dibenzofuran is that of Krishnamurthy and Shah (1979). However, our product distributions differ from theirs in several significant ways and we note that in some cases they did not recover a major portion of their products. We are presently attempting to see if their study and ours can be reconciled. 6 figs., 2 tabs.

  2. 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.

  3. A scale for identifying "Stockholm syndrome" reactions in young dating women: factor structure, reliability, and validity.

    PubMed

    Graham, D L; Rawlings, E I; Ihms, K; Latimer, D; Foliano, J; Thompson, A; Suttman, K; Farrington, M; Hacker, R

    1995-01-01

    The factor structure, reliability, and validity of a 49-item scale designed to measure Stockholm Syndrome (also referred to as "traumatic bonding" and "terror bonding"), that is, bonding with an abusive partner, were assessed for college women in heterosexual dating relationships. Factor analysis identified three major factors: Core Stockholm Syndrome, characterized by cognitive distortions and other strategies for coping with abuse; Psychological Damage, marked by depression, low self-esteem, and loss of sense of self; and Love-Dependence, typified by the feeling that one cannot survive without one's partner's love. The scale and factors had excellent internal consistency and good test-retest reliabilities. They correlated negatively with the Marlowe-Crowne Social Desirability scale and positively with Horowitz, Wilner, & Alvarez' (1979) Impact of Event Scale, Hyler and Rieder's (1987) Borderline Personality Disorder Scale, Hatfield and Sprecher's (1986) Passionate Love Scale, and Straus' (1979) Verbal Aggression and Violence scales of the Conflict Tactics Scales. PMID:8555117

  4. 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.

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

    PubMed Central

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

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

  7. Reaction pathways of 2-iodoacetic acid on Cu(100): coverage-dependent competition between C-I bond scission and COOH deprotonation and identification of surface intermediates.

    PubMed

    Lin, Yi-Shiue; Lin, Jain-Shiun; Liao, Yung-Hsuan; Yang, Che-Ming; Kuo, Che-Wei; Lin, Hong-Ping; Fan, Liang-Jen; Yang, Yaw-Wen; Lin, Jong-Liang

    2010-06-01

    The chemistry of 2-iodoacetic acid on Cu(100) has been studied by a combination of reflection-absorption infrared spectroscopy (RAIRS), X-ray photoelectron spectroscopy (XPS), temperature-programmed reaction/desorption (TPR/D), and theoretical calculations based on density functional theory for the optimized intermediate structures. In the thermal decomposition of ICH(2)COOH on Cu(100) with a coverage less than a half monolayer, three surface intermediates, CH(2)COO, CH(3)COO, and CCOH, are generated and characterized spectroscopically. Based on their different thermal stabilities, the reaction pathways of ICH(2)COOH on Cu(100) at temperatures higher than 230 K are established to be ICH(2)COOH --> CH(2)COO + H + I, CH(2)COO + H --> CH(3)COO, and CH(3)COO --> CCOH. Theoretical calculations suggest that the surface CH(2)COO has the skeletal plane, with delocalized pi electrons, approximately parallel to the surface. The calculated Mulliken charges agree with the detected binding energies for the two carbon atoms in CH(2)COO on Cu(100). The CCOH derived from CH(3)COO decomposition has a CC stretching frequency at 2025 cm(-1), reflecting its triple-bond character which is consistent with the calculated CCOH structure on Cu(100). Theoretically, CCOH at the bridge and hollow sites has a similar stability and is adsorbed with the molecular axis approximately perpendicular to the surface. The TPR/D study has shown the evolution of the products of H(2), CH(4), H(2)O, CO, CO(2), CH(2)CO, and CH(3)COOH from CH(3)COO decomposition between 500 and 600 K and the formation of H(2) and CO from CCOH between 600 and 700 K. However, at a coverage near one monolayer, the major species formed at 230 and 320 K are proposed to be ICH(2)COO and CH(3)COO. CH(3)COO becomes the only species present on the surface at 400 K. That is, there are two reaction pathways of ICH(2)COOH --> ICH(2)COO + H and ICH(2)COO + H --> CH(3)COO + I (possibly via CH(2)COO), which are different from those observed at lower coverages. Because the C-I bond dissociation of iodoethane on copper single crystal surfaces occurs at approximately 120 K and that the deprotonation of CH(3)COOH on Cu(100) occurs at approximately 220 K, the preferential COOH dehydrogenation of monolayer ICH(2)COOH is an interesting result, possibly due to electronic and/or steric effects. PMID:20356026

  8. Unimolecular dissociation of the CH3OCO radical: an intermediate in the CH3O + CO reaction.

    PubMed

    McCunn, Laura R; Lau, Kai-Chung; Krisch, Maria J; Butler, Laurie J; Tsung, Jieh-Wen; Lin, Jim J

    2006-02-01

    This work investigates the unimolecular dissociation of the methoxycarbonyl, CH(3)OCO, radical. Photolysis of methyl chloroformate at 193 nm produces nascent CH(3)OCO radicals with a distribution of internal energies, determined by the velocities of the momentum-matched Cl atoms, that spans the theoretically predicted barriers to the CH(3)O + CO and CH(3) + CO(2) product channels. Both electronic ground- and excited-state radicals undergo competitive dissociation to both product channels. The experimental product branching to CH(3) + CO(2) from the ground-state radical, about 70%, is orders of magnitude larger than Rice-Ramsperger-Kassel-Marcus (RRKM)-predicted branching, suggesting that previously calculated barriers to the CH(3)OCO --> CH(3) + CO(2) reaction are dramatically in error. Our electronic structure calculations reveal that the cis conformer of the transition state leading to the CH(3) + CO(2) product channel has a much lower barrier than the trans transition state. RRKM calculations using this cis transition state give product branching in agreement with the experimental branching. The data also suggest that our experiments produce a low-lying excited state of the CH(3)OCO radical and give an upper limit to its adiabatic excitation energy of 55 kcal/mol. PMID:16435825

  9. Cooperativity and intermediates in the equilibrium reactions of Fe(II,III) with ethanethiolate in N-methylformamide solution.

    PubMed

    Frank, Patrick; Hodgson, Keith O

    2005-06-01

    The reaction of FeCl(2) or FeCl(3) with sodium ethanethiolate (SEt) in N-methylformamide (NMF) has been reevaluated to rectify a previous Fe(II) oxidation artifact. On titrating Fe(II) with EtS(-) concentrations up to 12 mol Eq, new features in the UV/vis spectrum (epsilon(344)=(3.1+/-0.2)x10(3) M(-1) cm(-1); epsilon(486)=(4.5+/-0.1)x10(2) M(-1) cm(-1)) indicated that the first observable step was the formation of a single complex different from the known tetrahedral tetrathiolate, [Fe(SEt)(4)](2-) . As the EtS(-) concentration increased past 12.5 mol Eq the UV/vis spectrum gradually transformed to that of [Fe(SEt)(4)](2-) (lambda(max)=314 nm). A Hill-formalism fit to the titration data of the initially formed complex indicated cooperative ligation by three ethanethiolate ions, with K(coop)=(1.7+/-0.1)x10(3) M(-3) and Hill "n"=2.4+/-0.1 (r=0.997). The 3:1 EtS(-)-Fe(II) complex is proposed to be [Fe(2)(SEt)(6)](2-). Titration of Fe(III) with EtS(-) showed direct cooperative formation of [Fe(SEt)(4)](-) [epsilon(340)=(3.4+/-0.5)x10(3) M(-1) cm(-1)] with a Hill-formalism K(coop)=(4.3+/-0.1)x10(2) M(-4) and a Hill coefficient "n"=3.7+/-0.2 (r=0.996). Further ligation past [Fe(SEt)(4)](-) was observed at EtS(-) concentrations above 35 mol Eq. The Fe(III) Hill constants are at variance with our previous report. However, the UV/vis spectrum of Fe(III) in NMF solution was found to change systematically over time, consistent with a slow progressive deprotonation of [Fe(nmf)](3+). The observed time-to-time differences in the equilibrium chemistry of Fe(III) with ethanethiolate in NMF thus reflect variation in the microscopic solution composition of FeCl(3) in alkaline NMF solvent. These results are related to the chemistry of nitrogenase FeMo cofactor in alkaline NMF solution. PMID:15864505

  10. The thiolase reaction mechanism: the importance of Asn316 and His348 for stabilizing the enolate intermediate of the Claisen condensation.

    PubMed

    Meriläinen, Gitte; Poikela, Visa; Kursula, Petri; Wierenga, Rik K

    2009-11-24

    The biosynthetic thiolase catalyzes a Claisen condensation reaction between acetyl-CoA and the enzyme acetylated at Cys89. Two oxyanion holes facilitate this catalysis: oxyanion hole I stabilizes the enolate intermediate generated from acetyl-CoA, whereas oxyanion hole II stabilizes the tetrahedral intermediate of the acetylated enzyme. The latter intermediate is formed when the alpha-carbanion of acetyl-CoA enolate reacts with the carbonyl carbon of acetyl-Cys89, after which C-C bond formation is completed. Oxyanion hole II is made of two main chain peptide NH groups, whereas oxyanion hole I is formed by a water molecule (Wat82) and NE2(His348). Wat82 is anchored in the active site by an optimal set of hydrogen bonding interactions, including a hydrogen bond to ND2(Asn316). Here, the importance of Asn316 and His348 for catalysis has been studied; in particular, the properties of the N316D, N316A, N316H, H348A, and H348N variants have been determined. For the N316D variant, no activity could be detected. For each of the remaining variants, the k(cat)/K(m) value for the Claisen condensation catalysis is reduced by a factor of several hundred, whereas the thiolytic degradation catalysis is much less affected. The crystal structures of the variants show that the structural changes in the active site are minimal. Our studies confirm that oxyanion hole I is critically important for the condensation catalysis. Removing either one of the hydrogen bond donors causes the loss of at least 3.4 kcal/mol of transition state stabilization. It appears that in the thiolytic degradation direction, oxyanion hole I is not involved in stabilizing the transition state of its rate limiting step. However, His348 has a dual role in the catalytic cycle, contributing to oxyanion hole I and activating Cys89. The analysis of the hydrogen bonding interactions in the very polar catalytic cavity shows the importance of two conserved water molecules, Wat82 and Wat49, for the formation of oxyanion hole I and for influencing the reactivity of the catalytic base, Cys378, respectively. Cys89, Asn316, and His348 form the CNH-catalytic triad of the thiolase superfamily. Our findings are also discussed in the context of the importance of this triad for the catalytic mechanism of other enzymes of the thiolase superfamily. PMID:19842716

  11. 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

  12. 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

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

    PubMed

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

    2012-11-01

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

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

    PubMed

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

    2015-02-14

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

  15. 19: Cyclization and Pericyclic Reactions (Not Posted) Reactions That Make Rings

    E-print Network

    Reed, Christopher A.

    Intermediates Friedel-Crafts Reactions. Carbocation Addition to Alkenes. Carbocation Ring Contraction19: Cyclization and Pericyclic Reactions (Not Posted) Reactions That Make Rings Cyclization Reactions Enolate Ion Intermediates Intramolecular Aldol Reaction. Dieckmann Condensation. Malonic

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

    SciTech Connect

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

    2014-03-07

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  18. Polymerase chain reaction-based screening method applicable universally to environmental haloarchaea and halobacteria for identifying polyhydroxyalkanoate producers among them.

    PubMed

    Mahansaria, Riddhi; Choudhury, Jayanta Debabrata; Mukherjee, Joydeep

    2015-09-01

    The existing techniques for detection of polyhydroxyalkanoates (PHA) in halophilic archaea/bacteria are either imprecise or require prior PHA production before screening. The proposed method involves amplification of the approximately 280-300 bp conserved region of Class III PHA synthase (phaC) gene of halophiles using the primers codehopCF and codehopCR (Han et al. Appl Environ Microb 76:7811-7819, 2010). In this study, the best reaction condition was ascertained after repeated trials. This developed method was tested on nine haloarchaeal and halobacterial type strains and 28 environmental halophilic archaea and bacteria isolated from the salt pans of the east and west coasts of India. 29 strains were found to be phaC-positive, while eight were found to be phaC-negative although they appeared PHA positive through conventional Nile Red staining. 16S rRNA-based phylogenetic analysis identified 9 haloarchaeal and 9 halobacterial species as novel PHA producers. Multiple sequence alignment of the phaC gene-derived amino acid sequences showed that only 7 amino acid residues were conserved within all four classes of phaC enzymes, whereas 61 amino acids were identical among the phaC enzyme specific to the haloarchaeal and halobacterial strains presently investigated. All phaC-positive strains produced PHA in standard nutrient deficient medium, whereas the phaC-negative strains did not accumulate any PHA as detected by gas chromatography and nuclear magnetic resonance analyses, thus proving the precision of the developed method and elimination of false positives seen with the traditional Nile Red staining procedure. PMID:26240023

  19. 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.

    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 foods. UMD Dining does not assume liability for adverse reactions to foods consumed, or items one may

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

    PubMed Central

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

    2015-01-01

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

  1. Caffeoylquinic acid derived free radicals identified during antioxidant reactions of bitter tea (Ilex latifolia and Ilex kudincha).

    PubMed

    Pirker, Katharina Franziska; Goodman, Bernard Albert

    2010-12-01

    In order to provide some insight into the chemical basis for the antioxidant behaviour of bitter tea, the Chinese medicinal beverage derived from leaves of Ilex kudincha or Ilex latifolia, free radicals generated during the oxidation of aqueous extracts of dried leaves have been investigated by electron paramagnetic resonance (EPR) spectroscopy. With both beverages, the major components in the EPR spectra after accelerated autoxidation under alkaline conditions or oxidation with the superoxide anion radical were comparable to those derived from reactions of caffeoylquinic acids. Thus these reaction products have sufficient stability for biological activity, and the present results suggest that such molecules contribute appreciably to the antioxidant chemistry of these beverages. PMID:21776475

  2. A General Method for Identifying Recessive Diploid-Specific Mutations in Saccharomyces Cerevisiae, Its Application to the Isolation of Mutants Blocked at Intermediate Stages of Meiotic Prophase and Characterization of a New Gene Sae2

    PubMed Central

    McKee, AHZ.; Kleckner, N.

    1997-01-01

    We describe a general new approach for identifying recessive mutations that affect diploid strains of yeast Saccharomyces cerevisiae and the application of this method to the identification of mutations that confer an intermediate block in meiotic prophase chromosome metabolism. The method uses a temperature-sensitive conjugation mutation ste7-1 in combination with homothallism. The mutations of interest confer a defect in spore formation that is dependent upon a gene required for initiation of meiotic recombination and development of meiosis-specific chromosome structure (SPO11). Identified in this screen were null mutations of the DMC1 gene, nonnull mutations of RAD50 (rad50S), and mutations in three new genes designated SAE1, SAE2 and SAE3 (Sporulation in the Absence of Spo Eleven). Molecular characterization of the SAE2 gene and characterization of meiotic and mitotic phenotypes of sae2 mutants are also presented. The phenotypes conferred by a sae2 null mutation are virtually indistinguishable from those conferred by the previously identified nonnull mutations of RAD50 (rad50S). Most notably, both mutations confer only weak sensitivity to the radiomimetic agent methyl methane sulfonate (MMS) but completely block resection and turnover of meiosis-specific double-strand breaks. These observations provide further evidence that this constellation of phenotypes identifies a specific molecular function. PMID:9215888

  3. 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

  4. Identifying and managing an adverse food reaction in a polar bear (Ursus maritimus) by an elimination diet trial.

    PubMed

    Monson, Sara; Minter, Larry J; Krouse, Marissa; De Voe, Ryan S

    2014-06-01

    A 16-yr-old polar bear (Ursus maritimus) presented with severe diarrhea shortly following transfer to the North Carolina Zoological Park. Multiple diagnostic procedures were performed over several months and the cause of the chronic diarrhea was inconclusive. Histologically, colonic mucosal biopsies were consistent with severe chronic eosinophilic and lymphoplasmacytic colitis with no evidence of etiologic agents present. A dietary elimination trial was conducted and an adverse food reaction to the dog chow in the diet was confirmed. PMID:25000711

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

    PubMed

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

    2013-01-01

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

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

    SciTech Connect

    Sammarruca, Francesca; White, Larz

    2011-06-15

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

  7. Genes that encode botulism neurotoxins A, B, E and F in neotropical bee honey identified with the polymerase chain reaction.

    PubMed

    Fournier, Ana Teresa; Gamboa, María del Mar; Arias, María Laura

    2006-03-01

    Honey can be used for the treatment of wounds, sores and skin bums, but it might be contaminated with Clostridium botulinum spores. In order to evaluate Costa Rican raw honey samples, the detection of neurotoxin gene sequences (corresponding to the bacterium) C. botulinum A, B, E and F was done with the polymerase chain reaction. A total of 64 raw honey samples, coming from different Costa Rican sites were analyzed. Reference C. botulinum strains type A (ATCC 19397), type B (ATCC 7949), type E (ATCC 17786) and type F (ATCC 25764) were used as templates for testing the effectivity of the method. The process consisted in culturing the honey samples in prereduced triptose-peptone-glucose-yeast extract media (TGPY) for 5 days. After this, the bacteria lysate obtained was used for PCR. The amplicons, product of the reaction, were visualized using agarose gel 2%. From the 64 honey samples analyzed, none produced positive results in the PCR, since no amplicons were obtained. Even though, all the reference C. botulinum strains used as controls were visualized and showed the effectivity of the extraction method and of the PCR used. The results obtained show promising therapeutic uses for honey from Costa Rica, but further evaluations shall be done in order to be sure of the safety of the product. PMID:18457171

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

    PubMed

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

    2013-06-25

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

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

    SciTech Connect

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

    2008-04-15

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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Norman, B.

    2004-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Mahal, H. S.; Mukherjee, T.

    1999-01-01

    Resonance-stabilized 2-MT rad radicals, generated pulse radiolytically in neutral aqueous solutions from 2-MT by the reaction with OH rad , Br rad , and Br rad -2 radicals have a broad absorption band between 300-550 nm. The rate constants for the reactions of OH rad , T1 2+, Cl rad -2, Br rad and Br rad -2 with 2-MT have been determined at pH 2.2 and 6 and are close to the diffusion controlled values. At pH 6 the OH rad radicals react only to an extent of ˜45% with 2-MT. The 2-MT rad radicals are able to oxidize phenothiazine [PH] drugs [ E1?0.8 V] and ABTS with k?2-5×10 9 dm 3 mol -1 s -1. The semi-reduced species have been formed by the reaction of e -aq with 2-MT with a k?5.7×10 9 dm 3mol -1s -1 at pH 7. They show ?max ranging from 300-325 nm depending on the solution pH. The radical p Ka has been measured, p Ka=6. The semi-reduced form of 2-MT efficiently reduced MV 2+ to MV rad +. Our results indicate that if 2-MT is to be used as a corrosion inhibitor it will be more conducive to use it under reducing conditions than under oxidizing conditions.

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

    SciTech Connect

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

    1986-04-01

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

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

    SciTech Connect

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

    2011-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

    Janz, S; Brede, O; Müller, J

    1991-07-01

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

  17. 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.

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

    SciTech Connect

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

    1987-05-05

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

  19. Extensional flow convecting a reactant undergoing a first order homogeneous reaction and diffusional mass transfer from a sphere at low to intermediate Peclet and Damkohler numbers

    NASA Technical Reports Server (NTRS)

    Shah, N. Y.; Reed, X. B., Jr.

    1995-01-01

    Forced convective diffusion-reaction is considered for viscous axisymmetric extensional convecting velocity in the neighborhood of a sphere. For Peclet numbers in the range 0.1 less than or equal to Pe less than or equal to 500 and for Damkohler numbers increasing with increasing Pe but in the overall range 0.02 less than or equal to Da less than or equal to 10, average and local Sherwood numbers have been computed. By introducing the eigenfunction expansion c(r, Theta) = Sum of c(n)(r)P(n)(cos Theta) into the forced convective diffusion equation for the concentration of a chemical species undergoing a first order homogeneous reaction and by using properties of the Legendre functions Pn(cos Theta), the variable coefficient PDE can be reduced to a system of N + 1 second order ODEs for the radial functions c(sub n)(r), n = 0, 1, 2,..., N. The adaptive grid algorithm of Pereyra and Lentini can be used to solve the corresponding 2(N + 1) first order differential equations as a two-point boundary value problem on 1 less than or equal to r less than or equal to r(sub infinity). Convergence of the expansion for a specific value of N can thus be established and provides 'spectral' behavior as well as the full concentration field c(r, Theta).

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

    NASA Astrophysics Data System (ADS)

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

    1988-12-01

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

  1. A second GDP-L-galactose phosphorylase in arabidopsis en route to vitamin C. Covalent intermediate and substrate requirements for the conserved reaction.

    PubMed

    Linster, Carole L; Adler, Lital N; Webb, Kristofor; Christensen, Kathryn C; Brenner, Charles; Clarke, Steven G

    2008-07-01

    The Arabidopsis thaliana VTC2 gene encodes an enzyme that catalyzes the conversion of GDP-L-galactose to L-galactose 1-phosphate in the first committed step of the Smirnoff-Wheeler pathway to plant vitamin C synthesis. Mutations in VTC2 had previously been found to lead to only partial vitamin C deficiency. Here we show that the Arabidopsis gene At5g55120 encodes an enzyme with high sequence identity to VTC2. Designated VTC5, this enzyme displays substrate specificity and enzymatic properties that are remarkably similar to those of VTC2, suggesting that it may be responsible for residual vitamin C synthesis in vtc2 mutants. The exact nature of the reaction catalyzed by VTC2/VTC5 is controversial because of reports that kiwifruit and Arabidopsis VTC2 utilize hexose 1-phosphates as phosphorolytic acceptor substrates. Using liquid chromatography-mass spectroscopy and a VTC2-H238N mutant, we provide evidence that the reaction proceeds through a covalent guanylylated histidine residue within the histidine triad motif. Moreover, we show that both the Arabidopsis VTC2 and VTC5 enzymes catalyze simple phosphorolysis of the guanylylated enzyme, forming GDP and L-galactose 1-phosphate from GDP-L-galactose and phosphate, with poor reactivity of hexose 1-phosphates as phosphorolytic acceptors. Indeed, the endogenous activities from Japanese mustard spinach, lemon, and spinach have the same substrate requirements. These results show that Arabidopsis VTC2 and VTC5 proteins and their homologs in other plants are enzymes that guanylylate a conserved active site His residue with GDP-L-galactose, forming L-galactose 1-phosphate for vitamin C synthesis, and regenerate the enzyme with phosphate to form GDP. PMID:18463094

  2. 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.

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

    PubMed

    Shi, Hongchang; Wang, Yilei; Hua, Ruimao

    2015-11-11

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

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

    SciTech Connect

    Oganessian, Yu. Ts.; Abdullin, F. Sh.; Dmitriev, S. N.; Itkis, M. G.; Lobanov, Yu. V.; Mezentsev, A. N.; Polyakov, A. N.; Sagaidak, R. N.; Shirokovsky, I. V.; Subbotin, V. G.; Sukhov, A. M.; Tsyganov, Yu. S.; Utyonkov, V. K.; Voinov, A. A.; Vostokin, G. K.; Bailey, P. D.; Benker, D. E.; Ezold, J. G.; Porter, C. E.; Riley, F. D.

    2011-05-15

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

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

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

    PubMed

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

    2015-04-15

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2013-05-01

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

  10. Use of mitochondrial cytochrome oxidase I polymerase chain reaction-restriction fragment length polymorphism for identifying subclades of Bemisia tabaci Mediterranean group.

    PubMed

    Chu, Dong; Hu, Xiangshun; Gao, Changsheng; Zhao, Huiyan; Nichols, Robert L; Li, Xianchun

    2012-02-01

    The Mediterranean group (commonly known as Q biotype; hereafter MED) of the sweetpotato whitefly, Bemisia tabaci (Gennadius), originated in the Mediterranean region, but it now has been found in at least 10 countries outside the Mediterranean. Collections of B. tabaci from some of these countries exhibit different pest behaviors and pesticide resistance characteristics, yet all may be classified as MED. A phylogenetic analysis of 120 mitochondrial cytochrome oxidase I (mtCOI) sequences (JN966761-JN966880) of MED whiteflies collected in Arizona and of 417 retrieved from the GenBank database resolves the MED into five subclades, designated as Q1-Q5. Only subclades Q1 and Q2 have been detected in the United States. Q1 and the other four subclades (Q2-Q5) differ in the number or position of the AluI recognition sites. Based on the differences in the AluI recognition sites reported here and the previously reported differences in VspI recognition sites, we developed a simple diagnostic technique to identify subclades Q1-Q5 by using mtCOI polymerase chain reaction (PCR)-restriction fragment-length polymorphism (RFLP). A test of a worldwide collection of whiteflies demonstrates that this combination mtCOIPCR-RFLP technique can reliably distinguish not only the MED from the Middle East-Asia Minor 1 group but also the Q1 from any of the other four MED subclades. PMID:22420277

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

    USGS Publications Warehouse

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

    2004-01-01

    Bacteria in soil microcosm experiments oxidized elevated levels of methyl chloride (MeCl) and methyl bromide (MeBr), the former compound more rapidly than the latter. MeBr was also removed by chemical reactions while MeCl was not. Chemical degradation dominated the early removal of MeBr and accounted for more than half of its total loss. Fractionation of stable carbon isotopes during chemical degradation of MeBr resulted in a kinetic isotope effect (KIE) of 59 ?? 7???. Soil bacterial oxidation dominated the later removal of MeBr and MeCl and was characterized by different KIEs for each compound. The KIE for MeBr oxidation was 69 ?? 9??? and the KIE for MeCl oxidation was 49 ?? 3???. Stable isotope probing revealed that different populations of soil bacteria assimilated added 13C-labeled MeBr and MeCl. The identity of the active MeBr and MeCl degrading bacteria in soil was determined by analysis of 16S rRNA gene sequences amplified from 13C-DNA fractions, which identified a number of sequences from organisms not previously thought to be involved in methyl halide degradation. These included Burkholderia , the major clone type in the 13C-MeBr fraction, and Rhodobacter, Lysobacter and Nocardioides the major clone types in the 13C-MeCl fraction. None of the 16S rRNA gene sequences for methyl halide oxidizing bacteria currently in culture (including Aminobacter strain IMB-1 isolated from fumigated soil) were identified. Functional gene clone types closely related to Aminobacter spp. were identified in libraries containing the sequences for the cmuA gene, which codes for the enzyme known to catalyze the initial step in the oxidation of MeBr and MeCl. The cmuA gene was limited to members of the alpha-Proteobacteria whereas the greater diversity demonstrated by the 16S rRNA gene may indicate that other enzymes catalyze methyl halide oxidation in different groups of bacteria. Copyright ?? 2004 Elsevier Ltd.

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

    NASA Astrophysics Data System (ADS)

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

    2004-08-01

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

  13. 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,…

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  15. 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.

  16. Intermediate-energy nuclear chemistry workshop

    SciTech Connect

    Butler, G.W.; Giesler, G.C.; Liu, L.C.; Dropesky, B.J.; Knight, J.D.; Lucero, F.; Orth, C.J.

    1981-05-01

    This report contains the proceedings of the LAMPF Intermediate-Energy Nuclear Chemistry Workshop held in Los Alamos, New Mexico, June 23-27, 1980. The first two days of the Workshop were devoted to invited review talks highlighting current experimental and theoretical research activities in intermediate-energy nuclear chemistry and physics. Working panels representing major topic areas carried out indepth appraisals of present research and formulated recommendations for future research directions. The major topic areas were Pion-Nucleus Reactions, Nucleon-Nucleus Reactions and Nuclei Far from Stability, Mesonic Atoms, Exotic Interactions, New Theoretical Approaches, and New Experimental Techniques and New Nuclear Chemistry Facilities.

  17. Detection of Late Intermediates in Virus Capsid Assembly by Charge Detection Mass Spectrometry

    PubMed Central

    2015-01-01

    The assembly of hundreds of identical proteins into an icosahedral virus capsid is a remarkable feat of molecular engineering. How this occurs is poorly understood. Key intermediates have been anticipated at the end of the assembly reaction, but it has not been possible to detect them. In this work we have used charge detection mass spectrometry to identify trapped intermediates from late in the assembly of the hepatitis B virus T = 4 capsid, a complex of 120 protein dimers. Prominent intermediates are found with 104/105, 110/111, and 117/118 dimers. Cryo-EM observations indicate the intermediates are incomplete capsids and, hence, on the assembly pathway. On the basis of their stability and kinetic accessibility we have proposed plausible structures. The prominent trapped intermediate with 104 dimers is attributed to an icosahedron missing two neighboring facets, the 111-dimer species is assigned to an icosahedron missing a single facet, and the intermediate with 117 dimers is assigned to a capsid missing a ring of three dimers in the center of a facet. PMID:24548133

  18. 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.

  19. 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.

  20. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

    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.

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

    PubMed Central

    Gutiérrez Acosta, Olga B.; Hardt, Norman

    2013-01-01

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

  3. 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

  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. Oxide formation: reaction details studied,

    E-print Network

    Johnson, Edward A.

    Oxide formation: reaction details studied, reported in brief Sir -- Nineteen years ago, I published-nitrosohydroxylamines undergo an alternative decomposition under very similar reaction conditions to liberate nitrous oxide, N2O (refs 4,5). Moreover, this alternative reaction involves highly electrophilic intermediates analogous

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

    PubMed

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

    2011-09-19

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

  7. Highly enantioselective trapping of zwitterionic intermediates by imines

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

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

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

    PubMed

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

    2009-03-21

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

  9. Impact of sulfur dioxide oxidation by Stabilized Criegee Intermediate on sulfate

    EPA Science Inventory

    We revise the Carbon Bond chemical mechanism to explicitly represent three Stabilized Criegee Intermediates (SCIs) and their subsequent reactions with sulfur dioxide, water monomer, and water dimer, and incorporate the reactions into the Community Multiscale Air Quality model. Th...

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

    PubMed

    Song, Xinli; Zügner, Gábor L; Farkas, Mária; Illés, Ádám; Sarzy?ski, Dariusz; Rozgonyi, Tamás; Wang, Baoshan; Dóbé, Sándor

    2015-07-16

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

  11. Development of a multiplexed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay to identify common members of the Subgenera Culex (Culex) and Culex (Phenacomyia) in Guatemala.

    PubMed

    Kent, Rebekah J; Deus, Stephen; Williams, Martin; Savage, Harry M

    2010-08-01

    Morphological differentiation of mosquitoes in the subgenera Culex (Culex) and Culex (Phenacomyia) in Guatemala is difficult, with reliable identification ensured only through examination of larval skins from individually reared specimens and associated male genitalia. We developed a multiplexed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay to identify common Cx. (Cux.) and Cx. (Phc.). Culex (Cux.) chidesteri, Cx. (Cux.) coronator, Cx. (Cux.) interrogator, Cx. (Cux.) quinquefasciatus, Cx. (Cux.) nigripalpus/Cx. (Cux.) thriambus, and Cx. (Phc.) lactator were identified directly with a multiplexed primer cocktail comprising a conserved forward primer and specific reverse primers targeting ribosomal DNA (rDNA). Culex nigripalpus and Cx. thriambus were differentiated by restriction digest of homologous amplicons. The assay was developed and optimized using well-characterized specimens from Guatemala and the United States and field tested with unknown material from Guatemala. This assay will be a valuable tool for mosquito identification in entomological and arbovirus ecology studies in Guatemala. PMID:20682869

  12. 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…

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

    ERIC Educational Resources Information Center

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

    2011-01-01

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

  14. Exemplary Dissemination Programs for Intermediate Units Serving Rural Schools.

    ERIC Educational Resources Information Center

    Edington, Everett; Hays, Leonard

    Utilizing information derived from documents, site visits, correspondence, and personal interviews re: 6 intermediate education units serving rural schools which were initially identified via a mail survey, this report describes intermediate education units with exemplary information dissemination programs. Varying considerably, each program is…

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

    ERIC Educational Resources Information Center

    Kraak, Andre

    2008-01-01

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

  16. Covalent functionalization of graphene with reactive intermediates.

    PubMed

    Park, Jaehyeung; Yan, Mingdi

    2013-01-15

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

  17. The Intermediate Neutrino Program

    E-print Network

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

    2015-04-01

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

  18. 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...

  19. Intermediate water recovery system

    NASA Technical Reports Server (NTRS)

    Deckman, G.; Anderson, A. R. (editor)

    1973-01-01

    A water recovery system for collecting, storing, and processing urine, wash water, and humidity condensates from a crew of three aboard a spacecraft is described. The results of a 30-day test performed on a breadboard system are presented. The intermediate water recovery system produced clear, sterile, water with a 96.4 percent recovery rate from the processed urine. Recommendations for improving the system are included.

  20. 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.

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

    PubMed

    Svensson, Fredrik; Engen, Karin; Lundbäck, Thomas; Larhed, Mats; Sköld, Christian

    2015-09-28

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

  2. A mechanochemical switch to control radical intermediates.

    PubMed

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

    2014-06-17

    B??-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 AdoB??-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

  3. Accounting 306 Intermediate Accounting II

    E-print Network

    Barrash, Warren

    Accounting 306 Intermediate Accounting II Fall 2015 Syllabus Meeting Time: Section 1: T,TH 1-2190 email pbahnson@boisestate.edu Required Texts: Spiceland, Sepe, and Nelson, Intermediate Accounting (8th of the theory and practice of financial accounting. The intermediate series is considered by many

  4. Are copper(I) carbenes capable intermediates for cyclopropanations? The case for ylide intermediates.

    PubMed

    Aldajaei, Jamal T; Keeffe, James R; Swift, Christopher A; Gronert, Scott

    2015-09-01

    A novel approach is used to synthesize a stable, ligated copper(I) carbene in the gas phase that is capable of typical metal carbenoid chemistry. However, it is shown that copper(I) carbenes generally undergo rapid unimolecular rearrangements including insertions into copper-ligand bonds and Wolff rearrangements. The results indicate that most copper(I) carbenes are inherently unstable and would not be viable intermediates in condensed-phase applications; an alternative intermediate that is less prone to rearrangements is required. Computational data suggest that ylides formed by the complexation of the carbene with solvent or other weak nucleophiles are viable intermediates in the reactions of copper(I) carbenes. PMID:26179611

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

    PubMed

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

    2008-07-11

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

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

    2010-01-01

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

  8. 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.

  9. Photocatalytic mineralization of codeine by UV-A/TiO2-Kinetics, intermediates, and pathways.

    PubMed

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

    2016-01-15

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

  10. Chemistry and some biological effects of model melanoidins and pigments as Maillard intermediates.

    PubMed

    Hayase, Fumitaka; Usui, Teruyuki; Watanabe, Hirohito

    2006-12-01

    Various pigments were formed in the D-xylose-glycine reaction system. Blue pigments (Blue-M1 and Blue-M2) and red pigments (Red-M1 and Red-M2) were generated in the Maillard reaction. Blue-M2 is presented to have been generated by the reaction between Blue-M1, which involved two pyrrolopyrrole structures as the major blue pigment, and di-D-xyluloseglycine. We identified red pigments as the isomers of addition compounds of D-xyluloseglycine to condensated compound between pyrroropyrrole-2-carbaldehyde and pyrrole-2-carbaldehyde compounds. These pigments have polymerizing activities, suggesting that they are important Maillard reaction intermediates through the formation of melanoidins. Blue-M1 as well as melanoidins effectively suppressed the peroxidation of linoleic acid. The scavenging activity toward Blue-M1 on hydroxyl and DPPH radicals was also as strong as that of melanoidins. Furthermore, Blue-M1 prevents the oxidative cell injury. Therefore, Blue-M1 will be an antioxidant which protects against the oxidative stress in biological systems. Melanoidins induced IFN-gamma mRNA and IL-12 mRNA expressions in spleen cells exposed to allergen and in macrophage-like J774.1 cells, respectively. These findings suggest that melanoidins have suppressive effect on allergic reaction as a novel physiological effect. PMID:17131457

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

    SciTech Connect

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

    2013-04-08

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

  12. Nucleosynthesis in intermediate mass AGB stars

    E-print Network

    John Lattanzio; Corinne Charbonnel; Manuel Forestini

    1999-12-15

    We present a summary of the main sites for nucleosynthesis in intermediate mass Asymptotic Giant Branch (AGB) stars. We then discuss some detailed evolutionary models and how these have been used to create a synthetic evolution code which calculates the nucleosynthesis very rapidly, enabling us to investigate changes in some uncertain parameters in AGB evolution, such as mass-loss and dredge-up. We then present results for C, C/O, Mg and Al. We also discuss the changes due to the recent NACRE compilation of reaction rates.

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

    PubMed Central

    Rao, Arun Prasad; Austin, Ravi David

    2014-01-01

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

  14. 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

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

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

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

  16. Non-enzymatic synthesis of the coenzymes, uridine diphosphate glucose and cytidine diphosphate choline, and other phosphorylated metabolic intermediates

    NASA Technical Reports Server (NTRS)

    Mar, A.; Dworkin, J.; Oro, J.

    1987-01-01

    Using urea and cyanamide, the two condensing agents considered to have been present on the primitive earth, uridine diphosphate glucose (UDPG), cytidine diphosphate choline (CDP-choline), glucose-1-phosphate (G1P), and glucose-6-phosphate (G6P) were synthesized under simulated prebiotic conditions. The reaction products were separated and identified using paper chromatography, thin layer chromatography, enzymatic analyses, and ion-pair reverse-phase high performance liquid chromatography. The possibility of nonenzymatic synthesis of metabolic intermediates on the primitive earth from simple precursors was thus demonstrated.

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

    PubMed Central

    2015-01-01

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

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

    PubMed

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

    2014-05-21

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

  19. Welding. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Vincent, Kenneth

    Several intermediate performance objectives and corresponding criterion measures are listed for each of nine terminal objectives for an intermediate welding course. The materials were developed for a 36-week (3 hours daily) course designed to prepare the student for employment in the field of welding. Electric welding and specialized (TIG & MIG)…

  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. Formation of an intermediate phase in the ball milling synthesis of the sillenite phase of BSO and BTO

    NASA Astrophysics Data System (ADS)

    Carrasco, M. F.; Mendiratta, S. K.; Marques, L.

    2005-02-01

    High-energy ball milling is a relatively new process for the synthesis of technologically useful compounds that require high temperatures in the conventional solid-state reaction method. It is thought that high-impact energy transferred to microscopic amounts of powder momentarily trapped between two colliding balls leads to a local transient of high pressure and temperature that drives the reaction at the surface of the trapped particles. The technique of ball milling has been successfully used to produce nanocrystals of the sillenite phase of bismuth silicate (BSO), and its titanate (BTO) and germanate (BGO) homologues. Our aim in this paper is to see, experimentally, whether passage through an intermediate phase occurs en route to the final product. The results of our study using various analytical techniques show that indeed, in the case of BSO and BTO, an intermediate phase is formed temporarily along the grinding route. The SEM pictures of the powders in the various stages of the grinding process also indicate that a process of phase transformation takes place at the surface of the crystals. We have not been able to identify the precise structure of the intermediate phase, but show that it is an unstable phase that transforms with heat treatment preferentially into the desired sillenite phase in the case of BTO and to the reactants in the case of BSO.

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

    Cancer.gov

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

  3. Intermediate role of ?-keto acids in the formation of Strecker aldehydes.

    PubMed

    Hidalgo, Francisco J; Delgado, Rosa M; Zamora, Rosario

    2013-11-15

    The ability of ?-keto acids to covert amino acids into Strecker aldehydes was investigated in an attempt to both identify new pathways for Strecker degradation, and analyse the role of ?-keto acids as intermediate compounds in the formation of Strecker aldehydes by oxidised lipids. The results obtained indicated that phenylalanine was converted into phenylacetaldehyde to a significant extent by all ?-keto acids assayed; glyoxylic acid being the most reactive ?-keto acid for this reaction. It has been proposed that the reaction occurs by formation of an imine between the keto group of the ?-keto acid, and the amino group of the amino acid. This then undergoes an electronic rearrangement with the loss of carbon dioxide to produce a new imine. This final imine is the origin of both the Strecker aldehyde and the amino acid from which the ?-keto acid is derived. When glycine was incubated in the presence of 4,5-epoxy-2-decenal, the amino acid was converted into glyoxylic acid, and this ?-keto acid was then able to convert phenylalanine into phenylacetaldehyde. All these results suggest that Strecker aldehydes can be produced by amino acid degradation initiated by different reactive carbonyl compounds, included those coming from amino acids and proteins. In addition, ?-keto acids may act as intermediates for the Strecker degradation of amino acids by oxidised lipids. PMID:23790896

  4. General Method for Functionalized Polyaryl Synthesis via Aryne Intermediates

    PubMed Central

    2015-01-01

    A method for base-promoted arylation of arenes and heterocycles by aryl halides and aryl triflates is described. Additionally, in situ electrophilic trapping of ArLi intermediates generated in the reaction of benzyne with deprotonated arenes or heterocycles has been developed, providing rapid and easy access to a wide range of highly functionalized polyaryls. Base-promoted arylation methodology complements transition-metal-catalyzed direct arylation and allows access to structures that are not easily accessible via other direct arylation methods. The reactions are highly functional-group tolerant, with alkene, ether, dimethylamino, trifluoromethyl, ester, cyano, halide, hydroxyl, and silyl functionalities compatible with reaction conditions. PMID:24893069

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

    PubMed

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

    2015-12-21

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

  6. 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

  7. 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.

  8. 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

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

    PubMed Central

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

    1985-01-01

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

  10. 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.

  11. Moving beyond Intermediate English Proficiency

    ERIC Educational Resources Information Center

    Jewell, Mary

    2009-01-01

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

  12. Plasticity of Intermediate Filament Subunits

    E-print Network

    Kirmse, Robert

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

  13. Materials System for Intermediate Temperature Solid Oxide Fuel Cell

    SciTech Connect

    Uday B. Pal; Srikanth Gopalan

    2005-01-24

    AC complex impedance spectroscopy studies were conducted between 600-800 C on symmetrical cells that employed strontium-and-magnesium-doped lanthanum gallate electrolyte, La{sub 0.9}Sr{sub 0.1}Ga{sub 0.8}Mg{sub 0.2}O{sub 3} (LSGM). The objective of the study was to identify the materials system for fabrication and evaluation of intermediate temperature (600-800 C) solid oxide fuel cells (SOFCs). The slurry-coated electrode materials had fine porosity to enhance catalytic activity. Cathode materials investigated include La{sub 1-x}Sr{sub x}MnO{sub 3} (LSM), LSCF (La{sub 1-x}Sr{sub x}Co{sub y}Fe{sub 1-y}O{sub 3}), a two-phase particulate composite consisting of LSM-doped-lanthanum gallate (LSGM), and LSCF-LSGM. The anode materials were Ni-Ce{sub 0.85}Gd{sub 0.15}O{sub 2} (Ni-GDC) and Ni-Ce{sub 0.6}La{sub 0.4}O{sub 2} (Ni-LDC) composites. Experiments conducted with the anode materials investigated the effect of having a barrier layer of GDC or LDC in between the LSGM electrolyte and the Ni-composite anode to prevent adverse reaction of the Ni with lanthanum in LSGM. For proper interpretation of the beneficial effects of the barrier layer, similar measurements were performed without the barrier layer. The ohmic and the polarization resistances of the system were obtained over time as a function of temperature (600-800 C), firing temperature, thickness, and the composition of the electrodes. The study revealed important details pertaining to the ohmic and the polarization resistances of the electrode as they relate to stability and the charge-transfer reactions that occur in such electrode structures.

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

    PubMed

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

    2008-09-01

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

  15. Cryogenic Ion Vibrational Spectroscopy of - CH Activation Intermediates

    NASA Astrophysics Data System (ADS)

    Marsh, Brett; Garand, Etienne

    2013-06-01

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

  16. Applications of Reaction Rate

    ERIC Educational Resources Information Center

    Cunningham, Kevin

    2007-01-01

    This article presents an assignment in which students are to research and report on a chemical reaction whose increased or decreased rate is of practical importance. Specifically, students are asked to represent the reaction they have chosen with an acceptable chemical equation, identify a factor that influences its rate and explain how and why it…

  17. 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.

  18. Cofactor mobility determines reaction outcome in the IMPDH/GMPR (?/?)8 barrel enzymes

    PubMed Central

    Patton, Gregory C.; Stenmark, Pål; Gollapalli, Deviprasad R.; Sevastik, Robin; Kursula, Petri; Flodin, Susanne; Schuler, Herwig; Swales, Colin T.; Eklund, Hans; Himo, Fahmi; Nordlund, Pär; Hedstrom, Lizbeth

    2015-01-01

    IMP dehydrogenase (IMPDH) and GMP reductase (GMPR) belong to the same structural family, share a common set of catalytic residues and bind the same ligands. The structural and mechanistic features that determine reaction outcome in the IMPDH/GMPR family have not been identified. Here, we show that the GMPR reaction utilizes the same intermediate E-XMP* as IMPDH, but this intermediate reacts with ammonia instead of water. A single crystal structure of human GMPR type 2 with IMP and NADPH fortuitously captures three different states, each of which mimic a distinct step in the catalytic cycle of GMPR. The cofactor is found in two conformations, an "in" conformation poised for hydride transfer, and an "out" conformation where the cofactor is 6 Å from IMP. Mutagenesis, substrate/cofactor analog experiments demonstrate that the “out” conformation is required for the deamination of GMP. Remarkably, the cofactor is part of the catalytic machinery activating ammonia. PMID:22037469

  19. Structure and reaction of oxametallacycles derived from styrene oxide on Ag(1 1 0)

    NASA Astrophysics Data System (ADS)

    Lukaski, A. C.; Enever, M. C. N.; Barteau, M. A.

    2007-08-01

    Styrene oxide forms a strongly bound oxametallacycle intermediate via activated adsorption on the Ag(1 1 0) surface. The oxametallacycle species derived from styrene oxide on Ag(1 1 0) fits well with the family of oxametallacycles identified previously in studies of non-allylic 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(1 1 0) 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(1 1 0). Styrene oxide-derived oxametallacycles exhibit similar ring-closure behavior on the Ag(1 1 1) surface.

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

    SciTech Connect

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

    1999-08-01

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

  1. Diphosphine is an intermediate in the photolysis of phosphine to phosphorus and hydrogen. [Jupiter atmospheric chemistry

    NASA Technical Reports Server (NTRS)

    Ferris, J. P.; Benson, R.

    1980-01-01

    The photolysis of phosphine to red phosphorus (P4) and hydrogen is investigated in light of the potential significance of the reaction in the atmospheric chemistry of Jupiter. It is reported that the photolysis of PH3 at room temperature by a 206.2-nm light source gave rise to a product identified by its UV and IR spectra and gas chromatographic retention time as P2H4, the yield of which is found to increase to a maximum and then decrease to 20% of the maximum value with illumination time. A mechanism for phosphine photolysis including diphosphine formation as an intermediate step is proposed, and it is concluded that P2H4 is a likely constituent of the atmospheres of the Jovian planets.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  3. Fates of imine intermediates in radical cyclizations of N-sulfonylindoles and ene-sulfonamides

    PubMed Central

    Zhang, Hanmo; Hay, E Ben; Geib, Stephen J

    2015-01-01

    Summary Two new fates of imine intermediates formed on radical cyclizations of ene-sulfonamides have been identified, reduction and hydration/fragmentation. Tin hydride-mediated cyclizations of 2-halo-N-(3-methyl-N-sulfonylindole)anilines provide spiro[indoline-3,3'-indolones] or spiro-3,3'-biindolines (derived from imine reduction), depending on the indole C2 substituent. Cyclizations of 2-haloanilide derivatives of 3-carboxy-N-sulfonyl-2,3-dihydropyrroles also presumably form spiro-imines as primary products. However, the lactam carbonyl group facilitates the ring-opening of these cyclic imines by a new pathway of hydration and retro-Claisen-type reaction, providing rearranged 2-(2'-formamidoethyl)oxindoles.

  4. Allergic Reactions

    MedlinePLUS

    ... allergic reaction is actually a result of a chain reaction that begins in your genes and is expressed ... Tips • Allergy symptoms are the result of a chain reaction that starts in your immune system. • If you ...

  5. Evidence for an Ionic Intermediate in the Transformation of Fatty Acid Hydroperoxide by a Catalase-related Allene Oxide Synthase from the Cyanobacterium Acaryochloris marina*

    PubMed Central

    Gao, Benlian; Boeglin, William E.; Zheng, Yuxiang; Schneider, Claus; Brash, Alan R.

    2009-01-01

    Allene oxides are reactive epoxides biosynthesized from fatty acid hydroperoxides by specialized cytochrome P450s or by catalase-related hemoproteins. Here we cloned, expressed, and characterized a gene encoding a lipoxygenase-catalase/peroxidase fusion protein from Acaryochloris marina. We identified novel allene oxide synthase (AOS) activity and a by-product that provides evidence of the reaction mechanism. The fatty acids 18.4?3 and 18.3?3 are oxygenated to the 12R-hydroperoxide by the lipoxygenase domain and converted to the corresponding 12R,13-epoxy allene oxide by the catalase-related domain. Linoleic acid is oxygenated to its 9R-hydroperoxide and then, surprisingly, converted ?70% to an epoxyalcohol identified spectroscopically and by chemical synthesis as 9R,10S-epoxy-13S-hydroxyoctadeca-11E-enoic acid and only ?30% to the 9R,10-epoxy allene oxide. Experiments using oxygen-18-labeled 9R-hydroperoxide substrate and enzyme incubations conducted in H218O indicated that ?72% of the oxygen in the epoxyalcohol 13S-hydroxyl arises from water, a finding that points to an ionic intermediate (epoxy allylic carbocation) during catalysis. AOS and epoxyalcohol synthase activities are mechanistically related, with a reacting intermediate undergoing a net hydrogen abstraction or hydroxylation, respectively. The existence of epoxy allylic carbocations in fatty acid transformations is widely implicated although for AOS reactions, without direct experimental support. Our findings place together in strong association the reactions of allene oxide synthesis and an ionic reaction intermediate in the AOS-catalyzed transformation. PMID:19531485

  6. 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

  7. Compact intermediates in RNA folding

    SciTech Connect

    Woodson, S.A.

    2011-12-14

    Large noncoding RNAs fold into their biologically functional structures via compact yet disordered intermediates, which couple the stable secondary structure of the RNA with the emerging tertiary fold. The specificity of the collapse transition, which coincides with the assembly of helical domains, depends on RNA sequence and counterions. It determines the specificity of the folding pathways and the magnitude of the free energy barriers to the ensuing search for the native conformation. By coupling helix assembly with nascent tertiary interactions, compact folding intermediates in RNA also play a crucial role in ligand binding and RNA-protein recognition.

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

    NASA Astrophysics Data System (ADS)

    Savara, Aditya; Weitz, Eric

    2014-04-01

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

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

    PubMed

    Savara, Aditya; Weitz, Eric

    2014-01-01

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

  10. Microtubule and Intermediate Filament Patterns around the

    E-print Network

    Vorobjev, Ivan

    4 Microtubule and Intermediate Filament Patterns around the Centrosome in Interphase Cells I. B of the Centrosome III. Centrosome and Intermediate Filaments A. Intermediate Filament Foci in the Centrosome B. Effect of Ultracentrifugation of Living Cells on Their Intermediate Filament System: Identification

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

    PubMed Central

    2015-01-01

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

  12. The Time-Dependent Distribution of Phosphorylated Intermediates in Native Sarcoplasmic Reticulum Ca2+

    E-print Network

    Thomas, David D.

    (Pi) burst, reflecting increased turnover of E2P at the higher temperature. The Pi burst exceeded and breakdown of chemical intermediates in the Ca-ATPase reaction cycle (see Scheme 1). Coupling of the enzymatic reactions to the conformational events enables the chemical energy from ATP to be converted

  13. Vocabulary Learning Strategies of Iranian Upper-Intermediate EFL Learners

    ERIC Educational Resources Information Center

    Khatib, Mohammad; Hassanzadeh, Mohammad; Rezaei, Saeed

    2011-01-01

    This study examines the preferred vocabulary learning strategies of Iranian upper-intermediate EFL learners. In order to identify the aforementioned group in terms of language proficiency, a TOEFL test was administered to a population of 146 undergraduate EFL students at the university of Vali-e-Asr in Rafsanjan, Iran. Those scoring above 480 were…

  14. Error Analysis in Composition of Iranian Lower Intermediate Students

    ERIC Educational Resources Information Center

    Taghavi, Mehdi

    2012-01-01

    Learners make errors during the process of learning languages. This study examines errors in writing task of twenty Iranian lower intermediate male students aged between 13 and 15. A subject was given to the participants was a composition about the seasons of a year. All of the errors were identified and classified. Corder's classification (1967)…

  15. INTERMEDIATE ACCOUNTING II SUMMER 2015

    E-print Network

    Barrash, Warren

    1 ACCT 306 INTERMEDIATE ACCOUNTING II SUMMER 2015 PROFESSOR: Troy Hyatt, PhD, CPA SECTION: 1 OFFICE credit case that is due Wednesday, June 10, will also be distributed at a later date. EXAMS A total of four exams will be given, each worth 80 points. Exam dates are included on the attached schedule. All

  16. INTERMEDIATE ACCOUNTING I SUMMER 2015

    E-print Network

    Barrash, Warren

    1 ACCT 304 INTERMEDIATE ACCOUNTING I SUMMER 2015 PROFESSOR: Troy Hyatt, PhD, CPA SECTION: 1 OFFICE-WRITTEN RESPONSES WILL NOT BE ACCEPTED. EXAMS A total of four exams will be given, each worth 80 points. Exam dates are included on the attached schedule. All exams are "closed book." Exams will consist of multiple choice

  17. 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)…

  18. 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.

  19. A Caged, Destabilized Free Radical Intermediate in the Q Cycle

    PubMed Central

    Vennam, Preethi R.; Fisher, Nicholas; Krzyaniak, Matthew D.; Kramer, David M.

    2013-01-01

    The Rieske/cytochrome b complexes, also known as cytochrome bc complexes, catalyze a unique oxidant-induced reduction reaction at their quinol oxidase sites (Qo), in which substrate hydroquinone reduces two distinct electron transfer chains, one through a series of high-potential electron carriers, the second through low-potential cytochrome b. This reaction is a critical step in energy storage by the Q-cycle. The semiquinone intermediate in this reaction can reduce O2 to produce deleterious superoxide. It is yet unknown how the enzyme controls this reaction, though numerous models are proposed. In previous work we trapped a Q-cycle semiquinone anion intermediate, termed SQo, in bacterial cyt bc1 by rapid freeze-quenching. In this work, we apply pulsed EPR techniques to determine the location and properties of SQo in the mitochondrial complex. In contrast to semiquinone intermediates in other enzymes, SQo is not thermodynamically stabilized, and may even be destabilized with respect to solution. It is trapped in the Qo at a site, which is distinct from previously described inhibitor-binding sites, yet sufficiently close to cytochrome bL to allow rapid electron transfer. The binding site and EPR analysis show that SQo is not stabilized by hydrogen bonds to proteins. The formation of SQo involves “stripping” of both substrate -OH protons during the initial oxidation step, as well as conformational changes of the semiquinone and Qo proteins. The resulting charged radical is kinetically trapped, rather than thermodynamically stabilized (as in most enzymatic semiquinone species), conserving redox energy to drive electron transfer to cytochrome bL, while minimizing certain Q-cycle bypass reactions including oxidation of pre-reduced cytochrome b and reduction of O2. PMID:24009094

  20. Mechanistic Insight into the Dehydro-Diels-Alder Reaction of Styrene-Ynes.

    PubMed

    Kocsis, Laura S; Kagalwala, Husain N; Mutto, Sharlene; Godugu, Bhaskar; Bernhard, Stefan; Tantillo, Dean J; Brummond, Kay M

    2015-12-01

    The Diels-Alder reaction represents one of the most thoroughly studied and well-understood synthetic transformations for the assembly of six-membered rings. Although intramolecular dehydro-Diels-Alder (IMDDA) reactions have previously been employed for the preparation of naphthalene and dihydronaphthalene substrates, low yields and product mixtures have reduced the impact and scope of this reaction. Through the mechanistic studies described within, we have confirmed that the thermal IMDDA reaction of styrene-ynes produces a naphthalene product via loss of hydrogen gas from the initially formed cycloadduct, a tetraenyl intermediate. Alternatively, the dihydronaphthalene product is afforded from the same tetraenyl intermediate via a radical isomerization process. Moreover, we have identified conditions that can be used to achieve efficient, high-yielding, and selective IMDDA reactions of styrene-ynes to form either naphthalene or dihydronaphthalene products. The operational simplicity and retrosynthetic orthogonality of this method for the preparation of naphthalenes and dihydronaphthalenes makes this transformation appealing for the synthesis of medicinal and material targets. The mechanistic studies within may impact the development of other thermal transformations. PMID:25671399

  1. Structural insights into the reaction mechanism of S-adenosyl-L-homocysteine hydrolase

    PubMed Central

    Kusakabe, Yoshio; Ishihara, Masaaki; Umeda, Tomonobu; Kuroda, Daisuke; Nakanishi, Masayuki; Kitade, Yukio; Gouda, Hiroaki; Nakamura, Kazuo T.; Tanaka, Nobutada

    2015-01-01

    S-adenosyl-L-homocysteine hydrolase (SAH hydrolase or SAHH) is a highly conserved enzyme that catalyses the reversible hydrolysis of SAH to L-homocysteine (HCY) and adenosine (ADO). High-resolution crystal structures have been reported for bacterial and plant SAHHs, but not mammalian SAHHs. Here, we report the first high-resolution crystal structure of mammalian SAHH (mouse SAHH) in complex with a reaction product (ADO) and with two reaction intermediate analogues—3’-keto-aristeromycin (3KA) and noraristeromycin (NRN)—at resolutions of 1.55, 1.55, and 1.65?Å. Each of the three structures constitutes a structural snapshot of one of the last three steps of the five-step process of SAH hydrolysis by SAHH. In the NRN complex, a water molecule, which is an essential substrate for ADO formation, is structurally identified for the first time as the candidate donor in a Michael addition by SAHH to the 3’-keto-4’,5’-didehydroadenosine reaction intermediate. The presence of the water molecule is consistent with the reaction mechanism proposed by Palmer & Abeles in 1979. These results provide insights into the reaction mechanism of the SAHH enzyme. PMID:26573329

  2. Microfabricated electrochemiluminescence cell for chemical reaction detection

    DOEpatents

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

    2003-01-01

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

  3. Anaerobic Metabolism of Cyclohex-1-Ene-1-Carboxylate, a Proposed Intermediate of Benzoate Degradation, by Rhodopseudomonas palustris.

    PubMed

    Perrotta, J A; Harwood, C S

    1994-06-01

    Anaerobic benzoate degradation by the phototrophic bacterium Rhodopseudomonas palustris has been proposed to proceed via aromatic ring reduction reactions leading to cyclohex-1-ene-1-carboxyl-coenzyme A (CoA) formation. The alicyclic product is then proposed to undergo three beta-oxidation-like modifications resulting in ring cleavage. Illuminated suspensions of benzoate-grown cells converted [7-C]cyclohex-1-ene-1-carboxylate to intermediates that comigrated with cyclohex-1-ene-1-carboxyl-CoA, 2-hydroxycyclohexanecar-boxyl-CoA, 2-ketocyclohexanecarboxyl-CoA, and pimelyl-CoA by thin-layer chromatography. This set of intermediates was also formed by cells grown anaerobically or aerobically on cyclohex-1-ene-1-carboxylate, indicating that benzoate-grown and cyclohex-1-ene-1-carboxylate-grown cells degrade this alicyclic acid by the same catabolic route. Four enzymatic activities proposed to be required for conversion of cyclohex-1-ene-1-carboxylate to pimelyl-CoA were detected at 3- to 10-fold-higher levels in benzoate-grown cells than in succinate-grown cells. These were cyclohex-1-ene-1-carboxylate-CoA ligase, cyclohex-1-ene-1-carboxyl-CoA hydratase, 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase, and 2-ketocyclohexanecarboxyl-CoA hydrolase (ring cleaving). Pimelyl-CoA was identified in hydrolase reaction mixtures as the product of alicyclic ring cleavage. The results provide a first demonstration of an alicyclic ring cleavage activity. PMID:16349272

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

    SciTech Connect

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

    2000-01-20

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

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

    SciTech Connect

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

    2010-03-16

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

  6. PETER POULAY SPECIAL ISSUE, editor in charge H. F. SCAEFER The Mechanism of a Barrierless Reaction

    E-print Network

    Quapp, Wolfgang

    Reaction: Hidden Transition State and Hidden Intermediates in the Reaction of Methylene with Ethene Hyun: The chelotropic addition reaction of singlet methylene to ethene yielding cyclopropane (reaction 1) was investigated with the help of the Unified Reaction Valley approach (URVA) using different levels of theory (B3

  7. Transformation, products, and pathways of chlorophenols via electro-enzymatic catalysis: How to control toxic intermediate products.

    PubMed

    Du, Penghui; Zhao, He; Li, Haitao; Zhang, Di; Huang, Ching-Hua; Deng, Manfeng; Liu, Chenming; Cao, Hongbin

    2016-02-01

    Chlorophenols can be easily oxidized into chlorobenzoquinones (CBQs), which are highly toxic and have been linked to bladder cancer risk. Herein, we report the transformation, products, and pathways of 2,4-dichlorophenol (DCP) by horseradish peroxidase (HRP) and electro-generated hydrogen peroxide (H2O2) and suggest methods to control the formation of toxic intermediate products. After a 10-min electroenzymatic process, 99.7% DCP removal may be achieved under optimal conditions. A total of 16 reaction products, most of which are subsequently verified as DCP polymers and related quinone derivatives, are identified by using ultra-performance liquid chromatography-time-of-flight mass spectrometry (UPLC-TOF-MS). A five-step reaction pathway for DCP transformation, including HRP-driven substrate oxidation, substitution and radical coupling, quick redox equilibrium, nucleophilic reaction and precipitation from aqueous solution, is proposed. Current variations and the presence of CO2 could significantly affect these reaction pathways. In particular, higher currents enhance the hydroxylation process by promoting alkaline conditions and abundant H2O2 formation. As both OH(-) and H2O2 are strong nucleophiles, they easily react with CBQ products to form hydroxylated products, which can significantly reduce solution toxicity. An adequate supply of CO2 can provide favorable pH conditions and facilitate enzymatic steps, such as substrate oxidation and radical coupling, to generate precipitable polymerized products. All of the results suggest that toxic intermediate products can be effectively reduced and controlled during the electro-enzymatic process to remove DCP and other phenolic pollutants from wastewaters. PMID:26519798

  8. Mechanics of vimentin intermediate filaments

    NASA Technical Reports Server (NTRS)

    Wang, Ning; Stamenovic, Dimitrijie

    2002-01-01

    It is increasingly evident that the cytoskeleton of living cells plays important roles in mechanical and biological functions of the cells. Here we focus on the contribution of intermediate filaments (IFs) to the mechanical behaviors of living cells. Vimentin, a major structural component of IFs in many cell types, is shown to play an important role in vital mechanical and biological functions such as cell contractility, migration, stiffness, stiffening, and proliferation.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  10. Pineal parenchymal tumor of intermediate differentiation.

    PubMed

    Patil, Meena; Karandikar, Manjiri

    2015-01-01

    The 2007 World Health Organization classification of tumors of the central nervous system identified "pineal parenchymal tumor of intermediate differentiation" (PPTID) as a new pineal parenchymal neoplasm, located between pineocytoma and pineoblastoma as grade II or III. Because of the small number of reported cases, the classification of PPT is still a matter of controversy. We report a case of PPTID. A 25-year-old female patient was admitted to hospital with complaints of a headache, nausea, vomiting since 1-year. Computed tomography/magnetic resonance imaging of the brain showed well-defined, mildly enhancing lesion in the region of the pineal gland with areas of calcification. The tumor was excised. After 3 years, she presented with metastasis in thoracic and lumbosacral spinal region. This is a rare event. PMID:26549088

  11. EGRET sources at intermediate galactic latitude

    NASA Technical Reports Server (NTRS)

    Halpern, Jules P. (Principal Investigator)

    1996-01-01

    This paper presents the abstracts of four papers (using ROSAT data) that are submitted to refereed journals during the current reporting period. The papers are: (1) Extreme x-ray variability in the narrow-line QSO PHL 1092; (2) The Geminga pulsar (soft x-ray variability and an EUVE observation); (3) a broad-band x-ray study of the geminga pulsar; and (4) Classification of IRAS-selected x-ray galaxies in the ROSAT all-sky survey. The abstracts of these papers are given in the next four sections of this report, and their status is given in the Appendix. Finally, two new projects (De-identifying a non-AGN and EGRET sources at intermediate galactic latitude) for which ROSAT data were recently received are currently being studied under this grant. A summary of work in progress on these new projects is given in the last two sections of this report.

  12. Kinetics of a Criegee intermediate that would survive high humidity and may oxidize atmospheric SO2.

    PubMed

    Huang, Hao-Li; Chao, Wen; Lin, Jim Jr-Min

    2015-09-01

    Criegee intermediates are thought to play a role in atmospheric chemistry, in particular, the oxidation of SO2, which produces SO3 and subsequently H2SO4, an important constituent of aerosols and acid rain. However, the impact of such oxidation reactions is affected by the reactions of Criegee intermediates with water vapor, because of high water concentrations in the troposphere. In this work, the kinetics of the reactions of dimethyl substituted Criegee intermediate (CH3)2COO with water vapor and with SO2 were directly measured via UV absorption of (CH3)2COO under near-atmospheric conditions. The results indicate that (i) the water reaction with (CH3)2COO is not fast enough (kH2O < 1.5 × 10(-16) cm(3) s(-1)) to consume atmospheric (CH3)2COO significantly and (ii) (CH3)2COO reacts with SO2 at a near-gas-kinetic-limit rate (kSO2 = 1.3 × 10(-10) cm(3) s(-1)). These observations imply a significant fraction of atmospheric (CH3)2COO may survive under humid conditions and react with SO2, very different from the case of the simplest Criegee intermediate CH2OO, in which the reaction with water dimer predominates in the CH2OO decay under typical tropospheric conditions. In addition, a significant pressure dependence was observed for the reaction of (CH3)2COO with SO2, suggesting the use of low pressure rate may underestimate the impact of this reaction. This work demonstrates that the reactivity of a Criegee intermediate toward water vapor strongly depends on its structure, which will influence the main decay pathways and steady-state concentrations for various Criegee intermediates in the atmosphere. PMID:26283390

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

    SciTech Connect

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

    2010-06-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  15. Jet-Medium Interactions with Identified Particles

    E-print Network

    Anne M. Sickles

    2009-09-14

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

  16. Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase.

    PubMed

    Knoot, Cory J; Purpero, Vincent M; Lipscomb, John D

    2015-01-13

    Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe(3+) to activate O2 and catecholic substrates for reaction. The inability of Fe(3+) to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated here using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surrounding solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe(3+) species, and the anhydride-Fe(3+) intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe(2+)-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe(2+) intermediate that could bind O2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage. PMID:25548185

  17. Activation of the intermediate sum in intentional and automatic calculations

    PubMed Central

    Abramovich, Yael; Goldfarb, Liat

    2015-01-01

    Most research investigating how the cognitive system deals with arithmetic has focused on the processing of two addends. Arithmetic that involves more addends has specific cognitive demands such as the need to compute and hold the intermediate sum. This study examines the intermediate sums activations in intentional and automatic calculations. Experiment 1 included addition problems containing three operands. Participants were asked to calculate the sum and to remember the digits that appeared in the problem. The results revealed an interference effect in which it was hard to identify that the digit representing the intermediate sum was not actually one of the operands. Experiment 2, further examined if the intermediate sum is activated automatically when a task does not require calculation. Here, participants were presented with a prime of an addition problem followed by a target number. The task was to determine whether the target number is odd or even, while ignoring the addition problem in the prime. The results suggested that the intermediate sum of the addition problem in the prime was activated automatically and facilitated the target. Overall, the implications of those findings in the context of theories that relate to cognitive mathematical calculation is further discussed. PMID:26483749

  18. Top predators induce the evolutionary diversification of intermediate predator species.

    PubMed

    Zu, Jian; Yuan, Bo; Du, Jianqiang

    2015-12-21

    We analyze the evolutionary branching phenomenon of intermediate predator species in a tritrophic food chain model by using adaptive dynamics theory. Specifically, we consider the adaptive diversification of an intermediate predator species that feeds on a prey species and is fed upon by a top predator species. We assume that the intermediate predator?s ability to forage on the prey can adaptively improve, but this comes at the cost of decreased defense ability against the top predator. First, we identify the general properties of trade-off relationships that lead to a continuously stable strategy or to evolutionary branching in the intermediate predator species. We find that if there is an accelerating cost near the singular strategy, then that strategy is continuously stable. In contrast, if there is a mildly decelerating cost near the singular strategy, then that strategy may be an evolutionary branching point. Second, we find that after branching has occurred, depending on the specific shape and strength of the trade-off relationship, the intermediate predator species may reach an evolutionarily stable dimorphism or one of the two resultant predator lineages goes extinct. PMID:26431773

  19. Heuristics-Guided Exploration of Reaction Mechanisms.

    PubMed

    Bergeler, Maike; Simm, Gregor N; Proppe, Jonny; Reiher, Markus

    2015-12-01

    For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive species are involved that might cause a myriad of side reactions. Without automation, a complete investigation of complex reaction mechanisms is tedious and possibly unfeasible. Therefore, only the expected dominant reaction paths of a chemical reaction network (e.g., a catalytic cycle or an enzymatic cascade) are usually explored in practice. Here, we present a computational protocol that constructs such networks in a parallelized and automated manner. Molecular structures of reactive complexes are generated based on heuristic rules derived from conceptual electronic-structure theory and subsequently optimized by quantum-chemical methods to produce stable intermediates of an emerging reaction network. Pairs of intermediates in this network that might be related by an elementary reaction according to some structural similarity measure are then automatically detected and subjected to an automated search for the connecting transition state. The results are visualized as an automatically generated network graph, from which a comprehensive picture of the mechanism of a complex chemical process can be obtained that greatly facilitates the analysis of the whole network. We apply our protocol to the Schrock dinitrogen-fixation catalyst to study alternative pathways of catalytic ammonia production. PMID:26642988

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

    PubMed Central

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

    2010-01-01

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

  1. TOF-SIMS study of photocatalytic decomposition reactions on nanocrystalline TiO 2 films

    NASA Astrophysics Data System (ADS)

    Gnaser, Hubert; Orendorz, Adam; Ziegler, Christiane; Rowlett, Elisabeth; Bock, Wolfgang

    2006-07-01

    Nanocrystalline TiO 2 is known to be a very efficient photocatalyst. In order to elucidate the details of reaction pathways occurring on the surface, nanocrystalline TiO 2 films (with 12 nm average crystallite size) were covered by methylene blue (MB) and studied, both in the pristine state and upon UV exposure, by TOF-SIMS. Distinct mass signals related to the MB parent molecule ( m = 284.1 amu) and from fragment ions are observed for the as-prepared samples. Upon irradiation with UV light under atmospheric conditions, the surface composition is pronouncedly changed, an observation ascribed to photocatalytic reactions induced by UV photons: the amount of the parent molecule is diminished whereas intermediate reaction products are identified to be present at the TiO 2 surfaces. Eventually, the parent molecule and the characteristic fragment species disappear completely upon extended exposure to UV light.

  2. An alternative reaction for heme degradation catalyzed by the Escherichia coli O157:H7 ChuS protein: Release of hematinic acid, tripyrrole and Fe(III).

    PubMed

    Ouellet, Yannick H; Ndiaye, Cheikh Tidiane; Gagné, Stéphane M; Sebilo, Anne; Suits, Michael D L; Jubinville, Éric; Jia, Zongchao; Ivancich, Anabella; Couture, Manon

    2016-01-01

    As part of the machinery to acquire, internalize and utilize heme as a source of iron from the host, some bacteria possess a canonical heme oxygenase, where heme plays the dual role of substrate and cofactor, the later catalyzing the cleavage of the heme moiety using O2 and electrons, and resulting in biliverdin, carbon monoxide and ferrous non-heme iron. We have previously reported that the Escherichia coli O157:H7 ChuS protein, which is not homologous to heme oxygenases, can bind and degrade heme in a reaction that releases carbon monoxide. Here, we have pursued a detailed characterization of such heme degradation reaction using stopped-flow UV-visible absorption spectrometry, the characterization of the intermediate species formed in such reaction by EPR spectroscopy and the identification of reaction products by NMR spectroscopy and Mass spectrometry. We show that hydrogen peroxide (in molar equivalent) is the key player in the degradation reaction, at variance to canonical heme oxygenases. While the initial intermediates of the reaction of ChuS with hydrogen peroxide (a ferrous keto ? neutral radical and ferric verdoheme, both identified by EPR spectroscopy) are in common with heme oxygenases, a further and unprecedented reaction step, involving the cleavage of the porphyrin ring at adjacent meso-carbons, results in the release of hematinic acid (a monopyrrole moiety identified by NMR spectroscopy), a tripyrrole product (identified by Mass spectrometry) and non-heme iron in the ferric oxidation state (identified by EPR spectroscopy). Overall, the unprecedented reaction of E. coli O157:H7 ChuS provides evidence for a novel heme degradation activity in a Gram-negative bacterium. PMID:26598215

  3. Intermediate sanctions for healthcare organizations.

    PubMed

    Samuels, David G; Shoretz, Morris

    2002-09-01

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

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

    PubMed

    Gençten, Metin; Özcan, Ali

    2015-10-01

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

  5. 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.

  6. Effect of Formaldehyde on the Heterogeneous Reaction of Nitrogen Dioxide on ?-Alumina.

    PubMed

    Sun, Zhenyu; Kong, Lingdong; Zhao, Xi; Ding, Xiaoxiao; Fu, Hongbo; Cheng, Tiantao; Yang, Xin; Chen, Jianmin

    2015-09-01

    Heterogeneous reactions of NO2 on various mineral aerosol particles have been investigated in many previous studies, but a fundamental understanding of how the adsorption of formaldehyde influences the heterogeneous reactions of NO2 remains unclear. In this work, the effect of formaldehyde preadsorption on heterogeneous reaction of NO2 on the surface of ?-Al2O3 at 298 K and ambient pressure was investigated by using diffuse reflectance infrared Fourier transform spectrometry (DRIFTS). It was found that the preadsorption of HCHO on ?-Al2O3 could suppress the formation of nitrate, and the rate of nitrate formation decreased with increasing amount of preadsorbed HCHO, whereas the following heterogeneous uptake of NO2 could suppress the hydration reaction of HCHO and promote the production of HCOO(-) during the reaction. Surface nitrite was formed and identified to be an intermediate product and gradually disappeared as the reaction proceeded. The amount of the formed nitrite decreased when the amount of HCHO increased. Uptake coefficients of heterogeneous reactions were calculated and found to be sensitive to the adsorption of HCHO. A possible mechanism for the influence of HCHO adsorption on the heterogeneous conversion of NO2 on ?-Al2O3 was proposed, and atmospheric implications based on these results were discussed. PMID:26285065

  7. Reaction Dynamics DOI: 10.1002/anie.201310612

    E-print Network

    Kaiser, Ralf I.

    to the carbon­carbon double bond of the 2-methyl-1,3-butadiene molecule. These initial addition complexes, such as in circumstellar envelopes of carbon stars. These high concentrations make them important reaction intermediates

  8. Carbenylative Amination and Alkylation of Vinyl Iodides via Palladium Alkylidene Intermediates.

    PubMed

    Premachandra, Ilandari Dewage Udara Anulal; Nguyen, Thi A; Shen, Chengtian; Gutman, Eugene S; Van Vranken, David L

    2015-11-01

    Most palladium-catalyzed reactions involving insertion of alkylidenes with ?-hydrogens undergo ?-hydride elimination from alkylpalladium(II) intermediates to form alkenes. Vinyl iodides were shown to generate ?(3)-allylpalladium intermediates that resist ?-hydride elimination, preserving the sp(3) center adjacent to the carbene moiety. Acyclic stereocontrol (syn/anti) for carbenylative amination and alkylation reactions was low, suggesting a lack of control in the migratory insertion step. Highly hindered carbene precursors inexplicably led to formation of Z-alkenes with high levels of stereocontrol. PMID:26496485

  9. Degradation of ibuprofen by hydrodynamic cavitation: Reaction pathways and effect of operational parameters.

    PubMed

    Musmarra, Dino; Prisciandaro, Marina; Capocelli, Mauro; Karatza, Despina; Iovino, Pasquale; Canzano, Silvana; Lancia, Amedeo

    2016-03-01

    Ibuprofen (IBP) is an anti-inflammatory drug whose residues can be found worldwide in natural water bodies resulting in harmful effects to aquatic species even at low concentrations. This paper deals with the degradation of IBP in water by hydrodynamic cavitation in a convergent-divergent nozzle. Over 60% of ibuprofen was degraded in 60min with an electrical energy per order (EEO) of 10.77kWhm(-3) at an initial concentration of 200?gL(-1) and a relative inlet pressure pin=0.35MPa. Five intermediates generated from different hydroxylation reactions were identified; the potential mechanisms of degradation were sketched and discussed. The reaction pathways recognized are in line with the relevant literature, both experimental and theoretical. By varying the pressure upstream the constriction, different degradation rates were observed. This effect was discussed according to a numerical simulation of the hydroxyl radical production identifying a clear correspondence between the maximum kinetic constant kOH and the maximum calculated OH production. Furthermore, in the investigated experimental conditions, the pH parameter was found not to affect the extent of degradation; this peculiar feature agrees with a recently published kinetic insight and has been explained in the light of the intermediates of the different reaction pathways. PMID:26584987

  10. Stepwise conversion of a single source precursor into crystalline AlN by transamination reaction

    SciTech Connect

    Schulz, Stephan Bauer, Tillmann; Hoffbauer, Wilfried; Schmedt auf der Guenne, Joern; Doerr, Markus; Marian, Christel M.; Assenmacher, Wilfried

    2008-03-15

    Ammonolysis of the monomeric, base-stabilized trisaminoalane Me{sub 3}N-Al[N(H)Dipp)]{sub 3} (Dipp=2,6-{sup i}Pr{sub 2}-C{sub 6}H{sub 3}) yielded Al-N oligomers, which were characterized in detail by solid state NMR spectroscopy ({sup 1}H, {sup 13}C, {sup 15}N, {sup 27}Al) and TGA/DTA. Pyrolysis of as-prepared oligomers at different temperatures in an argon steam yielded carbon-containing black solids, whereas pyrolysis under a steady flow of NH{sub 3} produced pure aluminum nitride (AlN). The role of the pyrolysis temperature and the influence of NH{sub 3} on the formation of crystalline materials were investigated. As-prepared AlN was characterized by solid state NMR spectroscopy ({sup 15}N, {sup 27}Al), X-ray diffraction (XRD), transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS). Theoretical calculations were performed in order to identify potential reaction intermediates. - Graphical abstract: Ammonolysis reactions of Me{sub 3}N-Al(NHDipp){sub 3} in liquid NH{sub 3} yielded Al-N oligomers, which can be transformed into nanocrystalline aluminum nitride particles under thermolysis conditions at 1000 deg. C. Theoretical calculations were performed in order to identify potential reaction intermediates.

  11. General properties of astrophysical reaction rates in explosive nucleosynthesis

    E-print Network

    T. Rauscher

    2012-09-25

    Fundamental differences in the prediction of reaction rates with intermediate and heavy target nuclei compared to the ones with light nuclei are discussed, with special emphasis on stellar modifications of the rates. Ground and excited state contributions to the stellar rates are quantified, deriving a linear weighting of excited state contributions despite of a Boltzmann population of the nuclear states. A Coulomb suppression effect of the excited state contributions is identified, acting against the usual Q-value rule in some reactions. The proper inclusion of experimental data in revised stellar rates is shown, containing revised uncertainties. An application to the s-process shows that the actual uncertainties in the neutron capture rates are larger than would be expected from the experimental errors alone. Sensitivities of reaction rates and cross sections are defined and their application in reaction studies is discussed. The conclusion provides a guide to experiment as well as theory on how to best improve the rates used in astrophysical simulations and how to assess their uncertainties.

  12. Involvement of ferryl in the reaction between nitrite and the oxy forms of globins.

    PubMed

    Hathazi, Denisa; Mahu?, Sonia Diana; Scurtu, Florina-Violeta; Bischin, Cristina; Stanciu, Corina; Attia, Amr Ali; Damian, Grigore; Silaghi-Dumitrescu, Radu

    2014-10-01

    The reaction between nitrite and the oxy forms of globins has complex autocatalytic kinetics with several branching steps and evolves through chain reactions mediated by reactive species (including radicals) such as hydrogen peroxide, ferryl and nitrogen dioxide, starting with a lag phase, after which it proceeds onto an autocatalytic phase. Reported here are UV-Vis spectra collected upon stopped-flow mixing of myoglobin with a supraphysiological excess of nitrite. The best fit to the experimental data follows an A ? B ? C reaction scheme involving the formation of a short-lived intermediate identified as ferryl. This is consistent with a mechanism where nitrite binds to oxy myoglobin to generate an undetectable ferrous-peroxynitrate intermediate, whose decay leads to nitrate and ferryl. The ferryl is then reduced to met by the excess nitrite. DFT calculations reveal an essentially barrierless reaction between nitrite and the oxy heme, with a notable outer-sphere component; the resulting metastable ferrous-peroxynitrate adduct is found to feature a very low barrier towards nitrate liberation, with ferryl as a final product-in good agreement with experiment. PMID:25064750

  13. Wind Variability in Intermediate Luminosity B Supergiants

    NASA Technical Reports Server (NTRS)

    Massa, Derck

    1996-01-01

    This study used the unique spectroscopic diagnostics of intermediate luminosity B supergiants to determine the ubiquity and nature of wind variability. Specifically, (1) A detailed analysis of HD 64760 demonstrated massive ejections into its wind, provided the first clear demonstration of a 'photospheric connection' and ionization shifts in a stellar wind; (2) The international 'IUE MEGA campaign' obtained unprecedented temporal coverage of wind variability in rapidly rotating stars and demonstrated regularly repeating wind features originating in the photosphere; (3) A detailed analysis of wind variability in the rapidly rotating B1 Ib, gamma Ara demonstrated a two component wind with distinctly different mean states at different epochs; (4) A follow-on campaign to the MEGA project to study slowly rotating stars was organized and deemed a key project by ESA/NASA, and will obtain 30 days of IUE observations in May-June 1996; and (5) A global survey of archival IUE time series identified recurring spectroscopic signatures, identified with different physical phenomena. Items 4 and 5 above are still in progress and will be completed this summer in collaboration with Raman Prinja at University College, London.

  14. Speciation of Iron (III) Oxide Nanoparticles and Other Paramagnetic Intermediates during High-Temperature Oxidative Pyrolysis of 1-Methylnaphthalene

    PubMed Central

    Herring, Michael P.; Khachatryan, Lavrent; Dellinger, Barry

    2015-01-01

    Low Temperature Matrix Isolation - Electron Paramagnetic Resonance (LTMI-EPR) Spectroscopy was utilized to identify the species of iron oxide nanoparticles generated during the oxidative pyrolysis of 1-methylnaphthalene (1-MN). The otherwise gas-phase reactions of 1--MN were impacted by a polypropylenimine tetra-hexacontaamine dendrimer complexed with iron (III) nitrate nonahydrate diluted in air under atmospheric conditions. The EPR fine structure of Fe (III)2O3 nanoparticles clusters, characterized by g-factors of 2.00, 2.28, 3.76 and 4.37 were detected on a cold finger maintained at 77 K after accumulation over a multitude of experiments. Additionally, a high valence Fe (IV) paramagnetic intermediate and superoxide anion-radicals, O2•? adsorbed on nanoparticle surfaces in the form of Fe (IV) --- O2•? were detected from the quenching area of Zone 1 in the gas-phase. PMID:26413257

  15. Kinetic Intermediates in RNA Folding

    NASA Astrophysics Data System (ADS)

    Zarrinkar, Patrick P.; Williamson, James R.

    1994-08-01

    The folding pathways of large, highly structured RNA molecules are largely unexplored. Insight into both the kinetics of folding and the presence of intermediates was provided in a study of the Mg2+-induced folding of the Tetrahymena ribozyme by hybridization of complementary oligodeoxynucleotide probes. This RNA folds via a complex mechanism involving both Mg2+-dependent and Mg2+-independent steps. A hierarchical model for the folding pathway is proposed in which formation of one helical domain (P4-P6) precedes that of a second helical domain (P3-P7). The overall rate-limiting step is formation of P3-P7, and takes place with an observed rate constant of 0.72 ± 0.14 minute-1. The folding mechanism of large RNAs appears similar to that of many multidomain proteins in that formation of independently stable substructures precedes their association into the final conformation.

  16. Heuristics-Guided Exploration of Reaction Mechanisms

    E-print Network

    Bergeler, Maike; Proppe, Jonny; Reiher, Markus

    2015-01-01

    For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is inevitable. The complexity of such a network may grow rapidly, in particular if reactive species are involved that might cause a myriad of side reactions. Without automation, a complete investigation of complex reaction mechanisms is tedious and possibly unfeasible. Therefore, only the expected dominant reaction paths of a chemical reaction network (e.g., a catalytic cycle or an enzymatic cascade) are usually explored in practice. Here, we present a computational protocol that constructs such networks in a parallelized and automated manner. Molecular structures of reactive complexes are generated based on heuristic rules and subsequently optimized by electronic-structure methods. Pairs of reactive complexes related by an elementary reaction are then automatically detected and subjected to an automated search for the connecting transition state. The results are...

  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. 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.

  19. 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.

  20. Gold(I)-catalyzed enantioselective cycloaddition reactions

    PubMed Central

    2013-01-01

    Summary In recent years there have been extraordinary developments of gold(I)-catalyzed enantioselective processes. This includes progress in the area of cycloaddition reactions, which are of particular interest due to their potential for the rapid construction of optically active cyclic products. In this article we will summarize some of the most remarkable examples, emphasizing reaction mechanisms and key intermediates involved in the processes. PMID:24204438

  1. Resonant photoemission spectroscopy for intermediate band materials

    NASA Astrophysics Data System (ADS)

    Mazzola, F.; Nematollahi, M.; Li, Z. S.; Cooil, S.; Yang, X.; Reenaas, T. W.; Wells, J. W.

    2015-11-01

    Resonant photoemission spectroscopy is used to study the intermediate-band material Cr doped ZnS. Using resonant photoemission, we show that the intermediate-band can be characterized, revealing the filling and specific orbital character of the states contributing to the resonant photoemission signal. We demonstrate that resonant photoemission spectroscopy is a powerful approach for understanding the origin of intermediate bands in doped ZnS. The methodology can be widely extended to a large variety of materials, providing useful information towards engineering of high efficiency intermediate band solar cells and of other optoelectronic devices.

  2. 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

  3. The aroma side of the Maillard reaction.

    PubMed

    Cerny, Christoph

    2008-04-01

    The Maillard reaction in food produces, among others, a diversity of sensory-active compounds (aroma, taste, color). The resulting key aroma compounds are often present only in trace concentrations of 1 microg/kg to 1 mg/kg. Nevertheless, they contribute to the respective flavor because of their low odor-perception thresholds. While Maillard intermediates, such as Amadori compounds and deoxyosones, are formed at percentage levels during model reactions, the yield of aroma compounds, in particular nitrogen and sulfur-containing ones, is often as low as 0.001-0.01 mol%, thus indicating their formation through chemical side reactions. The elucidation of the relevant precursors in food and the identification of previously unknown intermediates can throw light on these minor pathways. Also, model reactions with isotopically labeled precursors are of great value in gaining insight into the relevant formation mechanisms. Several examples of these studies are illustrated including work to elucidate the role of the solvent glycerol in the formation of pyrazines, trials to reveal the relative significance of 4-hydroxy-5-methyl-3(2H)-furanone as intermediate in the reaction between ribose and cysteine, and experiments to assess the proportional contribution of the precursors cysteine, xylose, and thiamine to the formation of the resulting aroma compounds in the thermal reaction. PMID:18079482

  4. 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

  5. Intermediates and the folding of proteins L and G

    SciTech Connect

    Brown, Scott; Head-Gordon, Teresa

    2003-07-01

    We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.

  6. A review of collector and energy storage technology for intermediate temperature applications

    NASA Astrophysics Data System (ADS)

    Wyman, C.; Castle, J.; Kreith, F.

    1980-01-01

    The technology and thermal performance of intermediate temperature solar collectors is summarized and the status of thermal and thermo-chemical storage methods is reviewed. It is concluded that collector technology is commercially available to achieve delivery temperatures up to 350 F at averaged yearly efficiencies better than 30 per cent in good solar climates and that linear parabolic, single-axis tracking troughs are the best types of collectors currently available for intermediate temperature applications. On the other hand, energy storage options commercially available today are generally limited to sensible heat systems, which are bulky and expensive for long-term storage. More research is necessary to develop new storage concepts such as intermediate temperature chemical heat pumps based on reversible reactions, suitable for intermediate temperature solar systems with significant storage capability.

  7. Synthesis of an Advanced Intermediate of the Jatrophane Diterpene Pl-4: A Dibromide Coupling Approach

    PubMed Central

    2013-01-01

    The preparation of an advanced intermediate toward the synthesis of the jatrophane diterpene Pl-4 is described. The key step is a regioselective chelation-controlled lithiation of the (Z)-configured bromide in the corresponding vinyl dibromide precursor. The method outlined within this Article is suitable for the facile access of sterically hindered internal vinyl halides for further coupling reactions. PMID:23895274

  8. 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...

  9. Visualizing virus assembly intermediates inside marine cyanobacteria.

    PubMed

    Dai, Wei; Fu, Caroline; Raytcheva, Desislava; Flanagan, John; Khant, Htet A; Liu, Xiangan; Rochat, Ryan H; Haase-Pettingell, Cameron; Piret, Jacqueline; Ludtke, Steve J; Nagayama, Kuniaki; Schmid, Michael F; King, Jonathan A; Chiu, Wah

    2013-10-31

    Cyanobacteria are photosynthetic organisms responsible for ?25% of organic carbon fixation on the Earth. These bacteria began to convert solar energy and carbon dioxide into bioenergy and oxygen more than two billion years ago. Cyanophages, which infect these bacteria, have an important role in regulating the marine ecosystem by controlling cyanobacteria community organization and mediating lateral gene transfer. Here we visualize the maturation process of cyanophage Syn5 inside its host cell, Synechococcus, using Zernike phase contrast electron cryo-tomography (cryoET). This imaging modality yields dramatic enhancement of image contrast over conventional cryoET and thus facilitates the direct identification of subcellular components, including thylakoid membranes, carboxysomes and polyribosomes, as well as phages, inside the congested cytosol of the infected cell. By correlating the structural features and relative abundance of viral progeny within cells at different stages of infection, we identify distinct Syn5 assembly intermediates. Our results indicate that the procapsid releases scaffolding proteins and expands its volume at an early stage of genome packaging. Later in the assembly process, we detected full particles with a tail either with or without an additional horn. The morphogenetic pathway we describe here is highly conserved and was probably established long before that of double-stranded DNA viruses infecting more complex organisms. PMID:24107993

  10. Modeling of intermediate phase growth

    SciTech Connect

    Umantsev, A.

    2007-01-15

    We introduced a continuum method for modeling of intermediate phase growth and numerically simulated three common experimental situations relevant to the physical metallurgy of soldering: growth of intermetallic compound layer from an unlimited amount of liquid and solid solders and growth of the compound from limited amounts of liquid solder. We found qualitative agreements with the experimental regimes of growth in all cases. For instance, the layer expands in both directions with respect to the base line when it grows from solid solder, and grows into the copper phase when the solder is molten. The quantitative agreement with the sharp-interface approximation was also achieved in these cases. In the cases of limited amounts of liquid solder we found the point of turnaround when the compound/solder boundary changed the direction of its motion. Although such behavior had been previously observed experimentally, the simulations revealed important information: the turnaround occurs approximately at the time of complete saturation of solder with copper. This result allows us to conclude that coarsening of the intermetallic compound structure starts only after the solder is practically saturated with copper.

  11. Multifragment Emission Times in Xe Induced Reactions

    NASA Astrophysics Data System (ADS)

    Moroni, A.; Bowman, D. R.; Bruno, M.; Buttazzo, P.; Celano, L.; Colonna, N.; D'Agostino, M.; Dinius, J. D.; Ferrero, A.; Fiandri, M. L.; Gelbke, K.; Glasmacher, T.; Gramegna, F.; Handzy, D. O.; Horn, D.; Hsi, Wen-Chien; Huang, M.; Iori, I.; Lisa, M.; Lynch, W. G.; Margagliotti, G. V.; Mastinu, P. F.; Milazzo, P. M.; Montoya, C.; Peaslee, G. F.; Phair, L.; Petruzzelli, F.; Rui, R.; Scardaoni, R.; Schwarz, C.; Tsang, B.; Vannini, G.; Williams, C.

    1995-02-01

    Multifragment emission is studied in 129Xe + natCu reactions. The emission process for central collisions occurs on a time scale of ? 200 fm/c at 30 MeV/n. Intermediate-mass-fragment yields, velocity correlation functions and emission velocities of Z=6 fragments are compared with predictions of statistical decay models.

  12. Hedging Your Bets: Intermediate Movements as Optimal Behavior in the Context of an Incomplete Decision

    PubMed Central

    Haith, Adrian M.; Huberdeau, David M.; Krakauer, John W.

    2015-01-01

    Existing theories of movement planning suggest that it takes time to select and prepare the actions required to achieve a given goal. These theories often appeal to circumstances where planning apparently goes awry. For instance, if reaction times are forced to be very low, movement trajectories are often directed between two potential targets. These intermediate movements are generally interpreted as errors of movement planning, arising either from planning being incomplete or from parallel movement plans interfering with one another. Here we present an alternative view: that intermediate movements reflect uncertainty about movement goals. We show how intermediate movements are predicted by an optimal feedback control model that incorporates an ongoing decision about movement goals. According to this view, intermediate movements reflect an exploitation of compatibility between goals. Consequently, reducing the compatibility between goals should reduce the incidence of intermediate movements. In human subjects, we varied the compatibility between potential movement goals in two distinct ways: by varying the spatial separation between targets and by introducing a virtual barrier constraining trajectories to the target and penalizing intermediate movements. In both cases we found that decreasing goal compatibility led to a decreasing incidence of intermediate movements. Our results and theory suggest a more integrated view of decision-making and movement planning in which the primary bottleneck to generating a movement is deciding upon task goals. Determining how to move to achieve a given goal is rapid and automatic. PMID:25821964

  13. Structural Evidence for a Dehydrated Intermediate in Green Fluorescent Protein Chromophore Biosynthesis

    SciTech Connect

    Pletneva, Nadya V.; Pletnev, Vladimir Z.; Lukyanov, Konstantin A.; Gurskaya, Nadya G.; Goryacheva, Ekaterina A.; Martynov, Vladimir I.; Wlodawer, Alexander; Dauter, Zbigniew; Pletnev, Sergei

    2010-11-03

    The acGFPL is the first-identified member of a novel, colorless and non-fluorescent group of green fluorescent protein (GFP)-like proteins. Its mutant aceGFP, with Gly replacing the invariant catalytic Glu-222, demonstrates a relatively fast maturation rate and bright green fluorescence ({lambda}{sub ex} = 480 nm, {lambda}{sub em} = 505 nm). The reverse G222E single mutation in aceGFP results in the immature, colorless variant aceGFP-G222E, which undergoes irreversible photoconversion to a green fluorescent state under UV light exposure. Here we present a high resolution crystallographic study of aceGFP and aceGFP-G222E in the immature and UV-photoconverted states. A unique and striking feature of the colorless aceGFP-G222E structure is the chromophore in the trapped intermediate state, where cyclization of the protein backbone has occurred, but Tyr-66 still stays in the native, non-oxidized form, with C{sup {alpha}} and C{sup {beta}} atoms in the sp{sup 3} hybridization. This experimentally observed immature aceGFP-G222E structure, characterized by the non-coplanar arrangement of the imidazolone and phenolic rings, has been attributed to one of the intermediate states in the GFP chromophore biosynthesis. The UV irradiation ({lambda} = 250-300 nm) of aceGFP-G222E drives the chromophore maturation further to a green fluorescent state, characterized by the conventional coplanar bicyclic structure with the oxidized double Tyr-66 C{sup {alpha}} = C{sup {beta}} bond and the conjugated system of {pi}-electrons. Structure-based site-directed mutagenesis has revealed a critical role of the proximal Tyr-220 in the observed effects. In particular, an alternative reaction pathway via Tyr-220 rather than conventional wild type Glu-222 has been proposed for aceGFP maturation.

  14. De novo synthesis of amino acids during the maillard reaction: qTOF/ESI mass spectrometric evidence for the mechanism of Akabori transformation.

    PubMed

    Nashalian, Ossanna; Yaylayan, Varoujan A

    2015-01-14

    The transformation of ?-amino acids into their hydroxymethyl derivatives during the Maillard reaction is an intriguing possibility for catalysis by metal salts in the presence of Strecker aldehydes; the process is commonly known as the Akabori reaction. The mechanism of this reaction was studied in the presence of glucose, using glycine copper complex and paraformaldehyde as Akabori model system in aqueous mixtures heated at 110 °C for 2 h and subsequently analyzed by qTOF/ESI/MS. Isotope-labeling studies of the various products identified have provided for the first time mass spectrometric evidence for the detailed mechanism of Akabori transformation, particularly the formation of Schiff base adducts prior to the final conversion into serine and hydroxymethyl-serine. Furthermore, the results have indicated that sugars do not interfere with such transformations and, on the contrary, the presence of glycine–copper complexes in the Maillard model systems can enhance the production of Maillard reaction intermediates. PMID:25514107

  15. 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

  16. 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,…

  17. 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…

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

    ERIC Educational Resources Information Center

    Jones, Marion

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

  19. Appliance Services. Intermediate Course. Career Education.

    ERIC Educational Resources Information Center

    Killough, Joseph

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

  20. Air Conditioning. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Long, William

    Several intermediate performance objectives and corresponding criterion measures are listed for each of seven terminal objectives for an intermediate air conditioning course. The titles of the seven terminal objectives are Refrigeration Cycle, Job Requirement Skills, Air Conditioning, Trouble Shooting, Performance Test, Shop Management, and S.I.E.…

  1. 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.…

  2. THE INTERMEDIATE TEACHER'S ROLE WITH INDIAN CHILDREN.

    ERIC Educational Resources Information Center

    1966

    THIS DOCUMENT PRESENTS DESIRABLE CHARACTERISTICS POSSESSED BY INTERMEDIATE GRADE TEACHERS OF INDIAN CHILDREN. TO BE EFFECTIVE WITH INDIAN CHILDREN, INTERMEDIATE GRADE TEACHERS SHOULD HAVE WARMTH, SUPPORTIVENESS, AN UNDERSTANDING PERSONALITY, AND AN ENCOURAGING APPROACH. IN ADDITION, THEY SHOULD HAVE INSERVICE TRAINING AND BE AWARE OF BILINGUAL…

  3. Magnetic properties of intermediate-mass stars

    E-print Network

    G. A. Wade

    2006-01-30

    Magnetic fields play an important role in producing and modifying the photospheric chemical peculiarities of intermediate-mass main sequence stars. This article discusses the basic theory and methods of measurement used to detect and characterise stellar magnetic fields, and reviews our current knowledge of selected characteristics of magnetic fields in intermediate-mass stars.

  4. Multicomponent kinetic analysis and theoretical studies on the phenolic intermediates in the oxidation of eugenol and isoeugenol catalyzed by laccase.

    PubMed

    Qi, Yan-Bing; Wang, Xiao-Lei; Shi, Ting; Liu, Shuchang; Xu, Zhen-Hao; Li, Xiqing; Shi, Xuling; Xu, Ping; Zhao, Yi-Lei

    2015-11-28

    Laccase catalyzes the oxidation of natural phenols and thereby is believed to initialize reactions in lignification and delignification. Numerous phenolic mediators have also been applied in laccase-mediator systems. However, reaction details after the primary O-H rupture of phenols remain obscure. In this work two types of isomeric phenols, EUG (eugenol) and ISO (trans-/cis-isoeugenol), were used as chemical probes to explore the enzymatic reaction pathways, with the combined methods of time-resolved UV-Vis absorption spectra, MCR-ALS, HPLC-MS, and quantum mechanical (QM) calculations. It has been found that the EUG-consuming rate is linear to its concentration, while the ISO not. Besides, an o-methoxy quinone methide intermediate, (E/Z)-4-allylidene-2-methoxycyclohexa-2,5-dienone, was evidenced in the case of EUG with the UV-Vis measurement, mass spectra and TD-DFT calculations; in contrast, an ISO-generating phenoxyl radical, a (E/Z)-2-methoxy-4-(prop-1-en-1-yl) phenoxyl radical, was identified in the case of ISO. Furthermore, QM calculations indicated that the EUG-generating phenoxyl radical (an O-centered radical) can easily transform into an allylic radical (a C-centered radical) by hydrogen atom transfer (HAT) with a calculated activation enthalpy of 5.3 kcal mol(-1) and then be fast oxidized to the observed eugenol quinone methide, rather than an O-radical alkene addition with barriers above 12.8 kcal mol(-1). In contrast, the ISO-generating phenoxyl radical directly undergoes a radical coupling (RC) process, with a barrier of 4.8 kcal mol(-1), while the HAT isomerization between O- and C-centered radicals has a higher reaction barrier of 8.0 kcal mol(-1). The electronic conjugation of the benzyl-type radical and the aromatic allylic radical leads to differentiation of the two pathways. These results imply that competitive reaction pathways exist for the nascent reactive intermediates generated in the laccase-catalyzed oxidation of natural phenols, which is important for understanding the lignin polymerization and may shed some light on the development of efficient laccase-mediator systems. PMID:26477512

  5. Intermediate scalings in holographic RG flows and conductivities

    E-print Network

    Jyotirmoy Bhattacharya; Sera Cremonini; Blaise Goutéraux

    2015-02-04

    We construct numerically finite density domain-wall solutions which interpolate between two $AdS_4$ fixed points and exhibit an intermediate regime of hyperscaling violation, with or without Lifshitz scaling. Such RG flows can be realized in gravitational models containing a dilatonic scalar and a massive vector field with appropriate choices of the scalar potential and couplings. The infrared $AdS_4$ fixed point describes a new ground state for strongly coupled quantum systems realizing such scalings, thus avoiding the well-known extensive zero temperature entropy associated with $AdS_2 \\times \\mathbb{R}^2$. We also examine the zero temperature behavior of the optical conductivity in these backgrounds and identify two scaling regimes before the UV CFT scaling is reached. The scaling of the conductivity is controlled by the emergent IR conformal symmetry at very low frequencies, and by the intermediate scaling regime at higher frequencies.

  6. Cofactor mobility determines reaction outcome in the IMPDH and GMPR (?-?)8 barrel enzymes.

    PubMed

    Patton, Gregory C; Stenmark, Pål; Gollapalli, Deviprasad R; Sevastik, Robin; Kursula, Petri; Flodin, Susanne; Schuler, Herwig; Swales, Colin T; Eklund, Hans; Himo, Fahmi; Nordlund, Pär; Hedstrom, Lizbeth

    2011-12-01

    Inosine monophosphate dehydrogenase (IMPDH) and guanosine monophosphate reductase (GMPR) belong to the same structural family, share a common set of catalytic residues and bind the same ligands. The structural and mechanistic features that determine reaction outcome in the IMPDH and GMPR family have not been identified. Here we show that the GMPR reaction uses the same intermediate E-XMP* as IMPDH, but in this reaction the intermediate reacts with ammonia instead of water. A single crystal structure of human GMPR type 2 with IMP and NADPH fortuitously captures three different states, each of which mimics a distinct step in the catalytic cycle of GMPR. The cofactor is found in two conformations: an 'in' conformation poised for hydride transfer and an 'out' conformation in which the cofactor is 6 Å from IMP. Mutagenesis along with substrate and cofactor analog experiments demonstrate that the out conformation is required for the deamination of GMP. Remarkably, the cofactor is part of the catalytic machinery that activates ammonia. PMID:22037469

  7. Observation of hydroxymethyl hydroperoxide in a reaction system containing CH2OO and water vapor through pure rotational spectroscopy

    NASA Astrophysics Data System (ADS)

    Nakajima, Masakazu; Endo, Yasuki

    2015-10-01

    Pure rotational transitions of hydroxymethyl hydroperoxide (HMHP) were observed in the discharged plasma of a CH2I2/O2/water gas mixture, where the water complex with the simplest Criegee intermediate CH2OO has been identified [M. Nakajima and Y. Endo, J. Chem. Phys. 140, 134302 (2014)]. Isotope experiments using heavy water support that the currently observed HMHP molecule was produced by the reaction of CH2OO with water vapor. The observed species was identified as the most stable conformer with the help of quantum chemical calculations. We also clarified that productions of formic acid and dioxirane are promoted by the existence of water vapor in the discharged reaction system.

  8. 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

  9. MCNP6 simulation of light and medium nuclei fragmentation at intermediate energies

    E-print Network

    Stepan G. Mashnik; Leslie M. Kerby

    2015-08-24

    Fragmentation reactions induced on light and medium nuclei by protons and light nuclei of energies around 1 GeV/nucleon and below are studied with the Los Alamos transport code MCNP6 and with its CEM03.03 and LAQGSM03.03 event generators. CEM and LAQGSM assume that intermediate-energy fragmentation reactions on light nuclei occur generally in two stages. The first stage is the intranuclear cascade (INC), followed by the second, Fermi breakup disintegration of light excited residual nuclei produced after the INC. CEM and LAQGSM account also for coalescence of light fragments (complex particles) up to 4He from energetic nucleons emitted during INC. We investigate the validity and performance of MCNP6, CEM, and LAQGSM in simulating fragmentation reactions at intermediate energies and discuss possible ways of further improving these codes

  10. Molecular Modeling Studies on Aromatic Sulfonation. 1. Intermediates Formed in the Sulfonation of Toluene.

    PubMed

    Morley, John O.; Roberts, D. W.

    1997-10-17

    Molecular modeling studies suggest that the mechanism of the sulfonation of toluene with sulfur trioxide proceeds via the formation of a pi-complex (4b) which rearranges to form a Wheland intermediate (5). This structure is unable to form toluenesulfonic acid (8) directly and prefers to react with a further molecule of sulfur trioxide to form a pyrosulfonate intermediate (6a) which undergoes a facile prototropic rearrangement involving the transfer of the ring hydrogen at the sp(3) carbon of 6a to the sulfonate oxygen atom to form the corresponding acid (7). The formation of toluenesulfonic acid (8) appears to arise from an exothermic reaction of between the pyrosulfonic acid (7) and toluene. The overall calculated thermodynamic change in moving from the reaction of one molecule of sulfur trioxide with toluene to the sulfonic acid (8b) is fully consistent with an estimated experimental value of -33.5 kcal mol(-1) for the same reaction using simple alkylbenzenes. PMID:11671852

  11. 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

  12. Dilatometric approach for the determination of the solid state reaction-onset of the lead based relaxor ferroelectric system

    SciTech Connect

    Bhat, V.V.; Radhika Rao, M.V.; Umarji, A.M

    2003-05-26

    Dilatometer based thermal expansion studies have been carried out on the starting oxide mixtures of some of the important relaxor ferroelectric compositions including lead iron niobate, lead magnesium niobate-lead titanate and lead zinc niobate-barium titanate. An anomalous thermal expansion behavior is observed between 550 and 650 deg. C corresponding to the onset of the solid state reaction. Further heating of the reaction mixture resulted in a decrease in the dimension of the sample. From the complementary evidence of DTA, X-ray diffraction (XRD) and scanning electron microscopy (SEM), it is shown that the initiation of solid state reaction results in the restructuring of the reacting grains to form the agglomerates of fine particles of reaction intermediates. This phenomenon is shown to be absent in the barium zinc niobate system where the pyrochlore intermediates do not exist. This novel dilatometric approach has been projected as a possible technique to identify optimum calcination temperatures to produce sinter-active powders in the above oxide system, thereby help in reducing the sintering temperatures.

  13. The stepwise Diels-Alder reaction of 4-nitrobenzodifuroxan with Danishefsky's diene.

    PubMed

    Steglenko, Dmitry V; Kletsky, Mikhail E; Kurbatov, Sergey V; Tatarov, Artem V; Minkin, Vladimir I; Goumont, Regis; Terrier, François

    2011-06-27

    The Diels-Alder reaction of 4-nitrobenzodifuroxan (NBDF) with 1-methoxy-3-trimethylsilyloxy-1,3-butadiene has been investigated experimentally and theoretically. Treatment of NBDF with excess diene in chloroform at room temperature was found to afford a single product that contained a carbonyl functionality. Based on an X-ray structure and NMR spectroscopic data, the product appeared to be a result of the hydrolysis of the OSiMe(3) moiety of the thermodynamically more stable endo [2+4] cycloadduct, characterized by a cis arrangement of the MeO and NO(2) functionalities. In situ NMR investigations of the interaction were carried out at room temperature in CDCl(3) and at -40?°C in deuterated acetonitrile. Calculations at the B3LYP/6-31G* level in the gas phase and in acetonitrile were carried out under the assumption that the most stable cis conformation of the diene is also the most reactive in the interaction. The analysis revealed the NBDF/cis diene interaction involves the formation of a zwitterionic intermediate. Importantly, this intermediate is formed in two preferred conformations, which correspond to the endo and exo modes of approach of the reagents. Cyclization of these two identified conformations afforded the experimentally characterized endo and exo [2+4] cycloadducts. According to the calculations, the interconversion of the two conformers can either take place through a return to the pre-reaction complexes or it can occur by rotation through an intermediate conformation of lesser stability. In view of the stepwise character of the interaction, the possibility that the intermediate zwitterion is the result of the interaction between NBDF and the trans diene could not be excluded. Calculations carried out with the most stable and more populated s-trans conformer confirmed this idea and supported the role of the zwitterion in the overall interaction. PMID:21590823

  14. Roaming dynamics in radical addition-elimination reactions.

    PubMed

    Joalland, Baptiste; Shi, Yuanyuan; Kamasah, Alexander; Suits, Arthur G; Mebel, Alexander M

    2014-01-01

    Radical addition-elimination reactions are a major pathway for transformation of unsaturated hydrocarbons. In the gas phase, these reactions involve formation of a transient strongly bound intermediate. However, the detailed mechanism and dynamics for these reactions remain unclear. Here we show, for reaction of chlorine atoms with butenes, that the Cl addition-HCl elimination pathway occurs from an abstraction-like Cl-H-C geometry rather than a conventional three-centre or four-centre transition state. Furthermore, access to this geometry is attained by roaming excursions of the Cl atom from the initially formed adduct. In effect, the alkene ? cloud serves to capture the Cl atom and hold it, allowing many subsequent opportunities for the energized intermediate to find a suitable approach to the abstraction geometry. These bimolecular roaming reactions are closely related to the roaming radical dynamics recently discovered to play an important role in unimolecular reactions. PMID:24905903

  15. Biodegradation of ichlorodiphenyltrichloroe-thane: Intermediates in dichlorodiphenylacetic acid metabolism by Aerobacter aerogenes

    USGS Publications Warehouse

    1967-01-01

    The final product of dichlorodiphenyltrichloroethane (DDT) degradation by vertebrates is commonly considered to be dichlorodiphenylacetic acid, DDA (J. E. Peterson and W. H. Robison, Toxicol. Appl. Pharmacol. 6:321, 1964). Recently, certain organisms (A. S. Perry, S. Miller, and A. J. Buckner. J. Agr. Food Chem. 11:457, 1963; J. D. Pinto, M. N. Comien, and M. S. Dunn. J. Biol. Chem. 240:2148, 1965) have been found to degrade further DDA to dichlorobenzophenone (DBP), but the possibility that such degradation was due to microbial action could not be excluded. Significantly, dichlorobenzhydrol (DBH), dichlorophenylmethane (DPM), and dichlorodiphenylethylene (DDE) have been tentatively identified in rats fed DDA (Pinto et al., J. Biol. Chem. 240:2148, 1965). Since DDA as well as DDT is degraded by the ubiquitous microorganism Aerobacter aerogenes (G. Wedemeyer, Appl. Microbiol. 15:569, 1967; J. L. Mendel, and M. S. Walton, Science 151:1527, 1966), it seemed reasonable that the intestinal microflora might be involved in DBP formation, DPM and DBH being intermediates in its pathway from DDA. Since DDA is a (3,y-unsaturated acid, ketone formation via an alkene and an alcohol would be expected (S. G. Waley, Mechanisms of Organic and Enzymatic Reactions, Oxford University Press, London, England 1962).

  16. Chemical trapping of labile aldehyde intermediates in the metabolism of propranolol and oxprenolol.

    PubMed

    Goldszer, F; Tindell, G L; Walle, U K; Walle, T

    1981-11-01

    Propranolol is N-dealkylated to N-desisopropylpropranolol (DIP) by microsomal enzymes. DIP was shown in this study to be rapidly deaminated by monoamine oxidase (MAO). Thus, incubation of DIP (10(-4) M) with rat liver mitochondria for 90 min demonstrated 74.8 +/- 4.1% metabolism which was almost completely blocked by the MAO inhibitor pargyline (10(-5) M). The end products of this deamination were 3-(alpha-naphthoxy)-1,2-propylene glycol (Glycol) and 3-(alpha-naphthoxy)lactic acid (NLA). In the presence of excess NADH the Glycol was the major product whereas NLA was the major product in the presence of excess NAD+. The intermediate aldehyde in this deamination reaction, 3-(alpha-naphthoxy)-2-hydroxypropanal (Ald), was extremely labile and decomposed quantitatively to alpha-naphthol when removed from the incubates. However, the addition of methoxyamine hydrochloride directly to the incubates made it possible to chemically trap the intact Ald as an O-methyloxime and prove its structure by gas chromatography-mass spectrometry. The deamination of the primary amine of oxprenolol also gave rise to a labile aldehyde which could be trapped and identified as its O-methyloxime. PMID:7335950

  17. Observation of the Simplest Criegee Intermediate CH_2OO in the Gas-Phase Ozonolysis of Ethylene

    NASA Astrophysics Data System (ADS)

    Womack, Carrie; Martin-Drumel, Marie-Aline; Brown, Gordon G.; Field, Robert W.; McCarthy, Michael C.

    2015-06-01

    Criegee intermediates (R_1R_2COO) are understood to be critical intermediates in the ozonolysis of alkenes, but their high reactivity has traditionally made them very difficult to study directly. Although the smallest Criegee intermediates have now been generated in the laboratory using a diiodomethane photolysis scheme, numerous questions still remain about the product branching ratios of Criegee intermediates formed directly from ozonolysis. This talk will discuss our recent detection of the simplest Criegee intermediate, CH_2OO, in the ozonolysis of ethylene, using Fourier transform microwave spectroscopy and a modified pulsed nozzle. Nine other product species of the reaction were also detected, in abundances that qualitatively support the published mechanisms and rate constants.

  18. 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

  19. Thermodynamics of random reaction networks.

    PubMed

    Fischer, Jakob; Kleidon, Axel; Dittrich, Peter

    2015-01-01

    Reaction networks are useful for analyzing reaction systems occurring in chemistry, systems biology, or Earth system science. Despite the importance of thermodynamic disequilibrium for many of those systems, the general thermodynamic properties of reaction networks are poorly understood. To circumvent the problem of sparse thermodynamic data, we generate artificial reaction networks and investigate their non-equilibrium steady state for various boundary fluxes. We generate linear and nonlinear networks using four different complex network models (Erd?s-Rényi, Barabási-Albert, Watts-Strogatz, Pan-Sinha) and compare their topological properties with real reaction networks. For similar boundary conditions the steady state flow through the linear networks is about one order of magnitude higher than the flow through comparable nonlinear networks. In all networks, the flow decreases with the distance between the inflow and outflow boundary species, with Watts-Strogatz networks showing a significantly smaller slope compared to the three other network types. The distribution of entropy production of the individual reactions inside the network follows a power law in the intermediate region with an exponent of circa -1.5 for linear and -1.66 for nonlinear networks. An elevated entropy production rate is found in reactions associated with weakly connected species. This effect is stronger in nonlinear networks than in the linear ones. Increasing the flow through the nonlinear networks also increases the number of cycles and leads to a narrower distribution of chemical potentials. We conclude that the relation between distribution of dissipation, network topology and strength of disequilibrium is nontrivial and can be studied systematically by artificial reaction networks. PMID:25723751

  20. 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.

  1. 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

  2. Investigating intermediates in 6-methylsalicylic acid biosynthesis

    E-print Network

    Potter, Helen Katherine

    2011-07-12

    orcinol (8) (Figure 1.2).20 He proposed that this could be formed via a polyketone intermediate. Further investigations such as the formation of a naphthalene derivative from diacetylacetone and the formation of orcinol from ethyl acetoacetate21 led...

  3. Physical Mechanisms for Earthquakes at Intermediate Depths

    NASA Astrophysics Data System (ADS)

    Green, H. W.; Green, H. W.

    2001-12-01

    Conventional brittle shear failure it is strongly inhibited by pressure because it relies on local tensile failure. In contrast, plastic flow processes are thermally activated, making them sensitive functions of temperature, but their pressure dependence is only moderate. As a consequence, in Earth, faulting by unassisted brittle failure is probably restricted to depths less than ~ 30 km because the rocks flow at lower stresses than they fracture. To enable faulting at greater depths, mineral reactions must occur that generate a fluid or fluid-like solid that is much weaker than the parent assemblage. Although a variety of plastic instabilities have been and continue to be proposed to explain earthquakes at depth, dehydration embrittlement remains the only experimentally verified faulting mechanism consistent with the pressures and compositions existing at depths of 50-300km within subducting lithosphere. However, low pressure hydrous phases potentially abundant in subducting lithosphere (e.g. chlorite and antigorite) exhibit a temperature maximum in their stability, implying that the bulk volume change at depths of more than 70-100 km. becomes negative, thereby raising questions about mechanical instability upon dehydration. Further, it is now well-accepted that intermediate-depth earthquakes occur within the descending slab (double seismic zones present in several slabs dramatically demonstrate this fact), in conflict with the maximum depth of 10-12 km accepted for hydration of the lithosphere at oceanic spreading centers. Thus, on the one hand these earthquakes may be evidence that hydrous phases exist deep within subducting slabs but on the other hand, a mechanism for hydration to such depths is not known. One possibility is that large earthquakes outboard of trenches break the surface and allow hydration of the fault zone that can later dehydrate to yield earthquakes at depth, but no mechanism is known for pumping H2O into such fault zones to depths of tens of km. In the laboratory, we have confirmed that dehydration of antigorite under stress can trigger faulting, even under conditions where the net volume change upon dehydration is negative. We also have preliminary evidence that "dehydration" of hydrous eclogite above its wet solidus may be capable of inducing faulting.

  4. 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.

  5. Improving interMediAte Risk management. MARK study

    PubMed Central

    2011-01-01

    Background Cardiovascular risk functions fail to identify more than 50% of patients who develop cardiovascular disease. This is especially evident in the intermediate-risk patients in which clinical management becomes difficult. Our purpose is to analyze if ankle-brachial index (ABI), measures of arterial stiffness, postprandial glucose, glycosylated hemoglobin, self-measured blood pressure and presence of comorbidity are independently associated to incidence of vascular events and whether they can improve the predictive capacity of current risk equations in the intermediate-risk population. Methods/Design This project involves 3 groups belonging to REDIAPP (RETICS RD06/0018) from 3 Spanish regions. We will recruit a multicenter cohort of 2688 patients at intermediate risk (coronary risk between 5 and 15% or vascular death risk between 3-5% over 10 years) and no history of atherosclerotic disease, selected at random. We will record socio-demographic data, information on diet, physical activity, comorbidity and intermittent claudication. We will measure ABI, pulse wave velocity and cardio ankle vascular index at rest and after a light intensity exercise. Blood pressure and anthropometric data will be also recorded. We will also quantify lipids, glucose and glycosylated hemoglobin in a fasting blood sample and postprandial capillary glucose. Eighteen months after the recruitment, patients will be followed up to determine the incidence of vascular events (later follow-ups are planned at 5 and 10 years). We will analyze whether the new proposed risk factors contribute to improve the risk functions based on classic risk factors. Discussion Primary prevention of cardiovascular diseases is a priority in public health policy of developed and developing countries. The fundamental strategy consists in identifying people in a high risk situation in which preventive measures are effective and efficient. Improvement of these predictions in our country will have an immediate, clinical and welfare impact and a short term public health effect. Trial Registration Clinical Trials.gov Identifier: NCT01428934 PMID:21992621

  6. Mapping the ? Integrase bridges in the nucleoprotein Holliday junction intermediates of viral integrative and excisive recombination.

    PubMed

    Tong, Wenjun; Warren, David; Seah, Nicole E; Laxmikanthan, Gurunathan; Van Duyne, Gregory D; Landy, Arthur

    2014-08-26

    The site-specific recombinase encoded by bacteriophage ? [? Integrase (Int)] is responsible for integrating and excising the viral chromosome into and out of the chromosome of its Escherichia coli host. In contrast to the other well-studied and highly exploited tyrosine recombinase family members, such as Cre and Flp, Int carries out a reaction that is highly directional, tightly regulated, and depends on an ensemble of accessory DNA bending proteins acting on 240 bp of DNA encoding 16 protein binding sites. This additional complexity enables two pathways, integrative and excisive recombination, whose opposite, and effectively irreversible, directions are dictated by different physiological and environmental signals. Int recombinase is a heterobivalent DNA binding protein that binds via its small amino-terminal domain to high affinity arm-type DNA sites and via its large, compound carboxyl-terminal domain to core-type DNA sites, where DNA cleavage and ligation are executed. Each of the four Int protomers, within a multiprotein 400-kDa recombinogenic complex, is thought to bind and, with the aid of DNA bending proteins, bridge one arm- and one core-type DNA site. Despite a wealth of genetic, biochemical, and functional information generated by many laboratories over the last 50 y, it has not been possible to decipher the patterns of Int bridges, an essential step in understanding the architectures responsible for regulated directionality of recombination. We used site-directed chemical cross-linking of Int in trapped Holliday junction recombination intermediates and recombination reactions with chimeric recombinases, to identify the unique and monogamous patterns of Int bridges for integrative and excisive recombination. PMID:25114247

  7. 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

  8. Unconventional actin conformations localize on intermediate filaments in mitosis

    SciTech Connect

    Hubert, Thomas; Vandekerckhove, Joel; Gettemans, Jan

    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.

  9. Ferryl intermediates of catalase captured by time-resolved Weissenberg crystallography and UV-VIS spectroscopy.

    PubMed

    Gouet, P; Jouve, H M; Williams, P A; Andersson, I; Andreoletti, P; Nussaume, L; Hajdu, J

    1996-11-01

    Various enzymes use semi-stable ferryl intermediates and free radicals during their catalytic cycle, amongst them haem catalases. Structures for two transient intermediates (compounds I and II) of the NADPH-dependent catalase from Proteus mirabilis (PMC) have been determined by time-resolved X-ray crystallography and single crystal microspectrophotometry. The results show the formation and transformation of the ferryl group in the haem, and the unexpected binding of an anion during this reaction at a site distant from the haem. PMID:8901874

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

    SciTech Connect

    Vikas, E-mail: qlabspu@yahoo.com; Kaur, Gurpreet

    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. Global reaction route mapping of isomerization pathways of exotic C6H molecular species

    NASA Astrophysics Data System (ADS)

    Vikas, Kaur, Gurpreet

    2013-12-01

    C6H radical is known to exist in the astrophysical environment in linear form; however, it may originate from nonlinear isomeric forms. Potential energy surface of C6H is explored to search isomers of C6H and transition states connecting them. This work reports first-ever identification of reaction pathways for isomerization of C6H. 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 C6H) 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-C6H can readily isomerize to a six-member ring isomer.

  12. Low energy ion-molecule reactions

    SciTech Connect

    Farrar, J.M.

    1993-12-01

    This project is concerned with elucidating the dynamics of elementary ion-molecule reactions at collision energies near and below 1 eV. From measurements of the angular and energy distributions of the reaction products, one can infer intimathe details about the nature of collisions leading to chemical reaction, the geometries and lifetimes of intermediate complexes that govern the reaction dynamics, and the collision energy dependence of these dynamical features. The author employs crossed-beam low energy mass spectrometry technology developed over the last several years, with the focus of current research on proton transfer and hydrogen atom transfer reactions of te O{sup {minus}} ion with species such as HF, H{sub 2}O, and NH{sub 3}.

  13. Insight into methanol synthesis from CO2 hydrogenation on Cu(111): Complex reaction network and the effects of H2O

    SciTech Connect

    Zhao, Yafan; Yang, Yong; Mims, Charles A.; Peden, Charles HF; Li, Jun; Mei, Donghai

    2011-05-31

    Methanol synthesis from CO2 hydrogenation on supported Cu catalysts is of considerable importance in the chemical and energy industries. Although extensive experimental and theoretical efforts have been carried out in the past decades, the most fundamental questions such as the reaction mechanisms and the key reaction intermediates are still in debate. In the present work, a comprehensive reaction network for CO2 hydrogenation to methanol on Cu(111) was studied using periodic density functional theory (DFT) calculations. All of the elementary reaction steps in the reaction network were identified in an unbiased way with the dimer method. Our calculation results show that methanol synthesis from direct hydrogenation of formate on Cu(111) is not feasible due to the high activation barriers for some of the elementary steps. Instead, we find that CO2 hydrogenation to hydrocarboxyl (trans-COOH) is kinetically more favorable than formate in the presence of H2O via a unique proton transfer mechanism. The trans-COOH is then converted into hydroxymethylidyne (COH) via dihydroxycarbene (COHOH) intermediates, followed by three consecutive hydrogenation steps to form hydroxymethylene (HCOH), hydroxymethyl (H2COH), and methanol. This is consistent with recent experimental observations [1], which indicate that direct hydrogenation of formate will not produce methanol under dry hydrogen conditions. Thus, both experiment and computational modeling clearly demonstrate the important role of trace amounts of water in methanol synthesis from CO2 hydrogenation on Cu catalysts. The proposed methanol synthesis route on Cu(111) not only provides new insights into methanol synthesis chemistry, but also demonstrates again that spectroscopically observed surface species are often not critical reaction intermediates but rather spectator species. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  14. Model-based analysis of keratin intermediate filament assembly

    NASA Astrophysics Data System (ADS)

    Martin, Ines; Leitner, Anke; Walther, Paul; Herrmann, Harald; Marti, Othmar

    2015-09-01

    The cytoskeleton of epithelial cells consists of three types of filament systems: microtubules, actin filaments and intermediate filaments (IFs). Here, we took a closer look at type I and type II IF proteins, i.e. keratins. They are hallmark constituents of epithelial cells and are responsible for the generation of stiffness, the cellular response to mechanical stimuli and the integrity of entire cell layers. Thereby, keratin networks constitute an important instrument for cells to adapt to their environment. In particular, we applied models to characterize the assembly of keratin K8 and K18 into elongated filaments as a means for network formation. For this purpose, we measured the length of in vitro assembled keratin K8/K18 filaments by transmission electron microscopy at different time points. We evaluated the experimental data of the longitudinal annealing reaction using two models from polymer chemistry: the Schulz-Zimm model and the condensation polymerization model. In both scenarios one has to make assumptions about the reaction process. We compare how well the models fit the measured data and thus determine which assumptions fit best. Based on mathematical modelling of experimental filament assembly data we define basic mechanistic properties of the elongation reaction process.

  15. 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

  16. Identifying Savings Opportunities 

    E-print Network

    Chari, S.

    1993-01-01

    process to identify any opportunity through change of process. Such opportunities to change end-use processes in the auto parts manufacturing facility were not identified. Change the Entire System Of all the DSM measures, this is the hardest one...

  17. Photocatalytic degradation of terephthalic acid on sulfated titania particles and identification of fluorescent intermediates.

    PubMed

    Lin, Xuan Hao; Lee, Si Ni; Zhang, Wenlin; Li, Sam Fong Yau

    2016-02-13

    Terephthalic acid (TA) is toxic and known as an endocrine disruptor. In this paper, the photocatalytic degradation of TA using sulfated titanium dioxide SO4(2-)/TiO2 photocatalysts was investigated. The photocatalysts were prepared by sol-gel method and characterized by XRD, SEM, BET, ICP/MS and spectroscopic methods. Their activities were compared with bare TiO2 and Degussa P25. The effects of catalyst sulfur content, the initial TA concentration and pre-treatment conditions (O2, N2 or non-pretreated) were studied. O2 functions were also explored. Since there had been no comprehensive study of fluorescent intermediates reported yet, we investigated the intermediates and discovered 5 new intermediates (4 fluorescent and 1 non-fluorescent) which were identified by gas chromatography-mass spectrometry (GC/MS) and fluorescence spectroscopy. These intermediates are complementary to the previously identified carboxylic acid intermediates and might provide new insights to the mechanism of photocatalytic degradation of TA. Since TA is widely used as a probing molecule for photocatalytically generated (·)OH radicals, the ratios of fluorescent intermediates of TA degradation may provide new clues to the photocatalytic activity and mechanism. Based on the results obtained, the possible destruction pathway of TA is also proposed. PMID:26513565

  18. Aminolysis of phenyl N-phenylcarbamate via an isocyanate intermediate: theory and experiment.

    PubMed

    Ilieva, Sonia; Nalbantova, Didi; Hadjieva, Boriana; Galabov, Boris

    2013-07-01

    A comprehensive examination of the mechanism of the uncatalyzed and base-catalyzed aminolysis of phenyl N-phenylcarbamate by theoretical quantum mechanical methods at M06-2X/6-311+G(2d,2p) and B3LYP-D3/6-31G(d,p) levels, combined with an IR spectroscopic study of the reaction, was carried out. Three alternative reaction channels were theoretically characterized: concerted, stepwise via a tetrahedral intermediate, and stepwise involving an isocyanate intermediate. In contrast to dominating views, the theoretical results revealed that the reaction pathway through the isocyanate intermediate (E1cB) is energetically favored. These conclusions were supported by an IR spectroscopic investigation of the interactions of phenyl N-phenylcarbamate with several amines possessing varying basicities and nucleophilicities: n-butylamine, diethylamine, triethylamine, N-methylpyrrolidine, and trimethylamine. The reactivity of substituted phenyl N-phenylcarbamates in the aminolysis reaction was rationalized using theoretical and experimental reactivity indexes: electrostatic potential at nuclei (EPN), Hirshfeld and NBO atomic charges, and Hammett constants. The obtained quantitative relationships between these property descriptors and experimental kinetic constants reported in the literature emphasize the usefulness of theoretical parameters (EPN, atomic charges) in characterizing chemical reactivity. PMID:23734590

  19. Neurodevelopmental disabilities in children with intermediate and premutation range fragile X cytosine-guanine-guanine expansions.

    PubMed

    Renda, Meredith M; Voigt, Robert G; Babovic-Vuksanovic, Dusica; Highsmith, W Edward; Vinson, Sherry S; Sadowski, Christine M; Hagerman, Randi J

    2014-03-01

    To determine the range of neurodevelopmental diagnoses associated with intermediate (45-54 repeats) and premutation (55-200 repeats) range cytosine-guanine-guanine fragile X expansions, the medical records of children with intermediate or premutation range expansions were retrospectively reviewed, and all neurodevelopmental diagnoses were abstracted. Twenty-nine children (9 female, 20 male; age, 13 months to 17 years) with intermediate (n = 25) or premutation (n = 4) range expansions were identified with neurodevelopmental diagnoses, including global developmental delay/intellectual disability (n = 15), language and learning disorders (n = 9), attention-deficit hyperactivity disorder (n = 5), epilepsy (n = 5), and motor disorders (n = 12), including 2 boys younger than 4 years of age with tremor and ataxia. Thus, children with intermediate or premutation range fragile X cytosine-guanine-guanine expansions may be more susceptible than children without such expansions to other processes, both genetic and environmental, that contribute to neurodevelopmental disability. PMID:23266944

  20. The Mechanism of Iron(II)-Catalyzed Asymmetric Mukaiyama Aldol Reaction in Aqueous Media: Density Functional Theory and Artificial Force-Induced Reaction Study.

    PubMed

    Sameera, W M C; Hatanaka, Miho; Kitanosono, Taku; Kobayashi, Sh?; Morokuma, Keiji

    2015-09-01

    Density functional theory (DFT), combined with the artificial force-induced reaction (AFIR) method, is used to establish the mechanism of the aqueous Mukaiyama aldol reactions catalyzed by a chiral Fe(II) complex. On the bases of the calculations, we identified several thermodynamically stable six- or seven-coordinate complexes in the solution, where the high-spin quintet state is the ground state. Among them, the active intermediates for the selectivity-determining outer-sphere carbon-carbon bond formation are proposed. The multicomponent artificial force-induced reaction (MC-AFIR) method found key transition states for the carbon-carbon bond formation, and explained the enantioselectivity and diastereoselectivity. The overall mechanism consists of the coordination of the aldehyde, carbon-carbon bond formation, the rate-determining proton transfer from water to aldehyde, and dissociation of trimethylsilyl group. The calculated full catalytic cycle is consistent with the experiments. This study provides important mechanistic insights for the transition metal catalyzed Mukaiyama aldol reaction in aqueous media. PMID:26267294

  1. Palladium-catalyzed reaction of allyl halides with a-diazocarbonyl Shufeng Chen and Jianbo Wang*

    E-print Network

    Wang, Jianbo

    Palladium-catalyzed reaction of allyl halides with a-diazocarbonyl compoundsw Shufeng Chen-Allylic palladium complexes are important intermediates in palladium-catalyzed reactions.1 The p-allylic palladium,3-dicarbonyl compounds.2 In connection to our recent interest in the palladium-catalyzed reaction of diazo

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

    E-print Network

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

    2009-10-21

    Background: As a key player in suppression of colon tumorigenesis, Adenomatous Polyposis Coli (APC) has been widely studied to determine its cellular functions. However, inconsistencies of commercially available APC ...

  3. Storage stability and improvement of intermediate moisture foods

    NASA Technical Reports Server (NTRS)

    Labuza, T. P.

    1973-01-01

    The rates of chemical reactions which deteriorate foods prepared to an intermediate moisture content and water activity (A sub w 0.6 to 0.9) were studied. The phenomenon of sorption hysteresis was used to prepare model systems and foods to similar A sub w's but different moisture levels so that the separate effects of water binding and water content could be elucidated. It was found that water content is the controlling factor for lipid oxidation in model systems comprised of a solid support and an oxidizable liquid. It was proposed that metal chelating agents like EDTA should give good protection to oxidation. EDTA exhibited the highest efficacy, about 10-15 times better than BHA which is a radical scavenger when studied in the model systems.

  4. Biosynthesis of 20-hydroxyecdysone in plants: 3?-hydroxy-5?-cholestan-6-one as an intermediate immediately after cholesterol in Ajuga hairy roots.

    PubMed

    Fujimoto, Yoshinori; Maeda, Izumi; Ohyama, Kiyoshi; Hikiba, Juri; Kataoka, Hiroshi

    2015-03-01

    3?-Hydroxy-5?-cholestan-6-one was identified in the EtOAc extract of Ajuga hairy roots by micro-analysis using LC-MS/MS in the multiple reaction mode (MRM). Furthermore, administration of (2,2,4,4,7,7-(2)H6)- and (2,2,4,4,6,7,7-(2)H7)-cholesterols to the hairy roots followed by LC-MS/MS analysis of the EtOAc extract of the hairy roots indicated that cholesterol was converted to the 5?-ketone with hydrogen migration from the C-6 to the C-5 position. These findings, in conjunction with the previous observation that the ketone was efficiently converted to 20-hydroxyecdysone, strongly suggest that the 5?-ketone is an intermediate immediately formed after cholesterol during 20-hydroxyecdysone biosynthesis in Ajuga sp. In addition, the mechanism of the 5?-ketone formation from cholesterol is discussed. PMID:25593010

  5. A characterization of the two-step reaction mechanism of phenol decomposition by a Fenton reaction

    NASA Astrophysics Data System (ADS)

    Valdés, Cristian; Alzate-Morales, Jans; Osorio, Edison; Villaseñor, Jorge; Navarro-Retamal, Carlos

    2015-11-01

    Phenol is one of the worst contaminants at date, and its degradation has been a crucial task over years. Here, the decomposition process of phenol, in a Fenton reaction, is described. Using scavengers, it was observed that decomposition of phenol was mainly influenced by production of hydroxyl radicals. Experimental and theoretical activation energies (Ea) for phenol oxidation intermediates were calculated. According to these Ea, phenol decomposition is a two-step reaction mechanism mediated predominantly by hydroxyl radicals, producing a decomposition yield order given as hydroquinone > catechol > resorcinol. Furthermore, traces of reaction derived acids were detected by HPLC and GS-MS.

  6. Crystal Structure of Mycobacterium tuberculosis Polyketide Synthase 11 (PKS11) Reveals Intermediates in the Synthesis of Methyl-branched Alkylpyrones*

    PubMed Central

    Gokulan, Kuppan; O'Leary, Seán E.; Russell, William K.; Russell, David H.; Lalgondar, Mallikarjun; Begley, Tadhg P.; Ioerger, Thomas R.; Sacchettini, James C.

    2013-01-01

    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

  7. Snapshots of enzymatic Baeyer-Villiger catalysis: oxygen activation and intermediate stabilization.

    PubMed

    Orru, Roberto; Dudek, Hanna M; Martinoli, Christian; Torres Pazmiño, Daniel E; Royant, Antoine; Weik, Martin; Fraaije, Marco W; Mattevi, Andrea

    2011-08-19

    Baeyer-Villiger monooxygenases catalyze the oxidation of carbonylic substrates to ester or lactone products using NADPH as electron donor and molecular oxygen as oxidative reactant. Using protein engineering, kinetics, microspectrophotometry, crystallography, and intermediate analogs, we have captured several snapshots along the catalytic cycle which highlight key features in enzyme catalysis. After acting as electron donor, the enzyme-bound NADP(H) forms an H-bond with the flavin cofactor. This interaction is critical for stabilizing the oxygen-activating flavin-peroxide intermediate that results from the reaction of the reduced cofactor with oxygen. An essential active-site arginine acts as anchoring element for proper binding of the ketone substrate. Its positively charged guanidinium group can enhance the propensity of the substrate to undergo a nucleophilic attack by the flavin-peroxide intermediate. Furthermore, the arginine side chain, together with the NADP(+) ribose group, forms the niche that hosts the negatively charged Criegee intermediate that is generated upon reaction of the substrate with the flavin-peroxide. The fascinating ability of Baeyer-Villiger monooxygenases to catalyze a complex multistep catalytic reaction originates from concerted action of this Arg-NADP(H) pair and the flavin subsequently to promote flavin reduction, oxygen activation, tetrahedral intermediate formation, and product synthesis and release. The emerging picture is that these enzymes are mainly oxygen-activating and "Criegee-stabilizing" catalysts that act on any chemically suitable substrate that can diffuse into the active site, emphasizing their potential value as toolboxes for biocatalytic applications. PMID:21697090

  8. Blue outliers among intermediate redshift quasars

    E-print Network

    Marziani, P; Stirpe, G M; Dultzin, D; Del Olmo, A; Martínez-Carballo, M A

    2015-01-01

    [Oiii]{\\lambda}{\\lambda}4959,5007 "blue outliers" -- that are suggestive of outflows in the narrow line region of quasars -- appear to be much more common at intermediate z (high luminosity) than at low z. About 40% of quasars in a Hamburg ESO intermediate-z sample of 52 sources qualify as blue outliers (i.e., quasars with [OIII] {\\lambda}{\\lambda}4959,5007 lines showing large systematic blueshifts with respect to rest frame). We discuss major findings on what has become an intriguing field in active galactic nuclei research and stress the relevance of blue outliers to feedback and host galaxy evolution.

  9. Intermediate load-center photovoltaic application experiments

    SciTech Connect

    Burgess, E. L.

    1980-01-01

    A total of nine intermediate load-center photovoltaic systems were carried into the construction phase this year. These nine systems range in size from 20 to 225 kW/sub p/ electrical output and total almost 1 MW/sub p/. They are being installed in a diverse set of applications and locations and represent the bulk of the photovoltaic initial system evaluation experiments (ISEE) for the intermediate load-center sector. Each of these experiments are briefly described and the status of the construction phase is given for each project.

  10. 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

  11. 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

  12. 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.

  13. Chemistry of Furan Conversion into Aromatics and Olefins over HZSM-5: A Model Biomass Conversion Reaction

    SciTech Connect

    Cheng, Yu-Ting; Huber, George W.

    2011-06-03

    The conversion of furan (a model of cellulosic biomass) over HZSM-5 was investigated in a thermogravimetric analysis–mass spectrometry system, in situ Fourier transform infrared analysis, and in a continuous-flow fixed-bed reactor. Furan adsorbed as oligomers at room temperature with a 1.73 of adsorbed furan/Al ratio. These oligomers were polycyclic aromatic compounds that were converted to CO, CO?, aromatics, and olefins at temperatures from 400 to 600 °C. Aromatics (e.g., benzene, toluene, and naphthalene), oligomer isomers (e.g., benzofuran, 2,2-methylenebisfuran, and benzodioxane), and heavy oxygenates (C??{sub +} oligomers) were identified as intermediates formed inside HZSM-5 at different reaction temperatures. During furan conversion, graphite-type coke formed on the catalyst surface, which caused the aromatics and olefins formation to deactivate within the first 30 min of time on-stream. We have measured the effects of space velocity and temperature for furan conversion to help us understand the chemistry of biomass conversion inside zeolite catalysts. The major products for furan conversion included CO, CO?, allene, C?–C? olefins, benzene, toluene, styrene, benzofuran, indene, and naphthalene. The aromatics (benzene and toluene) and olefins (ethylene and propylene) selectivity decreased with increasing space velocity. Unsaturated hydrocarbons such as allene, cyclopentadiene, and aromatics selectivity increased with increasing space velocity. The product distribution was selective to olefins and CO at high temperatures (650 °C) but was selective to aromatics (benzene and toluene) at intermediate temperatures (450–600 °C). At low temperatures (450 °C), benzofuran and coke contributed 60% of the carbon selectivity. Several different reactions were occurring for furan conversion over zeolites. Some important reactions that we have identified in this study include Diels–Alder condensation (e.g., two furans form benzofuran and water), decarbonylation (e.g., furan forms CO and allene), oligomerization (allene forms olefins and aromatics plus hydrogen), and alkylation (e.g., furan plus olefins). The product distribution was far from thermodynamic equilibrium.

  14. Rapid Removal of Tetrabromobisphenol A by Ozonation in Water: Oxidation Products, Reaction Pathways and Toxicity Assessment

    PubMed Central

    Wang, Xinghao; Huang, Qingguo; Lu, Junhe; Wang, Liansheng; Wang, Zunyao

    2015-01-01

    Tetrabromobisphenol A (TBBPA) is one of the most widely used brominated flame retardants and has attracted more and more attention. In this work, the parent TBBPA with an initial concentration of 100 mg/L was completely removed after 6 min of ozonation at pH 8.0, and alkaline conditions favored a more rapid removal than acidic and neutral conditions. The presence of typical anions and humic acid did not significantly affect the degradation of TBBPA. The quenching test using isopropanol indicated that direct ozone oxidation played a dominant role during this process. Seventeen reaction intermediates and products were identified using an electrospray time-of-flight mass spectrometer. Notably, the generation of 2,4,6-tribromophenol was first observed in the degradation process of TBBPA. The evolution of reaction products showed that ozonation is an efficient treatment for removal of both TBBPA and intermediates. Sequential transformation of organic bromine to bromide and bromate was confirmed by ion chromatography analysis. Two primary reaction pathways that involve cleavage of central carbon atom and benzene ring cleavage concomitant with debromination were thus proposed and further justified by calculations of frontier electron densities. Furthermore, the total organic carbon data suggested a low mineralization rate, even after the complete removal of TBBPA. Meanwhile, the acute aqueous toxicity of reaction solutions to Photobacterium Phosphoreum and Daphnia magna was rapidly decreased during ozonation. In addition, no obvious difference in the attenuation of TBBPA was found by ozone oxidation using different water matrices, and the effectiveness in natural waters further demonstrates that ozonation can be adopted as a promising technique to treat TBBPA-contaminated waters. PMID:26430733

  15. Identification of surface intermediates during ethylidyne formation on Pt(111) by calculation of infrared intensities and deuterium isotope shifts

    NASA Astrophysics Data System (ADS)

    Zhao, Zhi-Jian; Greeley, Jeffrey P.

    2015-10-01

    The conversion of ethylene to ethylidyne on Pt(111) is a well-studied model reaction related to conversion of hydrocarbons over noble metal catalysts. For this chemistry, a two step mechanism that proceeds via an ethylidene intermediate has been generally accepted since the mid-1990s. However, recent DFT calculations (J. Phys Chem. C 2010, 114, 12190) have suggested that this intermediate may, in fact, be short-lived and should not be observed. Experimental verification of this prediction, though, is not straightforward, and to provide further theoretical results by which the prediction could be more easily evaluated, we present a set of benchmark calculations of infrared frequencies and intensities of candidate intermediates adsorbed on the Pt(111) surface at realistic coadsorbate coverages. The results show that only modest differences in frequencies and intensities exist between these intermediates, rendering direct spectroscopic differentiation difficult. However, by substituting the C2 species and intermediates with deuterium, it is shown that one characteristic vibrational band of vinylidene and ethylidene can be separated by well over 100 cm- 1. This result provides a clear prediction that, if coupled with measured vibrational spectra of deuterium-labeled C2 species, could definitively differentiate between the most likely intermediates in this reaction network.

  16. Garner’s aldehyde as a versatile intermediate in the synthesis of enantiopure natural products

    PubMed Central

    Passiniemi, Mikko

    2013-01-01

    Summary Since its introduction to the synthetic community in 1984, Garner’s aldehyde has gained substantial attention as a chiral intermediate for the synthesis of numerous amino alcohol derivatives. This review presents some of the most successful carbon chain elongation reactions, namely carbonyl alkylations and olefinations. The literature is reviewed with particular attention on understanding how to avoid the deleterious epimerization of the existing stereocenter in Garner’s aldehyde. PMID:24367429

  17. Capture of Reactive Monophosphine-Ligated Palladium(0) Intermediates by Mass Spectrometry.

    PubMed

    Zheng, Qiuling; Liu, Yong; Chen, Qinghao; Hu, Meihong; Helmy, Roy; Sherer, Edward C; Welch, Christopher J; Chen, Hao

    2015-11-11

    A long-sought-after reactive monophosphine-ligated palladium(0) intermediate, Pd(0)L (L = phosphine ligand), was detected for the first time from the activation of the Buchwald precatalyst with base. The detection was enabled using desorption electrospray ionization mass spectrometry (DESI-MS) in combination with online reaction monitoring. The subsequent oxidative addition of Pd(0)L with aryl halide and C-N coupling with amine via reductive elimination was also probed using DESI-MS. PMID:26498505

  18. CONTINUOUS TIME MARKOV CHAIN MODELS FOR CHEMICAL REACTION NETWORKS

    E-print Network

    Anderson, David F.

    Chapter 1 CONTINUOUS TIME MARKOV CHAIN MODELS FOR CHEMICAL REACTION NETWORKS David F. Anderson of identifying the different time scales and deriving the reduced models. Keywords: Reaction network, Markov for the reaction is that the probability of the reaction occurring in a small time inter- val (t, t + t] should

  19. Multistage reaction pathways in detonating high explosives

    SciTech Connect

    Li, Ying; Kalia, Rajiv K.; Nakano, Aiichiro; Nomura, Ken-ichi; Vashishta, Priya

    2014-11-17

    Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N{sub 2} and H{sub 2}O within ?10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct unimolecular and intermolecular reaction pathways, respectively, for the rapid N{sub 2} and H{sub 2}O productions.

  20. A hitherto unknown transketolase-catalyzed reaction.

    PubMed

    Sevostyanova, Irina A; Solovjeva, Olga N; Kochetov, German A

    2004-01-16

    Yeast transketolase, in addition to catalyzing the transferase reaction through utilization of two substrates--the donor substrate (ketose) and the acceptor substrate (aldose)--is also able to catalyze a one-substrate reaction with only aldose (glycolaldehyde) as substrate. The interaction of glycolaldehyde with holotransketolase results in formation of the transketolase reaction intermediate, dihydroxyethyl-thiamin diphosphate. Then the glycolaldehyde residue is transferred from dihydroxyethyl-thiamin diphosphate to free glycolaldehyde. As a result, the one-substrate transketolase reaction product, erythrulose, is formed. The specific activity of transketolase was found to be 0.23 U/mg and the apparent Km for glycolaldehyde was estimated as 140 mM. PMID:14697258

  1. A Computational Study of Acid Catalyzed Aerosol Reactions of Atmospherically Relevant Epoxides

    EPA Science Inventory

    Epoxides are important intermediates of atmospheric isoprene oxidation. Their subsequent reactions in the particle phase lead to the production of organic compounds detected in ambient aerosols. We apply density functional theory to determine the important kinetic factors that ...

  2. Experimental Observations in the Morita Baylis-Hillman Reaction in Methanol 

    E-print Network

    Plata, Robert Erik

    2013-05-22

    even defined a complete theoretical mechanistic energy profile for these reactions. This dissertation describes a combination of experimental and theoretical mechanistic probes, including the observation of intermediates, the independent generation...

  3. Ion Mobility-Mass Spectrometry Reveals the Energetics of Intermediates that Guide Polyproline Folding

    NASA Astrophysics Data System (ADS)

    Shi, Liuqing; Holliday, Alison E.; Glover, Matthew S.; Ewing, Michael A.; Russell, David H.; Clemmer, David E.

    2015-09-01

    Proline favors trans-configured peptide bonds in native proteins. Although cis/trans configurations vary for non-native and unstructured states, solvent also influences these preferences. Water induces the all-cis right-handed polyproline-I (PPI) helix of polyproline to fold into the all-trans left-handed polyproline-II (PPII) helix. Our recent work has shown that this occurs via a sequential mechanism involving six resolved intermediates [Shi, L., Holliday, A.E., Shi, H., Zhu, F., Ewing, M.A., Russell, D.H., Clemmer, D.E.: Characterizing intermediates along the transition from PPI to PPII using ion mobility-mass spectrometry. J. Am. Chem. Soc. 136, 12702-12711 (2014)]. Here, we use ion mobility-mass spectrometry to make the first detailed thermodynamic measurements of the folding intermediates, which inform us about how and why this transition occurs. It appears that early intermediates are energetically favorable because of the hydration of the peptide backbone, whereas late intermediates are enthalpically unfavorable. However, folding continues, as the entropy of the system increases upon successive formation of each new structure. When PPII is immersed in 1-propanol, the PPII?PPI transition occurs, but this reaction occurs through a very different mechanism. Early on, the PPII population splits onto multiple pathways that eventually converge through a late intermediate that continues on to the folded PPI helix. Nearly every step is endothermic. Folding results from a stepwise increase in the disorder of the system, allowing a wide-scale search for a critical late intermediate. Overall, the data presented here allow us to establish the first experimentally determined energy surface for biopolymer folding as a function of solution environment.

  4. Ion Mobility-Mass Spectrometry Reveals the Energetics of Intermediates that Guide Polyproline Folding.

    PubMed

    Shi, Liuqing; Holliday, Alison E; Glover, Matthew S; Ewing, Michael A; Russell, David H; Clemmer, David E

    2016-01-01

    Proline favors trans-configured peptide bonds in native proteins. Although cis/trans configurations vary for non-native and unstructured states, solvent also influences these preferences. Water induces the all-cis right-handed polyproline-I (PPI) helix of polyproline to fold into the all-trans left-handed polyproline-II (PPII) helix. Our recent work has shown that this occurs via a sequential mechanism involving six resolved intermediates [Shi, L., Holliday, A.E., Shi, H., Zhu, F., Ewing, M.A., Russell, D.H., Clemmer, D.E.: Characterizing intermediates along the transition from PPI to PPII using ion mobility-mass spectrometry. J. Am. Chem. Soc. 136, 12702-12711 (2014)]. Here, we use ion mobility-mass spectrometry to make the first detailed thermodynamic measurements of the folding intermediates, which inform us about how and why this transition occurs. It appears that early intermediates are energetically favorable because of the hydration of the peptide backbone, whereas late intermediates are enthalpically unfavorable. However, folding continues, as the entropy of the system increases upon successive formation of each new structure. When PPII is immersed in 1-propanol, the PPII?PPI transition occurs, but this reaction occurs through a very different mechanism. Early on, the PPII population splits onto multiple pathways that eventually converge through a late intermediate that continues on to the folded PPI helix. Nearly every step is endothermic. Folding results from a stepwise increase in the disorder of the system, allowing a wide-scale search for a critical late intermediate. Overall, the data presented here allow us to establish the first experimentally determined energy surface for biopolymer folding as a function of solution environment. Graphical Abstract ?. PMID:26362047

  5. Ion-Molecule Reactions and Ion Kinetics in DC Townsend Discharges in Dielectric Gases

    NASA Technical Reports Server (NTRS)

    Rao, M. V. V. S.; Arnold, James O. (Technical Monitor)

    1998-01-01

    In gas discharges the identify, transport, relative intensities, and kinetic energy distributions (KEDs) of ions may be dominated by ion-molecule reactions. In order to understand these discharges, there is a need for cross section data for various ion-molecule reactions, including symmetric and asymmetric charge-transfer, collisional detachment, and ion conversion reactions, especially for low to intermediate ion-impact energies. In view of the importance of dielectric gases, we have recently measured the KEDs of various positive and negative ions produced in DC Townsend discharges in SF6, CF4, CHF3, O2, and CO2. The relative abundance and mean energies of ions are obtained from the measured KEDs. The effective cross sections (Qeff) describing the KEDs of various ions can be derived by using the mean ion energies and the electric field-to-gas density ratios (E/N). In the case of SF6 and O2 discharges, the determined cross sections (Qeff) for the negative-ion molecule reactions are consistent with previously measured cross section data obtained by crossed-beam experiment. The availability of these cross section values enabled us to understand the ion data reasonably well. However, the lack of adequate cross section data for positive ions in all of the above gases is a major obstacle in understanding ion transport in these gas discharges.

  6. Iridium-Catalyzed Hydrogen Transfer Reactions

    NASA Astrophysics Data System (ADS)

    Saidi, Ourida; Williams, Jonathan M. J.

    This chapter describes the application of iridium complexes to catalytic hydrogen transfer reactions. Transfer hydrogenation reactions provide an alternative to direct hydrogenation for the reduction of a range of substrates. A hydrogen donor, typically an alcohol or formic acid, can be used as the source of hydrogen for the reduction of carbonyl compounds, imines, and alkenes. Heteroaromatic compounds and even carbon dioxide have also been reduced by transfer hydrogenation reactions. In the reverse process, the oxidation of alcohols to carbonyl compounds can be achieved by iridium-catalyzed hydrogen transfer reactions, where a ketone or alkene is used as a suitable hydrogen acceptor. The reversible nature of many hydrogen transfer processes has been exploited for the racemization of alcohols, where temporary removal of hydrogen generates an achiral ketone intermediate. In addition, there is a growing body of work where temporary removal of hydrogen provides an opportunity for using alcohols as alkylating agents. In this chemistry, an iridium catalyst "borrows" hydrogen from an alcohol to give an aldehyde or ketone intermediate, which can be transformed into either an imine or alkene under the reaction conditions. Return of the hydrogen from the catalyst provides methodology for the formation of amines or C-C bonds where the only by-product is typically water.

  7. Determination of penicillin susceptibility of Streptococcus pneumoniae using the polymerase chain reaction.

    PubMed Central

    Jalal, H.; Organji, S.; Reynolds, J.; Bennett, D.; O'Mason, E.; Millar, M. R.

    1997-01-01

    AIM: To develop a polymerase chain reaction (PCR) based method to detect penicillin susceptibility in isolates of Streptococcus pneumoniae (SP). METHOD: PCR primers were designed to amplify differential nucleotide sequences of the penicillin-binding protein (PBP) genes 2b, 2x, and 1a in penicillin susceptible and resistant strains of SP. Primers derived from the PBP 2x and 2b genes were designed to amplify products from penicillin susceptible S pneumoniae (PSSP), whereas primers derived from the PBP 1a gene were designed to amplify gene sequences of penicillin resistant S pneumoniae (PRSP). RESULTS: Two hundred and thirty clinical isolates of SP from the USA, UK, Kenya, Romania, and the Kingdom of Saudi Arabia were tested. Of the isolates, 116 were penicillin susceptible, 65 were intermediately resistant, and 49 were highly resistant. PCR identified 108 (93%) of 116 of PSSP isolates, 55 (85%) of 65 intermediately resistant isolates, and all of the 49 highly resistant isolates of SP. The susceptibility of 16 (7%) isolates could not be determined using PCR. All of these 16 isolates had a minimum inhibitory concentration (MIC) of penicillin < 1 mg/l. None of the highly resistant isolates was identified as penicillin susceptible by PCR, although two of the isolates with intermediate resistance (MIC = 0.125 mg/l) were. CONCLUSION: Using primers that differentially identify the genotypes of susceptible and resistant strains of SP, PCR provides a rapid method for determining the penicillin susceptibility of SP isolates and could potentially be used for testing clinical samples. Images PMID:9208813

  8. The RISE Report. Report of the California Commission for Reform of Intermediate and Secondary Education.

    ERIC Educational Resources Information Center

    California State Commission for Reform of Intermediate and Secondary Education, Sacramento.

    The commission was charged with drafting a framework for overhauling education in California's 1,600 intermediate and secondary schools. The Superintendent of Public Instruction asked the commission to envision an educational system that could respond continually to changing needs in the next quarter century; to identify the skills and…

  9. 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…

  10. Direct production of OH radicals upon CH overtone activation of (CH3)2COO Criegee intermediates

    NASA Astrophysics Data System (ADS)

    Liu, Fang; Beames, Joseph M.; Lester, Marsha I.

    2014-12-01

    Ozonolysis of alkenes, a principle non-photolytic source of atmospheric OH radicals, proceeds through unimolecular decay of energized carbonyl oxide intermediates, known as Criegee intermediates. In this work, cold dimethyl-substituted Criegee intermediates are vibrationally activated in the CH stretch overtone region to drive the 1,4 hydrogen transfer reaction that leads to OH radical products. IR excitation of (CH3)2COO reveals the vibrational states with sufficient oscillator strength, coupling to the reaction coordinate, and energy to surmount the effective barrier (? 16.0 kcal mol-1) to reaction. Insight on the dissociation dynamics is gleaned from homogeneous broadening of the spectral features, indicative of rapid intramolecular vibrational energy redistribution and/or reaction, as well as the quantum state distribution of the OH X2? (v = 0) products. The experimental results are compared with complementary electronic structure calculations, which provide the IR absorption spectrum and geometric changes along the intrinsic reaction coordinate. Additional theoretical analysis reveals the vibrational modes and couplings that permit (CH3)2COO to access to the transition state region for reaction. The experimental and theoretical results are compared with an analogous recent study of the IR activation of syn-CH3CHOO and its unimolecular decay to OH products [F. Liu, J. M. Beames, A. S. Petit, A. B. McCoy, and M. I. Lester, Science 345, 1596 (2014)].

  11. Reactive intermediates: Radicals with multiple personalities

    NASA Astrophysics Data System (ADS)

    Forbes, Malcolm D. E.

    2013-06-01

    A combined theoretical and experimental approach has revealed that radicals can be significantly stabilized by the presence of a remote anionic site in the same molecule. This finding has implications for understanding and potentially controlling the reactivity of these important reactive intermediates.

  12. Intermediate Tamil: A Self-Instructional Method.

    ERIC Educational Resources Information Center

    Schiffman, Harold

    This self-instructional method for learning an intermediate level of Tamil is designed to follow an elementary level such as "Conversational Tamil." The material in this text concentrates on grammatical constructions not covered in that elementary text, particularly negatives of all kinds; in addition, this text uses the same transcription and the…

  13. SOIL RESISTANCE UNDER GRAZED INTERMEDIATE WHEATGRASS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Intermediate wheatgrass [Thinopyrum intermedium (Host) Barkw. & D.R. Dewey subsp. intermedium] is a productive, high quality perennial forage that lacks persistence under grazing. Grazing effects on soil condition may contribute to this lack of persistence. An evaluation was undertaken to better u...

  14. What Should be Taught in Intermediate Macroeconomics?

    ERIC Educational Resources Information Center

    de Araujo, Pedro; O'Sullivan, Roisin; Simpson, Nicole B.

    2013-01-01

    A lack of consensus remains on what should form the theoretical core of the undergraduate intermediate macroeconomic course. In determining how to deal with the Keynesian/classical divide, instructors must decide whether to follow the modern approach of building macroeconomic relationships from micro foundations, or to use the traditional approach…

  15. INTERMEDIATE ACCOUNTING I FALL SEMESTER, 2015

    E-print Network

    Barrash, Warren

    1 ACCT 304 INTERMEDIATE ACCOUNTING I FALL SEMESTER, 2015 PROFESSOR: Troy Hyatt, PhD, CPA SECTION is due at the beginning of class on the due dates. HAND-WRITTEN RESPONSES WILL NOT BE ACCEPTED. EXAMS A total of four exams will be given, each worth 80 points. Exam dates are included on the attached

  16. Central Intermediate School. 1986-87 Profile.

    ERIC Educational Resources Information Center

    Cleveland Public Schools, OH. Dept. of Research and Analysis.

    This building profile provides standard information about one of the 129 schools of the Cleveland Public Schools (Ohio) in 1986-87. Information for the Central Intermediate School (CIS), serving grades 7 and 8, is presented along with comparative data for the school cluster and for the district as a whole. In 1986-87, 404 Black students and 237…

  17. Intermediate Charcot-Marie-Tooth disease.

    PubMed

    Liu, Lei; Zhang, Ruxu

    2014-12-01

    Charcot-Marie-Tooth (CMT) disease is a common neurogenetic disorder and its heterogeneity is a challenge for genetic diagnostics. The genetic diagnostic procedures for a CMT patient can be explored according to the electrophysiological criteria: very slow motor nerve conduction velocity (MNCV) (<15 m/s), slow MNCV (15-25 m/s), intermediate MNCV (25-45 m/s), and normal MNCV (>45 m/s). Based on the inheritance pattern, intermediate CMT can be divided into dominant (DI-CMT) and recessive types (RI-CMT). GJB1 is currently considered to be associated with X-linked DI-CMT, and MPZ, INF2, DNM2, YARS, GNB4, NEFL, and MFN2 are associated with autosomal DI-CMT. Moreover, GDAP1, KARS, and PLEKHG5 are associated with RI-CMT. Identification of these genes is not only important for patients and families but also provides new information about pathogenesis. It is hoped that this review will lead to a better understanding of intermediate CMT and provide a detailed diagnostic procedure for intermediate CMT. PMID:25326399

  18. 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...

  19. 40 CFR 721.3805 - Formaldehyde, reaction products with 1,3-benzenedimethanamine and bisphenol A.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...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 721.9484 - 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  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 721.10212 - 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...

  7. 40 CFR 721.3805 - Formaldehyde, reaction products with 1,3-benzenedimethanamine and bisphenol A.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. Advanced Intermediate-Temperature Na-S Battery

    SciTech Connect

    Lu, Xiaochuan; Kirby, Brent W.; Xu, Wu; Li, Guosheng; Kim, Jin Yong; Lemmon, John P.; Sprenkle, Vincent L.; Yang, Zhenguo

    2013-01-01

    In this study, we reported an intermediate-temperature (~150°C) sodium-sulfur (Na-S) battery. With a reduced operating temperature, this novel battery can potentially reduce the cost and safety issues associated with the conventional high-temperature (300~350°C) Na-S battery. A dense ?"-Al2O3 solid membrane and tetraglyme were utilized as the electrolyte separator and catholyte solvent in this battery. Solubility tests indicated that cathode mixture of Na2S4 and S exhibited extremely high solubility in tetraglyme (e.g., > 4.1 M for Na2S4 + 4 S). CV scans of Na2S4 in tetraglyme revealed two pairs of redox couples with peaks at around 2.22 and 1.75 V, corresponding to the redox reactions of polysulfide species. The discharge/charge profiles of the Na-S battery showed a slope region and a plateau, indicating multiple steps and cell reactions. In-situ Raman measurements during battery operation suggested that polysulfide species were formed in the sequence of Na2S5 + S ? Na2S5 + Na2S4? Na2S4 + Na2S2 during discharge and in a reverse order during charge. This battery showed dramatic improvement in rate capacity and cycling stability over room-temperature Na-S batteries, which makes it attractive for renewable energy integration and other grid related applications.

  13. 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.

    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.

  14. Moist air reaction with excess UF{sub 6}

    SciTech Connect

    Reiner, R.H.

    1989-08-01

    The moist air reaction with uranium hexafluoride (UF{sub 6}) has been studied at conditions simulating UF{sub 6} hydrolysis during air inleakage in the cascade. In excess UF{sub 6}, the reaction mechanism is more complicated than predicted by the simple gas-phase reaction of one UF{sub 6} molecule with two water molecules to form uranyl fluoride and hydrogen fluoride. The initial UF{sub 6} consumption is significantly greater than predicted, suggesting that a metastable uranium compound is formed during the hydrolysis reaction. This intermediate uranium compound may facilitate uranyl fluoride transport in the cascade.

  15. Can Chlorine Anion Catalyze the Reaction fo HOCl with HCl?

    NASA Technical Reports Server (NTRS)

    Richardson, S. L.; Francisco, J. S.; Mebel, A. M.; Morokuma, K.

    1997-01-01

    The reaction of HOCl + HCl -> Cl2 + H20 in the presence of Cl has been studied using ab initio methods. This reaction has been shown to have a high activation barrier of 46.5 kcal/mol. The chlorine anion, Cl- is found to catalyze the reaction, viz. two mechanisms. The first involves Cl- interacting through the concerted four-center transition state of the neutral reaction. The other mechanism involves the formation of a HCl-HOCl-Cl- intermediate which dissociates into Cl2 + Cl- + H20. The steps are found to have no barriers. The overall exothermicity is 15.5 kcal/mol.

  16. Femtosecond electron diffraction and spectroscopic studies of a solid state organic chemical reaction

    NASA Astrophysics Data System (ADS)

    Jean-Ruel, Hubert

    Photochromic diarylethene molecules are excellent model systems for studying electrocyclic reactions, in addition to having important technological applications in optoelectronics. The photoinduced ring-closing reaction in a crystalline photochromic diarylethene derivative was fully resolved using the complementary techniques of transient absorption spectroscopy and femtosecond electron crystallography. These studies are detailed in this thesis, together with the associated technical developments which enabled them. Importantly, the time-resolved crystallographic investigation reported here represents a highly significant proof-of-principle experiment. It constitutes the first study directly probing the molecular structural changes associated with an organic chemical reaction with sub-picosecond temporal and atomic spatial resolution---to follow the primary motions directing chemistry. In terms of technological development, the most important advance reported is the implementation of a radio frequency rebunching system capable of producing femtosecond electron pulses of exceptional brightness. The temporal resolution of this newly developed electron source was fully characterized using laser ponderomotive scattering, confirming a 435 +/- 75 fs instrument response time with 0.20 pC bunches. The ultrafast spectroscopic and crystallographic measurements were both achieved by exploiting the photoreversibility of diarylethene. The transient absorption study was first performed, after developing a novel robust acquisition scheme for thermally irreversible reactions in the solid state. It revealed the formation of an open-ring excited state intermediate, following photoexcitation of the open-ring isomer with an ultraviolet laser pulse, with a time constant of approximately 200 fs. The actual ring closing was found to occur from this intermediate with a time constant of 5.3 +/- 0.3 ps. The femtosecond diffraction measurements were then performed using multiple crystal orientations and a large number of different samples. To analyse the results, an innovative method was developed in which the apparently complex ring-closing reaction is distilled down to a small number of basic rotations. Immediately following photoexcitation, sub-picosecond structural changes associated with the formation of the intermediate are observed. The rotation of the thiophene rings is identified as the key motion. Subsequently, on the few picosecond time scale, the time-resolved diffraction patterns are observed to converge towards those associated with the closed-ring photoproduct. The formation of the closed-ring molecule is thus unambiguously witnessed.

  17. 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.

  18. SET-Induced Biaryl Cross-Coupling: An SRN1 Reaction

    PubMed Central

    2015-01-01

    The SET-induced biaryl cross-coupling reaction is established as the first example of a Grignard SRN1 reaction. The reaction is examined within the mechanistic framework of dissociative electron transfer in the presence of a Lewis acid. DFT calculations show that the reaction proceeds through a radical intermediate in the form of an Mg ion-radical cage, which eludes detection in trapping experiments by reacting quickly to form an MgPh2 radical anion intermediate. A new mechanism is proposed. PMID:24564385

  19. Identifying Extreme Exposure Values

    Cancer.gov

    There are various perspectives on whether to exclude potentially unlikely exposure values. If the researcher chooses to do so, several approaches exist for identifying extreme values. We examined the plausibility of the reported frequencies for each food item in the NHANES 2009-10 DSQ and chose to exclude extreme values using a method that identifies them based on the actual distribution of the sample, but also minimizes the number of values excluded.

  20. Reaction Dynamics and Multifragmentation in Fermi Energy Heavy Ion Reactions

    E-print Network

    R. Wada; T. Keutgen; K. Hagel; Y. G. Ma; J. Wang; M. Murray; L. Qin; P. Smith; J. B. Natowitz; R. Alfarro; J. Cibor; M. Cinausero; Y. El Masri; D. Fabris; E. Fioretto; A. Keksis; M. Lunardon; A. Makeev; N. Marie; E. Martin; A. Martinez-Davalos; A. Menchaca-Rocha; G. Nebbia; G. Prete; V. Rizzi; A. Ruangma; D. V. Shetty; G. Souliotis; P. Staszel; M. Veselsky; G. Viesti; E. M. Winchester; S. J. Yennello; Z. Majka; A. Ono

    2003-08-27

    The reaction systems, 64Zn + 58Ni, 64Zn + 92Mo, 64Zn + 197Au, at 26A, 35A and 47A MeV, have been studied both in experiments with a 4$\\pi$ detector array, NIMROD, and with Antisymmetrized Molecular Dynamics model calculations employing effective interactions corresponding to soft and stiff equations of state (EOS). Direct experimental observables, such as multiplicity distributions, charge distributions, energy spectra and velocity spectra, have been compared in detail with those of the calculations and a reasonable agreement is obtained. The velocity distributions of $\\alpha$ particles and fragments with Z >= 3 show distinct differences in calculations with the soft EOS and the stiff EOS. The velocity distributions of $\\alpha$ particle and Intermediate Mass Fragments (IMF's) are best described by the stiff EOS. Neither of the above direct observables nor the strength of the elliptic flow are sensitive to changes in the in-medium nucleon-nucleon (NN) cross sections. A detailed analysis of the central collision events calculated with the stiff EOS revealed that multifragmentation with cold fragment emission is a common feature predicted for all reactions studied here. A possible multifragmentation scenario is presented; after the preequilibrium emission ceases in the composite system, cold light fragments are formed in a hotter gas of nucleons and stay cold until the composite system underdoes multifragmentation. For reaction with 197Au at 47A MeV a significant radial expansion takes place. For reactions with 58Ni and 92Mo at 47A MeV semi-transparency becomes prominent. The differing reaction dynamics drastically change the kinematic characteristics of emitted fragments. This scenario gives consistent explanations for many existing experimental results in the Fermi energy domain.

  1. Inhomogeneous isospin distribution in the reactions of 28Si + 112Sn and 124Sn at 30 and 50 MeV/nucleon

    E-print Network

    M. Veselsky; R. W. Ibbotson; R. Laforest; E. Ramakrishnan; D. J. Rowland; A. Ruangma; E. M. Winchester; E. Martin; S. J. Yennello

    2000-10-18

    We have created quasiprojectiles of varying isospin via peripheral reactions of 28Si + 112Sn and 124Sn at 30 and 50 MeV/nucleon. The quasiprojectiles have been reconstructed from completely isotopically identified fragments. The difference in N/Z of the reconstructed quasiprojectiles allows the investigation of the disassembly as a function of the isospin of the fragmenting system. The isobaric yield ratio 3H/3He depends strongly on N/Z ratio of quasiprojectiles. The dependences of mean fragment multiplicity and mean N/Z ratio of the fragments on N/Z ratio of the quasiprojectile are different for light charged particles and intermediate mass fragments. Observation of a different N/Z ratio of light charged particles and intermediate mass fragments is consistent with an inhomogeneous distribution of isospin in the fragmenting system.

  2. 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

  3. The C(3P) + NH3 Reaction in Interstellar Chemistry. I. Investigation of the Product Formation Channels

    NASA Astrophysics Data System (ADS)

    Bourgalais, Jérémy; Capron, Michael; Abhinavam Kailasanathan, Ranjith Kumar; Osborn, David L.; Hickson, Kevin M.; Loison, Jean-Christophe; Wakelam, Valentine; Goulay, Fabien; Le Picard, Sébastien D.

    2015-10-01

    The product formation channels of ground state carbon atoms, C(3P), reacting with ammonia, NH3, have been investigated using two complementary experiments and electronic structure calculations. Reaction products are detected in a gas flow tube experiment (330 K, 4 Torr) using tunable vacuum-ultraviolet (VUV) photoionization coupled with time of flight mass spectrometry. Temporal profiles of the species formed and photoionization spectra are used to identify primary products of the C + NH3 reaction. In addition, H-atom formation is monitored by VUV laser induced fluorescence (LIF) from room temperature to 50 K in a supersonic gas flow generated by the Laval nozzle technique. Electronic structure calculations are performed to derive intermediates, transition states, and complexes formed along the reaction coordinate. The combination of photoionization and LIF experiments supported by theoretical calculations indicate that in the temperature and pressure range investigated, the H + H2CN production channel represents 100% of the product yield for this reaction. Kinetics measurements of the title reaction down to 50 K and the effect of the new rate constants on interstellar nitrogen hydride abundances using a model of dense interstellar clouds are reported in Paper II.

  4. 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

  5. Probing Isotope Effects in Chemical Reactions Using Single Ions

    NASA Astrophysics Data System (ADS)

    Staanum, Peter F.; Højbjerre, Klaus; Wester, Roland; Drewsen, Michael

    2008-06-01

    Isotope effects in reactions between Mg+ in the 3p P3/22 excited state and molecular hydrogen at thermal energies are studied through single reaction events. From only ˜250 reactions with HD, the branching ratio between formation of MgD+ and MgH+ is found to be larger than 5. From an additional 65 reactions with H2 and D2 we find that the overall fragmentation probability of the intermediate MgH2+, MgHD+, or MgD2+ complexes is the same. Our study shows that few single ion reactions can provide quantitative information on ion-neutral reactions. Hence, the method is well suited for reaction studies involving rare species, e.g., rare isotopes or short-lived unstable elements.

  6. Structural and Thermodynamic Characteristics of Amyloidogenic Intermediates of ?-2-Microglobulin

    PubMed Central

    Chong, Song-Ho; Hong, Jooyeon; Lim, Sulgi; Cho, Sunhee; Lee, Jinkeong; Ham, Sihyun

    2015-01-01

    ?-2-microglobulin (?2m) self-aggregates to form amyloid fibril in renal patients taking long-term dialysis treatment. Despite the extensive structural and mutation studies carried out so far, the molecular details on the factors that dictate amyloidogenic potential of ?2m remain elusive. Here we report molecular dynamics simulations followed by the solvation thermodynamic analyses on the wild-type ?2m and D76N, D59P, and W60C mutants at the native (N) and so-called aggregation-prone intermediate (IT) states, which are distinguished by the native cis- and non-native trans-Pro32 backbone conformations. Three major structural and thermodynamic characteristics of the IT-state relative to the N-state in ?2m protein are detected that contribute to the increased amyloidogenic potential: (i) the disruption of the edge D-strand, (ii) the increased solvent-exposed hydrophobic interface, and (iii) the increased solvation free energy (less affinity toward solvent water). Mutation effects on these three factors are shown to exhibit a good correlation with the experimentally observed distinct amyloidogenic propensity of the D76N (+), D59P (+), and W60C (?) mutants (+/? for enhanced/decreased). Our analyses thus identify the structural and thermodynamic characteristics of the amyloidogenic intermediates, which will serve to uncover molecular mechanisms and driving forces in ?2m amyloid fibril formation. PMID:26348154

  7. Reaction of alkylcobalamins with thiols

    SciTech Connect

    Hogenkamp, H.P.C.; Bratt, G.T.; Kotchevar, A.T.

    1987-07-28

    Carbon-13 NMR spectroscopy and phosphorus-31 NMR spectroscopy have been used to study the reaction of several alkylcobalamins with 2-mercaptoethanol. At alkaline pH, when the thiol is deprotonated, the alkyl-transfer reactions involve a nucleophilic attack of the thiolate anion on the Co-methylene carbon of the cobalamins, yielding alkyl thioethers and cob(II)alamin. In these nucleophilic displacement reactions cob(I)alamin is presumably formed as an intermediate. The higher alkylcobalamins react more slowly than methylcobalamin. The lower reactivity of ethyl- and propylcobalamin is probably the basis of the inhibition of the corrinoid-dependent methyl-transfer systems by propyl iodide. The transfer of the upper nucleoside ligand of adenosylcobalamin to 2-mercaptoethanol is a very slow process; S-adenosylmercaptoethanol and cob(II)alamin are the final products of the reaction. The dealkylation of (carboxymethyl)cobalamin is a much more facile reaction. At alkaline pH S-(carboxymethyl)mercaptoethanol and cob(II)alamin are produced, while at pH values below 8 the carbon-cobalt bond is cleaved reductively to acetate and cob(II)alamin. The reductive cleavage of the carbon-cobalt bond of (carboxymethyl)cobalamin by 2-mercaptoethanol is extremely fast when the cobalamin is in the base-off form. Because the authors have been unable to detect trans coordination of 2-mercaptoethanol, they favor a mechanism that involves a hydride attack on the Co-methylene carbon of (carboxymethyl) rather than a trans attack of the thiol on the cobalt atom.

  8. [Spectroscopic study on the combustion reaction characteristics of methylcyclohexane].

    PubMed

    Li, Cong-Shan; Li, Ping; Zhang, Chang-Hua; Nie, Xiao-Fei; Li, Xiang-Yuan

    2011-09-01

    Using a measurement system consisting of monochromators, photomultiplier tubes, piezoelectric pressure sensors and a digital oscilloscope, characteristic emissions of intermediate products OH, CH and C2 produced in the combustion reaction of methylcyclohexane were measured behind reflected shock waves in a shock tube, and ignition delay times of methylcyclohexane/ oxygen/argon were acquired. Experimental conditions cover temperatures from 1 164 to 1 566 K, pressures from 1.03 to 1.99 atm, a fuel concentration of 1.0%, and an equivalence ratio of 1.0. Combustion reaction characteristics of methylcyclohexane were obtained qualitatively by analyzing emissions from intermediate products OH, CH and C2. The measured ignition delay times agree with available experimental data and the prediction of a combustion reaction mechanism. Current work provides experimental data for constructing and validating the combustion reaction mechanism of methylcyclohexane. PMID:22097862

  9. Intermediate Heat Transfer Loop Study for High Temperature Gas-Cooled Reactor

    SciTech Connect

    C. H. Oh; C. Davis; S. Sherman

    2008-08-01

    A number of possible configurations for a system that transfers heat between the nuclear reactor and the hydrogen and/or electrical generation plants were identified. These configurations included both direct and indirect cycles for the production of electricity. Both helium and liquid salts were considered as the working fluid in the intermediate heat transport loop. Methods were developed to perform thermal-hydraulic and cycleefficiency evaluations of the different configurations and coolants. The thermal-hydraulic evaluations estimated the sizes of various components in the intermediate heat transport loop for the different configurations. This paper also includes a portion of stress analyses performed on pipe configurations.

  10. [The intermediate lobe of the pituitary, model of neuroendocrine communication].

    PubMed

    Lamacz, M; Tonon, M C; Louiset, E; Cazin, L; Vaudry, H

    1991-06-01

    The intermediate lobe of the pituitary is composed of a homogeneous population of endocrine cells, the melanotrophs, which secrete several bioactive peptides including alpha-melanocyte-stimulating hormone (alpha-MSH) and beta-endorphin. In contrast to most endocrine glands which are richly vascularized, the intermediate lobe of the pituitary contains very few blood vessels; in some species, the pars intermedia is virtually totally avascular. In contrast, pituitary melanotrophs are richly supplied by nerve fibers originating from the hypothalamus. The pars intermedia thus appears as a pure model of neuroendocrine communication, i.e. it is an archetype of the mode of transducing interface between the central nervous system and endocrine effectors. In mammalian species, different types of nerve terminals containing dopamine, norepinephrine, gamma-aminobutyric acid (GABA) and serotonin have been identified. In lower vertebrates, particularly in fish and amphibians, the pars intermedia is also innervated by peptidergic fibers which are though to take part in regulation of the secretory activity of the melanotroph. In these animals, the pars intermedia is regarded as a major center of neuroendocrine integration and an exceptional model to investigate the process of communication between the brain and the endocrine glands. The purpose of the present review is to summarize our current knowledge on the synthesis, processing and release of peptide hormones from pars intermedia cells and to survey the multiple regulatory mechanisms which are involved in the control of the activity of pituitary melanotrophs. Proopiomelanocortin, a multifunctional precursor. Pituitary melanotrophs synthetise a major precursor protein called proopiomelanocortin (POMC) which generates through proteolytic cleavage several biologically active peptides including adrenocorticotropic hormone (ACTH), endorphins and MSHs. In lower vertebrates, alpha-MSH is generally considered as the major hormone secreted by melanotrophs, in that it is involved in the process of skin colour adaptation. The post-translational processing of POMC, which yields to the mature hormones released by melanotrophs, includes a number of steps: glycosylation, phosphorylation, tissue-specific proteolytic cleavage, amidation and acetylation. Some of these posttranslational modifications can be regulated by neuroendocrine factors. For instance, in frogs, it has been shown that dopamine inhibits acetylation of alpha-MSH and thus reduces the secretion of the biologically active form of the peptide. The intermediate lobe of the pituitary: a model of neuroendocrine integration. In most vertebrate species, the intermediate lobe of the pituitary is innervated by catecholamine-containing fibers. In particular, the presence of dopaminergic nerve fibers has been observed in the pars intermedia of mammals and poikilotherms.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:1717055

  11. Catalytic reactions in ionic liquids.

    PubMed

    Sheldon, R

    2001-12-01

    The chemical industry is under considerable pressure to replace many of the volatile organic compounds (VOCs) that are currently used as solvents in organic synthesis. The toxic and/or hazardous properties of many solvents, notably chlorinated hydrocarbons, combined with serious environmental issues, such as atmospheric emissions and contamination of aqueous effluents is making their use prohibitive. This is an important driving force in the quest for novel reaction media. Curzons and coworkers, for example, recently noted that rigorous management of solvent use is likely to result in the greatest improvement towards greener processes for the manufacture of pharmaceutical intermediates. The current emphasis on novel reaction media is also motivated by the need for efficient methods for recycling homogeneous catalysts. The key to waste minimisation in chemicals manufacture is the widespread substitution of classical 'stoichiometric' syntheses by atom efficient, catalytic alternatives. In the context of homogeneous catalysis, efficient recycling of the catalyst is a conditio sine qua non for economically and environmentally attractive processes. Motivated by one or both of the above issues much attention has been devoted to homogeneous catalysis in aqueous biphasic and fluorous biphasic systems as well as in supercritical carbon dioxide. Similarly, the use of ionic liquids as novel reaction media may offer a convenient solution to both the solvent emission and the catalyst recycling problem. PMID:12239988

  12. Reaction Selectivity in Heterogeneous Catalysis

    SciTech Connect

    Somorjai, Gabor A.; Kliewer, Christopher J.

    2009-02-02

    The understanding of selectivity in heterogeneous catalysis is of paramount importance to our society today. In this review we outline the current state of the art in research on selectivity in heterogeneous catalysis. Current in-situ surface science techniques have revealed several important features of catalytic selectivity. Sum frequency generation vibrational spectroscopy has shown us the importance of understanding the reaction intermediates and mechanism of a heterogeneous reaction, and can readily yield information as to the effect of temperature, pressure, catalyst geometry, surface promoters, and catalyst composition on the reaction mechanism. DFT calculations are quickly approaching the ability to assist in the interpretation of observed surface spectra, thereby making surface spectroscopy an even more powerful tool. HP-STM has revealed three vitally important parameters in heterogeneous selectivity: adsorbate mobility, catalyst mobility, and selective site-blocking. The development of size controlled nanoparticles from 0.8 to 10 nm, of controlled shape, and of controlled bimetallic composition has revealed several important variables for catalytic selectivity. Lastly, DFT calculations may be paving the way to guiding the composition choice for multi-metallic heterogeneous catalysis for the intelligent design of catalysts incorporating the many factors of selectivity we have learned.

  13. 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.

  14. Grey Zone Lymphomas: Lymphomas with Intermediate Features

    PubMed Central

    Hoeller, Sylvia; Copie-Bergman, Christiane

    2012-01-01

    The current classification of lymphoid neoplasms is based on clinical information, morphology, immunophenotype, and molecular genetic characteristics. Despite technical and scientific progress, some aggressive B-cell lymphomas with features overlapping between two different types of lymphomas remain difficult to classify. The updated 2008 World Health Organization (WHO) classification of Tumours of the Hematopoietic and Lymphoid Tissues has addressed this problem by creation of two new provisional categories of B-cell lymphomas, unclassifiable; one with features intermediate between diffuse large B-cell lymphoma and classical Hodgkin lymphoma and the second with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma. We review here the diagnostic criteria of these two provisional entities and discuss new scientific findings in light of the 2008 WHO classification. PMID:22548066

  15. Colloidal Nanoparticles for Intermediate Band Solar Cells.

    PubMed

    Vörös, Márton; Galli, Giulia; Zimanyi, Gergely T

    2015-07-28

    The Intermediate Band (IB) solar cell concept is a promising idea to transcend the Shockley-Queisser limit. Using the results of first-principles calculations, we propose that colloidal nanoparticles (CNPs) are a viable and efficient platform for the implementation of the IB solar cell concept. We focused on CdSe CNPs and we showed that intragap states present in the isolated CNPs with reconstructed surfaces combine to form an IB in arrays of CNPs, which is well separated from the valence and conduction band edges. We demonstrated that optical transitions to and from the IB are active. We also showed that the IB can be electron doped in a solution, e.g., by decamethylcobaltocene, thus activating an IB-induced absorption process. Our results, together with the recent report of a nearly 10% efficient CNP solar cell, indicate that colloidal nanoparticle intermediate band solar cells are a promising platform to overcome the Shockley-Queisser limit. PMID:26042468

  16. Raman scattering as a probe of intermediate phases in glassy networks

    E-print Network

    P. Boolchand; Mingji Jin; D. I. Novita; S. Chakravarty

    2007-09-27

    Bulk glass formation occurs over a very small part of phase space, and "good" glasses (which form even at low quench rates ~ 10K/sec) select an even smaller part of that accessible phase space. An axiomatic theory provides the physical basis of glass formation, and identifies these sweet spots of glass formation with existence of rigid but stress-free networks for which experimental evidence is rapidly emerging. Recently, theory and experiment have come together to show that these sweet spots of glass formation occur over a range of chemical compositions identified as Intermediate Phases. These ranges appear to be controlled by elements of local and medium range molecular structures that form isostatically rigid networks. Intermediate Phase glasses possess non-hysteretic glass transitions (Tgs) that do not age much. Raman scattering has played a pivotal role in elucidating molecular structure of glasses in general, and in identifying domains of Intermediate Phases. Experiments reveal these phases to possess sharp phase boundaries and to be characterized by an optical elasticity that varies with network mean coordination number, r, as power-law. In this review, we provide examples in chalcogenide and oxide glass systems where these phases along with optical elasticity power-laws have been established. Intermediate Phase glasses represent self-organized nanostructured functional materials optimized by nature.

  17. In vitro synthesis of intermediates involved in the assembly of enterobacterial common antigen (ECA)

    SciTech Connect

    Barr, K.; Wolski, S.; Kroto, J.; Rick, P.D.

    1986-05-01

    ECA is a cell surface antigen found in all bacteria belonging to the family Enterobacteriaceae. The serological specificity of ECA is determined by a linear heteropolysaccharide comprised of trisaccharide repeat units; the component sugars are N-acetyl-D-glucosamine (GlcNAc), N-acetyl-D-mannosaminuronic acid (ManNAcUA), and 4-acetamido-D-fucose (Fuc4NAc). In vivo studies have suggested that GlcNAc-pyrophosphorylundecaprenol (GlcNAc-PP-lipid) is an intermediate in ECA synthesis. More recently, they have demonstrated UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase activity in cell envelope preparations of E. coli. Radioactivity from UDP-(/sup 3/H)Glc-NAc was incorporated into endogenous lipid acceptor, and the labeled product was characterized as GlcNAc-PP-lipid (lipid I). Transferase activity was inhibited by tunicamycin and UMP, but it was unaffected by UDP. The reaction was reversible, and the synthesis of UDP-(/sup 3/H)GlcNAc from UMP and (/sup 3/H)GlcNAc-PP-lipid was also sensitive to tunicamycin. The simultaneous addition of UDP-(/sup 14/C)ManNAcUA and UDP-(/sup 3/H)GlcNAc to cell envelope preparations resulted in the synthesis of a more polar lipid (lipid II) that contained both labeled sugars in equimolar amounts. Synthesis of lipid II was dependent on prior synthesis of lipid I. Accordingly, (/sup 3/H)GlcNAc-PP-lipid that had been synthesized in vivo served as an acceptor in vitro of ManNAcUA residues from UDP-ManNAcUA. Lipid II has been tentatively identified as ManNAcUA-GlcNAc-pyrophosphorylundecaprenol.

  18. Single step BP/LR combined Gateway reactions.

    PubMed

    Liang, Xiquan; Peng, Lansha; Baek, Chang-Ho; Katzen, Federico

    2013-11-01

    The Gateway recombination system is characterized by its ability to transfer DNA sequences back and forth between an intermediate clone (the entry clone) and a variety of destination vectors. However, a number of applications do not need to exploit the advantages offered by the entry clone. Here we report reaction conditions for cloning DNA fragments into destination vectors in a single step reaction, thus reducing the cost and overall time needed to obtain an expression clone from three days to one. PMID:24215642

  19. Lewis Acid Coupled Electron Transfer of Metal-Oxygen Intermediates.

    PubMed

    Fukuzumi, Shunichi; Ohkubo, Kei; Lee, Yong-Min; Nam, Wonwoo

    2015-12-01

    Redox-inactive metal ions and Brønsted acids that function as Lewis acids play pivotal roles in modulating the redox reactivity of metal-oxygen intermediates, such as metal-oxo and metal-peroxo complexes. The mechanisms of the oxidative C?H bond cleavage of toluene derivatives, sulfoxidation of thioanisole derivatives, and epoxidation of styrene derivatives by mononuclear nonheme iron(IV)-oxo complexes in the presence of triflic acid (HOTf) and Sc(OTf)3 have been unified as rate-determining electron transfer coupled with binding of Lewis acids (HOTf and Sc(OTf)3 ) by iron(III)-oxo complexes. All logarithms of the observed second-order rate constants of Lewis acid-promoted oxidative C?H bond cleavage, sulfoxidation, and epoxidation reactions of iron(IV)-oxo complexes exhibit remarkably unified correlations with the driving forces of proton-coupled electron transfer (PCET) and metal ion-coupled electron transfer (MCET) in light of the Marcus theory of electron transfer when the differences in the formation constants of precursor complexes were taken into account. The binding of HOTf and Sc(OTf)3 to the metal-oxo moiety has been confirmed for Mn(IV) -oxo complexes. The enhancement of the electron-transfer reactivity of metal-oxo complexes by binding of Lewis acids increases with increasing the Lewis acidity of redox-inactive metal ions. Metal ions can also bind to mononuclear nonheme iron(III)-peroxo complexes, resulting in acceleration of the electron-transfer reduction but deceleration of the electron-transfer oxidation. Such a control on the reactivity of metal-oxygen intermediates by binding of Lewis acids provides valuable insight into the role of Ca(2+) in the oxidation of water to dioxygen by the oxygen-evolving complex in photosystem?II. PMID:26404482

  20. New Cathode Materials for Intermediate Temperature Solid Oxide Fuel Cells

    SciTech Connect

    Allan J. Jacobson

    2005-11-17

    Operation of SOFCs at intermediate temperatures (500-800 C) requires new combinations of electrolyte and electrode materials that will provide both rapid ion transport across the electrolyte and electrode--electrolyte interfaces and efficient electrocatalysis of the oxygen reduction and fuel oxidation reactions. This project concentrates on materials and issues associated with cathode performance that are known to become limiting factors as the operating temperature is reduced. The specific objectives of the proposed research are to develop cathode materials that meet the electrode performance targets of 1.0 W/cm{sup 2} at 0.7 V in combination with YSZ at 700 C and with GDC, LSGM or bismuth oxide based electrolytes at 600 C. The performance targets imply an area specific resistance of {approx}0.5 {Omega}cm{sup 2} for the total cell. The research strategy is to investigate both established classes of materials and new candidates as cathodes, to determine fundamental performance parameters such as bulk diffusion, surface reactivity and interfacial transfer, and to couple these parameters to performance in single cell tests. In this report, the oxygen exchange kinetics of a P2 composition are described in detail. The oxygen exchange kinetics of the oxygen deficient double perovskite LnBaCo{sub 2}O{sub 5.5+{delta}} (Ln=Pr and Nd) have been determined by electrical conductivity relaxation. The high electronic conductivity and rapid diffusion and surface exchange kinetics of PBCO suggest its application as cathode material in intermediate temperature solid oxide fuel cells.